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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

​

​

FORM 10-Q

(Mark One)

​

☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

​

For the quarterly period ended June 30, 2019

​

OR

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☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

​

For the transition period from to

Commission file number: 001-34620

IRONWOOD PHARMACEUTICALS, INC.

(Exact name of registrant as specified in its charter)

​

Delaware | ​ | 04-3404176
(State or other jurisdiction of | ​ | (I.R.S. Employer
incorporation or organization) | ​ | Identification Number)

​

​

​ | ​ | ​
301 Binney Street | ​ | ​
Cambridge, Massachusetts | ​ | 02142
(Address of Principal Executive Offices) | ​ | (Zip Code)

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(617) 621-7722

(Registrant’s telephone number, including area code)

​

Securities registered pursuant to Section 12(b) of the Act:

​

​ | ​ | ​
Title of each class | Trading Symbol(s) | Name of each exchange on which registered
Class A common stock, $0.001 par value | IRWD | Nasdaq Global Select Market

​

​

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No ☐

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Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ⌧ No ◻

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Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

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Large Accelerated Filer ☒ | ​ | Accelerated Filer ☐
​ | ​ | ​
Non-accelerated Filer ☐ | ​ | Smaller Reporting Company ☐
​ | ​ | ​
​ | ​ | Emerging Growth Company ☐

​

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

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Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). ☐ Yes ☒ No

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As of July 26, 2019, there were 156,495,574 shares of Class A common stock outstanding.

​

​

​

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NOTE REGARDING FORWARD-LOOKING STATEMENTS

​

This Quarterly Report on Form 10-Q, including the sections titled “Management’s Discussion and Analysis of Financial Condition and Results of Operations” and “Risk Factors”, contains forward-looking statements. All statements contained in this Quarterly Report on Form 10-Q other than statements of historical fact are forward-looking statements. Forward-looking statements include statements regarding our future financial position, business strategy, budgets, projected costs, plans and objectives of management for future operations. The words “may,” “continue,” “estimate,” “intend,” “plan,” “will,” “believe,” “project,” “expect,” “seek,” “anticipate” and similar expressions may identify forward-looking statements, but the absence of these words does not necessarily mean that a statement is not forward-looking. These forward-looking statements include, among other things, statements about:

​

| ● | the demand and market potential for our products in the countries where they are approved for marketing, as well as the revenues therefrom;

| ● | the timing, investment and associated activities involved in commercializing LINZESS® by us and Allergan plc in the U.S.;

​

| ● | the timing and execution of the launches and commercialization of CONSTELLA® in Europe and LINZESS in Japan and China;

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| ● | the timing, investment and associated activities involved in developing, obtaining regulatory approval for, launching, and commercializing our products and product candidates by us and our partners worldwide;

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| ● | our ability and the ability of our partners to secure and maintain adequate reimbursement for our products;

​

| ● | our ability and the ability of our partners and third parties to manufacture and distribute sufficient amounts of linaclotide active pharmaceutical ingredient, drug product and finished goods, as applicable, on a commercial scale, as well as our expectations regarding revenue generated from Astellas for Japan;

​

| ● | our expectations regarding U.S. and foreign regulatory requirements for our products and our product candidates, including our post-approval development and regulatory requirements;

​

| ● | the ability of our product candidates to meet existing or future regulatory standards;

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| ● | the safety profile and related adverse events of our products and our product candidates;

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| ● | the therapeutic benefits and effectiveness of our products and our product candidates and the potential indications and market opportunities therefor;

​

| ● | our and our partners’ ability to obtain and maintain intellectual property protection for our products and our product candidates and the strength thereof, as well as Abbreviated New Drug Applications filed by generic drug manufacturers and potential U.S. Food and Drug Administration approval thereof, and associated patent infringement suits that we have filed or may file, or other action that we may take against such companies, and the timing and resolution thereof;

​

| ● | our and our partners’ ability to perform our respective obligations under our collaboration, license and other agreements, and our ability to achieve milestone and other payments under such agreements;

​

| ● | our plans with respect to the development, manufacture or sale of our product candidates and the associated timing thereof, including the design and results of pre-clinical and clinical studies;

​

| ● | the in-licensing or acquisition of externally discovered businesses, products or technologies, as well as partnering arrangements, including expectations relating to the completion of, or the realization of the expected benefits from, such transactions;

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2

Table of Contents

| ● | our expectations as to future financial performance, revenues, expense levels, payments, cash flows, profitability, tax obligations, capital raising and liquidity sources, real estate needs and concentration of voting control, as well as the timing and drivers thereof, and internal control over financial reporting;

​

| ● | our expectations as to the timing or costs associated with transitioning to a new headquarters location;

​

| ● | our ability to repay our outstanding indebtedness when due, or redeem or repurchase all or a portion of such debt, as well as the potential benefits of the note hedge transactions described herein;

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| ● | inventory levels and write downs, or asset impairments, and the drivers thereof, and inventory purchase commitments;

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| ● | our ability to compete with other companies that are or may be developing or selling products that are competitive with our products and product candidates;

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| ● | the status of government regulation in the life sciences industry, particularly with respect to healthcare reform;

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| ● | trends and challenges in our potential markets;

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| ● | our ability to attract and motivate key personnel;

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| ● | any benefits or costs of the separation of the Company’s operations into two independent, publicly traded companies, including the tax treatment; and

​

| ● | other factors discussed elsewhere in this Quarterly Report on Form 10-Q.

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Any or all of our forward-looking statements in this Quarterly Report on Form 10-Q may turn out to be inaccurate. These forward-looking statements may be affected by inaccurate assumptions or by known or unknown risks and uncertainties, including the risks, uncertainties and assumptions identified under the heading “Risk Factors” in this Quarterly Report on Form 10-Q. In light of these risks, uncertainties and assumptions, the forward-looking events and circumstances discussed in this Quarterly Report on Form 10-Q may not occur as contemplated, and actual results could differ materially from those anticipated or implied by the forward-looking statements.

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You should not unduly rely on these forward-looking statements, which speak only as of the date of this Quarterly Report on Form 10-Q. Unless required by law, we undertake no obligation to publicly update or revise any forward-looking statements to reflect new information or future events or otherwise. You should, however, review the factors and risks we describe in the reports we will file from time to time with the U.S. Securities and Exchange Commission, or the SEC, after the date of this Quarterly Report on Form 10-Q.

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NOTE REGARDING TRADEMARKS

​

LINZESS® and CONSTELLA® are trademarks of Ironwood Pharmaceuticals, Inc. ZURAMPIC® and DUZALLO® are trademarks of AstraZeneca AB. Any other trademarks referred to in this Quarterly Report on Form 10-Q are the property of their respective owners. All rights reserved.

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Table of Contents

IRONWOOD PHARMACEUTICALS, INC.

QUARTERLY REPORT ON FORM 10-Q

FOR THE QUARTER ENDED JUNE 30, 2019

TABLE OF CONTENTS

​

​ | ​ | ​ |
​ | ​ | ​ | ​
​ | ​ | ​ | Page
​ | ​ | ​ | ​
​ | PART I — FINANCIAL INFORMATION | ​ | ​
Item 1. | Financial Statements (unaudited) | ​ | ​
​ | Condensed Consolidated Balance Sheets as of June 30, 2019 and December 31, 2018 | ​ | 5
​ | Condensed Consolidated Statements of Operations for the Three and Six Months Ended June 30, 2019 and 2018 | ​ | 6
​ | Condensed Consolidated Statements of Comprehensive Income (Loss) for the Three and Six Months Ended June 30, 2019 and 2018 | ​ | 7
​ | Condensed Consolidated Statements of Stockholders’ Deficit for the Three and Six Months Ended June 30, 2019 and 2018 | ​ | 8
​ | Condensed Consolidated Statements of Cash Flows for the Six Months Ended June 30, 2019 and 2018 | ​ | 9
​ | Notes to Condensed Consolidated Financial Statements | ​ | 10
Item 2. | Management’s Discussion and Analysis of Financial Condition and Results of Operations | ​ | 40
Item 3. | Quantitative and Qualitative Disclosures About Market Risk | ​ | 54
Item 4. | Controls and Procedures | ​ | 55
​ | ​ | ​ | ​
​ | ​ | ​ | ​
​ | PART II — OTHER INFORMATION | ​ | ​
Item 1. | Legal Proceedings | ​ | 56
Item 1A. | Risk Factors | ​ | 57
Item 6. | Exhibits | ​ | 83
​ | ​ | ​ | ​
​ | Signatures | ​ | 85

​

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Table of Contents

PART I — FINANCIAL INFORMATION

Item 1. Financial Statement s

Ironwood Pharmaceuticals, Inc.

Condensed Consolidated Balance Sheet s

(In thousands, except share and per share amounts)

(unaudited)

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | June 30, | ​ | December 31,
​ |  | 2019 |  | 2018
ASSETS | ​ | ​ | ​ | ​ | ​ | ​
Current assets: | ​ | ​ | ​ | ​ | ​ | ​
Cash and cash equivalents | ​ | $ | 98,908 | ​ | $ | 173,172
Accounts receivable, net | ​ |  | 22,604 | ​ |  | 20,991
Related party accounts receivable, net | ​ |  | 81,182 | ​ |  | 59,959
Inventory, net | ​ |  | 1,735 | ​ |  | —
Prepaid expenses and other current assets | ​ |  | 8,880 | ​ |  | 10,216
Restricted cash | ​ | ​ | 7,676 | ​ | ​ | 1,250
Current assets of discontinued operations | ​ | ​ | — | ​ | ​ | 847
Total current assets | ​ |  | 220,985 | ​ |  | 266,435
Restricted cash, net of current portion | ​ |  | 971 | ​ |  | 6,426
Property and equipment, net | ​ |  | 6,665 | ​ |  | 7,652
Operating lease right-of-use assets | ​ | ​ | 25,569 | ​ | ​ | —
Convertible note hedges | ​ | ​ | 60,720 | ​ | ​ | 41,020
Goodwill | ​ | ​ | 785 | ​ | ​ | 785
Other assets | ​ |  | 26 | ​ |  | 89
Non-current assets of discontinued operations | ​ |  | — | ​ |  | 9,643
Total assets | ​ | $ | 315,721 | ​ | $ | 332,050
LIABILITIES AND STOCKHOLDERS' DEFICIT | ​ | ​ | ​ | ​ | ​ | ​
Current liabilities: | ​ | ​ | ​ | ​ | ​ | ​
Accounts payable | ​ | $ | 7,872 | ​ | $ | 14,891
Related party accounts payable, net | ​ |  | 2,036 | ​ |  | —
Accrued research and development costs | ​ |  | 6,270 | ​ |  | 2,963
Accrued expenses and other current liabilities | ​ |  | 33,982 | ​ |  | 38,001
Capital lease obligations | ​ |  | — | ​ |  | 73
Current portion of deferred rent | ​ |  | — | ​ |  | 252
Current portion of 2026 Notes | ​ | ​ | 48,797 | ​ | ​ | 47,554
Current portion of operating lease liabilities | ​ | ​ | 11,904 | ​ | ​ | —
Current portion of contingent consideration | ​ | ​ | — | ​ | ​ | 51
Current liabilities of discontinued operations | ​ | ​ | — | ​ | ​ | 15,739
Total current liabilities | ​ |  | 110,861 | ​ |  | 119,524
Capital lease obligations, net of current portion | ​ | ​ | — | ​ | ​ | 158
Deferred rent, net of current portion | ​ |  | — | ​ |  | 6,308
Note hedge warrants | ​ | ​ | 50,191 | ​ | ​ | 33,763
Convertible senior notes | ​ | ​ | 274,395 | ​ | ​ | 265,601
Operating lease liabilities, net of current portion | ​ | ​ | 18,685 | ​ | ​ | —
2026 Notes, net of current portion | ​ | ​ | 78,330 | ​ |  | 100,537
Other liabilities | ​ |  | 2,626 | ​ |  | 2,530
Commitments and contingencies | ​ | ​ | ​ | ​ | ​ | ​
Stockholders’ deficit: | ​ | ​ | ​ | ​ | ​ | ​
Preferred stock, $0.001 par value, 75,000,000 shares authorized, no shares issued and outstanding | ​ |  | — | ​ |  | —
Class A common stock, $0.001 par value, 500,000,000 shares authorized and 156,442,332 issued and outstanding at June 30, 2019 and 500,000,000 shares authorized and 154,414,691 shares issued and outstanding at December 31, 2018 | ​ |  | 156 | ​ |  | 154
Additional paid-in capital | ​ |  | 1,421,215 | ​ |  | 1,394,603
Accumulated deficit | ​ |  | (1,640,738) | ​ |  | (1,591,128)
Total stockholders’ deficit | ​ |  | (219,367) | ​ |  | (196,371)
Total liabilities and stockholders’ deficit | ​ | $ | 315,721 | ​ | $ | 332,050

​

The accompanying notes are an integral part of these condensed consolidated financial statements.

​

​

5

Table of Contents

Ironwood Pharmaceuticals, Inc.

Condensed Consolidated Statements of Operation s

(In thousands, except per share amounts)

(unaudited)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​ | June 30, | ​
​ |  | 2019 |  | 2018 |  | 2019 |  | 2018 |
Revenues: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Collaborative arrangements revenue | ​ | $ | 77,322 | ​ | $ | 71,207 | ​ | $ | 143,474 | ​ | $ | 134,293 | ​
Product revenue, net | ​ | ​ | — | ​ | ​ | 1,096 | ​ | ​ | — | ​ | ​ | 1,731 | ​
Sale of active pharmaceutical ingredient | ​ | ​ | 24,893 | ​ | ​ | 8,803 | ​ | ​ | 27,471 | ​ | ​ | 14,237 | ​
Total revenues | ​ |  | 102,215 | ​ |  | 81,106 | ​ |  | 170,945 | ​ |  | 150,261 | ​
Cost and expenses: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Cost of revenues, excluding amortization of acquired intangible assets | ​ |  | 11,313 | ​ |  | 4,065 | ​ | ​ | 12,356 | ​ | ​ | 6,672 | ​
Write-down of commercial supply and inventory to net realizable value and loss on non-cancellable purchase commitments | ​ | ​ | — | ​ | ​ | 1,836 | ​ | ​ | — | ​ | ​ | 1,836 | ​
Research and development | ​ |  | 28,758 | ​ |  | 23,187 | ​ | ​ | 60,956 | ​ | ​ | 43,663 | ​
Selling, general and administrative | ​ |  | 43,246 | ​ |  | 59,771 | ​ | ​ | 92,341 | ​ | ​ | 118,716 | ​
Amortization of acquired intangible assets | ​ | ​ | — | ​ | ​ | 3,476 | ​ | ​ | — | ​ | ​ | 6,952 | ​
Loss on fair value remeasurement of contingent consideration | ​ | ​ | — | ​ | ​ | 1,962 | ​ | ​ | — | ​ | ​ | 2,474 | ​
Gain on lease modification | ​ | ​ | (3,169) | ​ | ​ | — | ​ | ​ | (3,169) | ​ | ​ | — | ​
Restructuring expenses | ​ | ​ | 490 | ​ | ​ | 1,486 | ​ | ​ | 3,818 | ​ | ​ | 3,908 | ​
Total cost and expenses | ​ |  | 80,638 | ​ |  | 95,783 | ​ |  | 166,302 | ​ |  | 184,221 | ​
Income (loss) from operations | ​ |  | 21,577 | ​ |  | (14,677) | ​ |  | 4,643 | ​ |  | (33,960) | ​
Other (expense) income: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Interest expense | ​ |  | (9,430) | ​ |  | (9,383) | ​ | ​ | (19,022) | ​ | ​ | (18,656) | ​
Interest and investment income | ​ |  | 668 | ​ |  | 732 | ​ | ​ | 1,404 | ​ | ​ | 1,413 | ​
(Loss) gain on derivatives | ​ | ​ | (672) | ​ | ​ | (809) | ​ | ​ | 3,272 | ​ | ​ | 507 | ​
Other income | ​ | ​ | 140 | ​ | ​ | — | ​ | ​ | 140 | ​ | ​ | — | ​
Other expense, net | ​ |  | (9,294) | ​ |  | (9,460) | ​ |  | (14,206) | ​ |  | (16,736) | ​
Net income (loss) from continuing operations | ​ | ​ | 12,283 | ​ | ​ | (24,137) | ​ | ​ | (9,563) | ​ | ​ | (50,696) | ​
Net loss from discontinued operations | ​ | ​ | — | ​ | ​ | (25,243) | ​ | ​ | (37,438) | ​ | ​ | (41,828) | ​
Net income (loss) | ​ | $ | 12,283 | ​ | $ | (49,380) | ​ | $ | (47,001) | ​ | $ | (92,524) | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Net income (loss) per share from continuing operations—basic and diluted | ​ | $ | 0.08 | ​ | $ | (0.16) | ​ | $ | (0.06) | ​ | $ | (0.33) | ​
Net loss per share from discontinued operations—basic and diluted | ​ | $ | — | ​ | $ | (0.17) | ​ | $ | (0.24) | ​ | $ | (0.28) | ​
Net income (loss) per share—basic and diluted | ​ | $ | 0.08 | ​ | $ | (0.32) | ​ | $ | (0.30) | ​ | $ | (0.61) | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Weighted average number of common shares—basic and diluted: | ​ |  | 155,849 | ​ |  | 152,163 | ​ |  | 155,405 | ​ |  | 151,591 | ​

​

The accompanying notes are an integral part of these condensed consolidated financial statements.

​

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Ironwood Pharmaceuticals, Inc.

Condensed Consolidated Statements of Comprehensive Los s

(In thousands)

(unaudited)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​ | June 30, | ​
​ |  | 2019 |  | 2018 |  | 2019 |  | 2018 |
Net income (loss) | ​ | $ | 12,283 | ​ | $ | (49,380) | ​ | $ | (47,001) | ​ | $ | (92,524) | ​
Other comprehensive income: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Unrealized gains on available-for-sale securities | ​ |  | — | ​ |  | 47 | ​ |  | — | ​ |  | 35 | ​
Total other comprehensive income | ​ |  | — | ​ |  | 47 | ​ |  | — | ​ |  | 35 | ​
Comprehensive income (loss) | ​ | $ | 12,283 | ​ | $ | (49,333) | ​ | $ | (47,001) | ​ | $ | (92,489) | ​

​

The accompanying notes are an integral part of these condensed consolidated financial statements.

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Ironwood Pharmaceuticals, Inc.

Condensed Consolidated Statements of Stockholders’ Deficit

(In thousands, except share amounts)

(unaudited)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Class A | ​ | Additional | ​ | ​ | ​ | ​ | Total | ​
​ | ​ | common stock | ​ | paid-in | ​ | Accumulated | ​ | Stockholders’ | ​
​ | ​ | Shares |  | Amount | ​ | capital |  | deficit |  | deficit | ​
Balance at December 31, 2018 | ​ | 154,414,691 | ​ | $ | 154 | ​ | $ | 1,394,603 | ​ | $ | (1,591,128) | ​ | $ | (196,371) | ​
Issuance of common stock related to share-based awards and employee stock purchase plan | ​ | 1,210,858 | ​ | ​ | 2 | ​ | ​ | 3,486 | ​ | ​ | — | ​ | ​ | 3,488 | ​
Share-based compensation expense related to share-based awards and employee stock purchase plan | ​ | — | ​ | ​ | — | ​ | ​ | 14,988 | ​ | ​ | — | ​ | ​ | 14,988 | ​
Net loss | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (59,284) | ​ | ​ | (59,284) | ​
Balance at March 31, 2019 | ​ | 155,625,549 | ​ | $ | 156 | ​ | $ | 1,413,077 | ​ | $ | (1,650,412) | ​ | $ | (237,179) | ​
Issuance of common stock related to share-based awards and employee stock purchase plan, net of cancellations | ​ | 621,588 | ​ | ​ | — | ​ | ​ | 1,801 | ​ | ​ | — | ​ | ​ | 1,801 | ​
Share-based compensation expense related to share-based awards and employee stock purchase plan | ​ | 195,195 | ​ | ​ | — | ​ | ​ | 6,337 | ​ | ​ | — | ​ | ​ | 6,337 | ​
Dividend of sGC business | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (2,609) | ​ | ​ | (2,609) | ​
Net income | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 12,283 | ​ | ​ | 12,283 | ​
Balance at June 30, 2019 | ​ | 156,442,332 | ​ | $ | 156 | ​ | $ | 1,421,215 | ​ | $ | (1,640,738) | ​ | $ | (219,367) | ​

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | Accumulated | ​ | ​ | ​ | ​
​ | ​ | Class A | ​ | Class B | ​ | Additional | ​ | ​ | ​ | ​ | other | ​ | Total |
​ | ​ | common stock | ​ | common stock | ​ | paid-in | ​ | Accumulated | ​ | comprehensive | ​ | Stockholders’ |
​ |  | Shares |  | Amount |  | Shares |  | Amount |  | capital |  | deficit |  | loss |  | deficit |
Balance at December 31, 2017 | ​ | 136,465,526 | ​ | $ | 137 | ​ | 13,983,762 | ​ | $ | 14 | ​ | $ | 1,318,536 | ​ | $ | (1,308,760) | ​ | $ | (79) | ​ | $ | 9,848 |
Issuance of common stock related to share-based awards and employee stock purchase plan | ​ | 882,448 | ​ | ​ | 1 | ​ | 272,146 | ​ | ​ | — | ​ | ​ | 6,193 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 6,194 | ​
Issuance of common stock awards | ​ | 162 | ​ | ​ | — | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​
Conversion of Class B common stock to Class A common stock | ​ | 258,551 | ​ | ​ | — | ​ | (258,551) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​
Share-based compensation expense related to share-based awards and employee stock purchase plan | ​ | — | ​ | ​ | — | ​ | — | ​ | ​ | — | ​ | ​ | 9,062 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 9,062 | ​
Unrealized losses on available-for-sale securities | ​ | — | ​ | ​ | — | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (12) | ​ | ​ | (12) | ​
Net loss | ​ | — | ​ | ​ | — | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (43,144) | ​ | ​ | — | ​ | ​ | (43,144) | ​
Balance at March 31, 2018 |  | 137,606,687 | ​ | $ | 138 | ​ | 13,997,357 | ​ | $ | 14 | ​ | $ | 1,333,791 | ​ | $ | (1,351,904) | ​ | $ | (91) | ​ | $ | (18,052) | ​
Issuance of common stock related to share-based awards and employee stock purchase plan | ​ | 989,830 | ​ | ​ | 1 | ​ | 129,501 | ​ | ​ | — | ​ | ​ | 12,865 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 12,866 | ​
Issuance of common stock awards | ​ | 130,045 | ​ | ​ | — | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​
Conversion of Class B common stock to Class A common stock | ​ | 134,367 | ​ | ​ | — | ​ | (134,367) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​
Share-based compensation expense related to share-based awards and employee stock purchase plan | ​ | — | ​ | ​ | — | ​ | — | ​ | ​ | — | ​ | ​ | 10,568 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 10,568 | ​
Unrealized gains on available-for-sale securities | ​ | — | ​ | ​ | — | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 47 | ​ | ​ | 47 | ​
Net loss | ​ | — | ​ | ​ | — | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (49,380) | ​ | ​ | — | ​ | ​ | (49,380) | ​
Balance at June 30, 2018 | ​ | 138,860,929 | ​ | $ | 139 | ​ | 13,992,491 | ​ | $ | 14 | ​ | $ | 1,357,224 | ​ | $ | (1,401,284) | ​ | $ | (44) | ​ | $ | (43,951) | ​

​

The accompanying notes are an integral part of these condensed consolidated financial statements.

​

​

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​

Ironwood Pharmaceuticals, Inc.

Condensed Consolidated Statements of Cash Flow s

(In thousands)

(unaudited)

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​
​ |  | 2019 |  | 2018 |
Cash flows from operating activities: | ​ | ​ | ​ | ​ | ​ | ​ | ​
Net loss | ​ | $ | (47,001) | ​ | $ | (92,524) | ​
Adjustments to reconcile net loss to net cash used in operating activities: | ​ | ​ | ​ | ​ | ​ | ​ | ​
Depreciation and amortization | ​ |  | 1,539 | ​ | ​ | 2,189 | ​
Amortization of acquired intangible assets | ​ | ​ | — | ​ | ​ | 6,952 | ​
Loss (gain) on disposal of property and equipment | ​ | ​ | 109 | ​ | ​ | (275) | ​
Gain on lease modification | ​ | ​ | (3,169) | ​ | ​ | — | ​
Share-based compensation expense | ​ |  | 20,271 | ​ | ​ | 18,054 | ​
Change in fair value of note hedge warrants | ​ | ​ | 16,428 | ​ | ​ | 50,831 | ​
Change in fair value of convertible note hedges | ​ | ​ | (19,700) | ​ | ​ | (51,338) | ​
Write-down of commercial supply and inventory to net realizable value and loss on non-cancellable purchase commitments | ​ | ​ | — | ​ | ​ | 1,836 | ​
Write-down of excess non-cancellable ZURAMPIC and DUZALLO sample purchase commitments | ​ | ​ | — | ​ | ​ | 390 | ​
Accretion of discount/premium on investment securities | ​ |  | — | ​ | ​ | (138) | ​
Non-cash interest expense | ​ |  | 9,300 | ​ | ​ | 8,591 | ​
Non-cash change in fair value of contingent consideration | ​ | ​ | — | ​ | ​ | 2,474 | ​
Changes in assets and liabilities: | ​ | ​ | ​ | ​ | ​ | ​ | ​
Accounts receivable and related party accounts receivable, net | ​ |  | (21,529) | ​ | ​ | 1,638 | ​
Prepaid expenses and other current assets | ​ |  | 2,647 | ​ | ​ | (9,591) | ​
Inventory, net | ​ |  | (635) | ​ | ​ | (992) | ​
Other assets | ​ |  | (6) | ​ | ​ | 68 | ​
Accounts payable, related party accounts payable and accrued expenses | ​ |  | (25,205) | ​ | ​ | 2,096 | ​
Accrued research and development costs | ​ |  | 2,335 | ​ | ​ | 202 | ​
Operating lease right-of-use assets | ​ | ​ | 6,315 | ​ | ​ | — | ​
Operating lease liabilities | ​ | ​ | (4,685) | ​ | ​ | — | ​
Deferred rent | ​ |  | — | ​ | ​ | 655 | ​
Net cash used in continuing operating activities | ​ |  | (62,986) | ​ |  | (58,882) | ​
Net cash provided by discontinued operating activities | ​ | ​ | 11,364 | ​ | ​ | 5,305 | ​
Net cashed used in operating activities | ​ | ​ | (51,622) | ​ | ​ | (53,577) | ​
Cash flows from investing activities: | ​ | ​ | ​ | ​ | ​ | ​ | ​
Purchases of available-for-sale securities | ​ |  | — | ​ | ​ | (2,491) | ​
Sales and maturities of available-for-sale securities | ​ |  | — | ​ | ​ | 62,512 | ​
Purchases of property and equipment | ​ |  | (1,444) | ​ | ​ | (1,447) | ​
Proceeds from sale of property and equipment | ​ |  | 261 | ​ | ​ | 273 | ​
Net cash (used in) provided by continuing investing activities | ​ |  | (1,183) | ​ |  | 58,847 | ​
Net cash used in discontinued investing activities | ​ | ​ | (4,223) | ​ | ​ | (1,754) | ​
Net cash (used in) provided by investing activities | ​ | ​ | (5,406) | ​ | ​ | 57,093 | ​
Cash flows from financing activities: | ​ | ​ | ​ | ​ | ​ | ​ | ​
Proceeds from exercise of stock options and employee stock purchase plan | ​ |  | 5,204 | ​ | ​ | 19,044 | ​
Payments on capital lease obligations | ​ |  | — | ​ | ​ | (1,510) | ​
Principal payments on 2026 notes | ​ | ​ | (21,469) | ​ | ​ | — | ​
Payments on contingent purchase price consideration | ​ | ​ | — | ​ | ​ | (121) | ​
Net cash (used in) provided by continuing financing activities | ​ |  | (16,265) | ​ |  | 17,413 | ​
Net cash (used in) provided by discontinued financing activities | ​ | ​ | — | ​ | ​ | — | ​
Net cash (used in) provided by financing activities | ​ | ​ | (16,265) | ​ | ​ | 17,413 | ​
Net (decrease) increase in cash, cash equivalents and restricted cash | ​ |  | (73,293) | ​ |  | 20,929 | ​
Cash, cash equivalents and restricted cash, beginning of period | ​ |  | 180,848 | ​ |  | 132,792 | ​
Cash, cash equivalents and restricted cash, end of period | ​ | $ | 107,555 | ​ | $ | 153,721 | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Reconciliation of cash, cash equivalents, and restricted cash to the condensed consolidated balance sheets | ​ | ​ | ​ | ​ | ​ | ​ | ​
Cash and cash equivalents | ​ | $ | 98,908 | ​ | $ | 145,415 | ​
Restricted cash | ​ | ​ | 8,647 | ​ | ​ | 8,306 | ​
Total cash, cash equivalents, and restricted cash | ​ | $ | 107,555 | ​ | $ | 153,721 | ​

​

The accompanying notes are an integral part of these condensed consolidated financial statements.

​

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Ironwood Pharmaceuticals, Inc.

Notes to Condensed Consolidated Financial Statement s

(unaudited)

​

1. Nature of Business

​

Overview

​

Ironwood Pharmaceuticals, Inc. (“Ironwood” or the “Company”) is a gastrointestinal (“GI”) healthcare company dedicated to creating medicines that make a difference for people living with GI diseases. The Company is advancing innovative product opportunities in areas of large unmet need, capitalizing on its proven development and commercial capabilities and its deep expertise in GI diseases. On April 1, 2019, the Company completed its tax-free spin-off of its soluble guanylate cyclase (“sGC”) business into a separate, publicly traded company called Cyclerion Therapeutics, Inc. (“Cyclerion”).

​

The Company’s commercial product, linaclotide, is available to adult men and women suffering from irritable bowel syndrome with constipation (“IBS-C”), or chronic idiopathic constipation (“CIC”), in certain countries around the world. As many as 13 million adults suffer from IBS-C and as many as 35 million adults suffer from CIC in the U.S. alone, according to our analysis of studies including P Pare, et al. (published in 2001 in the American Journal of Gastroenterology) and J.F. Johanson, et al. (published in 2007 in Alimentary Pharmacology and Therapeutics) and American College of Gastroenterology Chronic Constipation Task Force (2005), American Journal of Gastroenterology Vol. 100, No. S1, 2005. Symptoms of IBS-C include abdominal pain, discomfort or bloating and constipation symptoms (for example, incomplete evacuation, infrequent bowel movements, hard/lumpy stools), while CIC is primarily characterized by constipation symptoms.

​

Linaclotide is available under the trademarked name LINZESS® (linaclotide) to adult men and women suffering from IBS-C or CIC in the United States (the “U.S.”) and Mexico and to adult men and women suffering from IBS-C in Japan. Linaclotide is available under the trademarked name CONSTELLA® to adult men and women suffering from IBS-C or CIC in Canada, and to adult men and women suffering from IBS-C in certain European countries.

​

The Company has formed strategic partnerships with leading pharmaceutical companies to support the development and commercialization of linaclotide throughout the world. The Company and its partner, Allergan plc (together with its affiliates, “Allergan”), began commercializing LINZESS in the U.S. in December 2012. Under the Company’s collaboration with Allergan for North America, total net sales of LINZESS in the U.S., as recorded by Allergan, are reduced by commercial costs incurred by each party, and the resulting amount is shared equally between the Company and Allergan. Allergan also has an exclusive license from the Company to develop and commercialize linaclotide in all countries other than China, Hong Kong, Macau, Japan and the countries and territories of North America (the “Allergan License Territory”). On a country-by-country and product-by-product basis in the Allergan License Territory, Allergan pays the Company a royalty as a percentage of net sales of products containing linaclotide as an active ingredient. In addition, Allergan has exclusive rights to commercialize linaclotide in Canada as CONSTELLA and in Mexico as LINZESS.

​

Astellas Pharma Inc. (“Astellas”), the Company’s partner in Japan, has an exclusive license to develop and commercialize linaclotide in Japan. In March 2017, Astellas began commercializing LINZESS for the treatment of adults with IBS-C in Japan, and in September 2018, Astellas began commercializing LINZESS for the treatment of adults with chronic constipation in Japan. The Company has a collaboration agreement with AstraZeneca AB (together with its affiliates, “AstraZeneca”), to co-develop and co-commercialize linaclotide in China, Hong Kong and Macau, with AstraZeneca having primary responsibility for the local operational execution. In January 2019, the National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China.

​

The Company and Allergan are exploring ways to enhance the clinical profile of LINZESS by studying linaclotide in additional indications, populations and formulations to assess its potential to treat various conditions. In June 2019, the Company announced positive topline data from its Phase IIIb trial demonstrating the efficacy and safety of LINZESS 290 mcg on the overall abdominal symptoms of bloating, pain and discomfort, in adult patients with IBS-C.

​

The Company and Allergan are also advancing MD-7246, a delayed release form of linaclotide, as an oral, intestinal, non-opioid pain relieving agent for patients suffering from abdominal pain associated with certain GI diseases.

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There are an estimated 16 million Americans who suffer from symptoms of IBS-D, according to Grundmann and Yoon in Irritable Bowel Syndrome: epidemiology, diagnosis and treatment: an update for health-care practitioners (published in the Journal of Gastroenterology and Hepatology in 2010) and the United States Census Bureau. In May 2019, the Company and Allergan initiated a Phase II clinical trial evaluating MD-7246 in adult patients with IBS with diarrhea (“IBS-D”).

​

The Company is advancing IW-3718, a gastric retentive formulation of a bile acid sequestrant, for the potential treatment of persistent gastroesophageal reflux disease (“GERD”). There are an estimated 10 million Americans who suffer regularly from symptoms of GERD, such as heartburn and regurgitation, despite receiving treatment with the current standard of care, a proton pump inhibitor, to suppress stomach acid, according to a study published in 2014 by HB El-Sarag, Sweet S, Winchester CC et al. in Gut; a Lieberman HCP Survey, 2019; a Lieberman GI patient landscape survey, 2010; a survey conducted by American Gastroenterological Association; and 2019 U.S. census data. In June 2018, the Company initiated two Phase III clinical trials evaluating the safety and efficacy of IW-3718 in patients with persistent GERD.

​

On April 1, 2019, Ironwood completed the separation of its sGC business, and certain other assets and liabilities, into Cyclerion (the “Separation”). The Separation was effected by means of a distribution of all of the outstanding shares of common stock, with no par value, of Cyclerion through a dividend of all outstanding shares of Cyclerion’s common stock, to Ironwood’s stockholders of record as of the close of business on March 19, 2019 (Note 2). Cyclerion is a clinical-stage biopharmaceutical company harnessing the power of sGC pharmacology to discover, develop, and commercialize breakthrough treatments for serious and orphan diseases.

​

On June 11, 2019, the Company entered into a non-cancelable operating lease (the “Summer Street Lease”) for approximately 39,000 square feet of office space on the 23rd floor of 100 Summer Street, Boston, Massachusetts (the “Summer Street Property”). The Summer Street Property is expected to serve as the Company’s new headquarters beginning in the fourth quarter of 2019, replacing its existing headquarters at 301 Binney Street (Note 8).

​

Additionally, the Company has periodically entered into co-promotion agreements to maximize its salesforce productivity, such as its co-promotion agreement with Allergan to perform sales detailing activities for VIBERZI for treatment for adults suffering from IBS-D (Note 4).

​

Basis of Presentation

​

The accompanying condensed consolidated financial statements and the related disclosures are unaudited and have been prepared in accordance with accounting principles generally accepted in the U.S. Additionally, certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. Accordingly, these interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2018, which was filed with the Securities and Exchange Commission on February 25, 2019 (the “2018 Annual Report on Form 10-K”).

​

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all normal recurring adjustments considered necessary for a fair presentation of the Company’s financial position as of June 30, 2019, and the results of its operations for the three and six months ended June 30, 2019 and 2018, its statements of stockholders’ deficit for the three and six months ended June 30, 2019 and 2018, and its cash flows for the six months ended June 30, 2019 and 2018. The results of operations for the three and six months ended June 30, 2019 and 2018 are not necessarily indicative of the results that may be expected for the full year or any other subsequent interim period.

​

The Company has presented its sGC business as discontinued operations in its condensed consolidated financial statements for all periods presented. The historical financial statements and footnotes have been recast accordingly (Note 2). For periods following the Separation, the Company continues to report financial results under one business segment.

​

Principles of Consolidation

​

The accompanying condensed consolidated financial statements include the accounts of Ironwood and its wholly-owned subsidiaries as of June 30, 2019, Ironwood Pharmaceuticals Securities Corporation and Ironwood

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Pharmaceuticals GmbH. Cyclerion was a wholly-owned subsidiary until it became an independent, publicly-traded company on April 1, 2019. All intercompany transactions and balances are eliminated in consolidation.

​

Use of Estimates

​

The preparation of condensed consolidated financial statements in accordance with U.S. generally accepted accounting principles requires the Company’s management to make estimates and judgments that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. On an on-going basis, the Company’s management evaluates its estimates, judgments and methodologies. Significant estimates and assumptions in the condensed consolidated financial statements include those related to revenue recognition; available-for-sale securities; accounts receivable; inventory valuation, and related reserves; impairment of long-lived assets, including goodwill; valuation procedures for right-of-use assets and operating lease liabilities; initial valuation procedures for the issuance of convertible notes; valuation of assets and liabilities held for disposition and losses related to discontinued operations; fair value of derivatives; balance sheet classification of notes payable and convertible notes; income taxes, including the valuation allowance for deferred tax assets; research and development expenses; contingencies and share-based compensation. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ materially from these estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known.

​

Reclassifications of Prior Period Financial Statements

​

Certain prior period financial statement items, such as discontinued operations, have been reclassified to conform to current period presentation.

​

Summary of Significant Accounting Policies

​

The Company’s significant accounting policies are described in Note 2, Summary of Significant Accounting Policies, in the 2018 Annual Report on Form 10-K. During the six months ended June 30, 2019, the Company adopted the following additional significant accounting policies:

​

Discontinued Operations

​

During the three months ended June 30, 2019, the Company determined that its sGC business met the criteria for classification as a discontinued operation in accordance with Accounting Standards Codification (“ASC”) Subtopic 205-20, Discontinued Operations. Accordingly, the accompanying condensed consolidated financial statements for all periods presented have been recast to present the assets and liabilities associated with the sGC business as held for disposition and the expenses directly associated with the sGC business as discontinued operations. For additional information related to discontinued operations, refer to Note 2, Cyclerion Separation, to these condensed consolidated financial statements.

​

Leases

Effective January 1, 2019, the Company adopted ASC Topic 842, Leases (“ASC 842”), using the optional transition method. The adoption of ASC 842 represents a change in accounting principle that aims to increase transparency and comparability among organizations by requiring the recognition of right-of-use assets and lease liabilities on the balance sheet for both operating and finance leases. In addition, the standard requires enhanced disclosures that meet the objective of enabling financial statement users to assess the amount, timing, and uncertainty of cash flows arising from leases. The reported results for the three and six months ended June 30, 2019 reflect the application of ASC 842 guidance, while the reported results for prior periods were prepared in conjunction with ASC Topic 840, Leases (“ASC 840”). Because there were no material changes to the values of capital leases as a result of adoption of ASC 842, the Company concluded that no cumulative-effect adjustment to the accumulated deficit as of January 1, 2019 was necessary.

​

The recognition of right-of-use assets and lease liabilities related to our operating leases under ASC 842 has had a material impact on the Company’s condensed consolidated financial statements.

12

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​

As part of the ASC 842 adoption, the Company elected certain practical expedients outlined in the guidance. These practical expedients include:

​

| ● | Accounting policy election to use the short-term lease exception by asset class;

| ● | Election of the practical expedient package during transition, which includes:

| o | An entity need not reassess whether any expired or existing contracts are or contain leases.

| o | An entity need not reassess the classification for any expired or existing leases. As a result, all leases that were classified as operating leases in accordance with ASC 840 are classified as operating leases under ASC 842, and all leases that were classified as capital leases in accordance with ASC 840 are classified as finance leases under ASC 842.

| o | An entity need not reassess initial direct costs for any existing leases.

​

Subsequent to the Company’s adoption of ASC 842, the Company elected the post-transition practical expedient, by class of underlying asset, to account for lease components and non-lease components together as a single component for the asset class of operating lease right-of-use real estate assets.

​

The Company’s lease portfolio includes: leases for its current and future headquarters locations, a data center colocation lease, vehicle leases for its salesforce representatives, and leases for computer and office equipment. The Company determines if an arrangement is a lease at the inception of the contract. The asset component of the Company’s operating leases is recorded as operating lease right-of-use assets, and the liability component is recorded as current portion of operating lease liabilities and operating lease liabilities, net of current portion in the Company’s condensed consolidated balance sheets. As of June 30, 2019, the Company did not have any finance leases.

​

Right-of-use assets and operating lease liabilities are recognized based on the present value of lease payments over the lease term at the lease inception date. Existing leases in the Company’s lease portfolio as of the adoption date were valued as of January 1, 2019. The Company uses an incremental borrowing rate based on the information available at lease inception in determining the present value of lease payments, if an implicit rate of return is not provided with the lease contract. Operating lease right-of-use assets are adjusted for incentives expected to be received.

​

Right-of-use assets and operating lease liabilities are remeasured upon certain modifications to leases using the present value of remaining lease payments and estimated incremental borrowing rate upon lease modification.

​

Lease cost is recognized on a straight-line basis over the lease term, and includes amounts related to short-term leases. The Company recognizes variable lease payments as operating expenses in the period in which the obligation for those payments is incurred. Variable lease payments primarily include common area maintenance, utilities, real estate taxes, insurance, and other operating costs that are passed on from the lessor in proportion to the space leased by the Company.

​

New Accounting Pronouncements

​

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (the “FASB”) or other standard setting bodies that are adopted by the Company as of the specified effective date. Except as set forth below, the Company did not adopt any new accounting pronouncements during the three and six months ended June 30, 2019 that had a material effect on its condensed consolidated financial statements.

​

In February 2016, the FASB issued ASU No. 2016-02, Leases (“ASU 2016-02”), which supersedes the lease accounting requirements in ASC 840 and most industry-specific guidance with ASC 842. ASU 2016-02 requires the identification of arrangements that should be accounted for as leases by lessees. In general, lease arrangements exceeding a 12-month term must now be recognized as assets and liabilities on the balance sheet of the lessee. Under ASU 2016-02, a right-of-use asset and lease obligation are recorded for all leases, whether operating or financing, while the income statement will reflect lease expense for operating leases and amortization and interest expense for financing leases. The balance sheet amounts recorded for existing leases at the date of adoption of ASU 2016-02 must be calculated using the applicable incremental borrowing rate at the date of adoption. ASU 2016-02 is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. Early adoption is permitted. Subsequent to the issuance of ASU 2016-02, the FASB issued ASU No. 2018-10, Leases (Topic 842),

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Codification Improvements (“ASU 2018-10”), ASU No. 2018-11, Leases (Topic 842), Targeted Improvements (“ASU 2018-11”), and ASU No. 2019-01 Leases (Topic 842), Codification Improvements (“ASU 2019-01”) to provide additional guidance for the adoption of Topic 842. ASU 2018-10 clarifies certain provisions and corrects unintended applications of the guidance, such as the rate implicit in a lease, impairment of the net investment in a lease, lessee reassessment of lease classifications, lessor reassessment of lease term and purchase options, variable payments that depend on an index or rate and certain transition adjustments. The amendments in ASU 2018-11 allow for an additional transition method, whereby at the adoption date the entity recognizes a cumulative-effect adjustment to the opening balance of retained earnings in the period of adoption, while the comparative period disclosures continue recognition under ASC 840. Additionally, ASU 2018-11 includes a practical expedient for separating contract components for lessors. The Company adopted ASC 842 using the optional transition method outlined in ASU 2018-11 as of January 1, 2019. The adoption of ASC 842 resulted in the recognition of operating lease right-of-use assets of approximately $88.3 million and corresponding lease liabilities of approximately $94.9 million. The adoption of these ASUs did not have a material impact on the Company’s results of operations; however, the adoption resulted in significant changes to the Company’s financial statement disclosures.

​

In June 2016, the FASB issued ASU No. 2016-13, Measurement of Credit Losses on Financial Instruments (“ASU 2016-13”). ASU 2016-13 will change how companies account for credit losses for most financial assets and certain other instruments. For trade receivables, loans and held-to-maturity debt securities, companies will be required to recognize an allowance for credit losses rather than reducing the carrying value of the asset. Subsequent to the issuance of ASU 2016-13, the FASB issued ASU No. 2019-04, Codification Improvements to Topic 326, Financial Instruments—Credit Losses, Topic 815, Derivatives and Hedging, and Topic 825, Financial Instruments (“ASU 2019-04”) and ASU No. 2019-05, Financial Instruments—Credit Losses (Topic 326): Targeted Transition Relief (“ASU 2019-05”) to provide additional guidance on the adoption of ASU 2016-13. ASU 2019-04 added Topic 326, Financial Instruments—Credit Losses, and made several amendments to the codification and also modified the accounting for available-for-sale debt securities. ASU 2019-05 provides targeted transition relief by providing an option to irrevocably elect the fair value option for certain financial assets previously measured at amortized cost basis. ASU 2016-13, ASU 2019-04 and ASU 2019-05 are effective for fiscal years beginning after December 15, 2019, including interim periods within those fiscal years. Early adoption is permitted. The Company is currently evaluating the potential impact that the adoption of these ASUs will have on the Company’s financial position and results of operations.

​

In January 2017, the FASB issued ASU No. 2017-04, Intangibles—Goodwill and Other (Topic 350) (“ASU 2017-04”) to simplify the accounting for goodwill impairment by removing Step 2 of the goodwill impairment test. ASU 2017-04 is effective for fiscal years beginning after December 15, 2019. Early adoption is permitted. The Company is evaluating the potential impact that the adoption of ASU 2017-04 may have on the Company’s financial position and results of operations.

​

In June 2018, the FASB issued ASU No. 2018-07, Compensation—Stock Compensation (Topic 718) (“Topic 718”): Improvements to Nonemployee Share-Based Payment Accounting (“ASU 2018-07”). ASU 2018-07 expands the scope of Topic 718 to include share-based payment transactions for acquiring goods and services from non-employees, and as a result, the accounting for share-based payments to non-employees will be substantially aligned. ASU 2018-07 is effective for fiscal years beginning after December 15, 2018, including interim periods within that fiscal year. Early adoption is permitted but not earlier than an entity’s adoption date of Topic 606. The Company adopted this standard during the three months ended March 31, 2019. The adoption of ASU 2018-07 did not have a material impact on the Company’s financial position and results of operations.

​

In July 2018, the FASB issued ASU 2018-09, Codification Improvements (“ASU 2018-09”). The amendments in ASU 2018-09 affect a wide variety of Topics in the FASB codification and apply to all reporting entities within the scope of the affected accounting guidance. The Company has evaluated ASU 2018-09 in its entirety and determined that the amendments related to Topic 718-740, Compensation—Stock Compensation—Income Taxes, are the only provisions that currently apply to the Company. The amendments in ASU 2018-09 related to Topic 718-740, Compensation—Stock Compensation—Income Taxes, clarify that an entity should recognize excess tax benefits related to stock compensation transactions in the period in which the amount of the deduction is determined. The amendments in ASU 2018-09 related to Topic 718-740 are effective for fiscal years beginning after December 15, 2018, with early adoption permitted. The Company adopted this standard during the three months ended March 31, 2019. The adoption of this standard did not have a material impact on the Company’s financial position and results of operations.

​

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In August 2018, the FASB issued ASU No. 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirement for Fair Value Measurement (“ASU 2018-13”) which amends the disclosure requirements for fair value measurements. The amendments in ASU 2018-13 are effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-13 may have on the Company’s financial position and results of operations.

​

In August 2018, the FASB issued ASU No. 2018-15, Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer's Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement that is a Service Contract (a consensus of the FASB Emerging Issues Task Force) (“ASU 2018-15)” which provides additional guidance on the accounting for costs of implementation activities performed in a cloud computing arrangement that is a service contract. The amendments in ASU 2018-15 are effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-15 may have on the Company’s financial position and results of operations.

​

In October 2018, the FASB issued ASU No. 2018-17, Consolidation (Topic 810): Targeted Improvements to Related Party Guidance for Variable Interest Entities (“ASU 2018-17”). The update is intended to improve general purpose financial reporting by considering indirect interests held through related parties in common control arrangements on a proportional basis for determining whether fees paid to decision makers and service providers are variable interests. The amendments in ASU 2018-17 will be effective for fiscal years beginning after December 15, 2019, with early adoption permitted. The Company is currently evaluating the potential impact that the adoption of ASU 2018-17 may have on the Company’s financial position and results of operations.

​

No other accounting standards known by the Company to be applicable to it that have been issued by the FASB or other standard-setting bodies and that do not require adoption until a future date are expected to have a material impact on the Company’s consolidated financial statements upon adoption.

​

2. Cyclerion Separation

​

On April 1, 2019, Ironwood completed the Separation of Cyclerion. The Separation was effected by means of a distribution of all of the outstanding shares of common stock, with no par value, of Cyclerion through a dividend of Cyclerion’s common stock, to Ironwood’s stockholders of record as of the close of business on March 19, 2019. Prior to the Separation on April 1, 2019, as described in Note 1, Nature of Business, Cyclerion was a wholly owned subsidiary of the Company. On March 30, 2019, the Company entered into certain agreements with Cyclerion relating to the Separation, including a separation agreement, a tax matters agreement, and an employee matters agreement.

​

Agreements with Cyclerion

​

The separation agreement with Cyclerion, dated as of March 30, 2019, sets forth, among other things, the Company’s agreements with Cyclerion regarding the principal actions to be taken in connection with the Separation, including the distribution, which was effective as of April 1, 2019. The separation agreement identifies assets transferred, liabilities assumed by and contracts assigned to each of Cyclerion and Ironwood as part of the Separation, and it provides for when and how these transfers, assumptions and assignments occur. The purpose of the separation agreement is to provide Cyclerion and Ironwood with assets to operate their respective businesses and retain or assume liabilities related to those assets.

​

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The transfer of assets and liabilities to Cyclerion was effected through a contribution in accordance with the separation agreement as summarized below (in thousands):

​

​ | ​ | ​ | ​ | ​
​ | ​ | ​ | As of April 1, 2019 | ​
Assets: | ​ | ​ | ​ | ​
Prepaid expenses and other current assets | ​ | $ | 1,169 | ​
Property and equipment, net | ​ | ​ | 10,241 | ​
Other assets | ​ | ​ | 21 | ​
​ | ​ | $ | 11,431 | ​
Liabilities: | ​ | ​ | ​ | ​
Accrued research and development costs | ​ | $ | 5,673 | ​
Accrued expenses and other current liabilities | ​ | ​ | 3,149 | ​
​ | ​ | $ | 8,822 | ​
Net Assets Transferred to Cyclerion | ​ | $ | 2,609 | ​
​ | ​ | ​ | ​ | ​

​

In addition, the Company is due approximately $1.3 million as of June 30, 2019 associated with tenant improvement reimbursement provisions related to the Cyclerion lease in accordance with the separation agreement, which has been included in related party accounts receivable.

​

The tax matters agreement, dated as of March 30, 2019, governs each party’s rights, responsibilities and obligations with respect to taxes, including taxes, if any, incurred as a result of any failure of the Separation to qualify as tax-free. In general, if the parties incur tax liabilities in the event that the Separation is not tax-free, each party is expected to be responsible for any taxes imposed on Ironwood or Cyclerion that arise from the failure of the Separation to qualify as a transaction that is generally tax-free for U.S. federal income tax purposes, under Sections 355 and 368(a)(1)(D) and certain other relevant provisions of the Internal Revenue Code of 1986, as amended, to the extent that the failure to so qualify is attributable to an acquisition of stock or assets of, or certain actions, omissions or failures to act of, such party. If both Ironwood and Cyclerion are responsible for such failure, liability will be shared according to relative fault. U.S. tax otherwise resulting from the failure of the Separation to qualify as a transaction that is tax-free generally will be the responsibility of Ironwood. Each party otherwise agreed to indemnify the other party from and against any liability for taxes allocated to such party under the tax matters agreement and any taxes resulting from breach of any such party’s covenants under the tax matters agreement, the separation agreement, or any ancillary agreement entered into in connection with the Separation. Cyclerion agreed to certain covenants that contain restrictions intended to preserve the tax-free status of the distribution and certain related transactions.

​

The employee matters agreement, dated as of March 30, 2019, allocates assets, liabilities and responsibilities relating to the employment, compensation, and employee benefits of Ironwood and Cyclerion employees, and other related matters in connection with the Separation, including the treatment of outstanding Ironwood incentive equity awards. Pursuant to the employee matters agreement, the outstanding Ironwood equity awards held by Cyclerion and Ironwood employees were adjusted in connection with the Separation, with the intent to maintain, immediately following the Separation, the economic value of the awards. No incremental stock-based compensation expense was recognized during the three months ended June 30, 2019 (Note 10).

​

Additionally, the Company entered into two transition services agreements and a development agreement with Cyclerion.

​

Pursuant to the transition service agreements, the Company is obligated to provide and is entitled to receive certain transition services related to corporate functions, such as finance, procurement, facilities and development. Services provided by the Company to Cyclerion will continue for an initial term of one to two years from the date of the Separation (as applicable), unless earlier terminated or extended according to the terms of the transition services agreement. Services provided by Cyclerion to the Company will continue for an initial term of one year from the date of the Separation, unless earlier terminated or extended according to the terms of such transition services agreement. Services received and performed are paid at a mutually agreed upon rate. Amounts for services provided to Cyclerion are recorded as other income and amounts for services provided by Cyclerion are recorded as selling, general and administrative expense and research and development expense, as applicable. During each of the three and six months ended June 30, 2019, the Company recorded an insignificant amount as other income for services provided to Cyclerion.

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During each of the three and six months ended June 30, 2019, the Company recorded an insignificant amount in both selling, general and administrative expense and research and development expense for services provided by Cyclerion.

​

Pursuant to the development agreement, Cyclerion is obligated to provide the Company with certain research and development services with respect to certain of Ironwood’s products and product candidates, including MD-7246 and IW-3718. Such research and development activities are governed by a joint steering committee comprised of representatives from both Cyclerion and Ironwood. Services received are paid at a mutually agreed upon rate. The Company recorded approximately $1.7 million in research and development expenses under the development agreement during the three months ended June 30, 2019.

​

Discontinued Operations

​

Upon Separation, the Company determined its sGC business qualified for discontinued operations accounting treatment in accordance with ASC Subtopic 205-20, Discontinued Operations. The following is a summary of expenses of Cyclerion for the three and six months ended June 30, 2019 and 2018 (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​ | June 30, | ​
​ | ​ | 2019 |  | 2018 | ​ | 2019 |  | 2018 |
Costs and expenses: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Research and development | ​ | ​ | — |  | ​ | 15,745 | ​ | ​ | 21,792 |  | ​ | 31,774 | ​
Selling, general and administrative | ​ | ​ | — |  | ​ | 8,592 | ​ | ​ | 15,646 |  | ​ | 9,148 | ​
Restructuring expenses | ​ | ​ | — | ​ | ​ | 906 | ​ | ​ | — | ​ | ​ | 906 | ​
Net loss from discontinued operations | ​ | ​ | — | ​ | ​ | 25,243 | ​ | ​ | 37,438 | ​ | ​ | 41,828 | ​

​

There were no assets and liabilities related to discontinued operations as of June 30, 2019, as all balances were transferred to Cyclerion upon Separation. The following is a summary of assets and liabilities of discontinued operations as of December 31, 2018 (in thousands):

​

​ | ​ | ​ | ​
Assets: | ​ | ​ | ​
Prepaid expenses and other current assets | ​ | $ | 847
Property and equipment, net | ​ | ​ | 9,618
Other assets | ​ | ​ | 25
​ | ​ | $ | 10,490
Liabilities: | ​ | ​ | ​
Accounts payable | ​ | $ | 3,232
Accrued research and development costs | ​ | ​ | 5,256
Accrued expenses and other current liabilities | ​ | ​ | 7,251
​ | ​ | $ | 15,739

​

​

​

​

3. Net Income (Loss) Per Share

​

Basic and diluted net income (loss) per common share is computed by dividing net (income) loss by the weighted average number of common shares outstanding during the period.

​

In June 2015, in connection with the issuance of approximately $335.7 million in aggregate principal amount of 2.25% Convertible Senior Notes due 2022 (the “2022 Notes”) (Note 9), the Company entered into convertible note hedge transactions (the “Convertible Note Hedges”). The Convertible Note Hedges are generally expected to reduce the potential dilution to the Company’s Class A common stockholders upon a conversion of the 2022 Notes and/or offset any cash payments the Company is required to make in excess of the principal amount of converted 2022 Notes in the event that the market price per share of the Company’s Class A common stock, as measured under the terms of the Convertible Note Hedges, is greater than the conversion price of the 2022 Notes. The Convertible Note Hedges are not considered for purposes of calculating the number of diluted weighted average shares outstanding, as their effect would be anti-dilutive.

​

Concurrently with entering into the Convertible Note Hedges, the Company also entered into certain warrant transactions in which it sold note hedge warrants (the “Note Hedge Warrants”) to the Convertible Note Hedge

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counterparties to acquire shares of the Company’s Class A common stock, subject to customary anti-dilution adjustments (Note 9). The Note Hedge Warrants could have a dilutive effect on the Company’s Class A common stock to the extent that the market price per share of the Class A common stock exceeds the applicable strike price of such warrants. The Note Hedge Warrants are not considered for purposes of calculating the number of diluted weighted averages shares outstanding, as their effect would be anti-dilutive.

​

The following potentially dilutive securities have been excluded from the computation of diluted weighted average shares outstanding, as applicable, as their effect would be anti-dilutive (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​
​ |  | 2019 |  | 2018 |
Options to purchase Class A common stock | ​ | 19,324 |  | 22,056 |
Shares subject to repurchase |  | 182 |  | 130 |
Restricted stock units | ​ | 2,799 | ​ | 3,207 | ​
Note Hedge Warrants | ​ | 23,135 | ​ | 20,250 | ​
2022 Notes | ​ | 23,135 | ​ | 20,250 | ​
Total |  | 68,575 |  | 65,893 |

​

​

During the three and six months ended June 30, 2019, the Company recorded net income of approximately $12.3 million and net loss of approximately $47.0 million, respectively. The inclusion of applicable securities in the calculation of diluted earnings per share was anti-dilutive for the three months ended June 30, 2019. As a result, diluted earnings per share is equivalent to basic earnings per share for the three and six months ended June 30, 2019.

​

​

4. Collaboration, License, Co-Promotion and Other Commercial Agreements

​

For the three and six months ended June 30, 2019, the Company had linaclotide collaboration agreements with Allergan for North America and AstraZeneca for China, Hong Kong and Macau, as well as linaclotide license agreements with Astellas for Japan and with Allergan for the Allergan License Territory. The Company also had agreements with Allergan to co-promote VIBERZI in the U.S. The following table provides amounts included in the Company’s condensed consolidated statements of operations as collaborative arrangements revenue and sale of active pharmaceutical ingredient (“API”) attributable to transactions from these arrangements (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​ | June 30, | ​
Collaborative Arrangements Revenue | ​ | 2019 |  | 2018 | ​ | 2019 |  | 2018 |
Linaclotide Agreements: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Allergan (North America) | ​ | $ | 75,498 | ​ | $ | 69,810 | ​ | $ | 140,283 | ​ | $ | 131,408 | ​
Allergan (Europe and other) | ​ | ​ | 262 | ​ | ​ | 304 | ​ | ​ | 682 | ​ | ​ | 576 | ​
Co-Promotion and Other Agreements: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Allergan (VIBERZI) | ​ | ​ | 1,239 | ​ | ​ | 750 | ​ | ​ | 1,239 | ​ | ​ | 1,500 | ​
Other | ​ | ​ | 323 | ​ | ​ | 343 | ​ | ​ | 1,270 | ​ | ​ | 809 | ​
Total collaborative arrangements revenue | ​ | $ | 77,322 | ​ | $ | 71,207 | ​ | $ | 143,474 | ​ | $ | 134,293 | ​
Sale of API (1) | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Linaclotide Agreements: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Astellas (Japan) | ​ | $ | 24,893 | ​ | $ | 8,803 | ​ | $ | 27,468 | ​ | $ | 14,237 | ​
Other (1) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 3 | ​ | ​ | — | ​
Total sale of API | ​ | $ | 24,893 | ​ | $ | 8,803 | ​ | $ | 27,471 | ​ | $ | 14,237 | ​

(1) Sale of API includes an insignificant amount of revenue from the sale of drug product to AstraZeneca in China during the six months ended June 30, 2019.

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​

Accounts receivable, net and related party accounts receivable, net included approximately $103.8 million related to collaborative arrangements revenue and sale of API as of June 30, 2019, net of approximately $4.3 million related to related party accounts payable.

​

As of June 30, 2019, there were no impairment indicators for the accounts receivable recorded. During the three and six months ended June 30, 2019, there was no significant unusual activity in accounts receivable.

​

Linaclotide Agreements

​

Collaboration Agreement for North America with Allergan

​

In September 2007, the Company entered into a collaboration agreement with Allergan to develop and commercialize linaclotide for the treatment of IBS-C, CIC and other GI conditions in North America. Under the terms of this collaboration agreement, the Company received a non-refundable, upfront licensing fee and shares equally with Allergan all development costs as well as net profits or losses from the development and sale of linaclotide in the U.S. The Company receives royalties in the mid-teens percent based on net sales in Canada and Mexico. Allergan is solely responsible for the further development, regulatory approval and commercialization of linaclotide in those countries and funding any costs. The collaboration agreement for North America also includes contingent milestone payments, as well as a contingent equity investment, based on the achievement of specific development and commercial milestones. At June 30, 2019, $205.0 million in license fees and all six development milestone payments had been received by the Company, as well as a $25.0 million equity investment in the Company’s capital stock (Note 11). The Company can also achieve up to $100.0 million in a sales-related milestone if certain conditions are met, which will be recognized as collaborative arrangements revenue when it is probable that a significant reversal of revenue would not occur and the associated constraints have been lifted.

​

As a result of the research and development cost-sharing provisions of the linaclotide collaboration for North America, the Company offset approximately $2.4 million and approximately $5.6 million in incremental research and development costs during the three and six months ended June 30, 2019, respectively, and offset approximately $1.9 million and approximately $3.3 million in incremental research and development costs during the three and six months ended June 30, 2018, respectively, to reflect the obligations of each party under the collaboration to bear half of the development costs incurred.

​

The Company and Allergan began commercializing LINZESS in the U.S. in December 2012. The Company receives 50% of the net profits and bears 50% of the net losses from the commercial sale of LINZESS in the U.S. Net profits or net losses consist of net sales of LINZESS to third-party customers and sublicense income in the U.S. less the cost of goods sold as well as selling, general and administrative expenses. LINZESS net sales are calculated and recorded by Allergan and may include gross sales net of discounts, rebates, allowances, sales taxes, freight and insurance charges, and other applicable deductions. If either party provided fewer calls on physicians in a particular year than it was contractually required to provide, such party’s share of the net profits would be adjusted as set forth in the collaboration agreement for North America. The Company has completed its obligations under the terms of the commercial agreement with Allergan, pursuant to which it promoted CANASA, and these adjustments to the share of the net profits have been eliminated, in full, in 2018 and all subsequent years.

​

The Company evaluated this collaboration arrangement under ASC 606, Revenue from Contracts with Customers (“ASC 606”), and concluded that all development-period performance obligations had been satisfied as of September 2012. However, the Company has determined that there are three remaining commercial-period performance obligations, which include the sales detailing of LINZESS, participation in the joint commercialization committee, and approved additional trials. The consideration remaining includes cost reimbursements in the U.S., as well as commercial sales-based milestones and net profit and loss sharing payments based on net sales in the U.S. Additionally, the Company receives royalties in the mid-teens percent based on net sales in Canada and Mexico. Royalties, commercial sales-based milestones, and net profit and loss sharing payments will be recorded as collaborative arrangements revenue or expense in the period earned, in accordance with the sales-based royalty exception, as these payments relate predominately to the license granted to Allergan. The Company records royalty revenue in the period earned based on royalty reports from its partner, if available, or based on the projected sales and historical trends. The cost reimbursements received from Allergan during the commercialization period will be recognized as billed in accordance

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with the right-to-invoice exemption, as the Company’s right to consideration corresponds directly with the value of the services transferred during the commercialization period.

Under the Company’s collaboration agreement with Allergan for North America, LINZESS net sales are calculated and recorded by Allergan and include gross sales net of discounts, rebates, allowances, sales taxes, freight and insurance charges, and other applicable deductions, as noted above. These amounts include the use of estimates and judgments, which could be adjusted based on actual results in the future. The Company records its share of the net profits or net losses from the sales of LINZESS in the U.S. on a net basis less commercial expenses, and presents the settlement payments to and from Allergan as collaboration expense or collaborative arrangements revenue, as applicable. This treatment is in accordance with the Company’s revenue recognition policy, given that the Company is not the primary obligor and does not have the inventory risks in the collaboration agreement with Allergan for North America. The Company relies on Allergan to provide accurate and complete information related to net sales of LINZESS in accordance with U.S. generally accepted accounting principles in order to calculate its settlement payments to and from Allergan and record collaboration expense or collaborative arrangements revenue, as applicable.

​

The Company recognized collaborative arrangements revenue from the Allergan collaboration agreement for North America during the three and six months ended June 30, 2019 and 2018 as follows (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​ | June 30, | ​
​ |  | 2019 |  | 2018 |  | 2019 |  | 2018 |
Collaborative arrangements revenue related to sales of LINZESS in the U.S. | ​ | $ | 74,973 | ​ | $ | 69,264 | ​ | $ | 139,267 | ​ | $ | 130,413 | ​
Royalty revenue | ​ |  | 525 |  | ​ | 546 | ​ |  | 1,016 |  | ​ | 995 | ​
Total collaborative arrangements revenue | ​ | $ | 75,498 | ​ | $ | 69,810 | ​ | $ | 140,283 | ​ | $ | 131,408 | ​

​

The collaborative arrangements revenue recognized in the three and six months ended June 30, 2019 and 2018 primarily represents the Company’s share of the net profits and net losses on the sale of LINZESS in the U.S.

​

The following table presents the amounts recorded by the Company for commercial efforts related to LINZESS in the U.S. in the three and six months ended June 30, 2019 and 2018 (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​ | June 30, | ​
​ |  | 2019 |  | 2018 |  | 2019 |  | 2018 |
Collaborative arrangements revenue related to sales of LINZESS in the U.S.(1)(2) | ​ | $ | 74,973 | ​ | $ | 69,264 | ​ | $ | 139,267 | ​ | $ | 130,413 | ​
Selling, general and administrative costs incurred by the Company(1) | ​ |  | (10,359) | ​ |  | (11,713) | ​ |  | (20,636) | ​ |  | (22,641) | ​
The Company’s share of net profit | ​ | $ | 64,614 | ​ | $ | 57,551 | ​ | $ | 118,631 | ​ | $ | 107,772 | ​

(1) | Includes only collaborative arrangement revenue or selling, general and administrative costs attributable to the cost-sharing arrangement with Allergan for the three and six months ended June 30, 2019 and 2018.

​

In May 2014, CONSTELLA became commercially available in Canada and in June 2014, LINZESS became commercially available in Mexico. The Company records royalties on sales of CONSTELLA in Canada and LINZESS in Mexico in the period earned. The Company recognized approximately $0.5 million and approximately $1.0 million of combined royalty revenues from Canada and Mexico during the three and six months ended June 30, 2019, respectively. The Company recognized approximately $0.6 million and approximately $1.0 million of combined royalty revenues from Canada and Mexico during the three and six months ended June 30, 2018, respectively.

​

License Agreement with Allergan (All countries other than the countries and territories of North America, China, Hong Kong, Macau, and Japan)

​

In April 2009, the Company entered into a license agreement with Almirall, S.A. (“Almirall”) to develop and commercialize linaclotide in Europe (including the Commonwealth of Independent States and Turkey) for the treatment of IBS-C, CIC and other GI conditions (the “European License Agreement”). In accordance with the European License Agreement, the Company granted Almirall a right to access its U.S. Phase III clinical trial data for the purposes of supporting European regulatory approval. Additionally, the Company was required to participate on a joint development

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committee during linaclotide’s development period and is required to participate in a joint commercialization committee while linaclotide is commercially available. In October 2015, Almirall transferred its exclusive license to develop and commercialize linaclotide in Europe to Allergan.

​

Additionally, in October 2015, the Company and Allergan separately entered into an amendment to the European License Agreement relating to the development and commercialization of linaclotide in Europe. Pursuant to the terms of the amendment, (i) certain sales-based milestones payable to the Company under the European License Agreement were modified to increase the total milestone payments such that, when aggregated with certain commercial launch milestones, they could total up to $42.5 million, (ii) the royalties payable to the Company during the term of the European License Agreement were modified such that the royalties based on sales volume in Europe begin in the mid-single digit percent and escalate to the upper-teens percent by calendar year 2019, and (iii) Allergan assumed responsibility for the manufacturing of linaclotide API for Europe from the Company, as well as the associated costs. The Company concluded that the 2015 amendment to the European License Agreement was not a modification to the linaclotide collaboration agreement with Allergan for North America.

​

In January 2017, concurrently with entering into the commercial agreement as described below in Commercial Agreement with Allergan, the Company and Allergan entered into an amendment to the European License Agreement (the “2017 Amendment”). The European License Agreement, as amended (the “Allergan License Agreement”), extended the license to develop and commercialize linaclotide in all countries other than China, Hong Kong, Macau, Japan, and the countries and territories of North America. On a country-by-country and product-by-product basis in such additional territory, Allergan is obligated to pay the Company a royalty as a percentage of net sales of products containing linaclotide as an active ingredient in the upper-single digits for five years following the first commercial sale of a linaclotide product in a country, and in the low-double digits thereafter. The royalty rate for products in the expanded territory will decrease, on a country-by-country basis, to the lower-single digits, or cease entirely, following the occurrence of certain events. Allergan is also obligated to assume certain purchase commitments for quantities of linaclotide API under the Company’s agreements with third-party API suppliers. The amendment to the European License Agreement did not modify any of the milestones or royalty terms related to Europe.

Prior to the adoption of ASC 606, the Company concluded that the 2017 Amendment was a material modification to the European License Agreement; however, this modification did not have a material impact on the Company's condensed consolidated financial statements as there was no deferred revenue associated with the European License Agreement. The Company also concluded that the 2017 Amendment was not a material modification to the linaclotide collaboration agreement with Allergan for North America.

In evaluating the terms of the 2009 European License Agreement under ASC 606, the Company determined that there are no remaining performance obligations as of September 2012. However, the Company continues to be eligible to receive consideration in the form of commercial launch milestones, sales-based milestones, and royalties.

The commercial launch milestones, sales-based milestones and royalties under the European License Agreement have historically been recognized as revenue as earned. Under ASC 606, the Company applied the sales-based royalty exception to royalties and sales-based milestones, as these payments relate predominantly to the license granted to Allergan (formerly Almirall). Accordingly, the royalties and sales-based milestones are recorded as revenue in the period earned. The Company records royalties on sales of CONSTELLA in Europe in the period earned based on royalty reports from its partner, if available, or the projected sales and historical trends. The commercial launch milestones are recognized as revenue when it is probable that a significant reversal of revenue would not occur and the associated constraint has been lifted.

Additionally, the Company evaluated the terms of the 2017 Amendment under ASC 606 and determined that it would be treated as a separate contract given that it adds a distinct good or service at an amount that reflects standalone selling price. The Company determined that all performance obligations in the 2017 Amendment were satisfied in January 2017 when the license for the additional territory was transferred. The Company continues to receive royalties under this agreement, which are recorded in the period earned pursuant to the sales-based royalty exception, as they related predominantly to the license granted to Allergan.

​

The Company recognized approximately $0.3 million and approximately $0.7 million of royalty revenue from the European License Agreement during the three and six months ended June 30, 2019, respectively, and recognized

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approximately $0.3 million and approximately $0.6 million during the three and six months ended June 30, 2018, respectively.

​

License Agreement for Japan with Astellas

​

In November 2009, the Company entered into a license agreement with Astellas, as amended, to develop and commercialize linaclotide for the treatment of IBS-C, CIC and other GI conditions in Japan (the “2009 License Agreement with Astellas”). Astellas is responsible for all activities relating to development, regulatory approval and commercialization in Japan as well as funding the associated costs and the Company is required to participate on a joint development committee over linaclotide’s development period. During the year ended December 31, 2017, the Company and Astellas entered into a commercial API supply agreement (the “Astellas Commercial Supply Agreement”). Pursuant to the Astellas Commercial Supply Agreement, the Company sells linaclotide API supply to Astellas at a contractually defined rate and recognizes related revenue as sale of API. Under the license agreement, the Company receives royalties which escalate based on sales volume, beginning in the low-twenties percent, less the transfer price paid for the API included in the product actually sold and other contractual deductions.

Under the 2009 License Agreement with Astellas, the Company received an up-front licensing fee of $30.0 million and three development milestone payments that totaled up to $45.0 million, which were recognized as revenue prior to the adoption of ASC 606 on January 1, 2018.

​

The Company had evaluated the terms of the 2009 License Agreement with Astellas under ASC 606 and determined that there were no remaining performance obligations as of the adoption of ASC 606. However, there continues to be consideration in the form of royalties on sales of LINZESS in Japan under the 2009 License Agreement with Astellas. Upon adoption of ASC 606, the Company concluded that the royalties on sales of LINZESS in Japan relate predominantly to the license granted to Astellas. Accordingly, the Company applies the sales-based royalty exception and records royalties on sales of LINZESS in Japan in the period earned based on royalty reports from its partner, if available, or the projected sales and historical trends.

​

Additionally, under the terms of the Astellas Commercial Supply Agreement, the Company continues to have an ongoing performance obligation to supply API. Upon adoption of ASC 606, product revenue is recognized when the customer obtains control of the Company’s product, which occurs at a point in time, typically upon shipment of the product to the customer. This results in earlier revenue recognition than the Company’s historical accounting.

​

The Company recognized approximately $24.9 million and approximately $27.5 million from the sale of API to Astellas under the license agreement and the Astellas Commercial Supply Agreement during the three and six months ended June 30, 2019, respectively, and recognized approximately $8.8 million and approximately $14.2 million during the three and six months ended June 30, 2018, respectively. The royalties on sales of LINZESS in Japan did not exceed the transfer price of API sold and other contractual deductions during each of the periods presented.

​

Collaboration Agreement for China, Hong Kong and Macau with AstraZeneca

​

In October 2012, the Company entered into a collaboration agreement with AstraZeneca (the “AstraZeneca Collaboration Agreement”) to co-develop and co-commercialize linaclotide in China, Hong Kong and Macau (the “License Territory”). The collaboration provides AstraZeneca with an exclusive nontransferable license to exploit the underlying technology in the License Territory. The parties share responsibility for continued development and commercialization of linaclotide under a joint development plan and a joint commercialization plan, respectively, with AstraZeneca having primary responsibility for the local operational execution.

The parties agreed to an Initial Development Plan (“IDP”) which includes the planned development of linaclotide in China, including the lead responsibility for each activity and the related internal and external costs. The IDP indicates that AstraZeneca is responsible for a multinational Phase III clinical trial (the “Phase III Trial”). The Company is responsible for nonclinical development and supplying clinical trial material and both parties are responsible for the regulatory submission process. The IDP indicates that the party specifically designated as being responsible for a particular development activity under the IDP shall implement and conduct such activities. The activities are governed by a Joint Development Committee (“JDC”), with equal representation from each party. The JDC is responsible for approving, by unanimous consent, the joint development plan and development budget, as well as approving protocols

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for clinical studies, reviewing and commenting on regulatory submissions, and providing an exchange of data and information.

The AstraZeneca Collaboration Agreement will continue until there is no longer a development plan or commercialization plan in place, however, it can be terminated by AstraZeneca at any time upon 180 days’ prior written notice. Under certain circumstances, either party may terminate the AstraZeneca Collaboration Agreement in the event of bankruptcy or an uncured material breach of the other party. Upon certain change in control scenarios of AstraZeneca, the Company may elect to terminate the AstraZeneca Collaboration Agreement and may re-acquire its product rights in a lump sum payment equal to the fair market value of such product rights.

​

There are no refund provisions in the AstraZeneca Collaboration Agreement.

Under the terms of the AstraZeneca Collaboration Agreement, the Company received a $25.0 million non-refundable up-front payment upon execution. The Company is also eligible for $125.0 million in additional commercial milestone payments contingent on the achievement of certain sales targets. The parties will also share in the net profits and losses associated with the development and commercialization of linaclotide in the License Territory, with AstraZeneca receiving 55% of the net profits or incurring 55% of the net losses until a certain specified commercial milestone is achieved, at which time profits and losses will be shared equally thereafter.

In August 2014, the Company and AstraZeneca, through the JDC, modified the IDP and development budget to include approximately $14.0 million in additional activities over the remaining development period, to be shared by the Company and AstraZeneca under the terms of the AstraZeneca Collaboration Agreement. These additional activities serve to support the continued development of linaclotide in the License Territory, including the Phase III Trial. Pursuant to the terms of the modified IDP and development budget, certain of the Company’s deliverables were modified, specifically the research, development and regulatory services pursuant to the IDP, as modified from time to time (the “R&D Services”) and the obligation to supply clinical trial material. The modification did not have a material impact on the Company’s condensed consolidated financial statements.

The total amount of the non-contingent consideration allocable to the AstraZeneca Collaboration Agreement and a co-promotion agreement was approximately $34.0 million (“Arrangement Consideration”), which includes the $25.0 million non-refundable up-front payment and approximately $9.0 million representing 55% of the costs for clinical trial material supply services and research, development and regulatory activities allocated to the Company in the IDP or as approved by the JDC in subsequent periods.

Prior to adoption of ASC 606, the Company allocated the Arrangement Consideration to the non-contingent deliverables based on management’s best estimated selling price (“BESP”) of each deliverable using the relative selling price method, as the Company did not have vendor-specific objective evidence or third-party evidence of selling price for such deliverables. Of the total Arrangement Consideration, approximately $29.7 million was allocated to the License Deliverable, approximately $1.8 million to the R&D Services, approximately $0.1 million to the JDC services, approximately $0.3 million to the clinical trial material supply services, and approximately $2.1 million to a co-promotion deliverable in the relative selling price model.

Because the Company shares development costs with AstraZeneca, payments from AstraZeneca with respect to both research and development and selling, general and administrative costs incurred by the Company prior to the commercialization of linaclotide in the License Territory are recorded as a reduction in expense, in accordance with the Company’s policy, which is consistent with the nature of the cost reimbursement. Development costs incurred by the Company that pertain to the joint development plan and subsequent amendments to the joint development plan, as approved by the JDC, are recorded as research and development expense as incurred. Payments to AstraZeneca are recorded as incremental research and development expense.

The following remaining performance obligations are ongoing as of June 30, 2019:

| ● | R&D Services,

| ● | JDC services,

| ● | obligation to supply clinical trial material, and

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| ● | Joint Commercialization Committee (“JCC”) services.

The Company determined that the supply of linaclotide drug product for commercial requirements was an optional service at inception of the arrangement and did not provide a material right to AstraZeneca.

Under ASC 606, the Company applied the contract modification practical expedient to the August 2014 amendment, which expanded the scope of the Company’s activities under the IDP and increased the development budget. This practical expedient allows an entity to reflect the aggregate effect of all modifications that occur before the beginning of the earliest period presented. The application of this practical expedient resulted in a total transaction price of approximately $34.0 million, which was allocable to the Company’s performance obligations on a relative standalone selling price (“SSP”) basis.

Under ASC 606, consideration allocated to the R&D Services will be recognized as such services are provided over the performance period using an output method based on full-time employee hours incurred. Consideration allocated to the JDC Services are recognized ratably over the development period using a time-based, straight-line attribution model. Revenue from the supply of clinical trial material is recognized as the clinical trial material is delivered to the customer.

​

Upon commercialization, the Company’s only remaining performance obligation will be JCC Services. During commercialization, the Company will be entitled to receive sales-based milestone payments from AstraZeneca. Additionally, the parties will share in the net profits and losses associated with the development and commercialization of linaclotide in the License Territory, with AstraZeneca receiving 55% of the net profits or incurring 55% of the net losses until a certain specified commercial milestone is achieved; from that point, profits and losses will be shared equally thereafter. Commercial sales-based milestones and net profit and loss sharing payments will be recorded as collaborative arrangements revenue or expense in the period earned, in accordance with the sales-based royalty exception, as these payments related predominately to the license granted to AstraZeneca. Any cost reimbursements received from AstraZeneca during the commercialization period will be recognized as incurred in accordance with the right-to-invoice exemption, as the Company’s right to consideration corresponds directly with the value of the services transferred during the commercialization period.

​

During the three and six months ended June 30, 2019, the Company incurred no costs and offset an insignificant amount of costs related to R&D Services and JDC Services, respectively. During each of the three and six months ended June 30, 2018, the Company offset costs of approximately $0.7 million related to R&D Services and JDC Services. During the three and six months ended June 30, 2019, the Company recognized no revenue and an insignificant amount of revenue related to linaclotide drug product as sale of API, respectively. The Company recorded no revenue related to linaclotide drug product and sale of API during each of the three and six months ended June 30, 2018. Additionally, the Company incurred approximately $0.3 million and approximately $0.5 million in costs related to pre-launch commercial services and supply chain services during the three and six months ended June 30, 2019, respectively.

​

Co-Promotion and Other Agreements

​

In January 2017, concurrently with entering into the amendment to the European License Agreement, the Company and Allergan entered into an agreement under which the adjustments to the Company’s or Allergan’s share of the net profits under the share adjustment provision of the collaboration agreement for linaclotide in North America relating to the contractually required calls on physicians in each year were eliminated, in full, in 2018 and all subsequent years (the “Commercial Agreement”). Pursuant to the Commercial Agreement, Allergan appointed the Company, on a non-exclusive basis, to promote CANASA, approved for the treatment of ulcerative proctitis in the U.S. for approximately two years through February 2019. Under the terms of the Commercial Agreement, the Company was obligated to perform third position sales details and offer samples of such products to gastroenterology prescribers who were on the then-current call panel for LINZESS to which the Company was providing first or second position details. On a product-by-product basis, Allergan paid the Company a royalty in the mid-teens on incremental sales of CANASA above a mutually agreed upon sales baseline. The Company discontinued its promotion of CANASA on December 31, 2018.

​

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Upon adoption of ASC 606, the Company evaluated the commercial agreement and the amendment to the European License Agreement under the contract combination and contract modification guidance in ASC 606. The Company determined that the agreements should be accounted for as separate contracts because each agreement adds distinct goods or services at an amount that reflects standalone selling price. The Company concluded that the CANASA sales detailing deliverable under ASC 605 was also considered a performance obligation in accordance with ASC 606. Accordingly, the Company recorded royalties on sales of CANASA and any estimated detailing shortfall penalty over the period of performance for the sales details; collaborative arrangements revenue was recognized when it was probable that a significant reversal of revenue would not occur and the associated constraint has been lifted. The Company estimated sales detailing royalties based on royalty reports from its partner, if available, or the projected sales and historical trends. At the inception of the arrangement, the consideration associated with the agreement comprised of royalties and a sales detailing shortfall penalty are fully constrained. During each of the three and six months ended June 30, 2018, the Company did not recognize royalty revenue related to the Commercial Agreement with Allergan for sales of CANASA.

​

In December 2017, the Company and Allergan entered into an amendment to the commercial agreement with Allergan (the “VIBERZI Amendment”), as described below, to include the VIBERZI promotional activities through December 31, 2018. Under the terms of the VIBERZI Amendment, the Company’s clinical sales specialists detailed VIBERZI in the second position to the same health care practitioners to whom they detailed LINZESS in the first position and provided certain medical education services. The Company had the potential to achieve a milestone payment of up to $7.5 million based on the net sales of VIBERZI during 2018, and was compensated approximately $3.0 million over the term of the agreement for its medical education initiatives. The Company evaluated the VIBERZI Amendment in accordance with ASC 606 and determined that it would be treated as a separate contract because it adds a distinct good or service at an amount that reflects standalone selling price. The following performance obligations under the VIBERZI Amendment were identified:

| ● | sales detailing of VIBERZI in either first or second position, and

| ● | medical education services.

​

The sales-based milestone payment was recognized as collaborative arrangements revenue when it was probable that a significant reversal of revenue would not occur and the associated constraint had been lifted. During the three months ended December 31, 2018, the Company determined the sales-based milestone payment was no longer constrained and recognized approximately $1.3 million in collaborative arrangements revenue. The consideration related to medical education events of approximately $3.0 million was recognized over the period of performance that medical education services are provided. During the three and six months ended June 30, 2018, the Company recognized approximately $0.8 million and approximately $1.5 million of collaborative arrangements revenue, respectively, related to VIBERZI medical education services. In December 2018 and in March 2019, the Company extended the VIBERZI Amendment through April 2019.

​

In April 2019, the Company entered into a new agreement with Allergan to perform sales detailing activities for VIBERZI, effective April 1, 2019 through December 31, 2019 (the “VIBERZI Promotion Agreement”). Under the terms of the VIBERZI Promotion Agreement, the Company’s clinical sales specialists will continue detailing VIBERZI in the second position to the same health care practitioners to whom they detail LINZESS in the first position. The Company has the potential to achieve a milestone payment of up to approximately $4.2 million based on the number of VIBERZI prescription extended units filled over the term of the agreement. The Company will be compensated based on the number of VIBERZI sales details performed, up to a maximum amount of approximately $4.1 million over the term of the agreement. In accordance with ASC 606, the VIBERZI Promotion Agreement will be accounted for as a separate contract as it contains distinct services at an amount that reflects standalone selling price, incremental to past agreements. The Company identified the performance of VIBERZI second position sales details as the sole performance obligation under the agreement.

​

The milestone payment will be recognized as collaborative arrangements revenue when it is probable that a significant reversal of revenue will not occur and the associated constraint has been lifted. As of June 30, 2019, the Company determined the milestone payment was fully constrained. The compensation related to the VIBERZI sales details will be recognized over the term of the agreement using an output method based on estimated amounts for which the Company has the right to invoice based on the number of sales details performed during the associated period. During each of the three and six months ended June 30, 2019, the Company recognized approximately $1.2 million of collaborative arrangements revenue related to VIBERZI sales details.

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​

Other Collaboration and License Agreements

​

The Company has other collaboration and license agreements that are not individually significant to its business. Pursuant to the terms of one agreement, the Company was required to pay $7.5 million for development milestones, all of which had been paid as of June 30, 2019. The Company may also be required to pay up to $18.0 million for regulatory milestones, none of which had been paid as of June 30, 2019. Pursuant to the terms of another license agreement, the Company recognized no revenue and approximately $0.5 million in collaborative arrangements revenue during the three and six months ended June 30, 2019, respectively, related to a nonrefundable upfront payment. The Company is eligible to receive up to $63.5 million in development and sales-based milestones, as well as a royalty as a percentage of net sales of a product, under the terms of this agreement. The Company did not record any research and development expense associated with the Company’s other collaboration and license agreements during each of the three and six months ended June 30, 2019 and 2018.

​

​

​

5. Fair Value of Financial Instruments

​

The tables below present information about the Company’s assets that are measured at fair value on a recurring basis as of June 30, 2019 and December 31, 2018 and indicate the fair value hierarchy of the valuation techniques the Company utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize observable inputs such as quoted prices in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are either directly or indirectly observable, such as quoted prices for similar instruments in active markets, interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points in which there is little or no market data, which require the Company to develop its own assumptions for the asset or liability.

​

The Company’s investment portfolio includes fixed income securities that do not always trade on a daily basis. As a result, the pricing services used by the Company apply other available information as applicable through processes such as benchmark yields, benchmarking of like securities, sector groupings and matrix pricing to prepare valuations. In addition, model processes are used to assess interest rate impact and develop prepayment scenarios. These models take into consideration relevant credit information, perceived market movements, sector news and economic events. The inputs into these models may include benchmark yields, reported trades, broker-dealer quotes, issuer spreads and other relevant data. The Company validates the prices provided by its third-party pricing services by obtaining market values from other pricing sources and analyzing pricing data in certain instances. The Company also invests in certain reverse repurchase agreements which are collateralized by deposits in the form of Government Securities and Obligations for an amount not less than 102% of their principal amount. The Company does not record an asset or liability for the collateral as the Company is not permitted to sell or re-pledge the collateral. The collateral has at least the prevailing credit rating of U.S. Government Treasuries and Agencies. The Company utilizes a third-party custodian to manage the exchange of funds and ensure the collateral received is maintained at 102% of the reverse repurchase agreements principal amount on a daily basis.

​

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The following tables present the assets and liabilities the Company has measured at fair value on a recurring basis (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | Fair Value Measurements at Reporting Date Using |
​ |  | ​ | ​ |  |  | Quoted Prices in |  | Significant Other |  | Significant |
​ | ​ | ​ | ​ | ​ | ​ | Active Markets for | ​ | Observable | ​ | Unobservable |
​ | ​ | ​ | ​ | ​ | Identical Assets | ​ | Inputs | ​ | Inputs |
​ | ​ | June 30, 2019 | ​ | ​ | (Level 1) | ​ | (Level 2) | ​ | (Level 3) | ​
Assets: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Cash and cash equivalents: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Money market funds | ​ | $ | 82,918 | ​ | ​ | $ | 82,918 | ​ | $ | — | ​ | $ | — | ​
Repurchase agreements | ​ | ​ | 15,875 | ​ | ​ | ​ | 15,875 | ​ | ​ | — | ​ | ​ | — | ​
Convertible Note Hedges | ​ | ​ | 60,720 | ​ | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 60,720 | ​
Total assets measured at fair value | ​ | $ | 159,513 | ​ | ​ | $ | 98,793 | ​ | $ | — | ​ | $ | 60,720 | ​
Liabilities: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Note Hedge Warrants | ​ | $ | 50,191 | ​ | ​ | $ | — | ​ | $ | — | ​ | $ | 50,191 | ​
Total liabilities measured at fair value | ​ | $ | 50,191 | ​ | ​ | $ | — | ​ | $ | — | ​ | $ | 50,191 | ​

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | Fair Value Measurements at Reporting Date Using |
​ |  | ​ | ​ |  |  | Quoted Prices in |  | Significant Other |  | Significant |
​ | ​ | ​ | ​ | ​ | ​ | Active Markets for | ​ | Observable | ​ | Unobservable |
​ | ​ | ​ | ​ | ​ | Identical Assets | ​ | Inputs | ​ | Inputs |
​ | ​ | December 31, 2018 | ​ | ​ | (Level 1) | ​ | (Level 2) | ​ | (Level 3) | ​
Assets: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Cash and cash equivalents: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Money market funds | ​ | $ | 142,218 | ​ | ​ | $ | 142,218 | ​ | $ | — | ​ | $ | — | ​
Repurchase agreements | ​ | ​ | 30,875 | ​ | ​ | ​ | 30,875 | ​ | ​ | — | ​ | ​ | — | ​
Convertible Note Hedges | ​ | ​ | 41,020 | ​ | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 41,020 | ​
Total assets measured at fair value | ​ | $ | 214,113 | ​ | ​ | $ | 173,093 | ​ | $ | — | ​ | $ | 41,020 | ​
Liabilities: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Note Hedge Warrants | ​ | $ | 33,763 | ​ | ​ | $ | — | ​ | $ | — | ​ | $ | 33,763 | ​
Contingent Consideration | ​ | ​ | 51 | ​ | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 51 | ​
Total liabilities measured at fair value | ​ | $ | 33,814 | ​ | ​ | $ | — | ​ | $ | — | ​ | $ | 33,814 | ​

​

There were no transfers between fair value measurement levels during each of the three and six months ended June 30, 2019 or 2018.

​

Cash equivalents, accounts receivable, related party accounts receivable, prepaid expenses and other current assets, accounts payable, related party accounts payable, accrued expenses and other current liabilities, the current portion of capital lease obligations, deferred rent, and operating lease obligations at June 30, 2019 and December 31, 2018 are carried at amounts that approximate fair value due to their short-term maturities.

​

Convertible Note Hedges and Note Hedge Warrants

​

The Company’s Convertible Note Hedges and the Note Hedge Warrants are recorded as derivative assets and liabilities, and are classified as Level 3 under the fair value hierarchy. These derivatives are not actively traded and are valued using the Black-Scholes option-pricing model which requires the use of subjective assumptions. Significant inputs used to determine the fair value as of June 30, 2019 included the price per share of the Company’s Class A common stock, time to maturity of the derivative instruments, strike prices of the derivative instruments, risk-free interest rate, expected volatility of the Company’s Class A common stock, and expected dividend yield. Changes to these inputs could materially affect the valuation of the Convertible Note Hedges and Note Hedge Warrants.

​

In April 2019, the Company announced an adjustment to the conversion rate applicable to the 2022 Notes, effective April 15, 2019 (Note 9).

​

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The following inputs were used in the fair market valuation of the Convertible Note Hedges and Note Hedge Warrants as of June 30, 2019 and December 31, 2018:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Six Months Ended | ​ | Year Ended | ​
​ | ​ | June 30, | ​ | December 31, | ​
​ |  | 2019 | ​ | 2018 | ​
​ | ​ | Convertible |  | Note Hedge | ​ | Convertible |  | Note Hedge |
​ | ​ | Note Hedges | ​ | Warrants |  | Note Hedges | ​ | Warrants |
Risk-free interest rate (1) | ​ | ​ | 1.7 | % | ​ | 1.7 | % | ​ | 2.5 | % | ​ | 2.5 | %
Time to maturity |  | ​ | 3.0 |  | ​ | 3.5 | ​ | ​ | 3.5 |  | ​ | 4.1 | ​
Stock price (2) | ​ | $ | 10.94 | ​ | $ | 10.94 | ​ | $ | 10.36 | ​ | $ | 10.36 | ​
Strike price (3) | ​ | $ | 14.51 | ​ | $ | 18.82 | ​ | $ | 16.58 | ​ | $ | 21.50 | ​
Common stock volatility (4) | ​ | ​ | 47.2 | % | ​ | 47.1 | % | ​ | 43.8 | % | ​ | 43.6 | %
Dividend yield | ​ |  | — | % |  | — | % |  | — | % |  | — | %

(1) | Based on U.S. Treasury yield curve, with terms commensurate with the terms of the Convertible Note Hedges and the Note Hedge Warrants.

(2) | The closing price of the Company’s Class A common stock on the last trading day of the quarter ended June 30, 2019 and December 31, 2018, respectively.

(3) | As per the respective agreements for the Convertible Note Hedges and Note Hedge Warrants. The strike prices for the Convertible Note Hedges and Note Hedge Warrants were adjusted in conjunction with the conversion rate adjustment in April 2019 (Note 9).

(4) | Expected volatility based on historical volatility of the Company’s Class A common stock.

(5) | The Company has not paid and does not anticipate paying cash dividends on its shares of common stock in the foreseeable future; therefore, the expected dividend yield is assumed to be zero.

​

The Convertible Note Hedges and the Note Hedge Warrants are recorded at fair value at each reporting period and changes in fair value are recorded in other expense, net within the Company’s condensed consolidated statements of operations. Gains and losses for these derivative financial instruments are presented separately in the Company’s condensed consolidated statements of cash flows.

​

The following table reflects the change in the Company’s Level 3 convertible note derivatives from December 31, 2018 through June 30, 2019 (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Convertible | ​ | Note Hedge | ​
​ |  | Note Hedges |  | Warrants |
Balance at December 31, 2018 | ​ | $ | 41,020 | ​ | $ | (33,763) | ​
Change in fair value, recorded as a component of gain (loss) on derivatives | ​ | ​ | 19,700 | ​ | ​ | (16,428) | ​
Balance at June 30, 2019 | ​ | $ | 60,720 | ​ | $ | (50,191) | ​

​

2.25% Convertible Senior Notes

​

In June 2015, the Company issued approximately $335.7 million of its 2022 Notes. The Company separately accounted for the liability and equity components of the 2022 Notes by allocating the proceeds between the liability component and equity component (Note 9). The fair value of the 2022 Notes, which differs from their carrying value, is influenced by interest rates, the price of the Company’s Class A common stock and the volatility thereof, and the prices for the 2022 Notes observed in market trading, which are Level 2 inputs. The estimated fair value of the 2022 Notes was approximately $359.1 million and approximately $315.0 million as of June 30, 2019 and December 31, 2018, respectively.

​

8.375% Notes Due 2026

​

In September 2016, the Company closed a direct private placement pursuant to which the Company issued $150.0 million in aggregate principal amount of the 2026 Notes in January 2017. The estimated fair value of the 2026 Notes was approximately $133.0 million and approximately $148.2 million as of June 30, 2019 and December 31, 2018, respectively. This valuation was calculated using a discounted cash flow estimate of expected interest and principal

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payments and was determined using Level 3 inputs, including significant estimates related to expected LINZESS sales and a discount rate equivalent to market participant interest rates.

​

6. Inventory

​

Inventory consisted of the following (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | June 30, 2019 |  | December 31, 2018 |  | ​
Raw Materials | ​ | $ | 1,475 | ​ | $ | — | ​ | ​
Work in Progress | ​ | ​ | 260 | ​ | ​ | — | ​ | ​
​ | ​ | $ | 1,735 | ​ | $ | — | ​ | ​

​

The Company’s inventory represents linaclotide API and drug product. The Company evaluates inventory levels quarterly and any inventory that has a cost basis in excess of its expected net realizable value, inventory that becomes obsolete, inventory in excess of expected sales requirements, inventory that fails to meet commercial sale specifications or is otherwise impaired is written down with a corresponding charge to the statement of operations in the period that the impairment is first identified.

​

No impairment of inventory was recorded during the three and six months ended June 30, 2019. The Company wrote down approximately $1.8 million related to lesinurad inventory and commercial supply purchase commitments during the three months ended June 30, 2018 as a result of revised demand forecasts. The adjustment was recorded as write-down of lesinurad commercial supply to net realizable value and loss on non-cancelable purchase commitments.

​

7. Accrued Expenses and Other Current Liabilities

​

Accrued expenses and other current liabilities consisted of the following (in thousands):

​

p | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​
​ |  | June 30, 2019 |  | December 31, 2018 |
Salaries | ​ | $ | 2,499 | ​ | $ | 3,054 | ​
Accrued vacation | ​ | ​ | 2,887 | ​ | ​ | 3,493 | ​
Accrued incentive compensation | ​ | ​ | 5,370 | ​ | ​ | 13,867 | ​
Other employee benefits | ​ | ​ | 536 | ​ | ​ | 1,883 | ​
Professional fees | ​ |  | 5,275 | ​ |  | 1,735 | ​
Accrued interest | ​ |  | 793 | ​ |  | 873 | ​
Restructuring accruals | ​ | ​ | 1,597 | ​ | ​ | 2,885 | ​
Other | ​ |  | 15,025 | ​ |  | 10,211 | ​
​ | ​ | $ | 33,982 | ​ | $ | 38,001 | ​

​

​

​

​

As of June 30, 2019, other accrued expenses of approximately $15.0 million includes approximately $5.0 million related to goods received but not yet invoiced, approximately $2.5 million related to linaclotide excess purchase commitments, approximately $0.9 million related to a portion of the activities associated with the Separation, and approximately $1.4 million related to excess non-cancelable ZURAMPIC and DUZALLO (the “Lesinurad Products”) commercial supply and sample purchase commitments.

​

As of December 31, 2018, other accrued expenses of approximately $10.2 million included approximately $2.5 million related to linaclotide excess purchase commitments, and approximately $1.4 million related to excess non-cancelable Lesinurad Products commercial supply and sample purchase commitments.

​

​

8. Leases

​

Effective January 1, 2019, the Company adopted ASC 842 using the optional transition method. The Company’s lease portfolio includes: leases for its current and future headquarters locations, a data center colocation lease, vehicle leases for its salesforce representatives, and leases for computer and office equipment.

​

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Lease cost is recognized on a straight-line basis over the lease term. The components of lease cost for the three and six months ended June 30, 2019 are as follows (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​ | June 30, | ​
​ | ​ | 2019 | ​ | 2019 | ​
Operating lease cost during period, net(1) | ​ | $ | 3,155 | ​ | ​ | 7,680 | ​
Variable lease payments | ​ | ​ | 654 | ​ | ​ | 654 | ​
Short-term lease cost | ​ | ​ | 379 | ​ | ​ | 768 | ​
Total lease cost | ​ | $ | 4,188 | ​ | ​ | 9,102 | ​

(1) Operating lease cost is presented net of approximately $0.3 million of sublease income for the three months ended June 30, 2019. Sublease income relates to a sublease agreement between Ironwood and Cyclerion executed upon Separation. The sublease agreement terminated in May 2019.

​

Supplemental cash flow information related to leases for the periods reported is as follows:

​

​ | ​ | ​ | ​ | ​
​ | ​ | Six Months Ended
​ | ​ | June 30,
​ | ​ | 2019
Right-of-use assets obtained in exchange for new operating lease upon adoption of ASC 842 (in thousands) | ​ | $ | 88,299 | ​
Adjustment to right-of-use assets as a result of the lease modification at the Separation date (in thousands) | ​ | ​ | (40,427) | ​
Adjustment to right-of-use assets as a result of the termination of the Binney Street Lease (in thousands) | ​ | ​ | (34,440) | ​
Right-of-use assets obtained in exchange for new operating lease liabilities(1) (in thousands) | ​ | ​ | 18,452 | ​
Cash paid for amounts included in the measurement of lease liabilities (in thousands) | ​ | ​ | 6,619 | ​
Weighted-average remaining lease term of operating leases (in years) | ​ | ​ | 7.9 | ​
Weighted-average discount rate of operating leases | ​ | ​ | 5.3 | %

​

(1) Relates to right-of-use assets and operating lease liabilities for the Summer Street Lease.

​

Future minimum lease payments under non-cancelable operating leases under ASC 842 as of June 30, 2019 are as follows (in thousands):

​

​ | ​ | ​ | ​
​ | ​ | Operating
​ |  | Lease
​ | ​ | Payments
2019(1) | ​ | $ | 11,979
2020 | ​ | ​ | 1,146
2021 | ​ | ​ | 3,128
2022 | ​ | ​ | 3,129
2023 | ​ | ​ | 3,065
2024 and thereafter | ​ |  | 21,170
Total future minimum lease payments | ​ | ​ | 43,617
Less: present value adjustment | ​ | ​ | 9,205
Operating lease liabilities at June 30, 2019 | ​ | ​ | 34,412
Less: current portion of operating lease liabilities | ​ | ​ | 11,904
Operating lease liabilities, net of current portion | ​ | $ | 22,508

(1) Amounts are for the six months ending December 31, 2019.

​

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At December 31, 2018, future minimum lease payments under non-cancelable leases under ASC 840 were as follows (in thousands):

​

​ | ​ | ​ | ​
​ | ​ | Operating
​ |  | Lease
​ | ​ | Payments
2019 | ​ | $ | 18,736
2020 | ​ | ​ | 18,312
2021 | ​ | ​ | 18,863
2022 | ​ | ​ | 19,365
2023 | ​ | ​ | 19,818
2024 and thereafter | ​ |  | 22,118
Total future minimum lease payments | ​ | $ | 117,212

​

Summer Street Lease (future headquarters)

​

On June 11, 2019, the Company entered into the Summer Street Lease, a non-cancelable operating lease with MA-100 Summer Street Owner, L.L.C. (the “Summer Street Landlord”) for the Summer Street Property. The Summer Street Property is expected to serve as the Company’s new headquarters beginning in the fourth quarter of 2019, replacing its existing headquarters at 301 Binney Street in Cambridge, Massachusetts. The Summer Street Lease terminates on June 11, 2030 and includes an option to extend the term of the lease for an additional five years at a market base rental rate, a 2% annual rent escalation, free rent periods, and a tenant improvement allowance. The rent expense for the Summer Street Property, inclusive of the escalating rent payments and lease incentives, is recognized on a straight-line basis over the lease term. Additionally, the Summer Street Lease requires a letter of credit to secure the Company’s obligations under the lease agreement of approximately $1.0 million, which is collateralized by a money market account recorded as restricted cash on the Company’s condensed consolidated balance sheets as of June 30, 2019.

​

At lease inception, the Company recorded a right-of-use asset and a lease liability associated with the Summer Street Lease using an incremental borrowing rate of approximately 5.8%. At June 30, 2019, the balance of the right-of-use asset for the Summer Street Lease was approximately $18.3 million. The balance of the lease liability for the Summer Street Lease was approximately $18.3 million, net of approximately $3.8 million related to the tenant improvement allowance reimbursement expected to be received.

​

Lease cost related to the Summer Street Lease recorded during each of the three and months ended June 30, 2019 was approximately $0.2 million.

​

Binney Street Lease (current headquarters)

​

The Company rents office space at 301 Binney Street, Cambridge, Massachusetts (“Binney Street Property”) under a non-cancelable operating lease, entered into in January 2007, as amended (“Binney Street Lease”). The Binney Street Property currently serves as the Company’s headquarters, but is expected to be replaced by the Summer Street Property, as discussed above.

​

Prior to the modifications discussed below, the term of the Binney Street Lease was through January 31, 2025 for the approximately 223,000 square feet of laboratory and office space. The Binney Street Lease includes an option to extend the term of the lease for an additional five years at a market base rental rate, a 3% annual rent escalation, free rent periods, a tenant improvement allowance, and an option to extend the term of the lease for an additional five years at a market base rental rate. The rent expense for the Binney Street Lease, inclusive of the escalating rent payments, lease incentives and free rent periods, is recognized on a straight-line basis over the lease term through January 2025. Additionally, the Binney Street Lease requires a letter of credit to secure the Company’s obligations under the lease agreement of approximately $6.4 million, which is recorded as restricted cash.

​

As of January 1, 2019, in conjunction with the adoption of ASC 842, the Company recorded a right-of-use asset of approximately $87.7 million and a lease liability of approximately $94.3 million associated with the Binney Street Lease.

​

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On April 1, 2019, the Company modified its lease with BMR-Rogers Street LLC (“Binney Street Landlord”), to reduce its leased premises to approximately 108,000 rentable square feet of office space on the first and third floors. The surrendered portion of approximately 114,000 rentable square feet on the first and second floor of the building is now occupied by Cyclerion under a direct lease between Cyclerion and the Binney Street Landlord. As a result of the modification, the Company adjusted the value of its right-of-use asset and operating lease liability using an incremental borrowing rate of approximately 5.1% in accordance with ASC 842, and recognized a gain of approximately $3.2 million, recorded as operating expenses on its condensed consolidated statement of operations. The Company elected to determine the proportionate reduction in the right-of-use asset based on the reduction to the lease liability and will apply that methodology consistently to all comparable modifications that decrease the scope of the lease.

​

On June 11, 2019, the Company entered into a lease termination agreement (the “Lease Termination”) with the Binney Street Landlord to terminate the Company’s existing lease for approximately 108,000 square feet of office space. The Lease Termination is expected to go into effect on or before November 1, 2019 (subject to the Company’s one-time right to extend the termination date for up to 30 days) in exchange for an approximately $9.0 million payment to the Binney Street Landlord. The Company determined that the Lease Termination would be accounted for as a lease modification that reduces the term of the existing lease. As a result of this modification, the Company adjusted the value of its right-of-use asset and operating lease liability using an incremental borrowing rate of approximately 4.0%.

​

At June 30, 2019, the balances of the right-of-use asset and lease liability for the Binney Street Lease were approximately $7.3 million and approximately $11.8 million, respectively.

​

Lease cost related to the Binney Street Lease recorded during the three and six months ended June 30, 2019 was approximately $3.6 million and approximately $8.0 million, respectively, net of sublease income of approximately $0.3 million and approximately $0.3 million, respectively. Under ASC 840, rent expense related to the Binney Street Lease recorded during the three and six months ended June 30, 2018 was approximately $2.5 million and $5.1 million, respectively.

​

Data center colocation lease

​

The Company rents space for its data center at a colocation in Boston, Massachusetts under a non-cancelable operating lease (the “Data Center Lease”). The Data Center Lease contains various provisions, including a 4% annual rent escalation. The rent expense, inclusive of the escalating rent payments, is recognized on a straight-line basis over the lease term through August 2022. The Company recorded a right-of-use asset of approximately $0.6 million, and a lease liability of approximately $0.6 million associated with the Data Center Lease upon adoption of ASC 842. During the three months ended March 31, 2019, the Company migrated its data management process to a cloud-based services system, rendering its current data center technology and assets obsolete. As a result, the Company considered the right-of-use asset associated with the Data Center Lease to be impaired. The Company recorded a charge of approximately $0.5 million to selling, general, and administrative expenses on its condensed consolidated statement of operations as a result of the impairment.

​

At June 30, 2019, the lease liability associated with the Data Center Lease was approximately $0.5 million, and the right-of-use asset remained fully impaired. The incremental borrowing rate for the outstanding Data Center Lease obligation upon adoption of ASC 842 was approximately 6.0%.

​

Under ASC 842, the lease costs related to the Data Center Lease were insignificant for each of the three and six months ended June 30, 2019. Under ASC 840, rent expenses related to the Data Center Lease were insignificant for each of the three and six months ended June 30, 2018, respectively.

​

​

Vehicle fleet leases

​

During April 2018, the Company entered into a master services agreement containing 12-month leases (the “2018 Vehicle Leases”) for certain vehicles within its fleet for its field-based sales force and medical science liaisons. These leases are classified as short-term in accordance with the practical expedient in ASC 842. The 2018 Vehicle Leases expire at varying times beginning in June 2019, with a monthly renewal provision. In accordance with the terms of the 2018 Vehicle Leases, the Company maintains a letter of credit securing its obligation under the lease agreements of $1.3 million, which is collateralized by a money market account recorded as restricted cash.

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​

Lease cost related to the 2018 Vehicle Leases was approximately $0.4 million and approximately $0.8 million for the three and six months ended June 30, 2019, respectively. There were no rent expenses incurred under ASC 840 during the three and six months ended June 30, 2018 related to the 2018 Vehicle Leases.

​

Prior to the adoption of ASC 842, during 2018, the Company had certain ongoing vehicle leases for its field-based sales force and medical science liaisons (the “2015 Vehicle Leases”). These leases were classified as capital leases under ASC 840. The 2015 Vehicle Leases expired at varying times through December 2018. In connection with entering into the 2018 Vehicle Leases, all of the 2015 Vehicle Leases were terminated through December 31, 2018. At December 31, 2018, the Company had no remaining capital lease obligations related to the 2015 Vehicle Leases.

​

Other leases

​

Prior to the adoption of ASC 842, the Company entered into leases for certain computer and office equipment that expired in 2018. These leases were classified as capital leases under ASC 840. At December 31, 2018, the Company had approximately $0.2 million in capital lease obligations. At December 31, 2018, the weighted average interest rate on the outstanding capital lease obligations was approximately 3.4%.

​

​

​

​

​

​

9. Notes Payable

​

8.375% Notes due 2026

​

On September 23, 2016, the Company closed a direct private placement, pursuant to which the Company issued $150.0 million in aggregate principal amount of 8.375% notes due 2026 on January 5, 2017. The Company capitalized approximately $0.5 million of debt issuance costs, which were netted against the carrying value of the 2026 Notes.

​

The 2026 Notes bear an annual interest rate of 8.375%, with interest payable March 15, June 15, September 15 and December 15 of each year (each an “8.375% Payment Date”) which began on June 15, 2017. Principal of the 2026 Notes are payable on the 8.375% Payment Dates beginning March 15, 2019. From March 15, 2019, the Company makes quarterly payments on the 2026 Notes equal to the greater of (i) 7.5% of net sales of linaclotide in the U.S. for the preceding quarter (the “8.375% Synthetic Royalty Amount”) and (ii) accrued and unpaid interest on the 2026 Notes (the “8.375% Required Interest Amount”). Principal on the 2026 Notes will be repaid in an amount equal to the 8.375% Synthetic Royalty Amount minus the 8.375% Required Interest Amount, when this is a positive number, until the principal has been paid in full. Given the principal payments on the 2026 Notes are based on the 8.375% Synthetic Royalty Amount, which will vary from quarter to quarter, the 2026 Notes may be repaid prior to September 15, 2026, the final legal maturity date. During the three and six months ended June 30, 2019, the Company made principal payments of approximately $9.2 million and approximately $21.5 million, respectively, and expects to pay approximately $48.8 million of the principal within twelve months following June 30, 2019.

​

The 2026 Notes are secured by a security interest in a segregated bank account established to receive the required quarterly payments as well as certain limited accounts receivables, payment intangibles or other rights to payment or proceeds, in each case, up to the 8.375% Synthetic Royalty Amount or estimated equivalent thereto, as applicable. Up to the amount of the required quarterly payments under the 2026 Notes, Allergan deposits its quarterly profit (loss) sharing payments due to the Company related to net sales of linaclotide in the U.S. pursuant to the collaboration agreement for North America, if any, into the segregated bank account. If the funds deposited by Allergan into the segregated bank account are insufficient to make a required payment of interest or principal on a particular 8.375% Payment Date, the Company is obligated to deposit such shortfall out of the Company’s general funds into the segregated bank account.

​

The 2026 Notes may be redeemed at any time prior to maturity, in whole or in part, at the option of the Company. If applicable, the Company will pay a redemption price equal to the percentage of outstanding principal balance of the

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2026 Notes being redeemed specified below for the period in which the redemption occurs (plus the accrued and unpaid interest to the redemption date on the 2026 Notes being redeemed):

​

​ | ​ | ​ | ​
​ |  | Redemption |
Payment Dates | ​ | Percentage |
From and including March 15, 2019 to and including March 14, 2020 |  | 105.50 | %
From and including March 15, 2020 to and including March 14, 2021 |  | 102.75 | %
From and including March 15, 2021 and thereafter |  | 100.00 | %

​

The 2026 Notes contain certain covenants related to the Company’s obligations with respect to the commercialization of linaclotide and the related collaboration agreement with Allergan for North America, as well as certain customary covenants, including covenants that limit or restrict the Company’s ability to incur certain liens, merge or consolidate or make dispositions of assets. The 2026 Notes also specify a number of events of default (some of which are subject to applicable cure periods), including, among other things, covenant defaults, other non-payment defaults, and bankruptcy and insolvency defaults. Upon the occurrence of an event of default, subject to cure periods in certain circumstances, all amounts outstanding may become immediately due and payable.

​

The accounting for the 2026 Notes requires the Company to make certain estimates and assumptions about the future net sales of linaclotide in the U.S. Linaclotide has been marketed as LINZESS in the U.S. since December 2012 and the estimates of the magnitude and timing of linaclotide net sales are subject to significant variability and uncertainty. These estimates and assumptions are likely to change, which may result in future adjustments to the portion of the 2026 Notes that is classified as a current liability, the amortization of debt issuance costs, the accretion of discounts and recognition of interest expense. Any such adjustments could be material to the Company’s condensed consolidated financial statements.

​

2.25% Convertible Senior Notes due 2022

​

In June 2015, the Company issued approximately $335.7 million aggregate principal amount of the 2022 Notes. The Company received net proceeds of approximately $324.0 million from the sale of the 2022 Notes, after deducting fees and expenses of approximately $11.7 million. The Company used approximately $21.1 million of the net proceeds from the sale of the 2022 Notes to pay the net cost of the Convertible Note Hedges (after such cost was partially offset by the proceeds to the Company from the sale of the Note Hedge Warrants), as described below.

​

The 2022 Notes are governed by an indenture (the “Indenture”) between the Company and U.S. Bank National Association, as the trustee. The 2022 Notes are senior unsecured obligations and bear cash interest at the annual rate of 2.25%, payable on June 15 and December 15 of each year, which began on December 15, 2015. The 2022 Notes will mature on June 15, 2022, unless earlier converted or repurchased. The Company may settle conversions of the 2022 Notes through payment or delivery, as the case may be, of cash, shares of Class A common stock of the Company or a combination of cash and shares of Class A common stock, at the Company’s option (subject to, and in accordance with, the settlement provisions of the Indenture). The initial conversion rate for the 2022 Notes was 60.3209 shares of Class A common stock (subject to adjustment as provided for in the Indenture) per $1,000 principal amount of the 2022 Notes, which was equal to an initial conversion price of approximately $16.58 per share and 20,249,665 shares.

​

In connection with the Separation in April 2019, the conversion rate under the Indenture was adjusted to equal 68.9172 shares of Ironwood Class A common stock per $1,000 principal amount of the 2022 Notes, which is equal to an adjusted conversion price of approximately $14.51 per share and 23,135,435 shares.

​

Holders of the 2022 Notes may convert their 2022 Notes at their option at any time prior to the close of business on the business day immediately preceding December 15, 2021 in multiples of $1,000 principal amount, only under the following circumstances:

​

| ● | during any calendar quarter commencing after the calendar quarter ending on September 30, 2015 (and only during such calendar quarter), if the last reported sale price of the Company’s Class A common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price for the 2022 Notes on each applicable trading day;

​

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| ● | during the five business day period after any five consecutive trading day period (the “measurement period”) in which the “trading price” (as defined in the Indenture) per $1,000 principal amount of the 2022 Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s Class A common stock and the conversion rate for the 2022 Notes on each such trading day; or

​

| ● | upon the occurrence of specified corporate events described in the Indenture.

​

On or after December 15, 2021, until the close of business on the second scheduled trading day immediately preceding June 15, 2022, holders may convert their 2022 Notes, in multiples of $1,000 principal amount, at the option of the holder regardless of the foregoing circumstances.

​

If a make-whole fundamental change, as described in the Indenture, occurs and a holder elects to convert its 2022 Notes in connection with such make-whole fundamental change, such holder may be entitled to an increase in the conversion rate as described in the Indenture. The Company may not redeem the 2022 Notes prior to the maturity date and no “sinking fund” is provided for by the 2022 Notes, which means that the Company is not required to periodically redeem or retire the 2022 Notes. Upon the occurrence of certain fundamental changes involving the Company, holders of the 2022 Notes may require the Company to repurchase for cash all or part of their 2022 Notes at a repurchase price equal to 100% of the principal amount of the 2022 Notes to be repurchased, plus accrued and unpaid interest.

​

The Indenture does not contain any financial covenants or restrict the Company’s ability to repurchase the Company’s securities, pay dividends or make restricted payments in the event of a transaction that substantially increases the Company’s level of indebtedness. The Indenture provides for customary events of default. In the case of an event of default with respect to the 2022 Notes arising from specified events of bankruptcy or insolvency, all outstanding 2022 Notes will become due and payable immediately without further action or notice. If any other event of default with respect to the 2022 Notes under the Indenture occurs or is continuing, the trustee or holders of at least 25% in aggregate principal amount of the then outstanding 2022 Notes may declare the principal amount of the 2022 Notes to be immediately due and payable. Notwithstanding the foregoing, the Indenture provides that, upon the Company’s election, and for up to 180 days, the sole remedy for an event of default relating to certain failures by the Company to comply with certain reporting covenants in the Indenture consists exclusively of the right to receive additional interest on the 2022 Notes.

​

In accordance with accounting guidance for debt with conversion and other options, the Company separately accounted for the liability and equity components of the 2022 Notes by allocating the proceeds between the liability component and the embedded conversion option, or equity component, due to the Company’s ability to settle the 2022 Notes in cash, its Class A common stock, or a combination of cash and Class A common stock at the option of the Company. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The allocation was performed in a manner that reflected the Company’s non-convertible debt borrowing rate for similar debt. The equity component of the 2022 Notes was recognized as a debt discount and represents the difference between the gross proceeds from the issuance of the 2022 Notes and the fair value of the liability of the 2022 Notes on their respective dates of issuance. The excess of the principal amount of the liability component over its carrying amount, or debt discount, is amortized to interest expense using the effective interest method over seven years, or the expected life of the 2022 Notes. The equity component is not remeasured as long as it continues to meet the conditions for equity classification.

​

The Company’s outstanding Convertible Note balances as of June 30, 2019 and December 31, 2018 consisted of the following (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | June 30, 2019 | ​ | ​ | ​ | December 31, 2018 | ​
Liability component: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Principal | ​ | $ | 335,699 | ​ | ​ | ​ | $ | 335,699 | ​
Less: unamortized debt discount | ​ | ​ | (56,855) | ​ | ​ | ​ | ​ | (65,094) | ​
Less: unamortized debt issuance costs | ​ | ​ | (4,449) | ​ | ​ | ​ | ​ | (5,004) | ​
Net carrying amount | ​ | $ | 274,395 | ​ | ​ | ​ | $ | 265,601 | ​
Equity component | ​ | $ | 114,199 | ​ | ​ | ​ | $ | 114,199 | ​

​

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In connection with the issuance of the 2022 Notes, the Company incurred approximately $11.7 million of debt issuance costs, which primarily consisted of initial purchasers’ discounts and legal and other professional fees. The Company allocated these costs to the liability and equity components based on the allocation of the proceeds. The portion of these costs allocated to the equity components totaling approximately $4.0 million were recorded as a reduction to additional paid-in capital. The portion of these costs allocated to the liability components totaling approximately $7.7 million were recorded as a reduction in the carrying value of the debt on the balance sheet and are amortized to interest expense using the effective interest method over the expected life of the 2022 Notes.

​

The Company determined the expected life of the 2022 Notes was equal to their seven-year term. The effective interest rate on the liability components of the 2022 Notes for the period from the date of issuance through June 30, 2019 was 9.34%. The following table sets forth total interest expense recognized related to the 2022 Notes during the three and six months ended June 30, 2019 and 2018 (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​ | June 30, | ​
​ |  | 2019 |  | 2018 |  | 2019 |  | 2018 |
Contractual interest expense | ​ | $ | 1,889 | ​ | $ | 1,888 | ​ | $ | 3,777 | ​ | $ | 3,777 | ​
Amortization of debt issuance costs | ​ | ​ | 283 | ​ | ​ | 237 | ​ | ​ | 555 | ​ | ​ | 464 | ​
Amortization of debt discount | ​ | ​ | 4,164 | ​ | ​ | 3,816 | ​ | ​ | 8,239 | ​ | ​ | 7,550 | ​
Total interest expense | ​ | $ | 6,336 | ​ | $ | 5,941 | ​ | $ | 12,571 | ​ | $ | 11,791 | ​

​

Convertible Note Hedge and Note Hedge Warrant Transactions with Respect to 2022 Notes

​

To minimize the impact of potential dilution to the Company’s Class A common stockholders upon conversion of the 2022 Notes, the Company entered into the Convertible Note Hedges covering 20,249,665 shares of the Company’s Class A common stock in connection with the issuance of the 2022 Notes. The Convertible Note Hedges had an initial exercise price of $16.58 per share, subject to adjustment upon the occurrence of certain corporate events or transactions, and were exercisable if the 2022 Notes were converted. In connection with the adjustment to the conversion rate of the Indenture, the exercise price of the Convertible Note Hedges and the Note Hedge Warrants were adjusted to $14.51 per share and $18.82 per share, respectively (Note 5). If upon conversion of the 2022 Notes, the price of the Company’s Class A common stock is above the exercise price of the Convertible Note Hedges, the counterparties are obligated to deliver shares of the Company’s Class A common stock and/or cash with an aggregate value approximately equal to the difference between the price of the Company’s Class A common stock at the conversion date and the exercise price, multiplied by the number of shares of the Company’s Class A common stock related to the Convertible Note Hedge being exercised.

​

Concurrently with entering into the Convertible Note Hedges, the Company also sold Note Hedge Warrants to the Convertible Note Hedge counterparties to acquire 20,249,665 shares of the Company’s Class A common stock, subject to customary anti-dilution adjustments. The strike price of the Note Hedge Warrants was initially $21.50 per share, subject to adjustment, and such warrants are exercisable over the 150 trading day period beginning on September 15, 2022. In connection with the Separation in April 2019, the exercise price was adjusted to $18.82 per share and the number of shares underlying the Note Hedge Warrants was increased to 23,135,435 shares. The Note Hedge Warrants could have a dilutive effect on the Class A common stock to the extent that the market price per share of the Company’s Class A common stock exceeds the applicable strike price of such warrants.

​

The Convertible Note Hedges and the Note Hedge Warrants are separate transactions entered into by the Company and are not part of the terms of the 2022 Notes. Holders of the 2022 Notes and the Note Hedge Warrants do not have any rights with respect to the Convertible Note Hedges. The Company paid approximately $91.9 million for the Convertible Note Hedges and recorded this amount as a long-term asset on the condensed consolidated balance sheet. The Company received approximately $70.8 million for the Note Hedge Warrants and recorded this amount as a long-term liability, resulting in a net cost to the Company of approximately $21.1 million. The Convertible Note Hedges and Note Hedge Warrants are accounted for as derivative assets and liabilities, respectively, in accordance with ASC Topic 815, Derivatives and Hedging (Note 5).

​

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10. Employee Stock Benefit Plans

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The Company has several share-based compensation plans under which stock options, restricted stock awards, restricted stock units (“RSUs”), and other share-based awards are available for grant to employees, officers, directors and consultants of the Company.

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In May 2019, the Company’s stockholders approved the 2019 Equity Incentive Plan (the “2019 Equity Plan) under which stock options, restricted stock awards, RSUs, and other stock-based awards may be granted to employees, officers, directors, or consultants of the Company. Under the 2019 Equity Plan, 10,000,000 shares of Class A common stock were initially reserved for issuance. As of June 30, 2019, 9,923,183 shares are available for future grant under the 2019 Equity Plan.

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The following table summarizes share-based compensation expense reflected in the condensed consolidated statements of operations for the three and six months ended June 30, 2019 and 2018 (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​ | June 30, | ​
​ |  | 2019 |  | 2018 |  | 2019 |  | 2018 |
Research and development | ​ | $ | 1,179 | ​ | $ | 2,920 | ​ | $ | 4,098 | ​ | $ | 5,472 | ​
Selling, general and administrative | ​ | ​ | 5,021 | ​ |  | 6,539 | ​ |  | 15,519 | ​ | ​ | 12,065 | ​
Restructuring expenses | ​ | ​ | 137 | ​ | ​ | 324 | ​ |  | 654 | ​ |  | 517 | ​
​ | ​ | $ | 6,337 | ​ | $ | 9,783 | ​ | $ | 20,271 | ​ | $ | 18,054 | ​

​

During the three months ended March 31, 2018, the Company reduced its field-based workforce by approximately 60 employees, primarily consisting of field-based sales representatives that promoted DUZALLO or ZURAMPIC in the first position, resulting in a modification to certain share-based payment awards. As a result of the modification, the Company recorded stock-based compensation expense of approximately $0.2 million to restructuring expenses during the three months ended March 31, 2018.

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During the three months ended June 30, 2018, the Company initiated a reduction in headquarter-based workforce by approximately 40 employees associated with the Separation. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded approximately $0.3 million of restructuring expenses during each of the three and six months ended June 30, 2018.

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In February 2019, following further analysis of the Company’s strategy and core business needs, and in an effort to further strengthen the operational efficiency of the organization, the Company commenced a reduction in workforce by approximately 35 employees, primarily based in the home office. Certain share-based payment awards were modified in connection with the reduction in workforce. As a result of the modifications, the Company recorded an insignificant amount of share-based compensation expense and approximately $0.7 million to restructuring expenses during the three and six months ended June 30, 2019, respectively.

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In April 2019, in connection with the Separation, all outstanding share-based payment awards were modified in accordance with the equity conversion-related provisions of the employee matters agreement. No share-based compensation expense was recognized in connection with the modifications. Additionally, modifications with respect to the Company’s Employee Stock Purchase Plan (“ESPP”) were made due to the change in share price as a result of the Separation. As a result of the modification to the ESPP, the Company recorded share-based compensation expense of approximately $0.3 million during each of the three and six months ended June 30, 2019.

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In connection with certain other modifications of share-based payment awards during the six months ended June 30, 2019, the Company recognized approximately $2.4 million in share-based compensation expense.

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11. Related Party Transactions

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In September 2009, Allergan became a related party when the Company sold to Allergan 2,083,333 shares of the Company’s convertible preferred stock. Under the collaboration agreement, the Company and Allergan equally support the development and commercialization of linaclotide (Note 4). Amounts due to and due from Allergan are

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reflected as related party accounts payable and related party accounts receivable, respectively. These balances are reported net of any balances due to or from the related party. As of June 30, 2019 and December 31, 2018, the Company had approximately $79.4 million and approximately $60.0 million, respectively, in related party accounts receivable, net of related party accounts payable, associated with Allergan.

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The Company has and currently obtains health insurance services for its employees from an insurance provider whose President and Chief Executive Officer became a member of the Company’s Board of Directors in April 2016. The Company paid approximately $1.6 million and approximately $4.1 million in insurance premiums to this insurance provider during the three and six months ended June 30, 2019, respectively, and paid approximately $3.0 million and approximately $6.3 million during the three and six months ended June 30, 2018, respectively. At June 30, 2019 and December 31, 2018, the Company had no accounts payable due to this related party.

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The Company has and currently obtains commercial market and prescription data from a vendor whose Senior Vice President of Strategy, Marketing and Communications became a member of the Company’s Board of Directors in April 2019. The Company paid approximately $0.7 million and approximately $1.2 million in fees to this company during the three and six months ended June 30, 2019, respectively, and approximately $1.1 million and approximately $1.8 million during the three and six months ended June 30, 2018, respectively. As of June 30, 2019 and December 31, 2018, the Company had approximately $0.3 million and an insignificant amount of accounts payable due to this related party, respectively.

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In connection with the Separation, the Company executed certain contracts with Cyclerion whose President became a member of the Company’s Board of Directors in April 2019 (Note 2). As of June 30, 2019, the Company had an insignificant amount of accounts receivable, net of accounts payable due from Cyclerion.

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12. Workforce Reduction

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On January 30, 2018, the Company commenced an initiative to evaluate the optimal mix of investments for the lesinurad franchise. As part of this effort, the Company reduced its field-based workforce by approximately 60 employees, primarily consisting of field-based sales representatives that promoted DUZALLO or ZURAMPIC in the first position. During the three months ended March 31, 2018, the Company substantially completed the implementation of this reduction in field-based workforce and, in accordance with ASC Topic 420, Exit or Disposal Activities (“ASC 420”), recorded approximately $2.4 million of costs in its condensed consolidated statement of operations.

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On June 27, 2018, the Company determined the initial organizational designs of the two new businesses, including employees’ roles and responsibilities, in connection with the Separation. As part of this process, the Company initiated a reduction in its headquarter-based workforce by approximately 40 employees. During the three months ended June 30, 2019, the Company did not record any costs in connection with this workforce reduction. During the six months ended June 30, 2019, the Company recorded an insignificant amount of costs in connection with the reduction in workforce in accordance with ASC 420. During each of the three and six months ended June 30, 2018, the Company recorded approximately $1.5 million of costs in connection with the reduction in workforce in accordance with ASC 420. These costs are reflected in the condensed consolidated statement of operations as restructuring expenses.

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On August 16, 2018, the Company initiated a reduction in its workforce by approximately 100 employees, primarily consisting of field-based sales representatives in connection with the termination of the license related to the Lesinurad Products with AstraZeneca to develop, manufacture, and commercialize in the U.S products containing lesinurad as an active ingredient. During the three and six months ended June 30, 2019, the Company did not record any restructuring costs related to this workforce reduction. These costs are reflected in the condensed consolidated statement of operations as restructuring expenses.

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On February 7, 2019, following further analysis of the Company’s strategy and core business needs, and in an effort to further strengthen the operational efficiency of the organization, the Company commenced a reduction in workforce by approximately by 35 employees, primarily based in the home office. During the three and six months ended June 30, 2019, the Company recorded approximately $0.5 million and approximately $3.8 million, respectively, of costs that are reflected in the condensed consolidated statement of operations as restructuring expenses.

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The following table summarizes the accrued liabilities activity recorded in connection with the reduction in workforce for the three and six months ended June 30, 2019 (in thousands):

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Amounts | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | Amounts | ​
​ | ​ | Accrued at | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | Accrued at | ​
​ |  | December 31, 2018 | ​ | Charges |  | Amount Paid | ​ | Adjustments | ​ | June 30, 2019 | ​
Employee severance, benefits and related costs | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
June 2018 Reduction | ​ | ​ | 696 | ​ | ​ | 16 | ​ | ​ | (556) | ​ | ​ | (15) | ​ | ​ | 141 | ​
August 2018 Reduction | ​ | ​ | 1,756 | ​ | ​ | — | ​ | ​ | (1,708) | ​ | ​ | (44) | ​ | ​ | 4 | ​
February 2019 Reduction | ​ | ​ | — | ​ | ​ | 3,182 | ​ | ​ | (1,878) | ​ | ​ | — | ​ | ​ | 1,304 | ​
Total |  | $ | 2,452 | ​ | $ | 3,198 | ​ | $ | (4,142) | ​ | $ | (59) | ​ | $ | 1,449 | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Contract related costs | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
August 2018 Reduction | ​ | $ | 433 | ​ | $ | — | ​ | $ | (287) | ​ | $ | (42) | ​ | $ | 104 | ​
Total |  | $ | 433 | ​ | $ | — | ​ | $ | (287) | ​ | $ | (42) | ​ | $ | 104 | ​

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During the three and six months ended June 30, 2019, the Company recorded approximately $0.5 million and approximately $3.8 million in restructuring expenses, respectively, and recorded approximately $1.5 million and approximately $3.9 million during the three and six months ended June 30, 2018, respectively.

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Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

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Forward-Looking Information

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The following discussion of our financial condition and results of operations should be read in conjunction with our condensed consolidated financial statements and the notes to those financial statements appearing elsewhere in this Quarterly Report on Form 10-Q and the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K. This discussion contains forward-looking statements that involve significant risks and uncertainties. As a result of many factors, such as those set forth under “Risk Factors” in Item 1A of this Quarterly Report on Form 10-Q, our actual results may differ materially from those anticipated in these forward-looking statements.

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Overview

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We are a gastrointestinal, or GI, healthcare company dedicated to creating medicines that make a difference for people living with GI diseases. We are advancing innovative product opportunities in areas of large unmet need, capitalizing on our proven development and commercial capabilities and our deep expertise in GI diseases. On April 1, 2019, we completed our tax-free spin-off of our soluble guanylate cyclase, or sGC, business into a separate, publicly traded company, called Cyclerion Therapeutics, Inc., or Cyclerion.

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Our commercial product, linaclotide, is available to adult men and women suffering from irritable bowel syndrome with constipation, or IBS-C, or chronic idiopathic constipation, or CIC, in certain countries around the world. As many as 13 million adults suffer from IBS-C and as many as 35 million adults suffer from CIC in the U.S. alone, according to our analysis of studies including P Pare, et al. (published in 2001 in the American Journal of Gastroenterology) and J.F. Johanson, et al. (published in 2007 in Alimentary Pharmacology and Therapeutics) and American College of Gastroenterology Chronic Constipation Task Force (2005), American Journal of Gastroenterology Vol. 100, No. S1, 2005. Symptoms of IBS-C include abdominal pain, discomfort or bloating and constipation symptoms (for example, incomplete evacuation, infrequent bowel movements, hard/lumpy stools), while CIC is primarily characterized by constipation symptoms.

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Linaclotide is available under the trademarked name LINZESS® (linaclotide) to adult men and women suffering from IBS-C or CIC in the United States, or the U.S., and Mexico, and to adult men and women suffering from IBS-C in Japan. Linaclotide is available under the trademarked name CONSTELLA® to adult men and women suffering from IBS-C or CIC in Canada, and to adult men and women suffering from IBS-C in certain European countries.

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We have formed strategic partnerships with leading pharmaceutical companies to support the development and commercialization of linaclotide throughout the world. We and our partner Allergan plc (together with its affiliates), or Allergan, began commercializing LINZESS in the U.S. in December 2012. Under our collaboration with Allergan for North America, total net sales of LINZESS in the U.S., as recorded by Allergan, are reduced by commercial costs incurred by each party, and the resulting amount is shared equally between us and Allergan. Allergan has an exclusive license from us to develop and commercialize linaclotide in the Allergan License Territory, which is comprised of all countries other than China, Hong Kong, Macau, Japan and the countries and territories of North America. On a country-by-country and product-by-product basis in the Allergan License Territory, Allergan pays us royalties as a percentage of net sales of products containing linaclotide as an active ingredient. In addition, Allergan has exclusive rights to commercialize linaclotide in Canada as CONSTELLA and in Mexico as LINZESS.

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Astellas Pharma Inc., or Astellas, our partner in Japan, has an exclusive license to develop and commercialize linaclotide in Japan. In March 2017, Astellas began commercializing LINZESS for the treatment of adults with IBS-C in Japan, and in September 2018, Astellas began commercializing LINZESS for the treatment of adult patients with chronic constipation in Japan. In October 2012, we entered into a collaboration agreement with AstraZeneca AB (together with its affiliates), or AstraZeneca, to co-develop and co-commercialize linaclotide in China, Hong Kong and Macau, with AstraZeneca having primary responsibility for the local operational execution. In January 2019, the National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China.

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We and Allergan are exploring ways to enhance the clinical profile of LINZESS by studying linaclotide in additional indications, populations and formulations to assess its potential to treat various conditions. In June 2019, we announced positive topline data from our Phase IIIb trial demonstrating the efficacy and safety of LINZESS 290 mcg on the overall abdominal symptoms of bloating, pain and discomfort, in adult patients with IBS-C.

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​

We and Allergan are also advancing MD-7246, a delayed release form of linaclotide, as an oral, intestinal, non-opioid pain relieving agent for patients suffering from abdominal pain associated with certain GI diseases. There are an estimated 16 million Americans who suffer from symptoms of IBS-D, according to Grundmann and Yoon in Irritable Bowel Syndrome: epidemiology, diagnosis and treatment: an update for health-care practitioners (published in the Journal of Gastroenterology and Hepatology in 2010) and the United States Census Bureau. In May 2019, we and Allergan initiated a Phase II clinical trial evaluating MD-7246 in adult patients with IBS with diarrhea, or IBS-D.

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We are also advancing IW-3718, a gastric retentive formulation of a bile acid sequestrant, for the potential treatment of persistent gastroesophageal reflux disease, or persistent GERD. There are an estimated 10 million Americans who suffer regularly from symptoms of GERD, such as heartburn and regurgitation, despite receiving treatment with the current standard of care, a proton pump inhibitor, to suppress stomach acid, according to a study published in 2014 by HB El-Sarag, Sweet S, Winchester CC et al. in Gut; a Lieberman HCP Survey, 2019; a Lieberman GI patient landscape survey, 2010; a survey conducted by American Gastroenterological Association; and 2019 U.S. census data. In June 2018, we initiated two Phase III clinical trials evaluating the safety and efficacy of IW-3718 in patients with persistent GERD.

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As part of our strategy, we have established development and commercial capabilities that we plan to leverage as we seek to bring multiple medicines to patients. We intend to play an active role in the development and commercialization of our products in the U.S., and to establish a strong global brand by out-licensing commercialization rights in other territories to high-performing partners. Additionally, we have periodically entered into co-promotion agreements to maximize our salesforce productivity, such as our co-promotion agreement with Allergan to perform sales detailing activities for VIBERZI for treatment for adults suffering from IBS-D. This agreement is more fully described in Note 4, Collaborations, License, Co-Promotion and Other Commercial Agreements, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

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We were incorporated in Delaware on January 5, 1998 as Microbia, Inc. On April 7, 2008, we changed our name to Ironwood Pharmaceuticals, Inc. We operate in one reportable business segment—human therapeutics.

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To date, we have dedicated a majority of our activities to the research, development and commercialization of linaclotide and the commercialization of lesinurad, as well as to the research and development of our other product candidates. We have incurred significant operating losses since our inception in 1998. As of June 30, 2019, we had an accumulated deficit of approximately $1.6 billion. We are unable to predict the extent of any future losses or guarantee when, or if, our company will become cash flow positive.

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On April 1, 2019, we completed the separation of our sGC business, and certain other assets and liabilities, into a separate, independent publicly traded company, or the Separation. The Separation was effected by means of a distribution of all of the outstanding shares of common stock, with no par value, of Cyclerion, through a dividend of Cyclerion’s common stock to our stockholders of record as of the close of business on March 19, 2019. Cyclerion is a clinical-stage biopharmaceutical company harnessing the power of sGC pharmacology to discover, develop, and commercialize breakthrough treatments for serious and orphan diseases. Cyclerion’s portfolio is comprised of several sGC stimulators, including olinciguat a vascular sGC stimulator in Phase II development, praliciguat a systemic sGC stimulator in Phase II development, and IW-6463, a central nervous system-penetrant sGC stimulator in Phase I development. The Separation is more fully described in Note 2, Cyclerion Separation, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

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On June 11, 2019, we entered into a non-cancelable operating lease, or the Summer Street Lease, for approximately 39,000 square feet of office space on the 23rd floor of 100 Summer Street, Boston, Massachusetts, or the Summer Street Property. The Summer Street Property is expected to serve as our new headquarters beginning in the fourth quarter of 2019, replacing our existing headquarters at 301 Binney Street in Cambridge, Massachusetts. This agreement is more fully described in Note 8, Leases, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

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Financial Overview

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Revenues. Our revenues are generated primarily through our collaborative arrangements and license agreements related to research and development and commercialization of linaclotide, as well as co-promotion arrangements in the U.S. Effective January 1, 2018, we adopted Accounting Standards Codification, or ASC, Topic 606,

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Revenue from Contracts with Customers, or ASC 606, using the modified retrospective transition method. The adoption of ASC 606 represents a change in accounting principle that aims to more closely align revenue recognition with the delivery of our services and will provide financial statement readers with enhanced disclosures. In accordance with ASC 606, we recognize revenue when the customer obtains control of a promised good or service, in an amount that reflects the consideration which we expect to receive in exchange for the good or service. The reported results for the three and six months ended as of June 30, 2019 and 2018 reflect the application of ASC 606 guidance. Upon adoption of ASC 606, we concluded that no cumulative-effect adjustment to the accumulative deficit as of January 1, 2018 was necessary. The adoption of ASC 606 had no impact on our condensed consolidated statement of operations, condensed consolidated balance sheets, or condensed consolidated statement of cash flows.

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The terms of the collaborative research and development, license and co-promotion agreements contain multiple performance obligations which may include (i) licenses, (ii) research and development activities, (iii) the manufacture of finished drug product, active pharmaceutical ingredient, or API, or development materials for a partner which are reimbursed at a contractually determined rate, and (iv) co-promotion activities by our clinical sales specialists. Payments to us may include (i) up-front license fees, (ii) payments for research and development activities, (iii) payments for the manufacture of finished drug product, API or development materials, (iv) payments based upon the achievement of certain milestones, (v) payments for sales detailing, promotional support services and medical education initiatives and (vi) royalties on product sales. Additionally, we receive our share of the net profits or bear our share of the net losses from the sale of linaclotide in the U.S. and China.

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We record our share of the net profits and losses from the sales of LINZESS in the U.S. on a net basis and present the settlement payments to and from Allergan as collaboration expense or collaborative arrangements revenue, as applicable. Net profits or losses consist of net sales to third-party customers and sublicense income in the U.S. less the cost of goods sold as well as selling, general and administrative expenses. Although we expect net sales to increase over time, the settlement payments between Allergan and us, resulting in collaborative arrangements revenue or collaboration expense, are subject to fluctuation based on the ratio of selling, general and administrative expenses incurred by each party. In addition, our collaborative arrangements revenue may fluctuate as a result of the timing and amount of license fees and clinical and commercial milestones received and recognized under our current and future strategic partnerships as well as timing and amount of royalties from the sales of linaclotide in the European, Canadian or Mexican markets or any other markets where linaclotide receives approval.

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Through December 31, 2018, product revenue consisted of sales of ZURAMPIC and DUZALLO in the U.S. Product revenue was recognized when a particular national wholesaler or a selected regional wholesaler, or a Distributor, obtained control of our product, which occurred at a point in time, typically upon shipment of ZURAMPIC and DUZALLO, or the Lesinurad Products, to the Distributor.

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Cost of Revenues. Cost of revenues primarily includes cost of collaborative arrangements revenue related to the sales of linaclotide API and drug product. Cost related to the sales of linaclotide API and drug product are recognized upon shipment of linaclotide API and drug product to certain of our partners outside of the U.S. Our cost of collaborative arrangements revenue for linaclotide consists of the internal and external costs of producing such API and drug product for certain of our partners outside of the U.S.

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Research and Development Expense. Research and development expense consists of expenses incurred in connection with the research into and development of product candidates. These expenses consist primarily of compensation, benefits and other employee-related expenses, research and development related facility costs, third-party contract costs relating to nonclinical study and clinical trial activities, development of manufacturing processes, regulatory registration of third-party manufacturing facilities, as well as licensing fees for our product candidates. We charge all research and development expenses to operations as incurred. Under our linaclotide collaboration agreements with Allergan for the U.S. and AstraZeneca for China, Hong Kong and Macau, we are reimbursed for certain research and development expenses, and we net these reimbursements against our research and development expenses as incurred. Amounts owed to Allergan or AstraZeneca for such linaclotide territories are recorded as incremental research and development expense.

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The core of our research and development strategy is to leverage our development capabilities, as well as our pharmacologic expertise, to bring multiple medicines to patients. We are advancing innovative product opportunities in areas of large unmet need, including IBS-C and CIC, abdominal pain associated with lower GI disorders, and persistent GERD.

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Linaclotide. Our commercial product, linaclotide, is available to adult men and women suffering from IBS-C or CIC in certain countries around the world. LINZESS® (linaclotide) is the first FDA-approved guanylate cyclase type-C, or GC-C, agonist and is commercially available in the U.S. for the treatment of IBS-C or CIC. Linaclotide also is approved and commercially available in Japan and in a number of E.U. and other countries. In January 2019, the National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China.

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We and Allergan are exploring ways to enhance the clinical profile of LINZESS by studying linaclotide in additional indications, populations and formulations to assess its potential to treat various conditions. In June 2019, we announced positive topline data from our Phase IIIb trial demonstrating the efficacy and safety of linaclotide 290 mcg on the overall abdominal symptoms of bloating, pain and discomfort in adult patients with IBS-C. In addition, we and Allergan have established a plan with the FDA for clinical pediatric programs with linaclotide, as described below.

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MD-7246. We and Allergan are exploring MD-7246, a delayed release form of linaclotide, as an oral, intestinal, non-opioid pain-relieving agent for patients suffering from certain GI diseases. In May 2019, we and Allergan initiated patient dosing in Phase II clinical trial evaluating MD-7246 in adult patients with IBS-D.

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IW-3718. We are advancing our persistent GERD program through the development of IW-3718, a gastric retentive formulation of a bile acid sequestrant. IW-3718 is a novel formulation of bile acid sequestrant designed to release in the stomach over an extended period of time, bind to bile that refluxes into the stomach, and potentially provide symptomatic relief in patients with persistent GERD. In June 2018, we announced the initiation of two Phase III clinical trials evaluating the safety and efficacy of IW-3718 in patients with persistent GERD.

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Early research and development. Prior to the Separation, our early research and development efforts were primarily focused on identifying novel clinical candidates that drew on our proprietary and expanding expertise in GI disorders and GC pathways. Our early research and development efforts are now focused on supporting our development stage GI programs, including exploring strategic options for further development of certain of our internal programs, as well as evaluating potential external development stage GI programs.

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The following table sets forth our research and development expenses related to our product pipeline for the three and six months ended June 30, 2019 and 2018. These expenses relate primarily to internal compensation, benefits and other employee-related expenses and external costs associated with nonclinical studies and clinical trial costs for our product candidates. We allocate costs related to facilities, depreciation, share-based compensation, research and development support services, laboratory supplies and certain other costs directly to programs.

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​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended June 30, | ​ | Six Months Ended June 30, | ​
​ | ​ | 2019 |  | 2018 |  | 2019 |  | 2018 | ​
​ | ​ | (in thousands) | ​ | (in thousands) | ​
Linaclotide(1) |  | $ | 8,284 |  | $ | 8,187 |  | $ | 18,147 |  | $ | 15,478 |
Lesinurad(2) | ​ | ​ | 155 | ​ | ​ | 1,492 | ​ | ​ | 371 | ​ | ​ | 3,439 | ​
IW-3718 | ​ | ​ | 18,562 | ​ | ​ | 7,165 | ​ | ​ | 35,464 | ​ | ​ | 12,040 | ​
Early research and development | ​ |  | 1,757 | ​ |  | 6,343 | ​ |  | 6,974 | ​ |  | 12,706 | ​
Total research and development expenses | ​ | $ | 28,758 | ​ | $ | 23,187 | ​ | $ | 60,956 | ​ | $ | 43,663 | ​

(1) | Includes linaclotide immediate release in all indications, populations and formulations, and costs associated with MD-7246 (delayed release formulation).

(2) | Includes lesinurad in all indications, populations and formulations.

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Since 2004, the date we began tracking costs by program, we have incurred approximately $480.7 million of research and development expenses related to linaclotide. The expenses for linaclotide include both our portion of the research and development costs incurred by Allergan for the U.S. and AstraZeneca for China, Hong Kong and Macau and invoiced to us under the cost-sharing provisions of our collaboration agreements, as well as the unreimbursed portion of research and development costs incurred by us under such cost-sharing provisions.

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The lengthy process of securing regulatory approvals for new drugs requires the expenditure of substantial resources. Any failure by us to obtain, or any delay in obtaining, regulatory approvals would materially adversely affect our product development efforts and our business overall.

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In connection with the FDA approval of LINZESS, we are required to conduct certain nonclinical and clinical studies, including those aimed at understanding: (a) whether orally administered linaclotide can be detected in breast milk, (b) the potential for antibodies to be developed to linaclotide, and if so, (c) whether antibodies specific for linaclotide could have any therapeutic or safety implications. In addition, we and Allergan established a nonclinical and clinical post-marketing plan with the FDA to understand the efficacy and safety of LINZESS in pediatric patients, and clinical pediatric programs in IBS-C patients age seven to 17 and functional constipation patients age six to 17 are currently ongoing. We and Allergan are also exploring development opportunities to enhance the clinical profile of LINZESS by studying linaclotide in additional indications, populations and formulations to assess its potential to treat various conditions. We cannot currently estimate with any degree of certainty the amount of time or money that we will be required to expend in the future on linaclotide for other geographic markets within IBS-C and CIC, or in additional indications, populations or formulations.

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Given the inherent uncertainties that come with the development of pharmaceutical products, we cannot estimate with any degree of certainty how our programs will evolve, and therefore the amount of time or money that would be required to obtain regulatory approval to market them.

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As a result of these uncertainties surrounding the timing and outcome of any approvals, we are currently unable to estimate precisely when, if ever, linaclotide’s utility will be expanded within its currently approved indications; if or when linaclotide will be developed outside of its current markets, indications, populations or formulations; or when, if ever, any of our other product candidates will generate revenues and cash flows.

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We invest carefully in our pipeline, and the commitment of funding for each subsequent stage of our development programs is dependent upon the receipt of clear, supportive data. In addition, we intend to access externally discovered drug candidates that fit within our core strategy. In evaluating these potential assets, we apply the same investment criteria as those used for investments in internally discovered assets.

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The successful development of our product candidates is highly uncertain and subject to a number of risks including, but not limited to:

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| ● | The duration of clinical trials may vary substantially according to the type, complexity and novelty of the product candidate.

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| ● | The FDA and comparable agencies in foreign countries impose substantial and varying requirements on the introduction of therapeutic pharmaceutical products, typically requiring lengthy and detailed laboratory and clinical testing procedures, sampling activities and other costly and time-consuming procedures.

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| ● | Data obtained from nonclinical and clinical activities at any step in the testing process may be adverse and lead to discontinuation or redirection of development activity. Data obtained from these activities also are susceptible to varying interpretations, which could delay, limit or prevent regulatory approval.

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| ● | The duration and cost of early research and development, including nonclinical studies and clinical trials may vary significantly over the life of a product candidate and are difficult to predict.

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| ● | The costs, timing and outcome of regulatory review of a product candidate may not be favorable, and, even if approved, a product may face post-approval development and regulatory requirements.

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| ● | There may be substantial costs, delays and difficulties in successfully integrating externally developed product candidates into our business operations.

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| ● | The emergence of competing technologies and products and other adverse market developments may negatively impact us.

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As a result of the factors discussed above, including the factors discussed under “Risk Factors” in Item 1A of this Quarterly Report on Form 10-Q, we are unable to determine the duration and costs to complete current or future nonclinical and clinical stages of our product candidates or when, or to what extent, we will generate revenues from the commercialization and sale of our product candidates. Development timelines, probability of success and development costs vary widely. We anticipate that we will make determinations as to which additional programs to pursue and how

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much funding to direct to each program on an ongoing basis in response to the data of each product candidate, the competitive landscape and ongoing assessments of such product candidate’s commercial potential.

​

We expect to invest in our development programs for the foreseeable future. We will continue to invest in linaclotide, including the investigation of ways to enhance the clinical profile within its currently approved indications, and the exploration of its potential utility in other indications, populations and formulations. We will also continue to invest in our other GI-focused product candidates as we advance them through clinical trials, in addition to funding full-time equivalents for research and development activities under our external collaboration and license agreements.

​

Selling, General and Administrative Expense. Selling, general and administrative expense consists primarily of compensation, benefits and other employee-related expenses for personnel in our administrative, finance, legal, information technology, business development, commercial, sales, marketing, communications and human resource functions. Other costs include the legal costs of pursuing patent protection of our intellectual property, general and administrative related facility costs, insurance costs and professional fees for accounting and legal services. As we continue to invest in the commercialization of LINZESS, we expect our selling, general and administrative expenses will be substantial for the foreseeable future. We record all selling, general and administrative expenses as incurred.

​

Under our AstraZeneca collaboration agreement for linaclotide, we are reimbursed for certain selling, general and administrative expenses and we net these reimbursements against our selling, general and administrative expenses as incurred. We include Allergan’s selling, general and administrative cost-sharing payments in the calculation of the net profits and net losses from the sale of LINZESS in the U.S. and present the net payment to or from Allergan as collaboration expense or collaborative arrangements revenue, respectively.

​

Restructuring Expenses. We record costs and liabilities associated with exit and disposal activities in accordance with ASC Topic 420, Exit or Disposal Cost Obligations, or ASC 420. Such costs are based on estimates of fair value in the period the liabilities are incurred in accordance with ASC 420. We evaluate and adjust these costs as appropriate for changes in circumstances as additional information becomes available.

​

Other (Expense) Income. Interest expense consists primarily of cash and non-cash interest costs related to the 2022 Notes and the 2026 Notes. Non-cash interest expense consists of amortization of the debt discount and associated debt issuance costs associated with the 2.25% Convertible Senior Notes due 2022, or the 2022 Notes, and the 8.375% notes due 2026, or the 2026 Notes. We amortize these costs using the effective interest rate method over the life of the respective note agreements as interest expense in our condensed consolidated statements of operations.

​

​

In June 2015, in connection with the issuance of the 2022 Notes, we entered into convertible note hedge transactions, or the Convertible Note Hedges. Concurrently with entering into the Convertible Note Hedges, we also entered into certain warrant transactions in which we sold note hedge warrants, or the Note Hedge Warrants, to the Convertible Note Hedge counterparties to acquire 20,249,665 shares of our Class A common stock, subject to customary anti-dilution adjustments. In April 2019, in connection with the Separation, the number of shares underlying the Note Hedge Warrants was increased to 23,135,435 shares. Gain (loss) on derivatives consists of the change in fair value of the Convertible Note Hedges and Note Hedge Warrants, which are recorded as derivative assets and liabilities. The Convertible Note Hedges and the Note Hedge Warrants are recorded at fair value at each reporting period and changes in fair value are recorded in our condensed consolidated statements of operations. This transaction is more fully described in Note 9, Notes Payable, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

​

In September 2016, we closed a direct private placement, pursuant to which we issued $150.0 million in aggregate principal amount of 8.375% notes due 2026 on January 5, 2017, or the Funding Date. This transaction is more fully described in Note 9, Notes Payable, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

​

Interest income consists of interest earned on our cash, cash equivalents and marketable securities.

​

Discontinued Operations. We have recast all historical expenses directly associated with our sGC business as discontinued operations in accordance with ASC Subtopic 250-20, Discontinued Operations. For additional information refer to Note 2, Cyclerion Separation, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

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​

​

Critical Accounting Policies and Estimates

​

Our discussion and analysis of our financial condition and results of operations is based upon our condensed consolidated financial statements prepared in accordance with U.S. generally accepted accounting principles. The preparation of these financial statements requires us to make certain estimates and assumptions that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. Significant estimates and assumptions in our condensed consolidated financial statements include those related to revenue recognition; available-for-sale securities; accounts receivable; inventory valuation, and related reserves; impairment of long-lived assets, including goodwill; valuation procedures for right-of-use assets and operating lease liabilities; initial valuation procedures for the issuance of convertible notes; valuation of assets and liabilities held for disposition and losses related to discontinued operations; fair value of derivatives; balance sheet classification of notes payable and convertible notes; income taxes, including the valuation allowance for deferred tax assets; research and development expenses; contingencies and share-based compensation. We base our estimates on our historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ materially from our estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known.

​

Except as outlined below, during the three and six months ended June 30, 2019, there were no material changes to our critical accounting policies as reported in our Annual Report on Form 10-K for the year ended December 31, 2018, which was filed with the Securities and Exchange Commission, or SEC, on February 25, 2019, or the 2018 Annual Report on Form 10-K.

​

Discontinued Operations

​

During the three months ended June 30, 2019, we determined that the Separation of our sGC business on April 1, 2019 met the criteria for classification as a discontinued operation in accordance with ASC Topic 205-20, Discontinued Operations. Accordingly, the accompanying condensed consolidated financial statements for all periods presented have been recast to present the assets and liabilities associated with the sGC business as held for disposition and the expenses directly associated with the sGC business as discontinued operations. For additional information related to discontinued operations, refer to Note 2, Cyclerion Separation, to these condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

​

Leases

​

Effective January 1, 2019, we adopted ASC Topic 842, Leases, or ASC 842, using the optional transition method. The adoption of ASC 842 represents a change in accounting principle that aims to increase transparency and comparability among organizations by requiring the recognition of right-of-use, or ROU, assets and lease liabilities on the balance sheet for both operating and finance leases. In addition, the standard requires enhanced disclosures that meet the objective of enabling financial statement users to assess the amount, timing, and uncertainty of cash flows arising from leases. The reported results for the three and six months ended June 30, 2019 reflect the application of ASC 842 guidance, while the reported results for prior periods were prepared in conjunction with ASC Topic 840, Leases, or ASC 840. Because there were no material changes to the values of existing capital leases as a result of the adoption of ASC 842, we concluded that no cumulative-effect adjustment to the accumulated deficit as of January 1, 2019 was necessary. The recognition of right-of-use assets and lease liabilities related to our operating leases under ASC 842 has had a material impact on our condensed consolidated financial statements.

​

As part of the ASC 842 adoption, we elected certain practical expedients outlined in the guidance. These practical expedients include:

​

| ● | A policy election to use the short-term lease exception by asset class;

​

| ● | Election of the practical expedient package during transition, which includes:

| o | An entity need not reassess whether any expired or existing contracts are or contain leases.

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| o | An entity need not reassess the classification for any expired or existing leases. As a result, all leases that were classified as operating leases in accordance with ASC 840 are classified as operating leases under ASC 842, and all leases that were classified as capital leases in accordance with ASC 840 are classified as finance leases under ASC 842.

| o | An entity need not reassess initial direct costs for any existing leases.

Subsequent to our adoption of ASC 842, we elected the post-transition practical expedient, by class of underlying asset, to account for lease components and non-lease components together as a single component for the asset class of operating lease right-of-use real estate assets.

​

Our lease portfolio includes: a lease for our current and future headquarters locations, a data center colocation lease, vehicle leases for our salesforce representatives, and leases for computer and office equipment. We determine if an arrangement is a lease at the inception of the contract. The asset component of our operating leases are recorded as operating lease right-of-use asset, and the liability component of is recorded as current portion of operating lease liabilities and operating lease liabilities, net of current portion in our condensed consolidated balance sheet. As of June 30, 2019, we did not have any finance leases.

​

Right-of-use assets and operating lease liabilities are recognized based on the present value of lease payments over the lease term at the lease inception date. Existing leases in the Company’s lease portfolio as of the adoption date were valued as of January 1, 2019. We use an incremental borrowing rate based on the information available at lease inception in determining the present value of lease payments if an implicit rate of return is not provided with the lease contract. Operating lease right-of-use assets are adjusted for incentives expected to be received.

​

Right-of-use assets and operating lease liabilities are remeasured upon certain modifications to leases using the present value of remaining lease payments and estimated incremental borrowing rate upon lease modification.

​

Lease cost is recognized on a straight-line basis over the lease term, and includes amounts related to short-term leases. We recognize variable lease payments as operating expenses in the period in which the obligation for those payments is incurred. Variable lease payments under the Binney Street Lease primarily include common area maintenance, utilities, real estate taxes, insurance, and other operating costs that are passed on from the lessor in proportion to the space leased by us.

​

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Results of Operations

​

The following discussion summarizes the key factors our management believes are necessary for an understanding of our condensed consolidated financial statements.

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Six Months Ended | ​
​ | ​ | June 30, | ​ | June 30, | ​
​ |  | 2019 |  | 2018 |  | 2019 |  | 2018 |
​ | ​ | (in thousands) | ​ | (in thousands) | ​
Revenues: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Collaborative arrangements revenue | ​ | $ | 77,322 | ​ | $ | 71,207 | ​ | $ | 143,474 | ​ | $ | 134,293 |
Product revenue, net | ​ | ​ | — | ​ | ​ | 1,096 | ​ | ​ | — | ​ | ​ | 1,731 | ​
Sale of active pharmaceutical ingredient | ​ | ​ | 24,893 | ​ | ​ | 8,803 | ​ | ​ | 27,471 | ​ | ​ | 14,237 | ​
Total revenues | ​ | ​ | 102,215 | ​ | ​ | 81,106 | ​ | ​ | 170,945 | ​ | ​ | 150,261 | ​
Cost and expenses: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Cost of revenues, excluding amortization of acquired intangible assets | ​ |  | 11,313 | ​ |  | 4,065 | ​ |  | 12,356 | ​ |  | 6,672 | ​
Write-down of commercial supply and inventory to net realizable value and loss on non-cancellable purchase commitments | ​ |  | — | ​ |  | 1,836 | ​ |  | — | ​ |  | 1,836 | ​
Research and development | ​ |  | 28,758 | ​ |  | 23,187 | ​ |  | 60,956 | ​ |  | 43,663 | ​
Selling, general and administrative | ​ |  | 43,246 | ​ |  | 59,771 | ​ |  | 92,341 | ​ |  | 118,716 | ​
Amortization of acquired intangible assets | ​ | ​ | — | ​ | ​ | 3,476 | ​ | ​ | — | ​ | ​ | 6,952 | ​
Loss on fair value remeasurement of contingent consideration | ​ | ​ | — | ​ | ​ | 1,962 | ​ | ​ | — | ​ | ​ | 2,474 | ​
Gain on lease modification | ​ | ​ | (3,169) | ​ | ​ | — | ​ | ​ | (3,169) | ​ | ​ | — | ​
Restructuring expenses | ​ | ​ | 490 | ​ | ​ | 1,486 | ​ | ​ | 3,818 | ​ | ​ | 3,908 | ​
Total cost and expenses | ​ |  | 80,638 | ​ |  | 95,783 | ​ |  | 166,302 | ​ |  | 184,221 | ​
Income (loss) from operations | ​ |  | 21,577 | ​ |  | (14,677) | ​ |  | 4,643 | ​ |  | (33,960) | ​
Other (expense) income: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Interest expense | ​ |  | (9,430) | ​ |  | (9,383) | ​ |  | (19,022) | ​ |  | (18,656) | ​
Interest and investment income | ​ |  | 668 | ​ |  | 732 | ​ |  | 1,404 | ​ |  | 1,413 | ​
(Loss) gain on derivatives | ​ |  | (672) | ​ |  | (809) | ​ |  | 3,272 | ​ |  | 507 | ​
Other income | ​ |  | 140 | ​ |  | — | ​ |  | 140 | ​ |  | — | ​
Other expense, net | ​ |  | (9,294) | ​ |  | (9,460) | ​ |  | (14,206) | ​ |  | (16,736) | ​
Net income (loss) from continuing operations | ​ | ​ | 12,283 | ​ | ​ | (24,137) | ​ | ​ | (9,563) | ​ | ​ | (50,696) | ​
Net loss from discontinued operations | ​ | ​ | — | ​ | ​ | (25,243) | ​ | ​ | (37,438) | ​ | ​ | (41,828) | ​
Net income (loss) | ​ | $ | 12,283 | ​ | $ | (49,380) | ​ | $ | (47,001) | ​ | $ | (92,524) | ​

​

Three and six months ended June 30, 2019 Compared to Three and six months ended June 30, 2018

​

Revenues

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | ​ | ​ | ​ | ​ |  | ​ | Six Months Ended | ​ | ​ | ​ | ​ | ​ |
​ | ​ | June 30, | ​ | Change |  | ​ | June 30, | ​ | Change |
​ | ​ | 2019 | ​ | 2018 | ​ | $ | ​ | % |  | ​ | 2019 | ​ | 2018 | ​ | $ | ​ | % |
​ | ​ | (dollars in thousands) |  | ​ | (dollars in thousands) |
Revenues: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Collaborative arrangements revenue |  | $ | 77,322 |  | $ | 71,207 |  | $ | 6,115 |  | 9 | % |  | $ | 143,474 |  | $ | 134,293 |  | $ | 9,181 |  | 7 | %
Product revenue, net | ​ | ​ | — |  | ​ | 1,096 |  | ​ | (1,096) |  | (100) | % |  | ​ | — |  | ​ | 1,731 |  | ​ | (1,731) |  | (100) | %
Sale of active pharmaceutical ingredient | ​ | ​ | 24,893 | ​ | ​ | 8,803 | ​ | ​ | 16,090 | ​ | 183 | % | ​ | ​ | 27,471 | ​ | ​ | 14,237 | ​ | ​ | 13,234 | ​ | 93 | %
Total revenues | ​ | $ | 102,215 | ​ |  | 81,106 | ​ |  | 21,109 | ​ | 26 | % | ​ | ​ | 170,945 | ​ |  | 150,261 | ​ |  | 20,684 | ​ | 14 | %

​

Collaborative Arrangements Revenue. The increase in revenue from collaborative arrangements of approximately $6.1 million for the three months ended June 30, 2019 compared to the three months ended June 30, 2018 was primarily related to an approximately $5.7 million increase in our share of the net profits from the sale of LINZESS

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in the U.S. driven by increased prescription demand, partially offset by decreased net price, and an approximately $0.4 million net increase in revenue related to VIBERZI.

​

The increase in revenue from collaborative arrangements of approximately $9.2 million for the six months ended June 30, 2019 compared to the six months ended June 30, 2018 was primarily related to an approximately $8.9 million increase in our share of the net profits from the sale of LINZESS in the U.S. driven by increased prescription demand, partially offset by decreased net price, and approximately $0.5 million from an up-front payment received in connection with a license agreement. The increases were partially offset by an approximately $0.2 million decrease attributable to activities associated with VIBERZI and royalties.

​

Product Revenue, net. The decrease in net product revenue of approximately $1.1 million and approximately $1.7 million for the three and six months ended June 30, 2019 compared to the three and six months ended June 30, 2018, respectively, was due to our termination of the license agreement with AstraZeneca for the development, manufacture, and commercialization of products in the U.S. containing lesinurad as an active ingredient, or the Lesinurad License, in January 2019. As a result of this termination, we are no longer commercializing ZURAMPIC and DUZALLO.

​

Sale of Active Pharmaceutical Ingredient. The increase in sale of API of approximately $16.1 million and approximately $13.2 million for the three and six months ended June 30, 2019, compared to the three and six months ended June 30, 2018, respectively, was primarily due to increased shipments of linaclotide API to Astellas in Japan.

​

Cost and Expenses

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | ​ | ​ | ​ | ​ |  | ​ | Six Months Ended | ​ | ​ | ​ | ​ | ​ |
​ | ​ | June 30, | ​ | Change |  | ​ | June 30, | ​ | Change |
​ |  | 2019 |  | 2018 |  | $ |  | % |  |  | 2019 |  | 2018 |  | $ |  | % |
​ | ​ | (dollars in thousands) |  | ​ | (dollars in thousands) |
Cost and expenses: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Cost of revenues, excluding amortization of acquired intangible assets | ​ | $ | 11,313 | ​ | $ | 4,065 | ​ | $ | 7,248 | ​ | 178 | % | ​ | $ | 12,356 | ​ | $ | 6,672 | ​ | $ | 5,684 | ​ | 85 | %
Write-down of commercial supply and inventory to net realizable value and loss on non-cancellable purchase commitments | ​ |  | — | ​ |  | 1,836 | ​ |  | (1,836) | ​ | (100) | % | ​ |  | — | ​ |  | 1,836 | ​ |  | (1,836) | ​ | (100) | %
Research and development | ​ |  | 28,758 | ​ |  | 23,187 | ​ |  | 5,571 | ​ | 24 | % | ​ |  | 60,956 | ​ |  | 43,663 | ​ |  | 17,293 | ​ | 40 | %
Selling, general and administrative | ​ |  | 43,246 | ​ |  | 59,771 | ​ |  | (16,525) | ​ | (28) | % | ​ |  | 92,341 | ​ |  | 118,716 | ​ |  | (26,375) | ​ | (22) | %
Amortization of acquired intangible assets | ​ | ​ | — | ​ | ​ | 3,476 | ​ | ​ | (3,476) | ​ | (100) | % | ​ | ​ | — | ​ | ​ | 6,952 | ​ | ​ | (6,952) | ​ | (100) | %
Loss on fair value remeasurement of contingent consideration | ​ | ​ | — | ​ | ​ | 1,962 | ​ | ​ | (1,962) | ​ | (100) | % | ​ | ​ | — | ​ | ​ | 2,474 | ​ | ​ | (2,474) | ​ | (100) | %
Gain on lease modification | ​ | ​ | (3,169) | ​ | ​ | — | ​ | ​ | (3,169) | ​ | 100 | % | ​ | ​ | (3,169) | ​ | ​ | — | ​ | ​ | (3,169) | ​ | 100 | %
Restructuring expenses | ​ | ​ | 490 | ​ | ​ | 1,486 | ​ | ​ | (996) | ​ | (67) | % | ​ | ​ | 3,818 | ​ | ​ | 3,908 | ​ | ​ | (90) | ​ | (2) | %
Total cost and expenses | ​ | $ | 80,638 | ​ | $ | 95,783 | ​ | $ | (15,145) | ​ | (16) | % | ​ | $ | 166,302 | ​ | $ | 184,221 | ​ | $ | (17,919) | ​ | (10) | %

​

Cost of Revenue, excluding amortization of acquired intangible assets. The increase of approximately $7.2 million and approximately $5.7 million for the three and six months ended June 30, 2019 compared to the three and six months ended June 30, 2018, respectively, was primarily related to an increase in linaclotide API sales to Astellas in Japan.

​

Write-down of commercial supply and inventory to net realizable value and loss on non-cancellable purchase commitments. The decrease in write-down of commercial supply and inventory to net realizable value and loss on non-cancellable purchase commitments of approximately $1.8 million for the three and six months ended June 30, 2019 compared to the three and six months ended June 30, 2018, respectively, was due to the write-down of lesinurad inventory and commercial supply purchase commitments that occurred during the three months ended June 30, 2018 due to the expected termination of the Lesinurad License.

​

Research and Development Expense. The increase in research and development expense of approximately $5.6 million for the three months ended June 30, 2019 compared to the three months ended June 30, 2018 was primarily related to an increase of approximately $12.0 million in research costs related to our early research and development efforts; and an increase of approximately $1.5 million related to linaclotide development. These increases were partially offset by a decrease of approximately $6.2 million in compensation, benefits and other employee-related expenses; a decrease of approximately $1.0 million in operating expenses; and a decrease of approximately $0.4 million related to lesinurad development due to the termination of the Lesinurad License.

​

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The increase in research and development expense of approximately $17.3 million for the six months ended June 30, 2019 compared to the six months ended June 30, 2018 was primarily related to an increase of approximately $23.5 million in research costs related to our early research and development efforts; an increase of approximately $3.8 million related to linaclotide development; and an increase of approximately $0.6 million in costs associated with the Separation. These increases were partially offset by a decrease of approximately $7.6 million in compensation, benefits and other employee-related expenses; a decrease of approximately $1.7 million in facilities and operating expenses; and a decrease of approximately $0.9 million related to lesinurad development due to the termination of the Lesinurad License.

​

Selling, General and Administrative Expense. Selling, general and administrative expenses decreased for the three months ended June 30, 2019 compared to the three months ended June 30, 2018 primarily as a result of the Separation which was completed on April 1, 2019 and the termination of the Lesinurad License in January 2019. The approximately $16.6 million decrease in selling, general and administrative expense included an approximately $2.2 million decrease in costs associated with the Separation and an approximately $14.4 million decrease in non-Separation costs. The approximately $2.2 million decrease in costs associated with the Separation includes an approximately $6.0 million decrease in consulting and investment banking costs, offset by an approximately $2.1 million increase in compensation, benefits and employee-related expenses; an approximately $1.4 million increase in facilities and operating expenses; and an approximately $0.3 million increase in legal expenses. The decrease in non-Separation costs of approximately $14.4 million was primarily a result of an approximately $9.2 million decrease in sales and marketing programs; an approximately $10.8 million decrease in other compensation, benefits and employee-related expenses; an approximately $1.8 million decrease in professional service costs; and an approximately $0.2 million decrease in other facilities and operating costs. These decreases were partially offset by an approximately $4.8 million increase in consulting and investment banking costs; an approximately $2.6 million increase in legal costs; and an approximately $0.2 million increase in collaboration expenses.

​

Selling, general and administrative expenses decreased for the six months ended June 30, 2019 compared to the six months ended June 30, 2018 primarily as a result of the Separation which was completed on April 1, 2019 and the termination of the Lesinurad License in January 2019. The decrease of approximately $26.4 million was primarily due to decreases in non-Separation costs of approximately $42.9 million offset by an approximately $16.5 million increase in costs associated with the Separation. The approximately $42.9 million decrease in non-Separation costs of includes an approximately $17.2 million decrease in sales and marketing programs; an approximately $14.9 million decrease in other compensation, benefits and employee-related expenses; an approximately $8.0 million decrease in other consulting costs; an approximately $2.5 million decrease in professional services expenses; and an approximately $1.6 million decrease in other facilities and operating costs. These decreases were also partially offset by an approximately $1.1 million increase in non-Separation legal expenses. The decreases associated with the non-Separation costs were partially offset by an approximately $16.5 million increase in costs associated with the Separation, including an approximately $6.0 million increase in compensation, benefits and employee-related expenses; an approximately $5.5 million increase in consulting and investment banking costs; an approximately $2.6 million increase in facilities and operating expenses; and an approximately $2.3 million increase in legal expenses.

​

Amortization of Acquired Intangible Assets. The decrease in amortization of acquired intangible assets expense of approximately $3.5 million for the three months ended June 30, 2019 compared to the three months ended June 30, 2018 and approximately $7.0 million for the six months ended June 30, 2019 compared to the six months ended June 30, 2018, was due to the impairment of the ZURAMPIC and DUZALLO intangible assets as a result of revised cash flow assumptions and the termination of the Lesinurad License.

​

Loss on Fair Value Remeasurement of Contingent Consideration. The decrease in the loss on fair value of the contingent consideration obligation of approximately $2.0 million for the three months ended June 30, 2019 compared to the three months ended June 30, 2018 and approximately $2.5 million for the six months ended June 30, 2019 compared to the six months ended June 30, 2018, was due to the termination of the Lesinurad License.

​

Gain on Lease Modification. The increase in the gain on lease modification of approximately $3.2 million for each of the three and six months ended June 30, 2019 compared to the three and six months ended June 30, 2018 was due to the modification of the Binney Street Lease in connection with the Separation.

​

Restructuring Expenses. The decrease in restructuring expenses of approximately $1.0 million for the three months ended June 30, 2019 compared to the three months ended June 30, 2018, and an insignificant decrease for the six

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months ended June 30, 2019 compared to the six months ended June 30, 2018 was primarily due to costs associated with the workforce reductions in January 2018 and June 2018, which exceeded the costs incurred in the February 2019 workforce reduction.

​

​

Other (Expense) Income, Net

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | ​ | ​ | ​ | ​ |  | ​ | Six Months Ended | ​ | ​ | ​ | ​ | ​ |
​ | ​ | June 30, | ​ | Change |  | ​ | June 30, | ​ | Change |
​ |  | 2019 |  | 2018 |  | $ |  | % |  |  | 2019 |  | 2018 |  | $ |  | % |
​ | ​ | (dollars in thousands) |  | ​ | (dollars in thousands) |
Other (expense) income: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Interest expense | ​ | $ | (9,430) | ​ | $ | (9,383) | ​ | $ | (47) | ​ | 1 | % | ​ | $ | (19,022) | ​ | $ | (18,656) | ​ | $ | (366) | ​ | 2 | %
Interest and investment income | ​ |  | 668 | ​ |  | 732 | ​ |  | (64) | ​ | (9) | % | ​ |  | 1,404 | ​ |  | 1,413 | ​ |  | (9) | ​ | (1) | %
(Loss) gain on derivatives | ​ |  | (672) | ​ |  | (809) | ​ |  | 137 | ​ | (17) | % | ​ |  | 3,272 | ​ |  | 507 | ​ |  | 2,765 | ​ | 545 | %
Other income | ​ |  | 140 | ​ |  | — | ​ |  | 140 | ​ | 100 | % | ​ |  | 140 | ​ |  | — | ​ |  | 140 | ​ | 100 | %
Total other expense, net | ​ | $ | (9,294) | ​ | $ | (9,460) | ​ | $ | 166 | ​ | (2) | % | ​ | $ | (14,206) | ​ | $ | (16,736) | ​ | $ | 2,530 | ​ | (15) | %

​

Interest expense increased by an insignificant amount during the three months ended June 30, 2019 compared to the three months ended June 30, 2018, mainly due to an increase of approximately $0.4 million in interest expense associated with the 2022 Notes offset by a decrease of approximately $0.3 million in interest expense associated with the 2026 Notes. Interest expense increased by approximately $0.4 million during the six months ended June 30, 2019 compared to the six months ended June 30, 2018, mainly due to an increase of approximately $0.8 million in interest expense associated with the 2022 Notes partially offset by a decrease of $0.4 million in interest expense associated with the 2026 Notes.

​

Interest and investment income decreased by an insignificant amount during each of the three and six months ended June 30, 2019 compared to the three and six months ended June 30, 2018, mainly due to slightly lower yield return on investment securities in 2019.

​

For the three months ended June 30, 2019, we recorded a loss on derivatives of approximately $0.7 million resulting from an approximately $10.1 million increase in the fair value of the Convertible Note Hedges and an approximately $10.8 million increase in the fair value of the Note Hedge Warrants. For the three months ended June 30, 2018, we recorded a loss on derivatives of approximately $0.8 million resulting from an approximately $46.1 million increase in the fair value of the Convertible Note Hedges and an approximately $46.9 million increase in the fair value of the Note Hedge Warrants.

​

For the six months ended June 30, 2019, we recorded a gain on derivatives of approximately $3.3 million resulting from an approximately $19.7 million increase in the fair value of the Convertible Note Hedges and an approximately $16.4 million increase in the fair value of the Note Hedge Warrants. For the six months ended June 30, 2018, we recorded a gain on derivatives of approximately $0.5 million resulting from an approximately $51.3 million increase in the fair value of the Convertible Note Hedges and an approximately $50.8 million increase in the fair value of the Note Hedge Warrants.

​

Other income increased by an insignificant amount during each of the three and six months ended June 30, 2019 compared to the three and six months ended June 30, 2018 due to income related to a transition service agreement with Cyclerion.

​

Net Loss from Discontinued Operations

​

Net loss from discontinued operations was approximately $25.2 million for the three months ended June 30, 2018. There was no net loss from discontinued operations for the three months ended June 30, 2019 as the Separation was completed on April 1, 2019. Net loss from discontinued operations for the six months ended June 30, 2019 compared to the six months ended June 30, 2018 decreased by approximately $4.4 million primarily related to a decrease in research and development expense related to our sGC business. For additional information on discontinued operations, see Note 2, Cyclerion Separation, to our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q.

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Liquidity and Capital Resources

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At June 30, 2019, we had approximately $98.9 million of unrestricted cash and cash equivalents. Our cash equivalents include amounts held in money market funds and repurchase agreements. We invest cash in excess of immediate requirements in accordance with our investment policy, which limits the amounts we may invest in any one type of investment and requires all investments held by us to be at least A- rated, with a remaining final maturity when purchased of less than twenty-four months, so as to achieve liquidity and capital preservation objectives.

​

During the six months ended June 30, 2019, our balances of cash and cash equivalents decreased by approximately $73.3 million. This decrease is primarily due to approximately $51.6 million of cash used to operate our business, of which approximately $63.0 related to cash used in continuing operations and approximately $11.4 million related to cash provided by discontinued operations. The decrease in cash used to operate our business includes payments related to, among other things, research and development, and selling, general and administrative expenses, including payroll and compensation expense, and activities supporting the Separation that occurred on April 1, 2019. We also made principal payments on the 2026 Notes of approximately $21.5 million and invested approximately $1.4 million in capital expenditures. These cash outflows were partially offset by approximately $5.2 million in proceeds from the exercise of stock options.

​

We may from time to time seek to retire, redeem or repurchase all or part of our outstanding debt through cash purchases and/or exchanges, in open market purchases, privately negotiated transactions, by tender offer or otherwise. Such repurchases, redemptions or exchanges, if any, will depend on prevailing market conditions, liquidity requirements, contractual restrictions and other factors, and the amounts involved may be material.

​

Sources of Liquidity

​

We have incurred losses since our inception in 1998 and, as of June 30, 2019, we had an accumulated deficit of approximately $1.6 billion. We have financed our operations to date primarily through both the private sale of our preferred stock and the public sale of our Class A common stock, including approximately $203.2 million of net proceeds from our initial public offering, or IPO, in February 2010, and approximately $413.4 million of net proceeds from our follow-on public offerings; payments received under our strategic collaborative arrangements, including upfront and milestone payments, royalties and our share of net profits, as well as reimbursement of certain expenses; and debt financings, including approximately $324.0 million of net proceeds from the private placement of our 2022 Notes in June 2015 and approximately $11.2 million of net proceeds from the issuance of $150.0 million in aggregate principal amount of the 2026 Notes in January 2017.

​

Funding Requirements

​

We began commercializing LINZESS in the U.S. with our collaboration partner, Allergan, in the fourth quarter of 2012, and we currently derive a significant portion of our revenue from this collaboration. In addition, we are deploying significant resources to advance product opportunities in IBS-C and CIC, abdominal pain associated with IBS and persistent GERD, as well as to fulfill FDA requirements for linaclotide. We have also derived revenue from the sale of linaclotide API to Astellas for Japan. Our goal is to become cash flow positive, driven by increased revenue generated through sales of LINZESS and other commercial activities and financial discipline. We have not achieved positive cash flows from operations to date. We also expect revenue from Astellas for Japan to be significantly lower after 2019, particularly given Astellas’s buildup of linaclotide API inventory during the launch of LINZESS in Japan.

​

Under our collaboration with Allergan for North America, total net sales of LINZESS in the U.S., as recorded by Allergan, are reduced by commercial costs incurred by each party, and the resulting amount is shared equally between us and Allergan. Additionally, we receive royalties from Allergan based on sales of linaclotide in its licensed territories outside of the U.S. We believe revenues from our LINZESS partnership for the U.S. with Allergan will continue to constitute a significant portion of our total revenue for the foreseeable future and we cannot be certain that such revenues, as well as the revenues from our other commercial activities, will enable us to become cash flow positive, or to do so in the timeframes we expect. We also anticipate that we will continue to incur substantial expenses for the next several years as we further develop and commercialize linaclotide in the U.S., China and other markets, develop and commercialize other products, and invest in our pipeline and potentially other external opportunities. We believe that our cash on hand as of June 30, 2019 will be sufficient to meet our projected operating needs at least through the next twelve months from the issuance of these financial statements.

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Our forecast of the period of time through which our financial resources will be adequate to support our operations, including the underlying estimates regarding the costs to develop our product candidates and obtain regulatory approvals and the costs to commercialize linaclotide in the U.S., China and other markets, and develop and commercialize other products, our expectations regarding revenue from Astellas for Japan, as well as our goal to become cash flow positive, are forward-looking statements that involve risks and uncertainties. Our actual results could vary materially and negatively from these and other forward-looking statements as a result of a number of factors, including the factors discussed in the “Risk Factors” section of this Quarterly Report on Form 10-Q. We have based our estimates on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we currently expect.

​

Due to the numerous risks and uncertainties associated with the development and commercialization of our product candidates, we are unable to estimate precisely the amounts of capital outlays and operating expenditures necessary to develop, obtain regulatory approval for, and commercialize linaclotide and our other product candidates, in each case, for all of the markets, indications, populations and formulations for which we believe each is suited. Our funding requirements will depend on many factors, including, but not limited to, the following:

​

| ● | the revenue generated by sales of LINZESS, CONSTELLA and any other sources;

​

| ● | the rate of progress and cost of our commercialization activities, including the expense we incur in marketing and selling LINZESS and any other products;

​

| ● | the success of our third-party manufacturing activities;

​

| ● | the time and costs involved in developing, and obtaining regulatory approvals for, our product candidates, as well as the timing and cost of any post-approval development and regulatory requirements;

​

| ● | the success of our research and development efforts;

​

| ● | the emergence of competing or complementary products;

​

| ● | the costs of filing, prosecuting, defending and enforcing any patent claims and other intellectual property rights; ​

| ● | the terms and timing of any additional collaborative, licensing or other arrangements that we may establish, including royalties or other payments due or payable under such agreements; and

​

| ● | the acquisition of businesses, products and technologies and the impact of other strategic transactions, as well as the cost and timing of integrating any such assets into our business operations.

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Financing Strategy

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We may, from time to time, consider additional funding through a combination of new collaborative arrangements, strategic alliances, and additional equity and debt financings or from other sources. We will continue to manage our capital structure and to consider all financing opportunities, whenever they may occur, that could strengthen our long-term liquidity profile. Any such capital transactions may or may not be similar to transactions in which we have engaged in the past. There can be no assurance that any such financing opportunities will also be available on acceptable terms, if at all.

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Contractual Commitments and Obligations

​

The disclosure of our contractual obligations and commitments was reported in our 2018 Annual Report on Form 10-K. Except for commitments related to our current and future headquarters leases, there have not been any material changes from the contractual commitments and obligations previously disclosed in our 2018 Annual Report on Form 10-K. Refer to Note 8, Leases, to these condensed financial statements appearing elsewhere in this Quarterly Report on Form 10-Q for details on revised lease commitments.

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Off-Balance Sheet Arrangements

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We do not have any relationships with unconsolidated entities or financial partnerships, such as entities often referred to as structured finance or special purpose entities, that would have been established for the purpose of facilitating off-balance sheet arrangements (as that term is defined in Item 303(a)(4)(ii) of Regulation S-K) or other contractually narrow or limited purposes. As such, we are not exposed to any financing, liquidity, market or credit risk that could arise if we had engaged in those types of relationships. We enter into guarantees in the ordinary course of business related to the guarantee of our own performance and the performance of our subsidiaries.

​

New Accounting Pronouncements

​

For a discussion of recent accounting pronouncements, please refer to Note 2, Summary of Significant Accounting Policies, in our 2018 Annual Report on Form 10-K and Note 1, Nature of Business, appearing elsewhere in this Quarterly Report on Form 10-Q. We did not otherwise adopt any new accounting pronouncements during the three and six months ended June 30, 2019 that had a material effect on our condensed consolidated financial statements included in this report.

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Item 3. Quantitative and Qualitative Disclosures about Market Risk

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Interest Rate Risk

​

We are exposed to market risk related to changes in interest rates. We invest our cash in a variety of financial instruments, principally securities issued by the U.S. government and its agencies, collateralized reverse repurchase agreements, and money market instruments. The goals of our investment policy are preservation of capital, fulfillment of liquidity needs and fiduciary control of cash and investments. We also seek to maximize income from our investments without assuming significant risk.

​

Our primary exposure to market risk is interest income sensitivity, which is affected by changes in the general level of interest rates, particularly because our investments are in short-term marketable securities. Due to the primarily short-term duration of our investment portfolio and the low risk profile of our investments, an immediate 1% change in interest rates would not have a material effect on the fair market value of our portfolio. Accordingly, we would not expect our operating results or cash flows to be affected to any significant degree by the effect of a sudden change in market interest rates on our investment portfolio.

​

We do not believe our cash and cash equivalents have significant risk of default or illiquidity. While we believe our cash and cash equivalents do not contain excessive risk, we cannot provide absolute assurance that in the future our investments will not be subject to adverse changes in market value. In addition, we maintain significant amounts of cash and cash equivalents at one or more financial institutions that are in excess of federally insured limits. Given the potential instability of financial institutions, we cannot provide assurance that we will not experience losses on these deposits.

​

Our 2026 Notes and 2022 Notes bear interest at a fixed rate and therefore have minimal exposure to changes in interest rates; however, because these interest rates are fixed, we may be paying a higher interest rate, relative to market, in the future if our credit rating improves or other circumstances change.

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Equity Price Risk

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2022 Notes

​

Our 2022 Notes include conversion and settlement provisions that are based on the price of our Class A common stock at conversion or at maturity of the 2022 Notes. The amount of cash we may be required to pay is determined by the price of our Class A common stock. The fair value of our 2022 Notes is dependent on the price and volatility of our Class A common stock and will generally increase or decrease as the market price of our Class A common stock changes.

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The 2022 Notes are convertible into Class A common stock at an adjusted conversion rate of 68.9172 shares of Class A common stock (subject to adjustment as provided for in the Indenture) per $1,000 principal amount of the 2022 Notes, which is equal to a conversion price of approximately $14.51 per share. The 2022 Notes will mature on June 15, 2022 unless earlier converted or repurchased. The 2022 Notes bear cash interest at an annual rate of 2.25%, payable on June 15 and December 15 of each year, which began on December 15, 2015. As of June 30, 2019, the fair value of the 2022 Notes was estimated by us to be approximately $359.1 million. The 2022 Notes are more fully described in Note 5, Fair Value of Financial Instruments, and Note 9, Notes Payable, in the accompanying notes to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

​

Convertible Note Hedge and Note Hedge Warrant Transactions with Respect to 2022 Notes

​

To minimize the impact of potential dilution to our common stock upon conversion of the 2022 Notes, we entered into Convertible Note Hedges to acquire, subject to customary adjustments, 23,135,435 shares of our Class A common stock at a strike price of $14.51 per share, as adjusted. Concurrently with entering into the Convertible Note Hedges, we entered into warrant transactions whereby we sold Note Hedge Warrants to acquire, subject to customary adjustments, 23,135,435 shares of our Class A common stock at a strike price of $18.82 per share, as adjusted. The Convertible Note Hedges and Note Hedge Warrants are more fully described in Note 9, Notes Payable, in the accompanying notes to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

​

Foreign Currency Risk

​

We have no significant operations outside the U.S. and we do not expect to be impacted significantly by foreign currency fluctuations.

​

Effects of Inflation

​

We do not believe that inflation and changing prices over the three and six months ended June 30, 2019 and 2018 had a significant impact on our results of operations.

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Item 4. Controls and Procedure s

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Evaluation of Disclosure Controls and Procedures

​

As required by Rule 13a-15(b) of the Securities Exchange Act of 1934, or the Exchange Act, our management, including our principal executive officer and our principal financial officer, conducted an evaluation as of the end of the period covered by this Quarterly Report on Form 10-Q of the effectiveness of the design and operation of our disclosure controls and procedures. Based on that evaluation, our principal executive officer and principal financial officer concluded that our disclosure controls and procedures are effective at the reasonable assurance level in ensuring that information required to be disclosed by us in the reports that we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in the reports we file under the Exchange Act is accumulated and communicated to our management, including our principal executive officer and principal financial officer, as appropriate to allow timely decisions regarding required disclosure.

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Changes in Internal Control

​

As required by Rule 13a-15(d) of the Exchange Act, our management, including our principal executive officer and our principal financial officer, conducted an evaluation of the internal control over financial reporting to determine whether any changes occurred during the period covered by this Quarterly Report on Form 10-Q that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

​

On April 1, 2019, we completed the separation of Cyclerion. In connection with the Separation, we have implemented internal controls over discontinued operations.

​

Effective on April 1, 2019, Mark Mallon was appointed Chief Executive Officer of our Company by our Board of Directors.

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In addition, effective July 8, 2019, Kelly MacDonald was appointed Chief Accounting Officer of our Company by our Board of Directors.

​

Based on that evaluation, our principal executive officer and principal financial officer concluded no other changes during the period covered by this Quarterly Report on Form 10-Q materially affected, or were reasonably likely to materially affect, our internal control over financial reporting.

​

​

​

PART II OTHER INFORMATION

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Item 1. Legal Proceedings

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Actions in which we are the Plaintiff

​

LINZESS

​

We and Allergan have received Paragraph IV certification notice letters, or Notice Letters, regarding Abbreviated New Drug Applications, or ANDAs, submitted to the FDA by generic drug manufacturers requesting approval to engage in commercial manufacture, use, sale and offer for sale of (i) 145 mcg and 290 mcg linaclotide capsules, or the Potential Generic Products, and/or (ii) 72 mcg linaclotide capsules, or the Potential 72mcg Generic Products, each proposed generic versions of our FDA-approved drug LINZESS.

​

In October 2016, we received a Notice Letter relating to an ANDA that was submitted to the FDA by Teva Pharmaceuticals USA, Inc., or Teva. Teva’s Notice Letter contends that United States patents for LINZESS (U.S. Patent Nos. 7,371,727, 7,704,947, 7,745,409, 8,080,526, and 8,110,553 (expiring 2024); 7,304,036 (expiring 2026); and 8,748,573, 8,802,628, and 8,933,030 (expiring 2031), or the Challenged Patents) listed in the FDA’s list of Approved Drug Products with Therapeutic Equivalence Evaluations, commonly referred to as the Orange Book, are invalid, unenforceable and/or would not be infringed by Teva’s manufacture, use, sale or offer for sale of the Potential Generic Products. In September 2017, we received a second Notice Letter relating to the ANDA submitted to the FDA by Teva contending that U.S. Patent No. 9,708,371 (expiring 2033) listed in the Orange Book is invalid and/or would not be infringed by Teva’s manufacture, use, sale or offer for sale of the Potential Generic Products. In December 2017, we received a Notice Letter relating to an ANDA that was submitted to the FDA by Teva, contending that U.S. Patent Nos. 7,371,727, 7,704,947, 7,745,409, 8,080,526, and 8,110,553; 7,304,036; 8,933,030; and 9,708,371, or the 72mcg Challenged Patents, are invalid, unenforceable and/or would not be infringed by Teva’s manufacture, use, sale or offer for sale of the Potential 72 mcg Generic Product.

​

In November 2016, we received a Notice Letter relating to an ANDA that was submitted to the FDA by Sandoz Inc., or Sandoz, contending that all of the Challenged Patents are invalid, unenforceable and/or would not be infringed by Sandoz’s manufacture, use, sale or offer for sale of the Potential Generic Products. In January 2018, we received a second Notice Letter relating to the ANDA submitted to the FDA by Sandoz contending that U.S. Patent No. 9,708,371 is invalid and/or would not be infringed by Sandoz’s manufacture, use, sale or offer for sale of the Potential Generic Products.

​

In response to the ANDAs for which we received Notice Letters in 2016, we and Allergan filed a lawsuit against the generic drug manufacturers in Delaware District Court in November 2016. We asserted that the Challenged Patents are valid and infringed by Teva and Sandoz. In accordance with the Hatch-Waxman Act, the timely filing of the lawsuits against the ANDA filers with respect to the Challenged Patents triggered an automatic stay of the FDA’s approval of the ANDAs until as early as February 29, 2020 (unless there is a final court decision adverse to us and Allergan sooner). In October 2017 and January 2018, we and Allergan filed lawsuits against Teva and Sandoz, respectively, each in Delaware District Court, related to each of their respective second Notice Letters. We asserted that U.S. Patent No. 9,708,371 is valid and infringed by each of Teva and Sandoz. The lawsuits filed in October 2017 and January 2018 against Teva and Sandoz, respectively, have been consolidated with the lawsuit filed in November 2016.

​

In January 2017, each of Teva and Sandoz filed an answer and counterclaims seeking declaratory judgment of invalidity and non-infringement of the Challenged Patents. In November 2017 and February 2018, each of Teva and Sandoz, respectively, filed an answer and counterclaims seeking declaratory judgment of invalidity and non-infringement of U.S. Patent No. 9,708,371. In February 2018, we and Allergan filed a lawsuit against Teva in Delaware

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District Court asserting that the 72mcg Challenged Patents are valid and infringed. This lawsuit was consolidated with the lawsuit filed in November 2016.

​

In May 2018 and August 2018, we, Allergan, Teva and Sandoz stipulated to dismiss without prejudice all claims, counterclaims and defenses with respect to U.S. Patent Nos. 9,708,371 and 8,933,030, respectively. In May 2019, we, Allergan, Teva and Sandoz stipulated to dismiss without prejudice all claims, counterclaims and defenses with respect to U.S. Patent Nos. 7,745,409 and 8,110,553.

​

The trial for the action involving Teva and Sandoz was originally scheduled to begin in June 2019. However, the trial was postponed as a result of the unavailability of one of the expert witnesses for Teva and Sandoz to testify in person at the trial due to a serious health issue. On July 22, 2019, we, Allergan, Teva and Sandoz filed a proposed stipulation with the Delaware District Court. Subject to the court’s approval, the stipulation provides for the trial to be rescheduled to begin on January 7, 2020. In an effort to preserve the status quo, and subject to the court’s approval, the stipulation would prohibit Teva and Sandoz from commercially selling or importing into the U.S. any proposed generic version of LINZESS until the earlier of (i) the date the court issues its trial decision in the lawsuit, and (ii) September 20, 2020.

​

We and Allergan previously entered into settlement agreements with Sun Pharma Global FZE, Aurobindo Pharma Ltd. and an affiliate of Aurobindo, and Mylan Pharmaceuticals Inc.

​

​

Item 1A. Risk Factors

​

In addition to the other information in this Quarterly Report on Form 10-Q, any of the factors described below could significantly and negatively affect our business, financial condition, results of operations or prospects. The trading price of our common stock may decline due to these risks.

​

Risks Related to Our Business and Industry

​

We are highly dependent on the commercial success of LINZESS in the U.S. for the foreseeable future; we cannot guarantee that we will generate sufficient revenues from LINZESS to cover our expenses.

​

We and our partner, Allergan plc (together with its affiliates), or Allergan, began selling LINZESS in the U.S. during December 2012. Revenues from our LINZESS collaboration constitute a significant portion of our total revenue, and we believe they will continue to do so for the foreseeable future. The commercial success of LINZESS depends on a number of factors, including:

​

| ● | the effectiveness of LINZESS as a treatment for adult patients with IBS-C or CIC;

​

| ● | the size of the treatable patient population;

​

| ● | the effectiveness of the sales, managed markets and marketing efforts by us and Allergan;

​

| ● | the adoption of LINZESS by physicians, which depends on whether physicians view it as safe and effective treatment for adult patients with IBS-C and CIC;

​

| ● | our success in educating and activating adult IBS-C and CIC patients to enable them to more effectively communicate their symptoms and treatment history to their physicians;

​

| ● | our ability to both secure and maintain adequate reimbursement for, and optimize patient access to, LINZESS and our ability to demonstrate that LINZESS is safer, more efficacious and/or more cost-effective than alternative therapies;

​

| ● | the effectiveness of our partners’ distribution networks;

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| ● | the occurrence of any side effects, adverse reactions or misuse, or any unfavorable publicity in these or other areas, associated with linaclotide; and

​

| ● | the development or commercialization of competing products or therapies for the treatment of IBS-C or CIC, or their associated symptoms.

​

Our revenues from the commercialization of LINZESS are subject to these and other factors, and therefore may be unpredictable from quarter-to-quarter. Revenues from LINZESS or other sources in any quarter may be insufficient to cover our expenses or sustain net income.

​

Our products may cause undesirable side effects or have other properties that could limit their commercial potential.

The most commonly reported adverse reaction since linaclotide became commercially available, as well as in the clinical trials for linaclotide in IBS-C and CIC, has been diarrhea. In the linaclotide Phase III IBS-C and CIC trials, severe diarrhea was reported in 2% or less of the linaclotide-treated patients and its incidence was similar between the IBS-C and CIC populations. Linaclotide has been prescribed to millions of patients since its launch in the U.S. and other territories beginning in December 2012, and, as a result, it has been used in wider populations and in less rigorously controlled environments than in the clinical studies supporting its approval.

Further, if and as we and our partners conduct clinical trials, including in new or existing territories, indications, populations or formulations, as well as explore potential combination products, the number of patients treated with our products within and outside of such products’ currently approved indications and patient populations has grown and continues to do so.

As patient experience increases and expands, we and others may identify previously unknown side effects, known side effects may be found to be more frequent or severe than in the past, and we and others may detect unexpected safety signals for our products or any products perceived to be similar to our products. The foregoing, or the perception of the foregoing, may have the following effects, among others:

​

| ● | sales of our products may be impaired;

​

| ● | regulatory approvals for our products may be delayed, denied, restricted or withdrawn;

​

| ● | we or our partners may decide to, or be required to, change the products’ label or send product warning letters or field alerts to physicians, pharmacists and hospitals;

​

| ● | reformulation of the products, additional nonclinical or clinical studies, changes in labeling or changes to or re-approvals of manufacturing facilities may be required;

​

| ● | we or our partners may be precluded from pursuing approval of linaclotide in new territories or from studying additional development opportunities to enhance our products’ clinical profiles, including within new or existing indications, populations and formulations, as well as in potential combination products;

​

| ● | our or our products’ reputation in the marketplace may suffer; and

​

| ● | government investigations or lawsuits, including class action suits, may be brought against us or our partners.

​

Any of the above occurrences would harm or prevent sales of our products, increase expenses and impair our and our partners’ ability to successfully commercialize our products.

​

In addition, the U.S. Food and Drug Administration, or FDA, -approved label for LINZESS contains a boxed warning about its use in pediatric patients. LINZESS is contraindicated in pediatric patients up to six years of age based on nonclinical data from studies in neonatal mice approximately equivalent to human pediatric patients less than two years of age. There is also a warning advising physicians to avoid the use of LINZESS in pediatric patients six to less than 18 years of age. This warning is based on data in young juvenile mice and the lack of clinical safety and efficacy data in pediatric patients of any age group. We and Allergan have established a nonclinical and clinical post-

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marketing plan with the FDA to understand the safety and efficacy of LINZESS in pediatric patients, which is discussed below. These and other restrictions could limit the commercial potential of LINZESS.

​

We rely entirely on contract manufacturers, our partners and other third parties to manufacture and distribute linaclotide. If they are unable to comply with applicable regulatory requirements, unable to source sufficient raw materials, experience manufacturing or distribution difficulties, or are otherwise unable to manufacture and distribute sufficient quantities to meet demand, our commercialization efforts may be materially harmed.

​

We have no internal manufacturing or distribution capabilities. Instead, we rely on a combination of contract manufacturers and our partners to manufacture active pharmaceutical ingredient, or API, and final drug product. We rely on our partners to store and distribute linaclotide to third party purchasers. We and certain of our partners have commercial supply agreements with independent third parties to manufacture the linaclotide API used to support all of our partnered territories. Each of Allergan and Astellas is responsible for linaclotide drug product and finished goods manufacturing (including bottling and packaging) for its respective territories, and distributing the finished goods to wholesalers. Under our collaboration with AstraZeneca, we are accountable for drug product and finished goods manufacturing for China and for drug product manufacturing for Hong Kong and Macau, with AstraZeneca accountable for finished goods manufacturing for Hong Kong and Macau. Neither we nor AstraZeneca have experience manufacturing linaclotide on a commercial scale and we and AstraZeneca are working to achieve sufficient redundancy in this component of the linaclotide supply chain.

​

Each of our API and drug product manufacturers must comply with current good manufacturing practices, or GMP, and other stringent regulatory requirements enforced by the FDA and foreign regulatory authorities in other jurisdictions. These requirements include, among other things, quality control, quality assurance and the maintenance of records and documentation, which occur in addition to our own quality assurance releases. Manufacturers of our products may be unable to comply with these GMP requirements and with other regulatory requirements. We have little control over our manufacturers’ or partners’ compliance with these regulations and standards.

​

Our manufacturers may experience problems with their respective manufacturing and distribution operations and processes, including for example, quality issues, such as product specification and stability failures, procedural deviations, improper equipment installation or operation, utility failures, contamination and natural disasters. In addition, the raw materials necessary to make API for our products are acquired from a limited number of sources. Any delay or disruption in the availability of these raw materials or a change in raw material suppliers could result in production disruptions, delays or higher costs with consequent adverse effects on us.

​

The manufacture of pharmaceutical products requires significant expertise and capital investment, including the development of advanced manufacturing techniques and process controls. Manufacturers of pharmaceutical products often encounter difficulties in commercial production. These problems include difficulties with production costs and yields, quality control, including stability of the product and quality assurance testing, and shortages of qualified personnel, as well as compliance with federal, state and foreign regulations and the challenges associated with complex supply chain management. Even if our manufacturers or partners do not experience problems and commercial manufacturing is achieved, their maximum or available manufacturing capacities may be insufficient to meet commercial demand. Finding alternative manufacturers or adding additional manufacturers requires a significant amount of time and involves significant expense. New manufacturers would need to develop and implement the necessary production techniques and processes, which along with their facilities, would need to be inspected and approved by the regulatory authorities in each applicable territory.

​

If our API or drug product manufacturers fail to adhere to applicable GMP or other regulatory requirements, experience delays or disruptions in the availability of raw materials or experience manufacturing or distribution problems, we will suffer significant consequences, including product seizures or recalls, loss of product approval, fines and sanctions, reputational damage, shipment delays, inventory shortages, inventory write-offs and other product-related charges and increased manufacturing costs. If we experience any of these results, or if our manufacturers’ maximum or available capacities are insufficient to meet demand, we may not be able to successfully commercialize our products.

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​

The transition of lesinurad to AstraZeneca could require additional substantial financial and managerial resources, and we may not be successful.

​

In June 2016, we entered into a license agreement for exclusive rights to commercialize products containing lesinurad in the U.S., and we terminated such license effective January 2019. We have encountered and may continue to encounter costs and delays related to transitioning lesinurad to AstraZeneca. We have never undertaken the process of transitioning a marketed product to a third party, and we may encounter challenges and costs that we do not currently anticipate. Our reputation with patients or physicians may be harmed as a result of transitioning lesinurad, and unforeseen complications with the FDA or other regulatory agencies could arise. If we are unable to complete the orderly transition of lesinurad to AstraZeneca, this could potentially lead to costly administrative procedures or litigation, distract management from other business activities, and could have an adverse impact on our financial condition. For additional information relating to our costs and expenses of exiting lesinurad, see Note 12, Workforce Reduction, to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

​

If any of our linaclotide partners undergoes a change of control or in management, this may adversely affect our collaborative relationship or the success of the commercialization of linaclotide in the U.S. or in the other countries where it is approved, or the ability to achieve regulatory approval, launch and commercialize linaclotide in other territories.

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We work jointly and collaboratively with each of our partners on many aspects of the development, manufacturing and commercialization of linaclotide. In doing so, we have established relationships with several key members of the management teams of our linaclotide partners in functional areas such as development, quality, regulatory, drug safety and pharmacovigilance, operations, marketing, sales, field operations and medical science. Further, the success of our collaborations is highly dependent on the resources, efforts and skills of our partners and their key employees. As we and our partners commercialize linaclotide in the U.S. and the other countries where it is approved, and develop, launch and commercialize linaclotide in other parts of the world, the drug’s success becomes more dependent on us maintaining highly collaborative and well aligned partnerships. For example, in June 2019, Allergan and AbbVie, Inc. entered into a definitive agreement providing for the combination of the two companies. If the transaction is completed, or if any of our linaclotide partners otherwise undergo a change of control or in management, we would need to reestablish many relationships and confirm continued alignment on our development and commercialization strategy for linaclotide. Further, in connection with any change of control or in management, there is inherent uncertainty and disruption in operations, which could result in distraction, inefficiencies, and misalignment of priorities. As a result, in the event of a change of control or in management at one of our linaclotide partners, we cannot be sure that we will be able to successfully execute on our development and commercialization strategy for linaclotide in an effective and efficient manner and without disruption or reduced performance. Finally, any change of control or in management may result in a reprioritization of linaclotide within a partner’s portfolio, or such partner may fail to maintain the financial or other resources necessary to continue supporting its portion of the development, manufacturing or commercialization of linaclotide.

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If any of our linaclotide partners undergoes a change of control and the acquirer either (i) is unable to perform such partner’s obligations under its collaboration or license agreement with us or (ii) does not comply with the divestiture or certain other provisions of the applicable agreement, we have the right to terminate the collaboration or license agreement and reacquire that partner’s rights with respect to linaclotide. If we elect to exercise these rights in such circumstances, we will need to either establish the capability to develop, manufacture and commercialize linaclotide in that partnered territory on our own or we will need to establish a relationship with a new partner. We have assembled a team of specialists in manufacturing, quality, sales, marketing, payer, pricing and field operations, and specialized medical scientists, who represent the functional areas necessary for a successful commercial launch of a high potential, gastrointestinal, or GI, therapy and who support the commercialization of LINZESS in the U.S. If Allergan was subject to a change of control that allowed us to further commercialize LINZESS in the U.S. on our own, and we chose to do so, we would need to enhance each of these functional aspects to replace the capabilities that Allergan was previously providing to the collaboration. Any such transition might result in a period of reduced efficiency or performance by our operations and commercialization teams, which could adversely affect our ability to commercialize LINZESS.

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Although many members of our global operations, commercial and medical affairs teams have strategic oversight of, and a certain level of involvement in, their functional areas globally, we do not have corresponding operational capabilities in these areas outside of the U.S. If Allergan, Astellas or AstraZeneca was subject to a change of control that allowed us to continue linaclotide’s development or commercialization anywhere outside of the U.S. on our own, and we chose to do so rather than establishing a relationship with a new partner, we would need to build operational capabilities in the relevant territory. In any of these situations, the timeline and likelihood of achieving regulatory approval and, ultimately, the commercialization of linaclotide could be negatively impacted.

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We must work effectively and collaboratively with Allergan to market and sell LINZESS in the U.S. in order for it to achieve its maximum commercial potential.

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We are working closely with Allergan to execute our joint commercialization plan for LINZESS. The commercialization plan includes an agreed upon marketing campaign that targets the physicians who see patients who could benefit from LINZESS treatment. Our marketing campaign also targets the adult men and women who suffer from IBS-C or CIC. Our commercialization plan also includes an integrated call plan for our sales forces to optimize the education of specific gastroenterologists and primary care physicians on whom our and Allergan’s sales representatives call, and the frequency with which the representatives meet with them.

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In order to optimize the commercial potential of LINZESS, we and Allergan must execute upon this commercialization plan effectively and efficiently. In addition, we and Allergan must continually assess and modify our commercialization plan in a coordinated and integrated fashion in order to adapt to the promotional response. Further, we and Allergan must continue to focus and refine our marketing campaign to ensure a clear and understandable physician-patient dialogue around IBS-C, CIC and the potential for LINZESS as an appropriate therapy. In addition, we and Allergan must provide our sales forces with the highest quality support, guidance and oversight in order for them to continue to effectively promote LINZESS to gastroenterologists and primary care physicians. If we and Allergan fail to perform these commercial functions in the highest quality manner and in accordance with our joint commercialization plan and related agreements, LINZESS will not achieve its maximum commercial potential and we may suffer financial harm. Our efforts to further target and engage adult patients with IBS-C or CIC may not effectively increase appropriate patient awareness or patient/physician dialogue, and may not increase the revenues that we generate from LINZESS.

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We are subject to uncertainty relating to pricing and reimbursement policies in the U.S. which, if not favorable for our products, could hinder or prevent our products’ commercial success.

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Our and our partner’s ability to commercialize our products successfully depend in part on the coverage and reimbursement levels set by governmental authorities, private health insurers and other third-party payers. In determining whether to approve reimbursement for our products and at what level, we expect that third-party payers will consider factors that include the efficacy, cost effectiveness and safety of our products, as well as the availability of other treatments including generic prescription drugs and over-the-counter alternatives. Further, in order to obtain and maintain acceptable reimbursement levels and access for patients at copay levels that are reasonable and customary, we may face increasing pressure to offer discounts or rebates from list prices or discounts to a greater number of third-party payers or other unfavorable pricing modifications. Obtaining and maintaining favorable reimbursement can be a time consuming and expensive process, and there is no guarantee that we or Allergan will be able to negotiate or continue to negotiate pricing terms with third-party payers at levels that are profitable to us, or at all. Certain third-party payers also require prior authorization for, or even refuse to provide, reimbursement for our products, and others may do so in the future. Our business would be materially adversely affected if we and our partners are not able to receive approval for reimbursement of our products from third-party payers on a broad, timely or satisfactory basis; if reimbursement is subject to overly broad or restrictive prior authorization requirements; or if reimbursement is not maintained at satisfactory levels or becomes subject to prior authorization. In addition, our business could be adversely affected if government healthcare programs, private health insurers, including managed care organizations, or other reimbursing bodies or payers limit or reduce the indications for or conditions under which our products may be reimbursed.

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We expect to experience pricing pressures in connection with the sale of our current and future products due to the healthcare reforms discussed below, as well as the trend toward initiatives aimed at reducing healthcare costs, the increasing influence of managed care, the scrutiny of pharmaceutical pricing, the ongoing debates on reducing government spending and additional legislative proposals. There have been a number of recent federal and state efforts to address drug costs, which generally have focused on increasing transparency around drug costs or limiting drug prices or price increases. Healthcare reform efforts or any future legislation or regulatory actions aimed at controlling and

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reducing healthcare costs, including through measures designed to limit reimbursement, restrict access or impose unfavorable pricing modifications on pharmaceutical products, could impact our and our partners’ ability to obtain or maintain reimbursement for our products at satisfactory levels, or at all, which could materially harm our business and financial results.

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We and our linaclotide partners are subject to uncertainty relating to pricing and reimbursement policies outside the U.S., as well as risks relating to the improper importation of linaclotide and sale of counterfeit versions of linaclotide. If such policies are not favorable, or if linaclotide is improperly imported or is counterfeited, our business and financial results could be adversely affected.

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In some foreign countries, particularly Canada, the countries of Europe, Japan and China, the pricing and payment of prescription pharmaceuticals is subject to governmental control. In these countries, pricing negotiations with governmental authorities can take six to 12 months or longer after the receipt of regulatory approval and product launch. Reimbursement sources are different in each country, and each country may include a combination of distinct potential payers, including private insurance and governmental payers. Some countries may restrict the range of medicinal products for which their national health insurance systems provide reimbursement and control the prices of medicinal products for human use. To obtain favorable reimbursement for the indications sought or pricing approval in some countries, we and our partners may be required to conduct a clinical trial that compares the cost and clinical effectiveness of linaclotide to other available therapies. In addition, in countries in which linaclotide is the only approved therapy for a particular indication, such as CONSTELLA as the only prescription product approved for the symptomatic treatment of moderate to severe IBS-C in adults in Europe and LINZESS as the only prescription treatment approved for the treatment of adults with IBS-C in Japan, there may be disagreement as to what the most comparable product is, or if there even is one. Further, several countries have implemented government measures to either freeze or reduce pricing of pharmaceutical products. Many third-party payers and governmental authorities also consider the price for which the same product is being sold in other countries to determine their own pricing and reimbursement strategy, so if linaclotide is priced low or gets limited reimbursement in a particular country, this could result in similarly low pricing and reimbursement in other countries. If reimbursement for linaclotide is unavailable in any country in which reimbursement is sought, limited in scope or amount, or if pricing is set at or reduced to unsatisfactory levels, our and our partners’ ability to successfully commercialize linaclotide in such country would be impacted negatively. Furthermore, if these measures prevent us or any of our partners from selling linaclotide on a profitable basis in a particular country, they could prevent the commercial launch or continued sale of linaclotide in that country.

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CONSTELLA was first launched in certain European countries for the symptomatic treatment of moderate to severe IBS-C in adults in the second quarter of 2013 and our partner Allergan is currently commercializing CONSTELLA in a number of European countries, including the United Kingdom, Italy and Spain. LINZESS was first launched in Japan for the treatment of IBS-C in adults in the first quarter of 2017, and for the treatment of chronic constipation in adults in the third quarter of 2018, and our partner Astellas is currently commercializing LINZESS in Japan. In the first quarter of 2019, the National Medical Products Administration approved the marketing application for LINZESS for adults with IBS-C in China. The pricing and reimbursement strategy is a key component of our partners’ commercialization plans for CONSTELLA in Europe and LINZESS in Japan and China. Our revenues may suffer if our partners are unable to successfully and timely conclude reimbursement, price approval or funding processes and market CONSTELLA in key member states of the E.U. or LINZESS in Japan or China, or if coverage and reimbursement for either CONSTELLA or LINZESS is limited or reduced. If our partners are not able to obtain coverage, pricing or reimbursement on acceptable terms or at all, or if such terms change in any countries in its territory, our partners may not be able to, or may decide not to, sell either CONSTELLA or LINZESS in such countries.

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We and our partners also face the risk that linaclotide is imported or reimported into markets with relatively higher prices from markets with relatively lower prices, which would result in a decrease of sales and any payments we receive from the affected market. Additionally, third parties may illegally produce, distribute and/or sell counterfeit or otherwise unfit or adulterated versions of linaclotide. In either case, we and our partners may not be able to detect or, if detected, prevent or prohibit the sale of such products, which could result in dangerous health consequences for patients, loss of confidence in us, our partners and our products, and adverse regulatory or legal consequences. Any of the foregoing or other consequences could adversely impact our reputation, financial results and business.

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Because we work with partners to develop, manufacture and commercialize our products, we are dependent upon third parties, and our relationships with those third parties, in our efforts to obtain regulatory approval for, and to commercialize, our products, as well as to comply with regulatory and other obligations with respect to such products.

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Allergan played a significant role in the conduct of the clinical trials for linaclotide and in the subsequent collection and analysis of data, and Allergan holds the new drug application, or NDA, for LINZESS. In addition, we are commercializing LINZESS in the U.S. with Allergan. Allergan is also responsible for the development, regulatory approval and commercialization of linaclotide in countries worldwide other than Japan, China, Hong Kong and Macau. Allergan is commercializing LINZESS in Mexico and CONSTELLA in Canada, as well as commercializing CONSTELLA in certain countries in Europe. Astellas, our partner in Japan, is responsible for development and commercialization of linaclotide in its territory. Astellas is commercializing LINZESS in Japan. Further, we are jointly overseeing the development and commercialization of linaclotide in China, Hong Kong and Macau through our collaboration with AstraZeneca, with AstraZeneca having primary responsibility for the local operational execution. Each of Astellas, AstraZeneca and Allergan is responsible for commercializing linaclotide in its respective territory. Each of our partners is responsible for reporting adverse event information from its territory to us. Finally, each of our partners, other than AstraZeneca, is responsible for drug product manufacturing of linaclotide and making it into finished goods (including bottling and packaging) for its respective territory, and AstraZeneca is responsible for finished goods manufacturing for Hong Kong and Macau. The integration of our efforts with our partners’ efforts is subject to the uncertainty of the markets for pharmaceutical products in each partner’s respective territories, and accordingly, these relationships must evolve to meet any new challenges that arise in those regions.

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These integrated functions may not be carried out effectively and efficiently if we fail to communicate and coordinate with our linaclotide partners, and vice versa. Our linaclotide partnering strategy imposes obligations, risks and operational requirements on us as the central node in our global network of partners. If we do not effectively communicate with each partner and ensure that the entire network is making integrated and cohesive decisions focused on the global brand for linaclotide, linaclotide will not achieve its maximum commercial potential. Further, we have limited ability to control the amount or timing of resources that our partners devote to linaclotide. If any of our partners fails to devote sufficient time and resources to linaclotide, or if its performance is substandard, it will delay the potential submission or approval of regulatory applications for linaclotide, as well as the manufacturing and commercialization of linaclotide in the particular territory. A material breach by any of our partners of our collaboration or license agreement with such partner, or a significant disagreement between us and a partner, could also delay the regulatory approval and commercialization of linaclotide, potentially lead to costly litigation, and could have a material adverse impact on our financial condition. Moreover, although we have non-compete restrictions in place with each of our linaclotide partners, they may have competitive products or relationships with other commercial entities, some of which may compete with us. If any of our partners competes with us or assists our competitors, it could harm our competitive position.

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In addition, adverse event reporting requires significant coordination with our partners and third parties. We are the holder of the global safety database for linaclotide responsible for coordinating the safety surveillance and adverse event reporting efforts worldwide with respect to linaclotide, and an AstraZeneca partner is the holder of the global safety database for lesinurad responsible for coordinating the safety surveillance and adverse event reporting efforts worldwide with respect to lesinurad. If we or AstraZeneca’s partner fails to perform such activities and maintain each safety database or if such parties do not report adverse events related to such products, or fail to do so in a timely manner, we may not receive the information that we are required to report to the FDA regarding such products. Furthermore, we or such parties may fail to adequately monitor, identify or investigate adverse events, or to report adverse events to the FDA or foreign regulatory authority accurately and within the prescribed timeframe. If we or such parties are unsuccessful in any of the foregoing due to poor process, execution, systems, oversight, communication, adjudication or otherwise, then we may suffer any number of consequences, including the imposition of additional restrictions on the use of such products, removal of such products from the market, criminal prosecution, the imposition of civil monetary penalties, seizure of such products, or delay in approval of future products.

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Even though LINZESS is approved by the FDA, it faces post-approval development and regulatory requirements, which present additional challenges.

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In August 2012, the FDA approved LINZESS as a once-daily treatment for adult men and women suffering from IBS-C or CIC. LINZESS is subject to ongoing FDA requirements, including those governing the testing, manufacturing, labeling, packaging, storage, advertising, promotion, sale, distribution, recordkeeping and submission of safety and other post-market information.

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LINZESS is contraindicated in pediatric patients up to six years of age based on nonclinical data from studies in neonatal mice approximately equivalent to human pediatric patients less than two years of age. There is also a boxed warning advising physicians to avoid the use of LINZESS in pediatric patients six to less than 18 years of age. This warning is based on data in young juvenile mice and the lack of clinical safety and efficacy data in pediatric patients of any age group. We and Allergan have established a nonclinical and clinical post-marketing plan with the FDA to understand the safety and efficacy of LINZESS in pediatric patients, and clinical pediatric programs in IBS-C patients age seven to 17 and functional constipation patients age six to 17 currently are ongoing. Our ability to expand the indication or label information for LINZESS to pediatrics will depend on, among other things, our successful completion of pediatric clinical programs. In addition, we and Allergan have also committed to certain nonclinical and clinical studies aimed at understanding: (a) whether orally administered linaclotide can be detected in breast milk, (b) the potential for antibodies to be developed to linaclotide, and if so, (c) whether antibodies specific for linaclotide could have any therapeutic or safety implications. We expect to complete these studies over the next two to four years.

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In addition, as the holder of the approved NDA for each of ZURAMPIC and DUZALLO, we are obligated to monitor and report adverse events and any failure of such products to meet the specifications in the applicable NDA, to submit new or supplemental applications and to obtain FDA approval for certain changes to such products, including changes to product labeling and manufacturing processes. The FDA has required a post-marketing clinical study to further evaluate the renal and cardiovascular safety of lesinurad, and has required that enrollment include patients with moderate renal impairment. In connection with the termination of the lesinurad license, the post-marketing clinical study has been terminated.

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These post-approval requirements impose burdens and costs on us. Failure to effectively, appropriately and timely conduct and complete the required studies relating to our products, monitor and report adverse events and meet our other post-approval commitments would lead to negative regulatory action at the FDA, which could include withdrawal of regulatory approval of our products for their currently approved indications and patient populations.

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Manufacturers of drug products and their facilities are subject to continual review and periodic inspections by the FDA and other regulatory authorities for compliance with GMP and other applicable regulations. If we or a regulatory agency discovers previously unknown problems with a product, such as adverse events of unanticipated severity or frequency, or problems with a facility where the product is manufactured, a regulatory agency may impose restrictions on that product or the manufacturer, including withdrawal of the product from the market or suspension of manufacturing. If we, our partners or the manufacturing facilities for our products fail to comply with applicable regulatory requirements, a regulatory agency may take the following actions, among others:

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●issue warning letters or untitled letters;

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●impose civil or criminal penalties;

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●suspend or withdraw regulatory approval;

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●suspend any ongoing clinical trials;

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●refuse to approve pending applications or supplements to applications submitted by us or our partners;

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●impose restrictions on operations, including costly new manufacturing requirements; or

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●seize or detain products or require us to initiate a product recall.

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Even though linaclotide is approved for marketing in the U.S. and in a number of other countries, we or our partners may never receive approval to commercialize linaclotide in additional parts of the world.

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In order to market any products outside of the countries where linaclotide is currently approved, we or our partners must comply with numerous and varying regulatory requirements of other jurisdictions regarding, among other things, safety and efficacy. Approval procedures vary among jurisdictions and can involve product testing and

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administrative review periods different from, and greater than, those in the U.S. and the other countries where linaclotide is approved. Potential risks include that the regulatory authorities:

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| ● | may not deem linaclotide safe and effective;

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| ● | may not find the data from nonclinical studies and clinical trials sufficient to support approval;

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| ● | may not approve of manufacturing processes and facilities;

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| ● | may not approve linaclotide for any or all indications or patient populations for which approval is sought;

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| ● | may require significant warnings or restrictions on use to the product label for linaclotide; or

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| ● | may change their approval policies or adopt new regulations.

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If any of the foregoing were to occur, our receipt of regulatory approval in the applicable jurisdiction could be delayed or we may never receive approval at all. Further, regulatory approval in one jurisdiction does not ensure regulatory approval in another, but a failure or delay in obtaining regulatory approval in one jurisdiction may have a negative effect on the regulatory processes in others. If linaclotide is not approved for all indications or patient populations or with the label requested, this would limit the uses of linaclotide and have an adverse effect on its commercial potential or require costly post-marketing studies.

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We face potential product liability exposure, and, if claims brought against us are successful, we could incur substantial liabilities.

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The use of our product candidates in clinical trials and the sale of our approved products, including the sale of linaclotide and lesinurad, expose us to product liability claims. If we do not successfully defend ourselves against product liability claims, we could incur substantial liabilities. In addition, regardless of merit or eventual outcome, product liability claims may result in:

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| ● | decreased demand for approved products;

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| ● | impairment of our business reputation;

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| ● | withdrawal of clinical trial participants;

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| ● | initiation of investigations by regulators;

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| ● | litigation costs;

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| ● | distraction of management’s attention from our primary business;

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| ● | substantial monetary awards to patients or other claimants;

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| ● | loss of revenues; and

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| ● | the inability to commercialize our product candidates.

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We currently have product liability insurance coverage for the commercial sale of our products and for the clinical trials of our product candidates which is subject to industry-standard terms, conditions and exclusions. Our insurance coverage may not be sufficient to reimburse us for expenses or losses associated with claims. Moreover, insurance coverage is becoming increasingly expensive, and, in the future, we may not be able to maintain insurance coverage at a reasonable cost or in sufficient amounts to protect us against losses. On occasion, large judgments have been awarded in lawsuits based on drugs that had unanticipated side effects. A successful product liability claim or series

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of claims could cause our stock price to decline and, if judgments exceed our insurance coverage, could decrease our cash and adversely affect our business.

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We face competition and new products may emerge that provide different or better alternatives for treatment of the conditions that our products are approved to treat.

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The pharmaceutical industry and the markets in which we operate are intensely competitive. We compete in the marketing and sale of our products, the development of new products and the acquisition of rights to new products with commercial potential. Certain of our competitors have substantially greater financial, technical and human resources than us. Mergers and acquisitions in the pharmaceutical industry may result in even more resources being concentrated in our competitors and enable them to compete more effectively. For example, in March 2019, Bausch Health Companies Inc., or Bausch Health, acquired TRULANCE (plecanatide), which, as referenced below, is a competitor to LINZESS, from Synergy Pharmaceuticals, Inc. Competition may also increase further as a result of advances made in the commercial applicability of technologies and greater availability of capital for investment in these fields. Additionally, new developments, including the development of other drug technologies and methods of preventing the incidence of disease, occur in the pharmaceutical and medical technology industries at a rapid pace. These developments may render our products obsolete or noncompetitive.

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Our products compete with certain prescription therapies and over-the-counter products for the treatment of the indications for which they are approved, or their associated symptoms, and in many cases with products that have attained significant levels of market acceptance. The availability of prescription competitors and over-the-counter products for such conditions could limit the demand, and the price we are able to charge, for our products unless we are able to achieve market acceptance among the medical community and patients and differentiate our products on the basis of their cost and/or actual or perceived benefits. For example, Takeda’s AMITIZA (lubiprostone) is approved by the FDA for sale in the U.S. for the treatment of IBS-C, CIC and opioid-induced constipation, Bausch Health’s TRULANCE (plecanatide) is approved by the FDA for sale in the U.S. for the treatment of adults with IBS-C and CIC, Takeda’s MOTEGRITY (prucalopride) is approved by the FDA for sale in the U.S. for the treatment of CIC in adults, and Alfasigma USA Inc.’s ZELNORM (tegaserod) is approved for sale in the U.S. for treatment of IBS-C in women under the age of 65. Additionally, we believe other companies are developing products which could compete with our products, should they be approved by the FDA or foreign regulatory authorities. Currently, there are other compounds in late stage development and other potential competitors are in earlier stages of development for the treatment of the indications for which our products are approved. If our current or potential competitors are successful in completing drug development for their drug candidates and obtain approval from the FDA or foreign regulatory authorities, they could limit the demand for our products.

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We will incur significant liability if it is determined that we are promoting any “off-label” uses of our products.

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Physicians are permitted to prescribe drug products and medical devices for uses that are not described in the product’s labeling and that differ from those approved by the FDA or other applicable regulatory agencies. Such “off-label” uses are common across medical specialties. Although the FDA and other regulatory agencies do not regulate a physician’s choice of treatments, the FDA and other regulatory agencies do restrict manufacturer communications on off-label use. Companies are not permitted to promote drugs or medical devices for off-label uses or to promote unapproved drugs or medical devices. Accordingly, we do not permit promotion of any product that we develop, license, commercialize, promote, co-promote or otherwise partner prior to approval or for any indication, population or use not described in or consistent with such product’s label. The FDA and other regulatory and enforcement authorities actively enforce laws and regulations prohibiting promotion of off-label uses and the promotion of products for which marketing approval has not been obtained. A company that is found to have promoted off-label uses will be subject to significant liability, including civil and administrative remedies as well as criminal sanctions. Even if it is later determined that we were not in violation of these laws, we may be faced with negative publicity, incur significant expenses defending our actions and have to divert significant management resources from other matters.

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Notwithstanding the regulatory restrictions on off-label promotion, the FDA and other regulatory authorities allow companies to engage in truthful, non-misleading, and non-promotional scientific exchange concerning their products. We intend to engage in medical education activities and communicate with healthcare providers in compliance with all applicable laws, regulatory guidance and industry best practices. Although we believe we have put in place a robust compliance program, which is designed to ensure that all such activities are performed in a legal and compliant

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manner, we cannot be certain that our program will address all areas of potential exposure and the risks in this area cannot be entirely eliminated.

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If we fail to comply with healthcare and other regulations, we could face substantial penalties and our business, operations and financial condition could be adversely affected.

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The products that we promote are marketed in the U.S. and/or covered by federal healthcare programs, and, as a result, certain federal and state healthcare laws and regulations pertaining to product promotion and fraud and abuse are applicable to, and may affect, our business. These laws and regulations include:

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| ● | federal healthcare program anti-kickback laws, which prohibit, among other things, persons from offering, soliciting, receiving or providing remuneration, directly or indirectly, to induce either the referral of an individual, for an item or service or the purchasing or ordering of a good or service, for which payment may be made under federal healthcare programs such as Medicare and Medicaid;

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| ● | federal false claims laws which prohibit, among other things, individuals or entities from knowingly presenting, or causing to be presented, information or claims for payment from Medicare, Medicaid, or other third-party payers that are false or fraudulent, and which may apply to us for reasons including providing coding and billing advice to customers;

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| ● | the federal Health Insurance Portability and Accountability Act of 1996, which prohibits executing a scheme to defraud any healthcare benefit program or making false statements relating to healthcare matters and which also imposes certain requirements relating to the privacy, security and transmission of individually identifiable health information;

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| ● | the Federal Food, Drug, and Cosmetic Act, which among other things, strictly regulates drug product and medical device marketing, prohibits manufacturers from marketing such products prior to approval or for off-label use and regulates the distribution of samples;

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| ● | federal laws, including the Medicaid Drug Rebate Program, that require pharmaceutical manufacturers to report certain calculated product prices to the government or provide certain discounts or rebates to government authorities or private entities, often as a condition of reimbursement under government healthcare programs;

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| ● | the so-called “federal sunshine” law, which requires pharmaceutical and medical device companies to monitor and report certain financial interactions with physicians and teaching h ospitals (and additional categories of health care practitioners beginning with reports submitted in 2022) to the federal government for re-disclosure to the public; and

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| ● | state law equivalents of the above federal laws, such as anti-kickback and false claims laws which may apply to items or services reimbursed by any third-party payer, including commercial insurers, state transparency laws, state laws limiting interactions between pharmaceutical manufacturers and members of the healthcare industry, and state laws governing the privacy and security of health information in certain circumstances, many of which differ from each other in significant ways and often are not preempted by federal laws, thus complicating compliance efforts.

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Our global activities are subject to the U.S. Foreign Corrupt Practices Act which prohibits corporations and individuals from paying, offering to pay, or authorizing the payment of anything of value to any foreign government official, government staff member, political party, or political candidate in an attempt to obtain or retain business or to otherwise influence a person working in an official capacity. We are also subject to similar anti-bribery laws in the other countries in which we do business.

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In addition, we may be subject to privacy and security laws in the various jurisdictions in which we operate, obtain or store personally identifiable information. The legislative and regulatory landscape for privacy and data protection continues to evolve, and there has been an increasing focus on privacy and data protection issues with the potential to affect our business. For example, the processing of personal data in the European Economic Area, or the

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EEA, is subject to the General Data Protection Regulation, or the GDPR, which took effect in May 2018. The GDPR increases obligations with respect to clinical trials conducted in the EEA, such as in relation to the provision of fair processing notices, exercising data subject rights and reporting certain data breaches to regulators and affected individuals, as well as how we document our relationships with third parties that process GDPR-covered personal data on our behalf. The GDPR also increases the scrutiny applied to transfers of personal data from the EEA (including from clinical trial sites in the EEA) to countries that are considered by the European Commission to lack an adequate level of data protection, such as the United States. The compliance obligations imposed by the GDPR have required us to revise our operations. In addition, the GDPR imposes substantial fines and other regulatory penalties for breaches of data protection requirements, and it confers a private right of action on data subjects and their representatives for breaches of data protection requirements.

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If our operations are found to be in violation of any of the laws described above or any other laws, rules or regulations that apply to us, we will be subject to penalties, including civil and criminal penalties, damages, fines and the curtailment or restructuring of our operations. Any penalties, damages, fines, curtailment or restructuring of our operations could adversely affect our ability to operate our business and our financial results. Although compliance programs can mitigate the risk of investigation and prosecution for violations of these laws, rules or regulations, we cannot be certain that our program will address all areas of potential exposure and the risks in this area cannot be entirely eliminated, particularly because the requirements and government interpretations of the requirements in this space are constantly evolving. Any action against us for violation of these laws, rules or regulations, even if we successfully defend against it, could cause us to incur significant legal expenses and divert our management’s attention from the operation of our business, as well as damage our business or reputation. Moreover, achieving and sustaining compliance with applicable federal and state privacy, security, fraud and reporting laws may prove costly.

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Healthcare reform and other governmental and private payer initiatives may have an adverse effect upon, and could prevent, our products’ or product candidates’ commercial success.

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The U.S. government and individual states have been aggressively pursuing healthcare reform designed to impact delivery of, and/or payment for, healthcare, which include initiatives intended to reduce the cost of healthcare. For example, in March 2010, the U.S. Congress enacted the Patient Protection and Affordable Care Act, as modified by the Health Care and Education Reconciliation Act, or the ACA, which, among other things, expanded healthcare coverage through Medicaid expansion and the implementation of the individual health insurance mandate; included changes to the coverage and reimbursement of drug products under government healthcare programs; imposed an annual fee on manufacturers of branded drugs; and expanded government enforcement authority. We face uncertainties because there have been, and may be additional, federal legislative and administrative efforts to repeal, substantially modify or invalidate some or all of the provisions of the ACA. Such efforts may lead to fewer Americans having more comprehensive health insurance compliant with the ACA, even in the absence of a legislative repeal. For example, tax reform legislation was enacted at the end of 2017 that includes provisions to eliminate the tax penalty for individuals who do not maintain sufficient health insurance coverage beginning in 2019. The ACA has also been subject to judicial challenge. In December 2018, a federal district court judge, in a challenge brought by a number of state attorneys general, found the ACA unconstitutional in its entirety. Pending appeals, which could take some time, the ACA is still operational in all respects. Adoption of new healthcare reform legislation at the federal or state level could affect demand for, or pricing of, our products or product candidates if approved for sale. However, we cannot predict the ultimate content, timing or effect of any healthcare reform legislation or action, or its impact on us, and healthcare reform could increase compliance costs and may adversely affect our future business and financial results.

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In addition, other legislative changes have been adopted that could have an adverse effect upon, and could prevent, our products’ or product candidates’ commercial success. More broadly, the Budget Control Act of 2011, as amended, or the Budget Control Act, includes provisions intended to reduce the federal deficit, including reductions in Medicare payments to providers through 2027. Any significant spending reductions affecting Medicare, Medicaid or other publicly funded or subsidized health programs, or any significant taxes or fees imposed as part of any broader deficit reduction effort or legislative replacement to the Budget Control Act, or otherwise, could have an adverse impact on our anticipated product revenues.

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In addition to governmental efforts in the U.S., foreign jurisdictions as well as private health insurers and managed care plans are likely to continue challenging manufacturers’ ability to obtain reimbursement, as well as the level of reimbursement, for pharmaceuticals and other healthcare-related products and services. These cost-control initiatives could significantly decrease the available coverage and the price we might establish for our products, which would have an adverse effect on our financial results.

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The Food and Drug Administration Amendments Act of 2007 also provides the FDA enhanced post-marketing authority, including the authority to require post-marketing studies and clinical trials, labeling changes based on new safety information, and compliance with risk evaluations and mitigation strategies approved by the FDA. We and Allergan have established a nonclinical and clinical post-marketing plan with the FDA to understand the safety and efficacy of LINZESS in pediatrics. The FDA’s exercise of this authority has resulted (and is expected to continue to result) in increased development-related costs following the commercial launch of our products, and could result in potential restrictions on the sale and/or distribution of our products, even in such products’ approved indications and patient populations.

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If we are unable to successfully partner with other companies to develop and commercialize our products and/or product candidates, our ability to grow would be impaired and our business would be adversely affected.

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As part of our business strategy, we may partner with pharmaceutical, biotechnology or other companies to develop and commercialize our products or product candidates. Although we have entered into such arrangements with respect to the development and commercialization of linaclotide worldwide, there can be no assurance that we will be able to do so in the future with respect to other products or product candidates or that we will be able to gain the interest of potential partners; establish and maintain development, manufacturing, marketing, sales or distribution relationships on acceptable terms; that such relationships, if established, will be successful or on favorable terms; or that we will gain market acceptance for such products or product candidates. The process of proposing, negotiating and implementing a partnership arrangement is lengthy and complex. If we enter into any partnering arrangements with third parties, any revenues we receive will depend upon the efforts of such third parties. If we are unable to establish successful partnering arrangements, we may not gain access to the financial resources and industry experience necessary to develop, commercialize or successfully market our products or product candidates, may be forced to curtail, delay or stop a development program or one or more of our other development programs, delay commercialization, reduce the scope of our planned sales or marketing activities or undertake development or commercialization activities at our own expense, and therefore may be unable to generate revenue from our products or product candidates or do so to their full potential.

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In pursuing our growth strategy, we will incur a variety of costs and may devote resources to potential opportunities that are never completed or for which we never receive the benefit. Our failure to successfully discover, acquire, develop and market additional product candidates or approved products would impair our ability to grow and adversely affect our business.

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As part of our growth strategy, we intend to explore further linaclotide development opportunities. We and Allergan are exploring development opportunities to enhance the clinical profile of LINZESS by studying linaclotide in new or existing indications, populations and formulations to assess its potential to treat various conditions. These development efforts may fail or may not increase the revenues that we generate from LINZESS. Furthermore, they may result in adverse events, or perceived adverse events, in certain patient populations that are then attributed to the currently approved patient population, which may result in adverse regulatory action at the FDA or in other countries or harm linaclotide’s reputation in the marketplace, each of which could materially harm our revenues from linaclotide.

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We are also pursuing various other programs in our pipeline. We may spend several years and make significant investments in developing any current or future internal product candidate, and failure may occur at any point. Our product candidates are in various stages of development and must satisfy rigorous standards of safety and efficacy before they can be approved for sale by the FDA. To satisfy these standards, we must allocate resources among our various development programs and we must engage in costly and lengthy research and development efforts, which are subject to unanticipated delays and other significant uncertainties. Despite our efforts, our product candidates may not offer therapeutic or other improvement over existing competitive drugs, be proven safe and effective in clinical trials, or meet applicable regulatory standards. It is possible that none of the product candidates we are developing will be approved for commercial sale, which would impair our ability to grow.

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We have ongoing or planned nonclinical and clinical trials for linaclotide and our product candidates, including MD-7246, a delayed release form of linaclotide that is being developed as an oral, intestinal, non-opioid pain relieving agent for the potential treatment of IBS-D, and IW-3718, a gastric retentive formulation of a bile acid sequestrant for the potential treatment of persistent gastroesophageal reflux disease, and the strength of our company’s pipeline will depend in large part on the outcomes of these studies. Many companies in the pharmaceutical industry have suffered significant setbacks in clinical trials even after achieving promising results in earlier nonclinical or clinical trials. The findings from

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our completed nonclinical studies may not be replicated in later clinical trials, and our clinical trials may not be predictive of the results we may obtain in later-stage clinical trials or of the likelihood of regulatory approval. Results from our clinical trials and findings from our nonclinical studies could lead to abrupt changes in our development activities, including the possible limitation or cessation of development activities associated with a particular product candidate or program. Furthermore, our analysis of data obtained from nonclinical and clinical activities is subject to confirmation and interpretation by the FDA and other applicable regulatory authorities, which could delay, limit or prevent regulatory approval. Satisfaction of FDA or other applicable regulatory requirements is costly, time-consuming, uncertain and subject to unanticipated delays.

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In addition, because our internal research capabilities are limited, we may be dependent upon pharmaceutical and biotechnology companies, academic scientists and other researchers to sell or license products or technology to us. The success of this strategy depends partly upon our ability to identify, select, discover and acquire promising pharmaceutical product candidates and products. The process of proposing, negotiating and implementing a license or acquisition of a product candidate or approved product is lengthy and complex. Other companies, including some with substantially greater financial, marketing and sales resources, may compete with us for the license or acquisition of product candidates and approved products. We have limited resources to identify and execute the acquisition or in-licensing of third-party products, businesses and technologies and integrate them into our current infrastructure. Moreover, we may devote resources to potential acquisitions or in-licensing opportunities that are never completed, or we may fail to realize the anticipated benefits of such efforts. We may not be able to acquire the rights to additional products or product candidates on terms that we find acceptable, or at all.

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In addition, such acquisitions may entail numerous operational and financial risks, including:

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| ● | exposure to unknown liabilities;

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| ● | disruption of our business and diversion of our management’s time and attention to develop acquired products, product candidates or technologies;

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| ● | incurrence of substantial debt, dilutive issuances of securities or depletion of cash to pay for acquisitions;

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| ● | higher than expected acquisition and integration costs;

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| ● | difficulty in combining the operations and personnel of any acquired businesses with our operations and personnel;

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| ● | increased amortization expenses;

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| ● | impairment of relationships with key suppliers or customers of any acquired businesses due to changes in management and ownership; and

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| ● | inability to motivate key employees of any acquired businesses.

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Furthermore, we may have little or no insight or control over the development and commercialization of any product that we in-license outside the licensed territory. If other licensees do not effectively develop or commercialize any such product outside the licensed territory, our reputation or the reputation of any such product may be impacted. Also, any product candidate that we acquire may require additional development efforts prior to commercial sale, including extensive clinical testing and approval by the FDA and applicable foreign regulatory authorities. All product candidates are prone to risks of failure typical of pharmaceutical product development, including the possibility that a product candidate will not be shown to be sufficiently safe and effective for approval by regulatory authorities.

We may incur operational difficulties or be exposed to claims and liabilities as a result of the separation of Cyclerion.

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On April 1, 2019, we distributed all of the outstanding shares of Cyclerion Therapeutics, Inc., or Cyclerion, common stock to Ironwood stockholders in connection with the separation of our soluble guanylate cyclase business, or the Separation. In connection with the distribution, we entered into a separation agreement and various other agreements (including a tax matters agreement, an employee matters agreement, transition services agreements, an intellectual property license agreement and a development agreement). These agreements govern the separation and distribution and the relationship between the us and Cyclerion going forward, including with respect to potential tax-related losses

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associated with the separation and distribution. They also provide for the performance of services by each company for the benefit of the other for a period of time.

The separation agreement provides for indemnification obligations designed to make Cyclerion financially responsible for many liabilities that may exist relating to its business activities, whether incurred prior to or after the distribution, including any pending or future litigation, but we cannot guarantee that Cyclerion will be able to satisfy its indemnification obligations. It is also possible that a court would disregard the allocation agreed to between us and Cyclerion and require us to assume responsibility for obligations allocated to Cyclerion. Third parties could also seek to hold us responsible for any of these liabilities or obligations, and the indemnity rights we have under the separation agreement may not be sufficient to fully cover all of these liabilities and obligations. Even if we are successful in obtaining indemnification, we may have to bear costs temporarily. In addition, our indemnity obligations to Cyclerion, including those related to assets or liabilities allocated to us, may be significant. These risks could negatively affect our business, financial condition or results of operations.

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The separation of Cyclerion continues to involve a number of additional risks, including, among other things, the potential that management’s and our employees’ attention will be significantly diverted by the provision of transitional services or that we may incur other operational challenges or difficulties as a result of the separation. Certain of the agreements described above provide for the performance of services by each company for the benefit of the other for a period of time. If Cyclerion is unable to satisfy its obligations under these agreements, we could incur losses and may not have sufficient resources available for such services. These arrangements could also lead to disputes over rights to certain shared property and over the allocation of costs and revenues for products and operations. Our inability to effectively manage the transition activities and related events could adversely affect our business, financial condition or results of operations.

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If the distribution of the shares of Cyclerion common stock in connection with the separation is not generally tax-free for U.S. federal income tax purposes, we and our stockholders could be subject to significant tax liabilities.

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The distribution, together with certain related transactions, is intended to qualify for tax-free treatment to us and our stockholders for U.S. federal income tax purposes. We received a favorable private letter ruling from the Internal Revenue Service, or IRS, under the pilot program established in Revenue Procedure 2017-52 relating to the U.S. federal income tax treatment of the distribution. Consistent with the guidelines set forth in Revenue Procedure 2017-52, the IRS private letter ruling does not cover all of the issues that are relevant to determining whether the distribution is generally tax free for U.S. federal income tax purposes. Accordingly, completion of the distribution was conditioned upon, among other things, our receipt of an opinion from an outside tax advisor that the distribution will qualify as a transaction that is generally tax-free to both us and our stockholders for U.S. federal income tax purposes under Sections 355 and 368(a)(1)(D) of the Internal Revenue Code. The private letter ruling and opinion were based on and relied on, among other things, certain facts and assumptions, as well as certain representations, statements and undertakings from us and Cyclerion (including those relating to the past and future conduct of us and Cyclerion). If any of these facts, assumptions, representations, statements or undertakings is, or becomes, inaccurate or incomplete, or if we or Cyclerion breach any of our respective covenants relating to the distribution, the IRS private letter ruling and any tax opinion may be invalid. Moreover, the opinion is not binding on the IRS or any courts. Accordingly, notwithstanding receipt of the IRS private letter ruling and the opinion, the IRS could determine that the distribution and certain related transactions should be treated as taxable transactions for U.S. federal income tax purposes.

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If the distribution, together with certain related transactions, fails to qualify as a transaction that is generally tax-free under Sections 355 and 368(a)(1)(D) of the Internal Revenue Code, in general, for U.S. federal income tax purposes, we would recognize taxable gain with respect to Cyclerion’s distributed common stock and our stockholders who receive shares of Cyclerion common stock in the distribution would be subject to tax as if they had received a taxable distribution equal to the fair market value of such shares.

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We may not achieve some or all of the anticipated benefits of the Separation, which may adversely affect our business.

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We may not be able to achieve the full strategic, financial or other benefits expected to result from the Separation, or such benefits may be delayed or not occur at all. If we fail to achieve some or all of the expected benefits of the separation, or if such benefits are delayed, our business, financial condition, results of operations and the value of our stock could be adversely impacted. The combined value of the common stock of the two publicly traded companies may not be equal to or greater than what the value of our common stock would have been had the separation not

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occurred. The common stock price of each company may experience periods of extreme volatility. In addition, we are smaller and less diversified, with a narrower business focus, than we were before the separation and therefore may be more vulnerable to changing market conditions. The separation also presents a number of significant risks to our internal processes, including the failure to maintain an adequate control environment due to changes to our infrastructure technology systems and financial reporting processes.

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Completion of the Separation resulted in substantial changes in our board of directors and management.

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Completion of the Separation resulted in substantial changes in our board of directors and management. In particular, our former chief executive officer and director, Peter M. Hecht, resigned from each of those positions. In addition, William Huyett, our former chief operating officer, and Mark Currie, our former senior vice president, chief scientific officer and president of research and development, resigned from their positions with us to join management positions with Cyclerion. Furthermore, Marsha Fanucci, Terrance McGuire, Amy Schulman and Douglas Williams resigned as members of our board of directors upon the completion of the separation. These senior officer and board level changes could be disruptive to our operations, present significant management challenges and could harm our business.

Delays in the completion of clinical testing of any of our product candidates could result in increased costs and delay or limit our ability to generate revenues.

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Delays in the completion of clinical testing could significantly affect our product development costs. We do not know whether planned clinical trials will be completed on schedule, if at all. The commencement and completion of clinical trials can be delayed for a number of reasons, including delays related to:

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| ● | obtaining regulatory approval to commence a clinical trial;

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| ● | reaching agreement on acceptable terms with prospective clinical research organizations, or CROs, and trial sites, the terms of which can be subject to extensive negotiation and may vary significantly among different CROs and trial sites;

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| ● | manufacturing sufficient quantities of a product candidate for use in clinical trials;

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| ● | obtaining institutional review board approval to conduct a clinical trial at a prospective site;

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| ● | recruiting and enrolling patients to participate in clinical trials for a variety of reasons, including competition from other clinical trial programs for the treatment of similar conditions; and

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| ● | maintaining patients who have initiated a clinical trial but may be prone to withdraw due to side effects from the therapy, lack of efficacy or personal issues, or who are lost to further follow-up.

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Clinical trials may also be delayed as a result of ambiguous or negative interim results. In addition, a clinical trial may be suspended or terminated by us, an institutional review board overseeing the clinical trial at a clinical trial site (with respect to that site), the FDA, or other regulatory authorities due to a number of factors, including:

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| ● | failure to conduct the clinical trial in accordance with regulatory requirements or the study protocols;

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| ● | inspection of the clinical trial operations or trial sites by the FDA or other regulatory authorities resulting in the imposition of a clinical hold;

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| ● | unforeseen safety issues; or

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| ● | lack of adequate enrollment or funding to continue the clinical trial.

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Additionally, changes in regulatory requirements and guidance may occur, and we may need to amend clinical trial protocols to reflect these changes. Each protocol amendment would require institutional review board review and approval, which may adversely impact the costs, timing or successful completion of the associated clinical trials. If we or our partners terminate or experience delays in the completion of any clinical trials, the commercial prospects for our product candidates may be harmed, and our ability to generate product revenues will be delayed. In addition, many of

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the factors that cause, or lead to, a delay in the commencement or completion of clinical trials may also ultimately lead to the denial of regulatory approval.

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We may not be able to manage our business effectively if we lose any of our current management team or if we are unable to attract and motivate key personnel.

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We may not be able to attract or motivate qualified management and scientific, clinical, operations and commercial personnel in the future due to the intense competition for qualified personnel among biotechnology, pharmaceutical and other businesses, particularly in the greater-Boston area. If we are not able to attract and motivate necessary personnel to accomplish our business objectives, we will experience constraints that will significantly impede the achievement of our objectives.

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We are highly dependent on the drug research, development, regulatory, commercial, financial and other expertise of our management, particularly Mark Mallon, our chief executive officer; Gina Consylman, our senior vice president, chief financial officer, and treasurer; Halley E. Gilbert, our senior vice president, corporate development and chief administrative officer; and Thomas A. McCourt, our president. Transitions in our senior management team and other key employees, including as a result of the Separation, may result in operational disruptions, and our business may be harmed as a result. In addition to the competition for personnel, the Boston area in particular is characterized by a high cost of living. As such, we could have difficulty attracting experienced personnel to our company and may be required to expend significant financial resources in our employee recruitment efforts, which may or may not be successful.

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We also have scientific and clinical advisors who assist us in formulating our product development, clinical strategies and our global supply chain plans, as well as sales and marketing advisors who have assisted us in our commercialization strategy and brand plan for our products. These advisors are not our employees and may have commitments to, or consulting or advisory contracts with, other entities that may limit their availability to us, or may have arrangements with other companies to assist in the development and commercialization of products that may compete with ours.

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Security breaches and other disruptions to our information technology structure could compromise our information, disrupt our business and expose us to liability, which would cause our business and reputation to suffer.

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In the ordinary course of our business, we collect, process and store sensitive data, including intellectual property, our proprietary business information and that of our suppliers and business partners, as well as personally identifiable information of our patients, clinical trial participants and employees. We also rely to a large extent on information technology systems to operate our business, including to deliver our products. We have outsourced elements of our confidential information processing and information technology structure, and as a result, we are managing independent vendor relationships with third parties who may or could have access to our confidential information. Similarly, our business partners and other third-party providers possess certain of our sensitive data. The secure maintenance of this information is critical to our operations and business strategy. Despite our security measures, our large and complex information technology and infrastructure (and those of our partners, vendors and third-party providers) may be vulnerable to attacks by hackers or breached due to employee error, malfeasance or other disruptions. We, our partners, vendors and other third-party providers could be susceptible to third party attacks on our, and their, information security systems, which attacks are of ever-increasing levels of sophistication and are made by groups and individuals with a wide range of motives and expertise, including organized criminal groups, hacktivists, nation states and others. While we have invested in information technology and security and the protection of confidential information, there can be no assurance that our efforts will prevent service interruptions or security breaches. Any such interruptions or breach would substantially impair our ability to operate our business and would compromise our, and their, networks and the information stored there could be accessed, publicly disclosed, lost or stolen. Any such access, disclosure or other loss of information could result in legal claims or proceedings, liability under laws that protect the privacy of personal information, disrupt our operations, and damage our reputation, any of which could adversely affect our business. While we maintain cyber liability insurance, this insurance may not be sufficient to cover the losses that may result from an interruption or breach of our (or our partners’, vendors’ and third-party providers’) systems.

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Our business could be negatively affected as a result of a proxy contest or certain other stockholder actions.

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Responding to certain stockholder actions can be costly, disruptive and time-consuming, and could also impact our ability to attract, retain and motivate our employees. For example, a proxy contest for our annual meeting of

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stockholders relating to stockholder proposals or director nominees would require significant time and could divert the attention of our management, other employees and our board of directors. In addition, a proxy contest would require us to incur significant costs, including legal fees and proxy solicitation expenses.

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We intend to move our headquarters and may face disruption and additional costs.

We have entered into a lease to relocate our corporate headquarters to 100 Summer Street, Boston, Massachusetts, or the Summer Street Property, in the fourth quarter of 2019. In connection with this relocation, we could experience unexpected costs or business disruption and diversion of management attention. In addition, construction on the Summer Street Property may not be completed prior to the date we expect the lease for our current headquarters in Cambridge, Massachusetts to terminate. The occurrence of any of the foregoing would disrupt our business operations and result in additional costs to us.

We must comply with environmental laws and regulations, which can be expensive.

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We are subject to federal, state, city and local laws and regulations governing the use, manufacture, storage, handling and disposal of hazardous materials. Although we believe that the safety procedures we have used for handling and disposing of these materials comply with the standards prescribed by these laws and regulations, the risk of accidental contamination or injury from these materials cannot not be eliminated. Any such event could have an adverse effect on our business. We do not currently maintain hazardous materials insurance coverage.

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Risks Related to Intellectual Property

Limitations on the patent rights relating to our products and our product candidates may limit our ability to prevent third parties from competing against us.

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Our success depends on our ability to obtain and maintain patent protection for our products and product candidates, preserve our trade secrets, prevent third parties from infringing upon our proprietary rights and operate without infringing upon the proprietary rights of others.

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The strength of patents in the pharmaceutical industry involves complex legal and scientific questions and can be uncertain. Patent applications in the U.S. and most other countries are confidential for a period of time until they are published, and publication of discoveries in scientific or patent literature typically lags actual discoveries by several months or more. As a result, we cannot be certain that we were the first to conceive inventions covered by our patents and pending patent applications or that we were the first to file patent applications for such inventions. In addition, we cannot be certain that our patent applications will be granted, that any issued patents will adequately protect our intellectual property, or that such patents will not be challenged, narrowed, invalidated or circumvented.

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We have several issued patents and pending applications in the U.S. related to LINZESS, including a LINZESS composition of matter and methods of use patent (U.S. Patent 7,304,036) expiring in 2026. Additional U.S. patents and pending applications related to LINZESS include multiple patents relating to our commercial, room temperature stable formulation of linaclotide and methods of using this formulation, the latest of which expire in the early 2030s, as well as other patents and pending patent applications covering processes for making LINZESS, formulations and dosing regimens thereof, and molecules related to LINZESS. Although none of these issued patents currently is subject to a patent reexamination or review, we cannot guarantee that they will not be subject to reexamination or review by the U.S. Patent and Trademark Office, or the USPTO, in the future. We believe in the strength of our linaclotide patent portfolio and that we have sufficient freedom to operate; however, if any of our present or future patents is invalidated, this could have an adverse effect on our business and financial results. In March 2013, an opposition to one of our granted patents covering linaclotide was filed in Europe. In April 2015, the patent was upheld in its entirety by the European Patent Office, affirming the strength of our intellectual property and our belief that the opposition was without merit. The associated appeal was withdrawn by the opponent in January 2019.

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Furthermore, the America Invents Act, which was signed into law in 2011, has made several major changes in the U.S. patent statutes. These changes permit third parties to challenge our patents more easily and create uncertainty with respect to the interpretation and practice of U.S. patent law. Moreover, the U.S. Supreme Court has ruled on several patent cases in recent years, narrowing the scope of patent protection available and weakening the rights of patent owners in certain circumstances. Depending on the impact of these decisions and other actions by the U.S.

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Congress, the federal courts, the USPTO, and their foreign counterparts, the laws and regulations governing patents may change, or their interpretation or implementation may change, in unpredictable ways that could impact, potentially adversely, our ability to obtain new patents or to enforce and defend patents that we have already obtained or that we might obtain in the future. For example, such changes may increase the costs and complexity associated with obtaining, enforcing or defending our patents, including in abbreviated new drug application, or ANDA, litigation.

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We also rely upon unpatented trade secrets, unpatented know-how and continuing technological innovation to develop and maintain our competitive position, which we seek to protect, in part, by confidentiality agreements with our employees and our partners and consultants. We also have agreements with our employees and selected consultants that obligate them to assign their inventions to us. It is possible, however, that technology relevant to our business will be independently developed by a person that is not a party to such an agreement. Furthermore, if the employees and consultants that are parties to these agreements breach or violate the terms of these agreements, we may not have adequate remedies, and we could lose our trade secrets through such breaches or violations. Additionally, our trade secrets could otherwise become known or be independently discovered by our competitors.

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In addition, the laws of certain foreign countries do not protect proprietary rights to the same extent or in the same manner as the U.S., and, therefore, we may encounter problems in protecting and defending our intellectual property in certain foreign jurisdictions.

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If we are sued for infringing intellectual property rights of third parties, it will be costly and time consuming, and an unfavorable outcome in such litigation could have a material adverse effect on our business.

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Our commercial success depends on our ability, and the ability of our partners, to develop, manufacture, market and sell our products and use our proprietary technologies without infringing the proprietary rights of third parties. Numerous U.S. and foreign issued patents and pending patent applications, which are owned by third parties, exist in the fields in which we and our partners are developing products. As the biotechnology and pharmaceutical industry expands and more patents are issued, the risk increases that our potential products may give rise to claims of infringement of the patent rights of others. There may be issued patents of third parties of which we are currently unaware that may be infringed by linaclotide or our product candidates. Because patent applications can take many years to issue, there may be currently pending applications which may later result in issued patents that linaclotide or our product candidates may infringe.

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We may be exposed to, or threatened with, litigation by third parties alleging that linaclotide or our product candidates infringe their intellectual property rights. If linaclotide or one of our product candidates is found to infringe the intellectual property rights of a third party, we or our partners could be enjoined by a court and required to pay damages and could be unable to develop or commercialize linaclotide or the applicable product candidate unless we obtain a license to the intellectual property rights. A license may not be available to us on acceptable terms, if at all. In addition, during litigation, the counter-party could obtain a preliminary injunction or other equitable relief which could prohibit us from making, using or selling our products, pending a trial on the merits, which may not occur for several years.

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There is a substantial amount of litigation involving patent and other intellectual property rights in the biotechnology and pharmaceutical industries generally. If a third party claims that we or our partners infringe its intellectual property rights, we may face a number of issues, including, but not limited to:

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| ● | infringement and other intellectual property claims which, regardless of merit, may be expensive and time-consuming to litigate and may divert our management’s attention from our core business;

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| ● | substantial damages for infringement, which we may have to pay if a court decides that the product at issue infringes on or violates the third party’s rights, and, if the court finds that the infringement was willful, we could be ordered to pay treble damages and the patent owner’s attorneys’ fees;

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| ● | a court prohibiting us from selling our product unless the third party licenses its rights to us, which it is not required to do;

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| ● | if a license is available from a third party, we may have to pay substantial royalties, fees or grant cross-licenses to our intellectual property rights; and

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| ● | redesigning our products so they do not infringe, which may not be possible or may require substantial monetary expenditures and time.

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We have received notices of Paragraph IV certifications related to linaclotide in conjunction with ANDAs filed by generic drug manufacturers, and we may receive additional notices from others in the future. We have, and may continue to, become involved in legal proceedings to protect or enforce intellectual property rights relating to our products and our product candidates, which could be expensive and time consuming, and unfavorable outcomes in such proceedings could have a material adverse effect on our business.

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Competitors may infringe the patents relating to our products and our product candidates or may assert that such patents are invalid. To counter ongoing or potential infringement or unauthorized use, we may be required to file infringement claims, which can be expensive and time-consuming. Litigation with generic manufacturers has become increasingly common in the biotechnology and pharmaceutical industries. In addition, in an infringement or invalidity proceeding, a court or patent administrative body may determine that a patent of ours is not valid or is unenforceable, or may refuse to stop the other party from using the technology at issue on the grounds that our patents do not cover the technology in question. Generic drug manufacturers were first able to file ANDAs for generic versions of LINZESS in August 2016, but we may not become aware of these filings for several months after any such submission due to procedures specified under applicable FDA regulations. When filing an ANDA for one of our products, a generic drug manufacturer may choose to challenge one or more of the patents that cover such product. As such, we have brought, and may bring in the future, legal proceedings against generic drug manufacturers.

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We and Allergan have received Paragraph IV certification notice letters, or Notice Letters, regarding ANDAs submitted to the FDA by generic drug manufacturers requesting approval to engage in commercial manufacture, use, sale and offer for sale of linaclotide capsules (72 mcg, 145 mcg and 290 mcg), proposed generic versions of our FDA-approved drug LINZESS. For additional information relating to such ANDAs, see Item 1, Legal Proceedings, elsewhere in this Quarterly Report on Form 10-Q. Frequently, innovators receive multiple ANDA filings. Consequently, we expect to receive additional notice letters regarding ANDAs submitted to the FDA, and may receive amendments to the Notice Letters.

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After evaluation, we have in the past filed, and may, in the future, file patent infringement lawsuits or take other action against companies making ANDA filings. If a patent infringement suit has been filed within 45 days of receipt of a notice letter, the FDA is not permitted to approve any ANDA that is the subject of such lawsuit for 30 months from the date of the NDA holder’s and patent owner’s receipt of the ANDA filer’s notice letter, or until a court decides that the relevant patents are invalid, unenforceable and/or not infringed. In the case of suits filed before expiration of the new chemical entity, or NCE, exclusivity period for a particular drug, the 30-month stay would be calculated from the end of the applicable NCE exclusivity period. In addition to shortening the 30-month stay based on a decision that the relevant patents are invalid, unenforceable and/or not infringed, a court can also shorten or lengthen the 30-month stay under certain limited circumstances. The NCE exclusivity period for LINZESS expired on August 30, 2017, and the 30-month stay for each ANDA that is the subject of the current patent infringement lawsuits filed by us before such expiration date ends as early as February 29, 2020 (absent any of the foregoing adjustments). We have filed patent infringement lawsuits against the companies making such ANDA filings, and we have entered into settlement agreements with three such companies. For additional information relating to such lawsuits and settlements, see Item 1, Legal Proceedings, elsewhere in this Quarterly Report on Form 10-Q.

​

Additionally, the validity of the patents relating to our products and our product candidates may be challenged by third parties pursuant to administrative procedures introduced by the America Invents Act, specifically inter partes review, or IPR, and/or post grant review, or PGR, before the USPTO. Generic drug manufacturers may challenge our patents through IPRs or PGRs instead of or in addition to ANDA legal proceedings.

​

Patent litigation (including any lawsuits that we file against generic drug manufacturers in connection with the receipt of a notice letter), IPRs and PGRs involve complex legal and factual questions and we may need to devote significant resources to such legal proceedings. We can provide no assurance concerning the duration or the outcome of any such patent-related lawsuits or administrative proceedings, including any settlements or other resolutions thereof which could, in addition to other risks, result in a shortening of exclusivity periods. An adverse result in any litigation or defense proceedings could put one or more of the patents relating to our products and our product candidates at risk of being invalidated or interpreted narrowly, or could otherwise result in a loss of patent protection for the product or product candidate at issue, and could put our patent applications at risk of not issuing, which would materially harm our

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business. Upon any loss of patent protection for one of our products, or upon an “at-risk” launch (despite pending patent infringement litigation, before any court decision or while an appeal of a lower court decision is pending) by a manufacturer of a generic version of one of our patented products, our revenues for that product could be significantly reduced in a short period of time, which would materially and adversely affect our business.

​

Interference or derivation proceedings brought by the USPTO may be necessary to determine the priority of inventions with respect to the patents relating to our products and our product candidates and patent applications or those of our partners. An unfavorable outcome could require us to cease using the technology or to attempt to license rights to it from the prevailing party. Our business could be harmed if a prevailing party does not offer us a license on terms that are acceptable to us. Litigation or interference proceedings may fail and, even if successful, may result in substantial costs and distraction of our management and other employees. In addition, we may not be able to prevent, alone or with our partners, misappropriation of our proprietary rights, particularly in countries where the laws may not protect those rights as fully as in the U.S.

​

Furthermore, because of the substantial amount of discovery required in connection with intellectual property litigation, as well as the potential for public announcements of the results of hearings, motions or other interim proceeding or developments, there is a risk that some of our confidential information could be compromised by disclosure during this type of litigation.

​

Risks Related to Our Finances and Capital Requirements

​

We have incurred significant losses since our inception, and we may incur losses in future periods.

​

In recent years, we have focused primarily on developing, manufacturing and commercializing our products, as well as developing our other product candidates. We have financed our business to date primarily through the issuance of equity, our collaboration and license arrangements, and debt issuances, including our June 2015 issuance of our 2.25% Convertible Senior Notes due June 15, 2022, or the 2022 Notes, and our January 2017 issuance of our 8.375% Notes due 2026, or the 2026 Notes, related to the sales of LINZESS in the U.S., and we have incurred losses in each year since our inception in 1998. We currently derive a significant portion of our revenue from our LINZESS collaboration with Allergan for the U.S. We believe that the revenues from the LINZESS collaboration will continue to constitute a significant portion of our total revenue for the foreseeable future. Although we had net income of approximately $12.3 million in the three months ended June 30, 2019, we incurred net losses of approximately $47.0 million and approximately $92.5 million in the six months ended June 30, 2019 and 2018, respectively. As of June 30, 2019, we had an accumulated deficit of approximately $1.6 billion. We cannot be certain that sales of our products, and the revenue from our other commercial activities will not fall short of our projections or be delayed. Further, we expect to continue to incur substantial expenses in connection with our efforts to commercialize linaclotide and research and develop our product candidates. Because of the numerous risks and uncertainties associated with developing and commercializing pharmaceutical products, as well as those related to our expectations for our products and our other activities, we are unable to predict the extent of any future losses. Failure to achieve sustainable net income and positive cash flow would have an adverse effect on stockholders’ equity and working capital.

​

We may need additional funding and may be unable to raise capital when needed, which could cause us to delay, reduce or eliminate our product development programs or commercialization efforts.

​

In January 2017, we issued $150.0 million aggregate principal amount of our 2026 Notes bearing an annual interest rate of 8.375%. In June 2015, we issued approximately $335.7 million aggregate principal amount of our 2022 Notes and we have previously raised additional funds through other capital raising activities, including the sale of shares of our common stock in public offerings and other debt issuances. However, marketing and selling primary care drugs, purchasing commercial quantities of pharmaceutical products, developing product candidates, conducting clinical trials and accessing externally developed products are expensive and uncertain. Circumstances, our strategic imperatives, or opportunities to create or acquire new programs, as well as maturities, redemptions or repurchases of our outstanding debt securities, could require us to, or we may choose to, seek to raise additional funds. The amount and timing of our future funding requirements will depend on many factors, including, but not limited to:

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| ● | the level of underlying demand for our products by prescribers and patients in the countries in which they are approved;

​

| ● | the costs associated with commercializing our products in the U.S.;

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| ● | the costs of establishing, maintaining and/or expanding sales, marketing, distribution, and market access capabilities for our products;

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| ● | the regulatory approval of linaclotide outside of the U.S. and the other countries where it is approved and the timing of commercial launches in those countries, and the regulatory approval of linaclotide within new indications, populations and formulations, as well as the associated development and commercial milestones and royalties;

​

| ● | the rate of progress, the cost of our clinical trials and the other costs associated with our linaclotide product development programs, including our post-approval nonclinical and clinical studies of linaclotide in pediatrics and our investment to enhance the clinical profile of LINZESS within IBS-C and CIC, as well as to study linaclotide in additional indications, populations and formulations to assess its potential to treat various conditions;

​

| ● | the costs and timing of in-licensing additional products or product candidates or acquiring other complementary companies or assets;

​

| ● | the achievement and timing of milestone payments and royalties due or payable under our collaboration and license agreements;

​

| ● | the status, terms and timing of any collaboration, licensing, co-commercialization or other arrangements;

​

| ● | the timing of any regulatory approvals of our product candidates;

​

| ● | whether the holders of our 2022 Notes hold the notes to maturity without conversion into our common stock and whether we are required to repurchase our 2022 Notes prior to maturity upon a fundamental change, as defined in the indenture governing the 2022 Notes;

​

| ● | whether we seek to redeem or repurchase all or part of our outstanding debt through cash purchases and/or exchanges, in open market purchases, privately negotiated transactions, by tender offer or otherwise; and

​

| ● | any difficulties implementing the separation.

​

Additional funding may not be available on acceptable terms or at all. If adequate funds are not available, we may be required to delay or reduce the scope of our commercialization efforts, delay, reduce or eliminate one or more of our development programs or delay or abandon potential strategic opportunities.

​

Our ability to pay principal of and interest on our outstanding debt securities will depend in part on the receipt of payments from Allergan under our collaboration agreement for North America.

​

In January 2017, we issued $150.0 million aggregate principal amount of our 2026 Notes bearing an annual interest rate of 8.375% and in June 2015, we issued approximately $335.7 million aggregate principal amount of our 2022 Notes bearing an annual interest rate of 2.25%. Semi-annual payments on our 2022 Notes commenced on December 15, 2015. Quarterly interest payments on our 2026 Notes commenced on June 15, 2017 and, pursuant to the associated indenture, in March 2019 we began making quarterly payments on our 2026 Notes equal to the greater of (i) 7.5% of net sales of linaclotide in the U.S. for the preceding quarter and (ii) the accrued and unpaid interest on the 2026 Notes. Principal on the 2026 Notes is repaid in an amount equal to the difference between (i) and (ii) above, when this is a positive number, until the principal has been paid in full. We expect that for the next few years, at a minimum, the net quarterly payments from Allergan will be a significant source of cash flow from operations. If the cash flows derived from the net quarterly payments that we receive from Allergan under the collaboration agreement for North America are insufficient on any particular payment date to fund the interest payment on our outstanding indebtedness, at a minimum, we will be obligated to pay the amounts of such shortfall out of our general funds. The determination of whether Allergan will be obligated to make a net quarterly payment to us in respect of a particular quarterly period is a function of the revenue generated by LINZESS in the U.S. as well as the development, manufacturing and commercialization expenses incurred by each of us and Allergan under the collaboration agreement for North America. Accordingly, since we cannot guarantee that our company will sustain net income or attain or sustain positive cash flow, we cannot provide assurances that (i) we will have the available funds to fund the interest payment on our outstanding

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indebtedness, at a minimum, in the event that there is a deficiency in the net quarterly payment received from Allergan, (ii) there will be a net quarterly payment from Allergan at all or (iii) we will not also be required to make a true-up payment to Allergan under the collaboration agreement for North America, in each case, in respect of a particular quarterly period.

​

Our indebtedness could adversely affect our financial condition or restrict our future operations.

​

As of June 30, 2019, we had total indebtedness of approximately $464.2 million and available cash and cash equivalents of approximately $98.9 million. We chose to issue our 2026 Notes and our 2022 Notes based on the additional strategic optionality that they create for us, and the limited restrictions that these debt securities place on our ability to run our business compared to other potential available financing transactions. However, our indebtedness, combined with our other financial obligations and contractual commitments, could have other important consequences on our business, including:

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| ● | limiting our ability to obtain additional financing to fund future working capital, capital expenditures or other general corporate purposes, including product development, commercialization efforts, research and development activities, strategic arrangements, acquisitions and refinancing of our outstanding debt;

​

| ● | requiring a substantial portion of our cash flow to be dedicated to debt service payments instead of other purposes, thereby reducing the amount of cash flow available for working capital, capital expenditures, corporate transactions and other general corporate purposes;

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| ● | increasing our vulnerability to adverse changes in general economic, industry and competitive conditions;

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| ● | limiting our flexibility in planning for and reacting to changes in the industry in which we compete;

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| ● | placing us at a disadvantage compared to other, less leveraged competitors or competitors with comparable debt at more favorable interest rates; and

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| ● | increasing our cost of borrowing.

​

If we do not generate sufficient cash flow from operations or if future borrowings are not available to us in an amount sufficient to pay our indebtedness, including payments of principal when due on our outstanding indebtedness or, in the case of our 2022 Notes, in connection with a transaction involving us that constitutes a fundamental change under the indenture governing the 2022 Notes, or to fund our liquidity needs, we may be forced to refinance all or a portion of our indebtedness on or before the maturity dates thereof, sell assets, reduce or delay currently planned activities or curtail operations, seek to raise additional capital or take other actions. We may not be able to execute any of these actions on commercially reasonable terms or at all. This, together with any of the factors described above, could materially and adversely affect our business, financial condition and results of operations.

​

In addition, while our 2022 Notes do not include covenants restricting the operation of our business except in certain limited circumstances, in the event of a default under the 2022 Notes, the noteholders or the trustee under the indenture governing the 2022 Notes may accelerate our payment obligations under the 2022 Notes, which could have a material adverse effect on our business, financial condition and results of operations. We are also required to offer to repurchase the 2022 Notes upon the occurrence of a fundamental change, which could include, among other things, any acquisition of our company (other than an acquisition in which at least 90% of the consideration is common stock listed on The NASDAQ Global or Global Select Market or The New York Stock Exchange), subject to the terms of the 2022 Notes indenture. The repurchase price must be paid in cash, and this obligation may have the effect of discouraging, delaying or preventing an acquisition of our company that would otherwise be beneficial to our security holders.

​

Further, although we are not as restricted under our 2026 Notes as we might have been under a more traditional secured credit facility provided by a bank, the indenture governing our 2026 Notes contains a number of restrictive covenants that impose restrictions on us and may limit our ability to engage in certain acts, including restrictions on our ability to:

​

| ● | amend our collaboration agreement with Allergan for North America in a way that would have a material adverse effect on the noteholders’ rights, or terminate this collaboration agreement with respect to the U.S.;

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​

| ● | transfer our rights to commercialize the product under our collaboration agreement with Allergan for North America; and

​

| ● | incur certain liens.

​

Upon a breach of the covenants under our 2026 Notes indenture, or if certain other defaults thereunder occur, the holders of our 2026 Notes could elect to declare all amounts outstanding under our 2026 Notes to be immediately due and payable and we cannot be certain that we will have sufficient assets to repay them. If we are unable to repay those amounts, the holders of our 2026 Notes could proceed against the collateral granted to them to secure the debt securities and we could be forced into bankruptcy or liquidation. If we breach our covenants under our 2026 Notes indenture and seek a waiver, we may not be able to obtain a waiver from the required noteholders. If this occurs, we would be in default under our 2026 Notes indenture and the holders of our 2026 Notes could exercise their rights, as described above.

​

Each of our 2026 Notes and 2022 Notes also include cross-default features providing that a default under the indenture governing either the 2026 Notes or the 2022 Notes would likely result in a default under the indenture governing the other indebtedness. In the event of such default, the trustee or noteholders could elect to declare all amounts outstanding to be immediately due and payable under the applicable indenture, which could have a material adverse effect on our business, financial condition and results of operations.

​

Convertible note hedge and warrant transactions entered into in connection with our 2022 Notes may affect the value of our common stock.

​

In connection with our 2022 Notes, we entered into Convertible Note Hedges and separate Note Hedge Warrant transactions with certain financial institutions. These transactions are expected generally to reduce the potential dilution upon any conversion of our 2022 Notes or offset any cash payments we are required to make in excess of the principal amount of converted 2022 Notes, as the case may be.

​

In connection with these transactions, the financial institutions purchased our common stock in secondary market transactions and entered into various over-the-counter derivative transactions with respect to our common stock. These entities or their affiliates are likely to modify their hedge positions from time to time prior to conversion or maturity of the 2022 Notes by purchasing and selling shares of our common stock or other instruments they may wish to use in connection with such hedging. Any of these activities could adversely affect the value of our common stock and, as a result, the number of shares and the value of the common stock noteholders will receive upon conversion of the 2022 Notes. In addition, under certain circumstances the counterparties have the right to terminate the Convertible Note Hedges and settle the Note Hedge Warrants at fair value (as defined in the applicable confirmations), which may result in us not receiving all or any portion of the anticipated benefit of the Convertible Note Hedges. If the price of our common stock increases such that the hedge transactions settle in our favor, we could also be exposed to credit risk related to the counterparties to the Convertible Note Hedges, which would limit or eliminate the benefit of such transactions to us.

​

Our quarterly and annual operating results may fluctuate significantly.

​

We expect our operating results to be subject to frequent fluctuations. Our net loss and other operating results will be affected by numerous factors, including:

​

| ● | the level of underlying demand for our products in the countries in which they are approved;

​

| ● | wholesalers’ buying patterns with respect to our products;

​

| ● | the costs associated with commercializing our products in the U.S.;

​

| ● | the achievement and timing of milestone payments and royalties due or payable under our collaboration and license agreements;

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| ● | our execution of any collaboration, partnership, licensing or other strategic arrangements, and the timing of payments we may make or receive under these arrangements;

​

| ● | any excess or obsolete inventory or impairments of assets or goodwill, and associated write-downs;

​

| ● | any changes in the fair value of contingent consideration and the associated impact on our statement of operations;

​

| ● | any variations in the level of expenses related to our development programs;

​

| ● | addition or termination of clinical trials;

​

| ● | regulatory developments affecting our products and product candidates; and

​

| ● | any material lawsuit in which we may become involved.

​

If our operating results fall below the expectations of investors or securities analysts for any of the foregoing reasons or otherwise, the price of our common stock could decline substantially. Furthermore, any quarterly or annual fluctuations in our operating results may, in turn, cause the price of our stock to fluctuate substantially.

​

Our ability to use net operating loss and tax credit carryforwards and certain built-in losses to reduce future tax payments is limited by provisions of the Internal Revenue Code, and it is possible that our net operating loss and tax credit carryforwards may expire before we generate sufficient taxable income to use such carryforwards, or that certain transactions or a combination of certain transactions may result in material additional limitations on our ability to use our net operating loss and tax credit carryforwards.

​

We have incurred significant net losses since our inception. Although we achieved net income in the three months ended June 30, 2019, we cannot guarantee that we will sustain net income in the future. To the extent that we continue to generate federal and state taxable losses, unused net operating loss and tax credit carryforwards will carry forward to offset future taxable income, if any, until the date, if any, on which such unused carryforwards expire. Sections 382 and 383 of the Internal Revenue Code of 1986, as amended, contain rules that limit the ability of a company that undergoes an ownership change, which is generally any change in ownership of more than 50% of its stock over a three-year period, to utilize its net operating loss and tax credit carryforwards and certain built-in losses recognized in years after the ownership change. These rules generally operate by focusing on ownership changes involving stockholders owning directly or indirectly 5% or more of the stock of a company and any change in ownership arising from a new issuance of stock by the company. Generally, if an ownership change occurs, the yearly taxable income limitation on the use of net operating loss and tax credit carryforwards and certain built-in losses is equal to the product of the applicable long term tax exempt rate and the value of the company’s stock immediately before the ownership change.

​

If we do not generate sufficient taxable income prior to the expiration, if any, of the applicable carryforwards or if the carryforwards are subject to the limitations described above, we may be unable to offset our taxable income with losses, or our tax liability with credits, before such losses and credits expire and therefore would incur larger federal or state income tax liability. We have completed several financings since our inception which may have resulted in a change in control as defined by Section 382, or could result in a change in control in the future.

​

Risks Related to Securities Markets and Investment in Our Stock

​

Anti-takeover provisions under our charter documents and Delaware law could delay or prevent a change of control which could negatively impact the market price of our common stock.

​

Provisions in our certificate of incorporation and bylaws may have the effect of delaying or preventing a change of control. These provisions include the following:

​

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| ● | Our board of directors is currently divided into three classes serving staggered terms, such that not all members of the board are elected at one time. This staggered board structure prevents stockholders from

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|  | replacing the entire board at a single stockholders’ meeting. At our 2019 annual meeting of stockholders, our stockholders approved an amendment to our certificate of incorporation to declassify our board of directors to allow our stockholders to vote on the election of the entire board of directors on an annual basis, rather than on a staggered basis. This declassification will be phased in such that, once completed in 2022, stockholders will have the opportunity to replace the entire board at a single stockholders’ meeting. As required by Delaware law, the amendment to our certificate of incorporation also reflects that, once the board of directors is declassified, stockholders may remove directors with or without cause.

​

| ● | Our board of directors has the right to elect directors to fill a vacancy created by the expansion of the board of directors or the resignation, death or removal of a director, which prevents stockholders from being able to fill vacancies on our board of directors.

​

| ● | Our board of directors may issue, without stockholder approval, shares of preferred stock. The ability to authorize preferred stock makes it possible for our board of directors to issue preferred stock with voting or other rights or preferences that could impede the success of any attempt to acquire us.

​

| ● | Stockholders must provide advance notice to nominate individuals for election to the board of directors or to propose matters that can be acted upon at a stockholders’ meeting. Furthermore, as described above, until our board of directors is declassified, stockholders may only remove a member of our board of directors for cause. These provisions may discourage or deter a potential acquirer from conducting a solicitation of proxies to elect such acquirer’s own slate of directors or otherwise attempting to obtain control of our company.

​

| ● | Our stockholders may not act by written consent. As a result, a holder, or holders, controlling a majority of our capital stock are not able to take certain actions outside of a stockholders’ meeting.

​

| ● | Special meetings of stockholders may be called only by the chairman of our board of directors, our chief executive officer or a majority of our board of directors. As a result, a holder, or holders, controlling a majority of our capital stock are not able to call a special meeting.

​

| ● | A super-majority (80%) of the outstanding shares of common stock are required to amend our bylaws, which make it more difficult to change the provisions described above.

​

In addition, we are governed by the provisions of Section 203 of the Delaware General Corporation Law, which may prohibit certain business combinations with stockholders owning 15% or more of our outstanding voting stock. These and other provisions in our certificate of incorporation and our bylaws and in the Delaware General Corporation Law could make it more difficult for stockholders or potential acquirers to obtain control of our board of directors or initiate actions that are opposed by the then-current board of directors.

​

If we identify a material weakness in our internal control over financial reporting, it could have an adverse effect on our business and financial results and our ability to meet our reporting obligations could be negatively affected, each of which could negatively affect the trading price of our common stock.

​

A material weakness is a deficiency, or a combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of our annual or interim financial statements will not be prevented or detected on a timely basis. Accordingly, a material weakness increases the risk that the financial information we report contains material errors.

​

We regularly review and update our internal controls, disclosure controls and procedures, and corporate governance policies. In addition, we are required under the Sarbanes-Oxley Act of 2002 to report annually on our internal control over financial reporting. Our system of internal controls, however well-designed and operated, is based in part on certain assumptions and includes elements that rely on information from third parties, including our partners. Our system can provide only reasonable, not absolute, assurances that the objectives of the system are met. If we, or our independent registered public accounting firm, determine that our internal controls over financial reporting are not effective, or we discover areas that need improvement in the future, these shortcomings could have an adverse effect on our business and financial results, and the price of our common stock could be negatively affected.

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Further, we are dependent on our partners for information related to our results of operations. Our net profit or net loss generated from the sales of LINZESS in the U.S. is partially determined based on amounts provided by Allergan and involves the use of estimates and judgments, which could be modified in the future. We are highly dependent on our linaclotide partners for timely and accurate information regarding any revenues realized from sales of linaclotide in their respective territories, and in the case of Allergan for the U.S. and AstraZeneca for China, Hong Kong and Macau, the costs incurred in developing and commercializing it in order to accurately report our results of operations. Our results of operations are also dependent on the timeliness and accuracy of information from any other licensing, collaboration or other partners we may have, as well as our and our partners’ use of estimates and judgments. If we do not receive timely and accurate information or if estimated activity levels associated with the relevant collaboration or partnership at a given point in time are incorrect, whether the result of a material weakness or not, we could be required to record adjustments in future periods. Such adjustments, if significant, could have an adverse effect on our financial results, which could lead to a decline in our common stock price.

​

If we cannot conclude that we have effective internal control over our financial reporting, or if our independent registered public accounting firm is unable to provide an unqualified opinion regarding the effectiveness of our internal control over financial reporting, investors could lose confidence in the reliability of our financial statements, which could lead to a decline in our stock price. Failure to comply with reporting requirements could also subject us to sanctions and/or investigations by the SEC, The NASDAQ Stock Market or other regulatory authorities.

​

We expect that the price of our common stock will fluctuate substantially.

​

The market price of our common stock may be highly volatile due to many factors, including:

​

| ● | the commercial performance of our products in the countries in which they are approved, as well as the costs associated with such activities;

​

| ● | any third-party coverage and reimbursement policies for our products;

​

| ● | market conditions in the pharmaceutical and biotechnology sectors;

​

| ● | developments, litigation or public concern about the safety of our products or our potential products;

​

| ● | announcements of the introduction of new products by us or our competitors;

​

| ● | announcements concerning product development results, including clinical trial results, or intellectual property rights of us or others;

​

| ● | actual and anticipated fluctuations in our quarterly and annual operating results;

​

| ● | deviations in our operating results from any guidance we may provide or the estimates of securities analysts;

​

| ● | sales of additional shares of our common stock or sales of securities convertible into common stock or the perception that these sales might occur;

​

| ● | additions or departures of key personnel;

​

| ● | developments concerning current or future collaboration, partnership, licensing or other strategic arrangements, or the Separation; and

​

| ● | discussion of us or our stock price in the financial or scientific press or in online investor communities.

​

The realization of any of the risks described in these “Risk Factors” could have a dramatic and material adverse impact on the market price of our common stock. In addition, class action litigation has often been instituted against companies whose securities have experienced periods of volatility. Any such litigation brought against us could result in substantial costs and a diversion of management attention, which could hurt our business, operating results and financial condition.

​

​

Item 6. Exhibit s

​

See the Exhibit Index on the following page of this Quarterly Report on Form 10-Q.

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EXHIBIT INDEX

​

| ​ |
Exhibit No: | ​ | Description
3.1 ​ | ​ | Eleventh Amended and Restated Certificate of Incorporation. Incorporated by reference to Exhibit 3.1 of Ironwood Pharmaceuticals, Inc.’s Annual Report on Form 10-K for the year ended December 31, 2009, filed with the SEC on March 30, 2010. ​ ​
3.2 | ​ | Certificate of Amendment of Eleventh Amended and Restated Certificate of Incorporation. Incorporated by reference to Exhibit 3.1 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on May 31, 2019.
​ | ​ | ​
3.3 | ​ | Fifth Amended and Restated Bylaws. Incorporated by reference to Exhibit 3.2 of Ironwood Pharmaceuticals, Inc.’s Annual Report on Form 10-K for the year ended December 31, 2009, filed with the SEC on March 30, 2010. ​ ​
4.1 | ​ | Supplemental Indenture dated as of April 5, 2019 by and between Ironwood Pharmaceuticals, Inc. and U.S. Bank National Association, as Trustee. Incorporated by reference to Exhibit 4.1 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on April 8, 2019. ​
10.1*# | ​ | 2019 Equity Incentive Plan. ​
10.2*# | ​ | Form of Non-statutory Stock Option Agreement under the 2019 Equity Incentive Plan.
10.3*# | ​ | Form of Restricted Stock Unit Agreement under the 2019 Equity Incentive Plan. ​
10.4*# | ​ | Form of Restricted Stock Agreement under the 2019 Equity Incentive Plan. ​
10.5*# | ​ | Non-employee Director Compensation Policy, effective May 20, 2019. ​
10.6*# | ​ | Form of Non-Employee Director Restricted Stock Award Agreement under the Amended and Restated 2010 Employee, Director and Consultant Equity Incentive Plan. ​
10.7 | ​ | Thirteenth Amendment to Lease, dated as of April 1, 2019, by and between BMR-Rogers Street LLC and Ironwood Pharmaceuticals, Inc. Incorporated by reference to Exhibit 10.3 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on April 4, 2019.
10.8 | ​ | Lease Agreement for facilities at 100 Summer Street, Boston, Massachusetts, dated as of June 11, 2019, by and between Ironwood Pharmaceuticals, Inc. and MA-100 Summer Street Owner, L.L.C. Incorporated by reference to Exhibit 10.1 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on June 13, 2019. ​
10.9 | ​ | Lease Termination Agreement for facilities at 301 Binney Street, Cambridge, Massachusetts, dated as of June 11, 2019, by and between Ironwood Pharmaceuticals, Inc. and BMR-Rogers Street LLC. Incorporated by reference to Exhibit 10.2 of Ironwood Pharmaceuticals, Inc.’s Current Report on Form 8-K, filed with the SEC on June 13, 2019. ​
​ | ​ | ​
31.1* | ​ | Certification of Chief Executive Officer pursuant to Rules 13a-14 or 15d-14 of the Exchange Act.

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​ | ​ | ​
31.2* | ​ | Certification of Chief Financial Officer pursuant to Rules 13a-14 or 15d-14 of the Exchange Act.
​ | ​ | ​
32.1‡ | ​ | Certification of Chief Executive Officer pursuant to Rules 13a-14(b) or 15d-14(b) of the Exchange Act and 18 U.S.C. Section 1350.
​ | ​ | ​
32.2‡ | ​ | Certification of Chief Financial Officer pursuant to Rules 13a-14(b) or 15d-14(b) of the Exchange Act and 18 U.S.C. Section 1350.
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101.INS* | ​ | XBRL Instance Document – The Instance Document does not appear in the Interactive Data Files because its XBRL tags are embedded within the Inline XBRL document.
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101.SCH* | ​ | XBRL Taxonomy Extension Schema Document.
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101.CAL* | ​ | XBRL Taxonomy Extension Calculation Linkbase Document.
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101.LAB* | ​ | XBRL Taxonomy Extension Label Linkbase Database
​ | ​ | ​
101.PRE* | ​ | XBRL Taxonomy Extension Presentation Linkbase Document
​ | ​ | ​
101.DEF* | ​ | XBRL Taxonomy Extension Definition Linkbase Document

* Filed herewith.

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‡ Furnished herewith.

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# | Management contract or compensatory plan, contract, or arrangement.

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SIGNATURE S

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Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

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​ | Ironwood Pharmaceuticals, Inc.
​ | ​
Date: July 30, 2019 | By: | /s/ MARK MALLON
​ | ​ | Mark Mallon
​ | ​ | Chief Executive Officer and Director
​ | ​ | (Principal Executive Officer)
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​ | ​
Date: July 30, 2019 | By: | /s/ KELLY MACDONALD
​ | ​ | Kelly MacDonald
​ | ​ | Vice President, Finance and Chief Accounting Officer
​ | ​ | (Principal Accounting Officer)

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