AGIOS PHARMACEUTICALS, INC. 10-Q

Item 1. Financial Statements (Unaudited) AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Balance Sheets (Unaudited) (In thousands, except share and per share data) June 30, 2024 December 31, 2023 Assets Current assets: Cash and cash equivalents $ 84,518 $ 88,205 Marketable securities 485,374 688,723 Accounts receivable, net 3,762 2,810 Inventory 23,937 19,076 Prepaid expenses and other current assets 34,536 35,021 Total current assets 632,127 833,835 Marketable securities 75,404 29,435 Operating lease assets 48,750 54,409 Property and equipment, net 12,726 15,382 Other non-current assets 4,056 4,057 Total assets $ 773,063 $ 937,118 Liabilities and stockholders’ equity Current liabilities: Accounts payable $ 10,035 $ 9,780 Accrued expenses 36,742 43,167 Operating lease liabilities 15,860 15,008 Total current liabilities 62,637 67,955 Operating lease liabilities, net of current portion 48,760 56,988 Other non-current liabilities 1,156 1,156 Total liabilities 112,553 126,099 Stockholders’ equity: Preferred stock, $ 0.001 par value; 25,000,000 shares authorized; no shares issued or outstanding at June 30, 2024 and December 31, 2023 — — Common stock, $ 0.001 par value; 125,000,000 shares authorized; 73,091,490 shares issued and 56,875,079 shares outstanding at June 30, 2024, and 72,161,489 shares issued and 55,945,078 shares outstanding at December 31, 2023 73 72 Additional paid-in capital 2,464,284 2,436,523 Accumulated other comprehensive loss ( 1,045 ) ( 441 ) Treasury stock, at cost ( 16,216,411 shares at June 30, 2024 and December 31, 2023) ( 802,486 ) ( 802,486 ) Accumulated deficit ( 1,000,316 ) ( 822,649 ) Total stockholders’ equity 660,510 811,019 Total liabilities and stockholders’ equity $ 773,063 $ 937,118 See accompanying Notes to Condensed Consolidated Financial Statements. 1 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Operations (Unaudited) Three Months Ended June 30, Six Months Ended June 30, (In thousands, except share and per share data) 2024 2023 2024 2023 Revenues: Product revenue, net $ 8,615 $ 6,712 $ 16,804 $ 12,321 Total revenue 8,615 6,712 16,804 12,321 Operating expenses: Cost of sales $ 1,495 $ 1,108 $ 2,122 $ 1,662 Research and development 77,401 68,895 146,021 136,196 Selling, general and administrative 35,536 30,409 66,550 58,776 Total operating expenses 114,432 100,412 214,693 196,634 Loss from operations ( 105,817 ) ( 93,700 ) ( 197,889 ) ( 184,313 ) Interest income, net 8,120 8,254 17,009 16,345 Other income, net 1,579 1,640 3,213 3,144 Net loss $ ( 96,118 ) $ ( 83,806 ) $ ( 177,667 ) $ ( 164,824 ) Net loss per share - basic and diluted $ ( 1.69 ) $ ( 1.51 ) $ ( 3.14 ) $ ( 2.97 ) Weighted-average number of common shares used in computing net loss per share – basic and diluted 56,802,546 55,604,330 56,593,011 55,435,796 See accompanying Notes to Condensed Consolidated Financial Statements. 2 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Comprehensive Loss (Unaudited) Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2024 2023 2024 2023 Net loss $ ( 96,118 ) $ ( 83,806 ) $ ( 177,667 ) $ ( 164,824 ) Other comprehensive income (loss) Unrealized gain (loss) on available-for-sale securities 42 ( 459 ) ( 604 ) 3,665 Comprehensive loss $ ( 96,076 ) $ ( 84,265 ) $ ( 178,271 ) $ ( 161,159 ) See accompanying Notes to Condensed Consolidated Financial Statements. 3 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Stockholders' Equity (Unaudited) Common Stock Additional Paid-In Capital Accumulated Other Comprehensive Loss Accumulated Deficit Treasury Stock Total Stockholders’ Equity (in thousands, except share amounts) Shares Amount Shares Amount Balance at December 31, 2023 72,161,489 $ 72 $ 2,436,523 $ ( 441 ) $ ( 822,649 ) ( 16,216,411 ) $ ( 802,486 ) $ 811,019 Unrealized loss on available-for-sale securities — — — ( 646 ) — — — ( 646 ) Common stock issued under stock incentive plan and ESPP 806,433 1 5,863 — — — — 5,864 Stock-based compensation expense — — 9,234 — — — — 9,234 Net loss — — — — ( 81,549 ) — — ( 81,549 ) Balance at March 31, 2024 72,967,922 $ 73 $ 2,451,620 $ ( 1,087 ) $ ( 904,198 ) ( 16,216,411 ) $ ( 802,486 ) $ 743,922 Unrealized gain on available-for-sale securities — — — 42 — — — 42 Common stock issued under stock incentive plan and ESPP 123,568 — 1,099 — — — — 1,099 Stock-based compensation expense — — 11,565 — — — — 11,565 Net loss — — — — ( 96,118 ) — — ( 96,118 ) Balance at June 30, 2024 73,091,490 $ 73 $ 2,464,284 $ ( 1,045 ) $ ( 1,000,316 ) ( 16,216,411 ) $ ( 802,486 ) $ 660,510 Common Stock Additional Paid-In Capital Accumulated Other Comprehensive (Loss) Income Accumulated Deficit Treasury Stock Total Stockholders’ Equity (in thousands, except share amounts) Shares Amount Shares Amount Balance at December 31, 2022 71,256,118 $ 71 $ 2,386,325 $ ( 12,535 ) $ ( 470,561 ) ( 16,216,411 ) $ ( 802,486 ) $ 1,100,814 Unrealized gain on available-for-sale securities — — — 4,124 — — — 4,124 Common stock issued under stock incentive plan and ESPP 501,660 1 2,466 — — — — 2,467 Stock-based compensation expense — — 10,139 — — — — 10,139 Net loss — — — — ( 81,018 ) — — ( 81,018 ) Balance at March 31, 2023 71,757,778 $ 72 $ 2,398,930 $ ( 8,411 ) $ ( 551,579 ) ( 16,216,411 ) $ ( 802,486 ) $ 1,036,526 Unrealized loss on available-for-sale securities — — — ( 459 ) — — — ( 459 ) Common stock issued under stock incentive plan and ESPP 193,408 — 238 — — — — 238 Stock-based compensation expense — — 11,737 — — — — 11,737 Net loss — — — — ( 83,806 ) — — ( 83,806 ) Balance at June 30, 2023 71,951,186 $ 72 $ 2,410,905 $ ( 8,870 ) $ ( 635,385 ) ( 16,216,411 ) $ ( 802,486 ) $ 964,236 See accompanying Notes to Condensed Consolidated Financial Statements. 4 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Cash Flows (Unaudited) Six Months Ended June 30, (In thousands) 2024 2023 Operating activities Net loss $ ( 177,667 ) $ ( 164,824 ) Adjustments to reconcile net loss from operations to net cash used in operating activities: Depreciation and amortization 2,941 3,597 Stock-based compensation expense 20,799 21,876 Net accretion of discount on marketable securities ( 5,136 ) ( 5,738 ) Gain on disposal of property and equipment ( 39 ) ( 150 ) Non-cash operating lease expense 5,659 5,263 Realized gain on investments ( 153 ) — Changes in operating assets and liabilities: Accounts receivable, net ( 952 ) ( 45 ) Inventory ( 4,861 ) ( 7,179 ) Prepaid expenses and other current and non-current assets 486 2,103 Accounts payable 268 ( 6,837 ) Accrued expenses and other current liabilities ( 6,425 ) ( 1,161 ) Operating lease liabilities ( 7,376 ) ( 6,713 ) Other non-current liabilities — ( 2,123 ) Net cash used in operating activities ( 172,456 ) ( 161,931 ) Investing activities Purchases of marketable securities ( 348,604 ) ( 232,486 ) Proceeds from maturities and sales of marketable securities 510,669 337,453 Purchases of property and equipment ( 299 ) ( 396 ) Proceeds from sale of equipment 40 150 Net cash provided by investing activities 161,806 104,721 Financing activities Net proceeds from stock option exercises and employee stock purchase plan 6,963 2,704 Net cash provided by financing activities 6,963 2,704 Net change in cash and cash equivalents ( 3,687 ) ( 54,506 ) Cash and cash equivalents at beginning of the period 88,205 139,259 Cash and cash equivalents at end of the period $ 84,518 $ 84,753 Supplemental disclosure of non-cash investing and financing transactions Additions to property and equipment in accounts payable and accrued expenses $ 42 $ 6 Net cash taxes (returned) paid $ ( 603 ) $ 801 See accompanying Notes to Condensed Consolidated Financial Statements. 5 Table of Contents AGIOS PHARMACEUTICALS, INC. Notes to Condensed Consolidated Financial Statements (Unaudited) 1. Overview and Basis of Presentation References to Agios Throughout this Quarterly Report on Form 10-Q, "Agios," "the company," “we,” “us,” and “our,” and similar expressions, except where the context requires otherwise, refer to Agios Pharmaceuticals, Inc. and its consolidated subsidiaries, and “our Board of Directors” refers to the board of directors of Agios Pharmaceuticals, Inc. Overview We are a biopharmaceutical company committed to transforming patients’ lives through leadership in the field of cellular metabolism, with the goal of creating differentiated medicines for rare diseases, with a focus on classical hematology. With a history of focused study on cellular metabolism, we have a deep and mature understanding of this biology, which is involved in the healthy functioning of nearly every system in the body. Building on this expertise, these learnings can be rapidly applied to our clinical trials with the goal of developing medicines that can have a significant impact for patients. We accelerate the impact of our portfolio by cultivating connections with patient communities, healthcare professionals, partners and colleagues to discover, develop and deliver potential therapies for rare diseases. We are located in Cambridge, Massachusetts. The lead product candidate in our portfolio, PYRUKYND® (mitapivat), is an activator of both wild-type and mutant pyruvate kinase, or PK, enzymes for the potential treatment of hemolytic anemias. In February 2022, the U.S. Food and Drug Administration, or FDA, approved PYRUKYND® for the treatment of hemolytic anemia in adults with PK deficiency in the United States. In November 2022, we received marketing authorization from the European Commission for PYRUKYND® for the treatment of PK deficiency in adult patients in the European Union, or EU. In December 2022, we received marketing authorization in Great Britain for PYRUKYND® for the treatment of PK deficiency in adult patients under the European Commission Decision Reliance Procedure. In addition, we are currently evaluating PYRUKYND® in clinical trials for the treatment of thalassemia, sickle cell disease, or SCD, and in pediatric patients with PK deficiency. We are also developing (i) AG-946 (tebapivat), a novel PK activator, for the potential treatment of lower-risk myelodysplastic syndrome, or LR MDS, and hemolytic anemias, and (ii) AG-181, our phenylalanine hydroxylase, or PAH, stabilizer for the potential treatment of phenylketonuria, or PKU. In addition to the aforementioned development programs, in July 2023 we entered into a license agreement with Alnylam Pharmaceuticals, Inc., or Alnylam, for the development and commercialization of products containing or comprised of an siRNA preclinical development candidate discovered by Alnylam and targeting the transmembrane serine protease 6, or TMPRSS6, gene, and we have begun preclinical development of a product candidate for the potential disease-modifying treatment of patients with polycythemia vera, or PV, a rare blood disorder. We are subject to risks common to companies in our industry including, but not limited to, uncertainties relating to conducting preclinical and clinical research and development, the manufacture and supply of products for clinical and commercial use, obtaining and maintaining regulatory approvals and pricing and reimbursement for our products, market acceptance, managing global growth and operating expenses, availability of additional capital, competition, obtaining and enforcing patents, stock price volatility, dependence on collaborative relationships and third-party service providers, dependence on key personnel, potential litigation, potential product liability claims and potential government investigations. Alnylam License Agreement On July 28, 2023, we entered into a license agreement with Alnylam under which we acquired the rights to develop and commercialize Alnylam’s novel preclinical siRNA targeting the TMPRSS6 gene, as a potential disease-modifying treatment for patients with PV. Because the acquired assets do not meet the definition of a business in accordance with Accounting Standards Codification, or ASC, 805, Business Combinations , we accounted for the agreement as an asset acquisition. In accordance with the license agreement, in the twelve months ended December 31, 2023, we made an up-front payment to Alnylam and recognized in-process research and development of $ 17.5 million. We will also pay Alnylam for certain expenses associated with the development of the TMPRSS6 program, and these will be recorded in our Consolidated Statements of Operations as incurred. Additionally, we are responsible to pay up to $ 130.0 million in potential development and regulatory milestones, in addition to sales milestones as well as tiered royalties on annual net sales, if any, of licensed products, which may be subject to specified reductions and offsets. 6 Table of Contents Sale of Oncology Business to Servier and Sale of Contingent Payments and Royalty Rights On March 31, 2021, we completed the sale of our oncology business to Servier Pharmaceuticals, LLC, or Servier, which represented a discontinued operation. The transaction included the sale of our oncology business, including TIBSOVO®, our clinical-stage product candidates vorasidenib, AG-270 and AG-636, and our oncology research programs for a payment of approximately $ 1.8 billion in cash at the closing, subject to certain adjustments, and a payment of $ 200.0 million in cash, if, prior to January 1, 2027, vorasidenib is granted new drug application, or NDA, approval from the FDA with an approved label that permits vorasidenib’s use as a single agent for the adjuvant treatment of patients with Grade 2 glioma that have an isocitrate dehydrogenase, or IDH, 1 or 2 mutation (and, to the extent required by such approval, the vorasidenib companion diagnostic test is granted an FDA premarket approval), or the Vorasidenib Milestone Payment, as well as a royalty of 5 % of U.S. net sales of TIBSOVO® from the close of the transaction through loss of exclusivity, and a royalty of 15 % of U.S. net sales of vorasidenib from the first commercial sale of vorasidenib through loss of exclusivity, or the Vorasidenib Royalty Rights. The Vorasidenib Milestone Payment, Vorasidenib Royalty Rights and royalty payments related to TIBSOVO® are referred to as contingent payments and recognized as income when realizable. Servier also acquired our co-commercialization rights for Bristol Myers Squibb’s IDHIFA® and the right to receive a $ 25.0 million potential milestone payment under our prior collaboration agreement with Celgene Corporation, or Celgene, and following the sale Servier will conduct certain clinical development activities within the IDHIFA® development program. In October 2022, we sold our rights to future contingent payments associated with the royalty of 5 % of U.S. net sales of TIBSOVO® from the close of the transaction through the loss of exclusivity to entities affiliated with Sagard Healthcare Partners, or Sagard, and recognized income of $ 127.9 million within the gain on sale of contingent payments line item in our Consolidated Statements of Operations for the year ended December 31, 2022. In February 2024, Servier announced that it received filing acceptance and priority review from the FDA for its NDA for vorasidenib for the treatment of certain IDH-mutant diffuse glioma and accelerated assessment from the European Medicines Agency, or EMA, for its Marketing Authorization Application, or MAA, for vorasidenib. The FDA assigned the NDA a Prescription Drug User Fee Act, or PDUFA, action date of August 20, 2024, and Servier anticipates that the European Commission will approve its MAA in the second half of 2024. In May 2024, we entered into a purchase and sale agreement to sell the Vorasidenib Royalty Rights to Royalty Pharma Investments 2019 ICAV, or Royalty Pharma, for $ 905.0 million in cash, which sale is contingent upon NDA approval of vorasidenib by the FDA on or before October 31, 2024, and other customary closing conditions. Upon consummation of the sale, Royalty Pharma will acquire 100% of the Vorasidenib Royalty Rights payments made by Servier on account of up to $1.0 billion in net sales for each calendar year. In addition, any such Vorasidenib Royalty Rights payments made by Servier on account of U.S. net sales in each calendar year in excess of $1.0 billion will be split, with Royalty Pharma having the rights to a 12 % earn-out on those excess payments and Agios retaining the rights to a 3 % earn-out on those excess payments, or the Retained Earn-Out Rights. We retain our rights to the potential Vorasidenib Milestone Payment. Basis of Presentation The condensed consolidated balance sheet as of June 30, 2024, the condensed consolidated statements of operations, comprehensive loss and stockholders' equity for the three and six months ended June 30, 2024 and 2023, and the condensed consolidated statements of cash flows for the six months ended June 30, 2024 and 2023 are unaudited. The unaudited condensed consolidated financial statements have been prepared on the same basis as the annual financial statements and, in the opinion of our management, reflect all adjustments, which include only normal recurring adjustments, necessary to fairly state our financial position as of June 30, 2024, our results of operations and stockholders' equity for the three and six months ended June 30, 2024 and 2023, and cash flows for the six months ended June 30, 2024 and 2023. The financial data and the other financial information disclosed in these notes to the condensed consolidated financial statements related to the three and six-month periods are also unaudited. The results of operations for the three and six months ended June 30, 2024 are not necessarily indicative of the results to be expected for the year ending December 31, 2024 or for any other future annual or interim period. The condensed consolidated balance sheet data as of December 31, 2023 was derived from our audited financial statements, but does not include all disclosures required by U.S. generally accepted accounting principles, or U.S. GAAP. The condensed consolidated interim financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the year ended December 31, 2023 that was filed with the Securities and Exchange Commission, or SEC, on February 15, 2024. Our condensed consolidated financial statements include our accounts and the accounts of our wholly owned subsidiaries. All intercompany transactions have been eliminated in consolidation. The condensed consolidated financial statements have been prepared in conformity with U.S. GAAP. 7 Table of Contents Use of Estimates The preparation of our condensed consolidated financial statements requires us to make estimates, judgments and assumptions that may affect the reported amounts of assets, liabilities, equity, revenues and expenses and related disclosure of contingent assets and liabilities. On an ongoing basis we evaluate our estimates, judgments and methodologies. We base our estimates on historical experience and on various other assumptions that we believe are reasonable, the results of which form the basis for making judgments about the carrying values of assets, liabilities and equity and the amount of revenues and expenses. The full extent to which pandemics or public health emergencies, may in the future directly or indirectly impact our business, results of operations and financial condition, including expenses, reserves and allowances, clinical trials, research and development costs and employee-related amounts, will depend on future developments that are highly uncertain. Liquidity As of June 30, 2024, we had cash, cash equivalents and marketable securities of $ 645.3 million. Although we have incurred recurring losses and expect to continue to incur losses for the foreseeable future, we expect our cash, cash equivalents and marketable securities to be sufficient to fund current operations for at least the next twelve months from the issuance of the financial statements. If we are unable to raise additional funds through equity or debt financings, we may be required to delay, limit, reduce or terminate product development or future commercialization efforts or grant rights to develop and market products or product candidates that we would otherwise prefer to develop and market ourselves. 2. Summary of Significant Accounting Policies There have been no material changes to the significant accounting policies previously disclosed in our Annual Report on Form 10-K for the year ended December 31, 2023. Recent Accounting Pronouncements Accounting standards that have been issued by the Financial Accounting Standards Board or other standards-setting bodies that do not require adoption until a future date are not expected to have a material impact on our financial statements upon adoption. 3. Fair Value Measurements We record cash equivalents and marketable securities at fair value. ASC 820, Fair Value Measurements and Disclosures , establishes a fair value hierarchy for those instruments measured at fair value that distinguishes between assumptions based on market data (observable inputs) and our own assumptions (unobservable inputs). The hierarchy consists of three levels: Level 1 – Unadjusted quoted prices in active markets for identical assets or liabilities. Level 2 – Quoted prices for similar assets and liabilities in active markets, quoted prices in markets that are not active, or inputs which are observable, directly or indirectly, for substantially the full term of the asset or liability. Level 3 – Unobservable inputs that reflect our own assumptions about the assumptions market participants would use in pricing the asset or liability in which there is little, if any, market activity for the asset or liability at the measurement date. The following table summarizes our cash equivalents and marketable securities measured at fair value and by level on a recurring basis as of June 30, 2024: (In thousands) Level 1 Level 2 Level 3 Total Cash equivalents $ 16,203 $ 29,474 $ — $ 45,677 Total cash equivalents 16,203 29,474 — 45,677 Marketable securities: Certificates of deposit $ — $ 11,878 $ — $ 11,878 U.S. Treasuries — 102,260 — 102,260 Government securities — 150,793 — 150,793 Corporate debt securities — 295,847 — 295,847 Total marketable securities — 560,778 — 560,778 Total cash equivalents and marketable securities $ 16,203 $ 590,252 $ — $ 606,455 Cash equivalents and marketable securities have been initially valued at the transaction price and are subsequently valued, at the end of each reporting period, utilizing third-party pricing services or other observable market data. The pricing services utilize industry standard valuation models, including both income and market-based approaches, and observable market inputs to 8 Table of Contents determine value. After completing our validation procedures, we did not adjust or override any fair value measurements provided by the pricing services as of June 30, 2024. There have been no changes to the valuation methods during the six months ended June 30, 2024, and we had no financial assets or liabilities that were classified as Level 3 at any point during the six months ended June 30, 2024. 4. Marketable Securities Our marketable securities are classified as available-for-sale pursuant to ASC 320, Investments – Debt and Equity Securities , and are recorded at fair value. Unrealized gains and losses are included as a component of accumulated other comprehensive loss in the condensed consolidated balance sheets and statements of stockholders’ equity, and a component of total comprehensive loss in the condensed consolidated statements of comprehensive loss, until realized. Unrealized losses are evaluated for impairment under ASC 326, Financial Instruments - Credit Losses , to determine if the impairment is credit-related or noncredit-related. Credit-related impairment is recognized as an allowance on the condensed consolidated balance sheets with a corresponding adjustment to earnings, and noncredit-related impairment is recognized in other comprehensive income, net of taxes. Realized gains and losses are included in investment income on a specific-identification basis. There were no material realized gains or losses on marketable securities for the three and six months ended June 30, 2024 or 2023. Marketable securities at June 30, 2024 consisted of the following: (In thousands) Amortized Cost Unrealized Gains Unrealized Losses Fair Value Current: Certificates of deposit $ 11,885 $ — $ ( 7 ) $ 11,878 U.S. Treasuries 77,271 — ( 93 ) 77,178 Government securities 147,335 — ( 311 ) 147,024 Corporate debt securities 249,719 1 ( 426 ) 249,294 Total Current 486,210 1 ( 837 ) 485,374 Non-current: U.S. Treasuries 25,132 8 ( 58 ) 25,082 Government securities 3,800 — ( 31 ) 3,769 Corporate debt securities 46,681 5 ( 133 ) 46,553 Total Non-current 75,613 13 ( 222 ) 75,404 Total marketable securities $ 561,823 $ 14 $ ( 1,059 ) $ 560,778 Marketable securities at December 31, 2023 consisted of the following: (In thousands) Amortized Cost Unrealized Gains Unrealized Losses Fair Value Current: U.S. Treasuries $ 30,876 $ — $ ( 56 ) $ 30,820 Government securities 247,460 194 ( 695 ) 246,959 Corporate debt securities 411,045 874 ( 975 ) 410,944 Total Current 689,381 1,068 ( 1,726 ) 688,723 Non-current: U.S. Treasuries 4,802 30 — 4,832 Government securities 9,986 75 — 10,061 Corporate debt securities 14,430 112 — 14,542 Total Non-current 29,218 217 — 29,435 Total marketable securities $ 718,599 $ 1,285 $ ( 1,726 ) $ 718,158 As of June 30, 2024 and December 31, 2023, we held both current and non-current investments. Investments classified as current have maturities of less than one year. Investments classified as non-current are those that: (i) have a maturity of greater 9 Table of Contents than one year, and (ii) we do not intend to liquidate within the next twelve months, although these funds are available for use and, therefore, are classified as available-for-sale. As of June 30, 2024 and December 31, 2023, we held 194 and 151 debt securities, respectively, that were in an unrealized loss position for less than one year. We did no t record an allowance for credit losses as of June 30, 2024 and December 31, 2023 related to these securities. The aggregate fair value of debt securities in an unrealized loss position at June 30, 2024 and December 31, 2023 was $ 538.0 million and $ 513.5 million, respectively. There were no individual securities that were in a significant unrealized loss position as of June 30, 2024 and December 31, 2023. We regularly review the securities in an unrealized loss position and evaluate the current expected credit loss by considering factors such as historical experience, market data, issuer-specific factors, and current economic conditions. We do not consider these marketable securities to be impaired as of June 30, 2024 and December 31, 2023. 5. Inventory Inventory, which consists of commercial supply of PYRUKYND®, consisted of the following: (In thousands) June 30, 2024 December 31, 2023 Raw materials $ 90 $ 51 Work-in-process 21,691 17,568 Finished goods 2,156 1,457 Total inventory $ 23,937 $ 19,076 6. Leases Our building leases are comprised of office and laboratory space under non-cancelable operating leases. These lease agreements have remaining lease terms of approximately four years and contain various clauses for renewal at our option. The renewal options were not included in the calculation of the operating lease assets and the operating lease liabilities as the renewal options are not reasonably certain of being exercised. The lease agreements do not contain residual value guarantees. The components of lease expense and other information related to leases were as follows: Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2024 2023 2024 2023 Operating lease costs $ 3,806 $ 3,806 $ 7,613 $ 7,613 Cash paid for amounts included in the measurement of operating lease liabilities 4,678 4,544 $ 9,331 $ 9,064 We have not entered into any material short-term leases or financing leases as of June 30, 2024. In arriving at the operating lease liabilities as of June 30, 2024 and December 31, 2023, we applied the weighted-average incremental borrowing rate of 5.7 % for both periods over a weighted-average remaining lease term of 3.7 and 4.2 years, respectively. As of June 30, 2024, undiscounted minimum rental commitments under non-cancelable leases were as follows: (In thousands) Remaining 2024 $ 7,810 2025 19,507 2026 20,151 2027 20,755 2028 3,479 Undiscounted minimum rental commitments $ 71,702 Interest ( 7,082 ) Operating lease liabilities $ 64,620 We provided our landlord a security deposit of $ 2.9 million as security for our leases, which is included within other non-current assets on our condensed consolidated balance sheet. 10 Table of Contents In August 2021, we entered into a long-term sublease agreement for 13,000 square feet of the office space at 38 Sidney Street, Cambridge, Massachusetts, with the term of the lease running through December 2024. In April 2022, we entered into a long-term sublease agreement for 27,000 square feet of the office space at 64 Sidney Street, Cambridge, Massachusetts, with the term of the lease running through April 2025. In May 2023, we entered into a long-term sublease agreement for 7,407 square feet of office space on the first floor of 64 Sidney Street, Cambridge, Massachusetts, with the term of the lease running through April 2025. We recorded operating sublease income of $ 1.6 million and $ 1.4 million for the three months ended June 30, 2024 and 2023, respectively, and $ 3.2 million and $ 2.8 million for the six months ended June 30, 2024 and 2023, respectively, in other income, net in the condensed consolidated statements of operations. We hold security deposits from our sublessees of approximately $ 1.2 million which is recorded within other non-current assets on our condensed consolidated balance sheet. As of June 30, 2024, the future minimum lease payments to be received under the long-term sublease agreements were as follows: (In thousands) Remaining 2024 $ 2,565 2025 1,310 Total $ 3,875 7. Accrued Expenses Accrued expenses consisted of the following: (In thousands) June 30, 2024 December 31, 2023 Accrued compensation $ 11,965 $ 23,232 Accrued research and development costs 19,265 15,463 Accrued professional fees 3,439 3,115 Accrued other 2,073 1,357 Total accrued expenses $ 36,742 $ 43,167 8. Product Revenue We sell PYRUKYND®, our wholly owned product, to a limited number of specialty distributors and specialty pharmacy providers, or collectively, the Customers. These Customers subsequently resell PYRUKYND® to pharmacies or dispense PYRUKYND® directly to patients. In addition to distribution agreements with Customers, we enter into arrangements with healthcare providers and payors that provide for government-mandated and/or privately-negotiated rebates, chargebacks and discounts with respect to the purchase of PYRUKYND®. The performance obligation related to the sale of PYRUKYND® is satisfied and revenue is recognized when the Customer obtains control of the product, which occurs at a point in time, typically upon delivery to the Customer. Product revenue, net, were as follows: Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2024 2023 2024 2023 Product revenue, net $ 8,615 $ 6,712 $ 16,804 $ 12,321 Reserves for Variable Consideration Revenues from product sales are recorded at the net sales price, or transaction price, which includes estimates of variable consideration for which reserves are established and result from contractual adjustments, government rebates, returns and other allowances that are offered within the contracts with our Customers, healthcare providers, payors and other indirect customers relating to the sale of our products. Contractual Adjustments We generally provide Customers with discounts, including prompt pay discounts, and allowances that are explicitly stated in the contracts and are recorded as a reduction of revenue in the period the related product revenue is recognized. In addition, we receive sales order management, data and distribution services from certain Customers. 11 Table of Contents Chargebacks and discounts represent the estimated obligations resulting from contractual commitments to sell products to qualified healthcare providers at prices lower than the list prices charged to Customers who directly purchase the product from us. Customers charge us for the difference between what they pay for the product and the ultimate selling price to the qualified healthcare providers. These reserves are estimated using the expected value method, based upon a range of possible outcomes that are probability-weighted for the estimated channel mix and are established in the same period that the related revenue is recognized, resulting in a reduction of product revenue. Government Rebates Government rebates include Medicare, TriCare, and Medicaid rebates, which we estimate using the expected value method, based upon a range of possible outcomes that are probability-weighted for the estimated payor mix. These reserves are recorded in the same period the related revenue is recognized, resulting in a reduction of product revenue. For Medicare, we also estimate the number of patients in the prescription drug coverage gap for whom we will owe an additional liability under the Medicare Part D program. Returns / Replacement We estimate the amount of product sales that may be returned by Customers or replaced by Agios and record this estimate as a reduction of revenue in the period the related product revenue is recognized. We currently estimate product return and replacement liabilities using the expected value method, based on available industry data, including our visibility into the inventory remaining in the distribution channel. The following table summarizes balances and activity in each of the product revenue allowance and reserve categories for the six months ended June 30, 2024: (In thousands) Contractual Adjustments Government Rebates Returns/ Replacement Total Balance at December 31, 2023 $ 156 $ 1,084 $ 232 $ 1,472 Current provisions relating to sales in the current year 772 1,245 189 2,206 Adjustments relating to prior years ( 39 ) ( 49 ) 40 ( 48 ) Payments/returns relating to sales in the current year ( 632 ) ( 306 ) — ( 938 ) Payments/returns relating to sales in the prior years ( 85 ) ( 371 ) ( 71 ) ( 527 ) Balance at June 30, 2024 $ 172 $ 1,603 $ 390 $ 2,165 Total revenue-related reserves above, included in our condensed consolidated balance sheets, are summarized as follows: (In thousands) June 30, 2024 December 31, 2023 Reduction of accounts receivable $ 102 $ 151 Component of accrued expenses 2,063 1,321 Total revenue-related reserves $ 2,165 $ 1,472 The following table presents changes in our contract assets during the six months ended June 30, 2024: (In thousands) December 31, 2023 Additions Deductions June 30, 2024 Contract assets (1) Accounts receivable, net $ 2,810 $ 18,940 $ ( 17,988 ) $ 3,762 (1) Additions to contract assets relate to amounts billed to Customers for product sales and deductions to contract assets primarily relate to collection of receivables during the reporting period. 9. Share-Based Payments 2023 Stock Incentive Plan and Inducement Grants In June 2023, our stockholders approved the 2023 Stock Incentive Plan, or the 2023 Plan. The 2023 Plan provides for the grant of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units, or RSUs, performance-based share units, or PSUs, and other stock-based awards to employees, advisors, consultants and non-employee directors. 12 Table of Contents Following the adoption of the 2023 Plan, we ceased granting equity awards under the 2013 Stock Incentive Plan, or the 2013 Plan. Any outstanding equity awards that were previously granted under the 2013 Plan continue to be governed by their terms. Following adoption of the 2013 Plan, we ceased granting equity awards under the 2007 Stock Incentive Plan, or the 2007 Plan. There are no outstanding equity awards under the 2007 Plan. In connection with the start of employment of our Chief Executive Officer and Chief Financial Officer in 2022, and our Chief Commercial Officer in 2023, our board of directors granted each of them equity awards in the form of stock options, RSUs and PSUs, which awards were made outside our equity incentive plans as inducements material to their respective entry into employment with us in accordance with Nasdaq Listing Rule 5635(c)(4). As of June 30, 2024, the maximum number of shares reserved under the 2013 Plan, the 2023 Plan and the inducement grants described above was 11,127,064 , and we had 2,896,048 shares available for future issuance under the 2023 Plan. Stock options The following table presents stock option activity for the six months ended June 30, 2024: Number of Stock Options Weighted-Average Exercise Price Outstanding at December 31, 2023 5,263,681 $ 44.94 Granted 960,488 33.39 Exercised ( 184,331 ) 30.96 Cancelled/Forfeited ( 21,063 ) 41.52 Expired ( 22,750 ) 34.41 Outstanding at June 30, 2024 5,996,025 $ 43.57 Exercisable at June 30, 2024 3,727,328 $ 51.07 Vested and expected to vest at June 30, 2024 5,996,025 $ 43.57 At June 30, 2024, there was approximately $ 36.8 million of total unrecognized compensation expense related to unvested stock option awards, which we expect to recognize over a weighted-average period of approximately 2.61 years. Restricted stock units The following table presents RSU activity for the six months ended June 30, 2024: Number of Stock Units Weighted-Average Grant Date Fair Value Unvested shares at December 31, 2023 1,346,701 $ 29.67 Granted 1,054,565 31.23 Vested ( 522,606 ) 33.04 Forfeited ( 18,252 ) 29.17 Unvested shares at June 30, 2024 1,860,408 $ 29.62 As of June 30, 2024, there was approximately $ 43.8 million of total unrecognized compensation expense related to RSUs, which we expect to recognize over a weighted-average period of approximately 2.14 years. Performance-based stock units The following table presents PSU activity for the six months ended June 30, 2024: Number of Stock Units Weighted-Average Grant Date Fair Value Unvested shares at December 31, 2023 362,133 $ 30.66 Granted 183,000 32.27 Vested ( 170,550 ) 35.04 Unvested shares at June 30, 2024 374,583 $ 29.45 Stock-based compensation expense associated with these PSUs is recognized if the underlying performance condition is considered probable of achievement using our management’s best estimates. 13 Table of Contents As of June 30, 2024, there was no unrecognized compensation expense related to PSUs with performance-based vesting criteria that are considered probable of achievement, and $ 11.0 million of total unrecognized compensation expense related to PSUs with performance-based vesting criteria that are considered not probable of achievement. Market-based stock units The following table presents market-based stock unit, or MSU, activity for the six months ended June 30, 2024: Number of Stock Units Weighted-Average Grant Date Fair Value Unvested shares at December 31, 2023 42,695 $ 41.50 Expired ( 42,695 ) 41.50 Unvested shares at June 30, 2024 — $ — The fair value of MSUs are estimated using a Monte Carlo simulation model. Assumptions and estimates utilized in the model include the risk-free interest rate, dividend yield, expected stock volatility and the estimated period to achievement of the market condition. As of June 30, 2024, there was no remaining unrecognized compensation expense related to MSUs. 2013 Employee Stock Purchase Plan In June 2013, our Board of Directors adopted, and in July 2013 our stockholders approved, the 2013 Employee Stock Purchase Plan, or the 2013 ESPP. We issued and sold 52,514 and 54,867 shares of common stock during the six months ended June 30, 2024 and 2023, respectively, under the 2013 ESPP. The 2013 ESPP provides participating employees with the opportunity to purchase up to an aggregate of 2,363,636 shares of our common stock. As of June 30, 2024, we had 1,633,525 shares of common stock available for future issuance under the 2013 ESPP. Stock-based compensation expense Stock-based compensation expense by award type included within the condensed consolidated statements of operations is as follows: Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2024 2023 2024 2023 Stock options $ 4,361 $ 3,937 $ 8,432 $ 8,894 Restricted stock units 6,211 4,754 11,177 9,701 Performance-based stock units 750 2,784 750 2,784 Employee stock purchase plan 243 262 440 497 Total stock-based compensation expense $ 11,565 $ 11,737 $ 20,799 $ 21,876 Expenses related to stock options and stock-based awards were allocated as follows in the condensed consolidated statements of operations: Three Months Ended June 30, Six Months Ended June 30, (In thousands) 2024 2023 2024 2023 Research and development expense $ 4,460 $ 4,540 $ 8,235 $ 8,895 Selling, general and administrative expense 7,105 7,197 12,564 12,981 Total stock-based compensation expense $ 11,565 $ 11,737 $ 20,799 $ 21,876 10. Loss per Share Basic net loss per share is calculated by dividing net loss by the weighted-average shares outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is calculated by adjusting the weighted-average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury stock method. For purposes of the dilutive net loss per share calculation, stock options, RSUs, PSUs and MSUs for which the performance and market vesting conditions, respectively, have been deemed probable, and 2013 ESPP shares are considered to be common stock equivalents, while PSUs and MSUs with performance and market vesting conditions, respectively, that were not deemed probable as of June 30, 2024 are not considered to be common stock equivalents. 14 Table of Contents We utilize the control number concept in the computation of diluted earnings per share to determine whether potential common stock equivalents are dilutive. The control number used is net loss from continuing operations. The control number concept requires that the same number of potentially dilutive securities applied in computing diluted earnings per share from continuing operations be applied to all other categories of income or loss, regardless of their anti-dilutive effect on such categories. Since we had a net loss for all periods presented, no dilutive effect has been recognized in the calculation of loss per share. Basic and diluted net loss per share was the same for all periods presented. The following common stock equivalents were excluded from the calculation of diluted net loss per share applicable to common stockholders for the periods indicated because including them would have had an anti-dilutive effect: Three and Six Months Ended June 30, 2024 2023 Stock options 5,996,025 5,789,272 Restricted stock units 1,860,408 1,415,219 Employee stock purchase plan shares 39,381 50,942 Total common stock equivalents 7,895,814 7,255,433 11. Subsequent Events In July 2024, we entered into a distribution agreement with NewBridge Pharmaceuticals FZ-LLC, or NewBridge, pursuant to which we granted NewBridge the right to commercialize PYRUKYND® in Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, and the United Arab Emirates. We do not expect this agreement to have a material impact on our business, financial condition or results of operations for the fiscal year ending December 31, 2024. 15 Table of Contents