ALNYLAM PHARMACEUTICALS, INC. 10-Q

ITEM 1. FINANCIAL STATEMENTS (Unaudited) ALNYLAM PHARMACEUTICALS, INC. CONDENSED CONSOLIDATED BALANCE SHEETS (In thousands, except per share amounts) (Unaudited) March 31, 2023 December 31, 2022 ASSETS Current assets: Cash and cash equivalents $ 672,245 $ 866,394 Marketable debt securities 1,372,574 1,297,890 Marketable equity securities 25,856 28,122 Accounts receivable, net 219,434 237,963 Inventory 131,879 128,962 Prepaid expenses and other current assets 119,030 132,916 Total current assets 2,541,018 2,692,247 Property, plant and equipment, net 523,032 523,494 Operating lease right-of-use assets 215,049 215,136 Restricted investments 49,388 49,390 Other assets 63,453 66,092 Total assets $ 3,391,940 $ 3,546,359 LIABILITIES AND STOCKHOLDERS’ DEFICIT Current liabilities: Accounts payable $ 62,237 $ 98,094 Accrued expenses 508,599 545,460 Operating lease liability 43,055 41,967 Deferred revenue 35,794 42,105 Liability related to the sale of future royalties 23,706 40,289 Total current liabilities 673,391 767,915 Operating lease liability, net of current portion 259,399 261,339 Deferred revenue, net of current portion 191,257 193,791 Convertible debt 1,017,887 1,016,942 Liability related to the sale of future royalties, net of current portion 1,285,200 1,252,015 Other liabilities 224,046 212,580 Total liabilities 3,651,180 3,704,582 Commitments and contingencies (Note 13) Stockholders’ deficit: Preferred stock, $ 0.01 par value per share, 5,000 shares authorized and no shares issued and outstanding as of March 31, 2023 and December 31, 2022 — — Common stock, $ 0.01 par value per share, 250,000 shares authorized; 124,241 shares issued and outstanding as of March 31, 2023; 123,925 shares issued and outstanding as of December 31, 2022 1,243 1,240 Additional paid-in capital 6,522,091 6,454,540 Accumulated other comprehensive loss ( 39,124 ) ( 44,654 ) Accumulated deficit ( 6,743,450 ) ( 6,569,349 ) Total stockholders’ deficit ( 259,240 ) ( 158,223 ) Total liabilities and stockholders’ deficit $ 3,391,940 $ 3,546,359 The accompanying notes are an integral part of these condensed consolidated financial statements. 5 Table of Contents ALNYLAM PHARMACEUTICALS, INC. CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS (In thousands, except per share amounts) (Unaudited) Three Months Ended March 31, 2023 2022 Statements of Operations Revenues: Net product revenues $ 276,328 $ 186,872 Net revenues from collaborations 36,462 25,945 Royalty revenue 6,500 442 Total revenues 319,290 213,259 Operating costs and expenses: Cost of goods sold 41,432 23,457 Cost of collaborations and royalties 13,437 12,170 Research and development 230,569 169,893 Selling, general and administrative 183,659 154,471 Total operating costs and expenses 469,097 359,991 Loss from operations ( 149,807 ) ( 146,732 ) Other (expense) income: Interest expense ( 28,955 ) ( 42,362 ) Interest income 18,655 1,012 Other expense, net ( 12,255 ) ( 51,274 ) Total other expense, net ( 22,555 ) ( 92,624 ) Loss before income taxes ( 172,362 ) ( 239,356 ) Provision for income taxes ( 1,739 ) ( 985 ) Net loss $ ( 174,101 ) $ ( 240,341 ) Net loss per common share - basic and diluted $ ( 1.40 ) $ ( 2.00 ) Weighted-average common shares used to compute basic and diluted net loss per common share 124,111 120,393 Statements of Comprehensive Loss Net loss $ ( 174,101 ) $ ( 240,341 ) Other comprehensive income (loss): Unrealized gain (loss) on marketable securities 4,125 ( 7,217 ) Foreign currency translation gain 1,410 2,376 Defined benefit pension plans, net of tax ( 5 ) 35 Total other comprehensive income (loss) 5,530 ( 4,806 ) Comprehensive loss $ ( 168,571 ) $ ( 245,147 ) The accompanying notes are an integral part of these condensed consolidated financial statements. 6 Table of Contents ALNYLAM PHARMACEUTICALS, INC. CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ (DEFICIT) EQUITY (In thousands) (Unaudited) Common Stock Additional Paid-in Capital Accumulated Other Comprehensive Loss Accumulated Deficit Total Stockholders’ Deficit Shares Amount Balance as of December 31, 2022 123,925 $ 1,240 $ 6,454,540 $ ( 44,654 ) $ ( 6,569,349 ) $ ( 158,223 ) Exercise of common stock options, net of tax withholdings 269 3 26,415 — — 26,418 Issuance of common stock under equity plans 47 — — — — — Stock-based compensation expense — — 41,136 — — 41,136 Other comprehensive income — — — 5,530 — 5,530 Net loss — — — — ( 174,101 ) ( 174,101 ) Balance as of March 31, 2023 124,241 $ 1,243 $ 6,522,091 $ ( 39,124 ) $ ( 6,743,450 ) $ ( 259,240 ) Common Stock Additional Paid-in Capital Accumulated Other Comprehensive Loss Accumulated Deficit Total Stockholders’ Equity Shares Amount Balance as of December 31, 2021 120,182 $ 1,202 $ 6,058,453 $ ( 33,259 ) $ ( 5,438,193 ) $ 588,203 Exercise of common stock options, net of tax withholdings 524 5 28,054 — — 28,059 Issuance of common stock under equity plans 23 — — — — — Stock-based compensation expense — — 30,051 — — 30,051 Other comprehensive loss — — — ( 4,806 ) — ( 4,806 ) Net loss — — — — ( 240,341 ) ( 240,341 ) Balance as of March 31, 2022 120,729 $ 1,207 $ 6,116,558 $ ( 38,065 ) $ ( 5,678,534 ) $ 401,166 The accompanying notes are an integral part of these condensed consolidated financial statements. 7 Table of Contents ALNYLAM PHARMACEUTICALS, INC. CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (In thousands) (Unaudited) Three Months Ended March 31, 2023 2022 Cash flows from operating activities: Net loss $ ( 174,101 ) $ ( 240,341 ) Non-cash adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 14,065 9,460 Amortization and interest accretion related to operating leases 12,014 10,318 Non-cash interest expense on liability related to the sale of future royalties 25,275 27,702 Stock-based compensation 39,947 29,293 Realized and unrealized loss on marketable equity securities 2,267 31,161 Change in fair value of development derivative liability 6,471 13,782 Other ( 6,276 ) 7,395 Changes in operating assets and liabilities: Accounts receivable, net 19,153 39,696 Inventory ( 403 ) 1,926 Prepaid expenses and other assets ( 1,235 ) ( 29,852 ) Accounts payable, accrued expenses and other liabilities ( 81,975 ) ( 48,736 ) Operating lease liability ( 12,827 ) ( 10,672 ) Deferred revenue ( 8,850 ) ( 12,325 ) Net cash used in operating activities ( 166,475 ) ( 171,193 ) Cash flows from investing activities: Purchases of property, plant and equipment ( 13,891 ) ( 17,859 ) Purchases of marketable securities ( 435,746 ) ( 634,705 ) Sales and maturities of marketable securities 373,420 505,220 Proceeds from maturity of restricted investments 49,225 9,400 Purchases of restricted investments ( 49,225 ) ( 9,400 ) Other investing activities — ( 75 ) Net cash used in investing activities ( 76,217 ) ( 147,419 ) Cash flows from financing activities: Proceeds from exercise of stock options and other types of equity, net 42,371 27,123 Proceeds from development derivative 4,000 7,833 Net cash provided by financing activities 46,371 34,956 Effect of exchange rate changes on cash, cash equivalents and restricted cash 2,176 ( 2,238 ) Net decrease in cash, cash equivalents and restricted cash ( 194,145 ) ( 285,894 ) Cash, cash equivalents and restricted cash, beginning of period 868,556 822,153 Cash, cash equivalents and restricted cash, end of period $ 674,411 $ 536,259 Supplemental disclosure of cash flows: Cash paid for interest $ 13,912 $ 14,120 Supplemental disclosure of noncash investing activities: Capital expenditures included in accounts payable and accrued expenses $ 4,034 $ 8,318 The accompanying notes are an integral part of these condensed consolidated financial statements. 8 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) 1. NATURE OF BUSINESS Alnylam Pharmaceuticals, Inc. (also referred to as Alnylam, we, our or us) commenced operations on June 14, 2002 as a biopharmaceutical company seeking to develop and commercialize novel therapeutics based on ribonucleic acid interference, or RNAi. We are committed to the advancement of our company strategy of building a multi-product, global, commercial biopharmaceutical company with a deep and sustainable clinical pipeline of RNAi therapeutics for future growth and a robust, organic research engine for sustainable innovation and great potential for patient impact. Since inception, we have focused on discovering, developing and commercializing RNAi therapeutics by establishing and maintaining a strong intellectual property position in the RNAi field, establishing strategic alliances with leading pharmaceutical and life sciences companies, generating revenues through licensing agreements, and ultimately developing and commercializing RNAi therapeutics globally, either independently or with our strategic partners. We have devoted substantially all of our efforts to business planning, research, development, manufacturing and early commercial efforts, acquiring, filing and expanding intellectual property rights, recruiting management and technical staff, and raising capital. In early 2021, we launched our Alnylam P 5 x25 strategy, which focuses on our planned transition to a top-tier biotech company by the end of 2025. With Alnylam P 5 x25 , we aim to deliver transformative rare and prevalent disease medicines for patients around the world through sustainable innovation, while delivering exceptional financial performance. As of March 31, 2023, we have five marketed products, including one partnered product, and multiple late-stage investigational programs advancing towards potential commercialization. We currently generate worldwide product revenues from four commercialized products, ONPATTRO, AMVUTTRA, GIVLAARI and OXLUMO, primarily in the United States, or U.S., Europe and Japan. 2. BASIS OF PRESENTATION AND PRINCIPLES OF CONSOLIDATION The accompanying condensed consolidated financial statements of Alnylam are unaudited and have been prepared in accordance with accounting principles generally accepted in the United States of America, or GAAP, applicable to interim periods and, in the opinion of management, include all normal and recurring adjustments that are necessary to state fairly the results of operations for the reported periods. Our condensed consolidated financial statements have also been prepared on a basis substantially consistent with, and should be read in conjunction with, our audited consolidated financial statements for the year ended December 31, 2022, which were included in our Annual Report on Form 10-K that was filed with the Securities and Exchange Commission on February 23, 2023. The year-end condensed consolidated balance sheet data was derived from our audited financial statements but does not include all disclosures required by GAAP. The results of our operations for any interim period are not necessarily indicative of the results of our operations for any other interim period or for a full fiscal year. The accompanying condensed consolidated financial statements reflect the operations of Alnylam and our wholly-owned subsidiaries. All intercompany accounts and transactions have been eliminated. Our significant accounting policies are described in Note 2 of the Notes to Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2022. Use of Estimates The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America, or GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. In our condensed consolidated financial statements, we use estimates and assumptions related to our inventory valuation and related reserves, liability related to the sale of future royalties, development derivative liability, income taxes, revenue recognition, research and development expenses, and stock-based compensation. We base our estimates on historical experience and on various other assumptions that we believe to be reasonable. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known. Liquidity Based on our current operating plan, we believe that our cash, cash equivalents and marketable securities as of March 31, 2023, together with the cash we expect to generate from product sales and under our current alliances, will be sufficient to enable us to advance our Alnylam P 5 x25 strategy for at least the next 12 months from the filing of this Quarterly Report on Form 10-Q. 9 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) 3. NET PRODUCT REVENUES Net product revenues consist of the following: Three Months Ended March 31, (In thousands) 2023 2022 ONPATTRO United States $ 29,817 $ 62,307 Europe 59,678 53,181 Rest of World 12,998 21,521 Total 102,493 137,009 AMVUTTRA United States 79,013 — Europe 6,768 — Rest of World 15,987 — Total 101,768 — GIVLAARI United States 30,291 23,675 Europe 14,471 9,688 Rest of World 3,144 1,914 Total 47,906 35,277 OXLUMO United States 9,057 5,412 Europe 13,309 8,158 Rest of World 1,795 1,016 Total 24,161 14,586 Total net product revenues $ 276,328 $ 186,872 The following table presents the balance of our receivables related to our net product revenues: (In thousands) As of March 31, 2023 As of December 31, 2022 Receivables included in “Accounts receivable, net” $ 190,931 $ 203,844 10 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) 4. NET REVENUES FROM COLLABORATIONS Net revenues from collaborations consist of the following: Three Months Ended March 31, (In thousands) 2023 2022 Regeneron Pharmaceuticals $ 19,990 $ 12,412 Novartis AG 14,933 13,136 Other 1,539 397 Total $ 36,462 $ 25,945 The following table presents the balance of our receivables and contract liabilities related to our collaboration agreements: (In thousands) As of March 31, 2023 As of December 31, 2022 Receivables included in “Accounts receivable, net” $ 22,572 $ 32,342 Contract liabilities included in “Deferred revenue” $ 226,789 $ 235,528 We recognized revenue of $ 15.4 million and $ 9.5 million in the three months ended March 31, 2023 and 2022, respectively, that was included in the contract liability balance at the beginning of the period. In order to determine revenue recognized in the period from contract liabilities, we first allocate revenue to the individual contract liability balance outstanding at the beginning of the period until the revenue exceeds that balance. If additional consideration is received on those contracts in subsequent periods, we assume all revenue recognized in the reporting period first applies to the beginning contract liability as opposed to a portion applying to the new consideration for the period. The following table provides research and development expenses incurred by type, for which we recognize net revenue, that are directly attributable to our collaboration agreements, by collaboration partner: Three Months Ended March 31, 2023 2022 (In thousands) Clinical Trial and Manufacturing External Services Other Clinical Trial and Manufacturing External Services Other Regeneron Pharmaceuticals $ 8,516 $ 1,240 $ 9,363 $ 1,437 $ 622 $ 9,308 Other 312 126 360 156 42 160 Total $ 8,828 $ 1,366 $ 9,723 $ 1,593 $ 664 $ 9,468 The research and development expenses incurred for the agreements included in the table above consist of costs incurred for (i) clinical expenses, including manufacturing of clinical product, (ii) external services including consulting services and lab supplies and services, and (iii) other expenses, including professional services, facilities and overhead allocations, and a reasonable estimate of compensation and related costs as billed to our counterparties, for which we recognize net revenues from collaborations. For the three months ended March 31, 2023 and 2022, we did not incur material selling, general and administrative expenses related to our collaboration agreements. In addition, we recognized a reduction to our research and development expenses of $ 5.7 million and $ 3.9 million for the three months ended March 31, 2023 and 2022, respectively, from cost reimbursement due under certain of our collaboration agreements with Regeneron Pharmaceuticals, Inc., or Regeneron, accounted for under Accounting Standards Codification, or ASC, Topic 808, Collaborative Arrangements, or ASC 808. Product Alliances Regeneron Pharmaceuticals, Inc. In April 2019, we entered into a global, strategic collaboration with Regeneron to discover, develop and commercialize RNAi therapeutics for a broad range of diseases by addressing therapeutic targets expressed in the eye and central nervous system, or CNS, in addition to a select number of targets expressed in the liver, which we refer to as the Regeneron Collaboration. The Regeneron Collaboration is governed by a Master Agreement, referred to as the Regeneron Master Agreement, which became effective on May 21, 2019. In connection with the Regeneron Master Agreement, we and Regeneron entered into (i) a binding co-co collaboration term sheet covering the continued development of cemdisiran, our C5 small 11 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) interfering RNA, or siRNA, currently in Phase 2 development for C5 complement-mediated diseases, as a monotherapy and (ii) a binding license term sheet to evaluate anti-C5 antibody-siRNA combinations for C5 complement-mediated diseases including evaluating the combination of Regeneron’s pozelimab (REGN3918), currently in Phase 3 development, and cemdisiran. The C5 co-co collaboration and license agreements were executed in August 2019. Under the terms of the Regeneron Collaboration, we are working exclusively with Regeneron to discover RNAi therapeutics for eye and CNS diseases for an initial research period of approximately five years , which we refer to as the Initial Research Term. Regeneron has an option to extend the Initial Research Term (referred to as the Research Term Extension Period, and together with the Initial Research Term, the Research Term) for up to an additional five years , for a research term extension fee of $ 300.0 million. The Regeneron Collaboration also covers a select number of RNAi therapeutic programs designed to target genes expressed in the liver, including our previously announced collaboration with Regeneron to identify RNAi therapeutics for the chronic liver disease nonalcoholic steatohepatitis. We retain broad global rights to all of our other unpartnered liver-directed clinical and pre-clinical pipeline programs. The Regeneron Collaboration is governed by a joint steering committee that is comprised of an equal number of representatives from each party. Regeneron leads development and commercialization for all programs targeting eye diseases (subject to limited exceptions), entitling us to certain potential milestone and royalty payments pursuant to the terms of a license agreement, the form of which has been agreed upon by the parties. We and Regeneron are alternating leadership on CNS and liver programs covered by the Regeneron Collaboration, with the lead party retaining global development and commercial responsibility. For such CNS and liver programs, both we and Regeneron have the option at lead candidate selection to enter into a co-co collaboration agreement, the form of which has been agreed upon by the parties, whereby both companies will share equally all costs of, and profits from, all development and commercialization activities under the program. If the non-lead party elects to not enter into a co-co collaboration agreement with respect to a given CNS or liver program, we and Regeneron will enter into a license agreement with respect to such program and the lead party will be the “Licensee” for the purposes of the license agreement. If the lead party for a CNS or liver program elects to not enter into the co-co collaboration agreement, then we and Regeneron will enter into a license agreement with respect to such program and leadership of the program will transfer to the other party and the former non-lead party will be the “Licensee” for the purposes of the license agreement. With respect to the programs directed to C5 complement-mediated diseases, we retain control of cemdisiran monotherapy development, and Regeneron is leading combination product development. Pursuant to the C5 co-co collaboration agreement, Regeneron notified us in November 2022 of its decision to exercise its right to opt-out of the further development and commercialization of cemdisiran monotherapy. As a result, Regeneron no longer shares costs and potential future profits on any monotherapy program with us. We continue to perform our obligations under the agreement and we are solely responsible for all development and commercialization costs. Regeneron will be eligible to receive tiered double-digit royalties on net sales. Under the C5 license agreement, for cemdisiran to be used as part of a combination product, Regeneron is solely responsible for all development and commercialization costs and we will receive low double-digit royalties and commercial milestones of up to $ 325.0 million on any potential combination product sales. The C5 co-co collaboration agreement, the C5 license agreement, and the Master Agreement have been combined for accounting purposes and treated as a single agreement. In connection with the Regeneron Master Agreement, Regeneron made an upfront payment of $ 400.0 million. We are also eligible to receive up to an additional $ 200.0 million in milestone payments upon achievement of certain criteria during early clinical development for eye and CNS programs. We and Regeneron plan to advance programs directed to up to 30 targets in the first five years under the Regeneron Collaboration during the Initial Research Term. For each program, Regeneron will provide us with $ 2.5 million in funding at program initiation and an additional $ 2.5 million at lead candidate identification, with the potential for approximately $ 30.0 million in annual discovery funding to us as the Regeneron Collaboration reaches steady state. Regeneron has the right to terminate the Regeneron Master Agreement for convenience upon ninety days ’ notice. The termination of the Regeneron Master Agreement does not affect the term of any license agreement or co-co collaboration agreement then in effect. In addition, either party may terminate the Regeneron Master Agreement for a material breach by, or insolvency of, the other party. Unless earlier terminated pursuant to its terms, the Regeneron Master Agreement will remain in effect with respect to each program until (a) such program becomes a terminated program or (b) the parties enter into a license agreement or co-co collaboration agreement with respect to such program. The Regeneron Master Agreement includes various representations, warranties, covenants, dispute escalation and resolution mechanisms, indemnities and other provisions customary for transactions of this nature. For any license agreement subsequently entered into, the licensee will generally be responsible for its own costs and expenses incurred in connection with the development and commercialization of the collaboration products. The licensee will pay to the licensor certain development and/or commercialization milestone payments totaling up to $ 150.0 million for each collaboration product. In addition, following the first commercial sale of the applicable collaboration product under a license 12 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) agreement, the licensee is required to make certain tiered royalty payments, ranging from low double-digits up to 20 %, to the licensor based on the aggregate annual net sales of the collaboration product, subject to customary reductions. For any co-co collaboration agreement subsequently entered into, we and Regeneron will share equally all costs of, and profits from, development and commercialization activities. Reimbursement of our share of costs will be recognized as a reduction to research and development expense in the condensed consolidated statements of operations and comprehensive loss. In the event that a party exercises its opt-out right, the lead party will be responsible for all costs and expenses incurred in connection with the development and commercialization of the collaboration products under the applicable co-co collaboration agreement, subject to continued sharing of costs through defined points. If a party exercises its opt-out right, following the first commercial sale of the applicable collaboration product under a co-co collaboration agreement, the lead party is required to make certain tiered royalty payments, ranging from low double-digits up to 20 %, to the other party based on the aggregate annual net sales of the collaboration product and the timing of the exercise of the opt-out right, subject to customary reductions and a reduction for opt-out transition costs. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any milestone or royalty payments from Regeneron under the Regeneron Master Agreement, the C5 license agreement, or any future license agreement, or under any co-co collaboration agreement in the event we exercise our opt-out right. Our obligations under the Regeneron Collaboration include: (i) a research license and research services, collectively referred to as the Research Services Obligation; (ii) a worldwide license to cemdisiran for combination therapies, and manufacturing and supply, and development service obligations, collectively referred to as the C5 License Obligation; and (iii) development, manufacturing and commercialization activities for cemdisiran monotherapies, referred to as the C5 Co-Co Obligation. The research license is not distinct from the research services primarily as a result of Regeneron being unable to benefit on its own or with other resources reasonably available, as the license is providing access to specialized expertise, particularly as it relates to RNAi technology that is not available in the marketplace. Similarly, the worldwide license to cemdisiran for combination therapies is not distinct from the manufacturing and supply, and development service obligations, as Regeneron cannot benefit on its own from the value of the license without receipt of supply. Separately, prior to Regeneron’s decision in November 2022 to exercise its right to opt-out of the further development and commercialization of cemdisiran monotherapy, the cemdisiran monotherapy co-co collaboration agreement was under the scope of ASC 808 as we and Regeneron were both active participants in the development and manufacturing activities and were exposed to significant risks and rewards that were dependent on commercial success of the activities of the arrangement. Regeneron’s decision to exercise its right to opt-out of the arrangement caused a change in the role of Regeneron and its exposure to significant risks and rewards under the arrangement. As a result, we determined that the arrangement no longer represents a collaborative arrangement. The arrangement now represents a vendor-customer relationship under ASC 606 as we perform our obligation to provide development and manufacturing activities under the arrangement. The transaction price allocated to the C5 Co-Co obligation unit of account will be recognized over time using an input method based on cost incurred relative to the total estimated costs for the identified performance obligation by determining the proportion of effort incurred as a percentage of total effort we expect to expend. The total transaction price is comprised of the $ 400.0 million upfront payment and additional variable consideration related to research, development, manufacturing and supply activities related to the Research Services Obligation and the C5 License Obligation. We utilized the expected value method to determine the amount of reimbursement for these activities. We determined that any variable consideration related to sales-based royalties and milestones related to the worldwide license to cemdisiran for combination therapies is deemed to be constrained and therefore has been excluded from the transaction price. In addition, we are eligible to receive future milestones upon the achievement of certain criteria during early clinical development for the eye and CNS programs. We are also eligible to receive royalties on future commercial sales for certain eye, CNS or liver targets, if any; however, these amounts are excluded from variable consideration under the Regeneron Collaboration as we are only eligible to receive such amounts if, after a drug candidate is identified, the form of license agreement is subsequently executed resulting in a license that is granted to Regeneron. Any such subsequently granted license would represent a separate transaction under ASC 606. 13 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) We allocated the initial transaction price to each unit of account based on the applicable accounting guidance as follows, in thousands: Performance Obligations Standalone Selling Price Transaction Price Allocated Research Services Obligation $ 130,700 $ 183,100 C5 License Obligation 97,600 92,500 C5 Co-Co Obligation 364,600 246,000 $ 521,600 The transaction price was allocated to the obligations based on the relative estimated standalone selling prices of each obligation, over which management has applied significant judgment. We developed the estimated standalone selling price for the licenses included in the Research Services Obligation and the C5 License Obligation primarily based on the probability-weighted present value of expected future cash flows associated with each license related to each specific program. In developing such estimate, we applied judgment in the determination of the forecasted revenues, taking into consideration the applicable market conditions and relevant entity-specific factors, the expected number of targets or indications expected to be pursued under each license, the probability of success, the time needed to develop a product candidate pursuant to the associated license and the discount rate. We developed the estimated standalone selling price for the services and/or manufacturing and supply included in each of the obligations, as applicable, primarily based on the nature of the services to be performed and/or goods to be manufactured and estimates of the associated costs. The estimated standalone selling price of the C5 Co-Co Obligation was developed by estimating the present value of expected future cash flows that Regeneron is entitled to receive. In developing such estimate, we applied judgment in determining the indications that will be pursued, the forecasted revenues for such indications, the probability of success and the discount rate. For the Research Services Obligation, the C5 License Obligation, and the C5 Co-Co Obligation accounted for under ASC 606, we measure proportional performance over time using an input method based on cost incurred relative to the total estimated costs for each of the identified obligations, on a quarterly basis, by determining the proportion of effort incurred as a percentage of total effort we expect to expend. This ratio is applied to the transaction price allocated to each obligation. Management has applied significant judgment in the process of developing our estimates. Any changes to these estimates will be recognized in the period in which they change as a cumulative catch up. We re-evaluate the transaction price as of the end of each reporting period and as of March 31, 2023, the total transaction price was determined to be $ 559.6 million. Revenue recognized under this agreement is accounted for as collaboration revenue. The following tables provide a summary of the transaction price allocated to each unit of account based on the applicable accounting guidance, in addition to revenue activity during the period, in thousands: Transaction Price Allocated Deferred Revenue Performance Obligations As of March 31, 2023 As of March 31, 2023 As of December 31, 2022 Research Services Obligation $ 215,680 $ 23,000 $ 26,200 C5 License Obligation 97,900 6,000 7,000 C5 Co-Co Obligation 246,000 191,100 193,600 $ 559,580 $ 220,100 $ 226,800 Revenue Recognized During Performance Obligations Three Months Ended March 31, 2023 Three Months Ended March 31, 2022 Research Services Obligation $ 10,700 $ 7,200 C5 License Obligation 2,200 1,300 C5 Co-Co Obligation 2,500 2,300 $ 15,400 $ 10,800 As of March 31, 2023, the aggregate amount of the transaction price allocated to the remaining Research Services Obligation, C5 License Obligation and C5 Co-Co Obligation that was unsatisfied was $ 274.4 million, which is expected to be recognized through the term of the Regeneron Collaboration as the services are performed. Deferred revenue related to the Regeneron Collaboration is classified as either current or non-current in the condensed consolidated balance sheets based on the period the revenue is expected to be recognized. 14 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) Novartis AG 2013 Collaboration with The Medicines Company In February 2013, we and The Medicines Company, or MDCO, entered into a license and collaboration agreement pursuant to which we granted to MDCO an exclusive, worldwide license to develop, manufacture and commercialize RNAi therapeutics targeting proprotein convertase subtilisin/kexin type 9, or PCSK9, for the treatment of hypercholesterolemia and other human diseases, including inclisiran. We refer to this agreement, as amended through the date hereof, as the MDCO License Agreement. In 2020, Novartis AG, or Novartis, completed its acquisition of MDCO and assumed all rights and obligations under the MDCO License Agreement. Additional details regarding the terms, milestones earned upon the achievement of certain events and additional milestones we are entitled to receive upon the achievement of future events under the MDCO License Agreement are described in Note 4 of the Notes to Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2022, as filed with the Securities and Exchange Commission on February 23, 2023. Novartis License Agreement In December 2021, we and Novartis entered into a collaboration and license agreement, or the Novartis License Agreement, pursuant to which we granted to Novartis an exclusive, worldwide license to develop, manufacture and commercialize siRNAs targeting end-stage liver disease, or ESLD, potentially leading to the development of a treatment designed to promote the regrowth of functional liver cells and to provide an alternative to transplantation for patients with liver failure. Additional details regarding the terms and transaction price under the Novartis License Agreement are described in Note 4 of the Notes to Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2022, as filed with the Securities and Exchange Commission on February 23, 2023. Other In addition to the collaboration agreements discussed above, we have various other collaboration agreements that are not individually significant to our operating results or financial condition at this time. Pursuant to the terms of those agreements, we may be required to pay, or we may receive, additional amounts contingent upon the occurrence of various future events (e.g., upon the achievement of various development and commercial milestones) which in the aggregate could be significant. We may also incur, or be reimbursed for, significant research and development costs. In addition, if any products related to these collaborations are approved for sale, we may be required to pay, or we may receive, royalties on future sales. The payment or receipt of these amounts, however, is contingent upon the occurrence of various future events. 5 . LIABILITY RELATED TO THE SALE OF FUTURE ROYALTIES In April 2020, we entered into a purchase and sale agreement, or Purchase Agreement, with BX Bodyguard Royalties L.P. (an affiliate of The Blackstone Group Inc.), or Blackstone Royalties, under which Blackstone Royalties acquired 50 % of royalties payable, or Royalty Interest, with respect to net sales by MDCO, its affiliates or sublicensees of inclisiran (or the branded drug product, Leqvio) and any other licensed products under the MDCO License Agreement, and 75 % of the commercial milestone payments payable under the MDCO License Agreement, together with the Royalty Interest, the Purchased Interest. If Blackstone Royalties does not receive payments in respect of the Royalty Interest by December 31, 2029, equaling at least $ 1.00 billion, Blackstone Royalties will receive 55 % of the Royalty Interest beginning on January 1, 2030. In consideration for the sale of the Purchased Interest, Blackstone Royalties paid us $ 1.00 billion. We continue to own or control all inclisiran intellectual property rights and are responsible for certain ongoing manufacturing and supply obligations related to the generation of the Purchased Interest. Due to our continuing involvement, we will continue to account for any royalties and commercial milestones due to us under the MDCO License Agreement as revenue on our condensed consolidated statement of operations and comprehensive loss and record the proceeds from this transaction as a liability, net of closing costs, on our condensed consolidated balance sheet. In order to determine the amortization of the liability related to the sale of future royalties, we are required to estimate the total amount of future payments to Blackstone Royalties over the life of the Purchase Agreement. The $ 1.00 billion liability, recorded at execution of the agreement, will be accreted to the total of these royalty and commercial milestone payments as interest expense over the life of the Purchase Agreement. As of March 31, 2023, our estimate of this total interest expense resulted in an effective annual interest rate of 8 %. These estimates contain assumptions that impact both the amount recorded at execution and the interest expense that will be recognized in future periods. As payments are made to Blackstone Royalties, the balance of the liability will be effectively repaid over the life of the Purchase Agreement. The exact timing and amount of repayment is likely to change each reporting period. A significant increase or decrease in Leqvio global net revenue will materially impact the liability related to the sale of future royalties, interest expense and the time period for repayment. We will periodically assess the expected payments to Blackstone Royalties 15 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) and to the extent the amount or timing of such payments is materially different than our initial estimates, we will prospectively adjust the amortization of the liability related to the sale of future royalties and the related interest expense. As of March 31, 2023, the carrying value of the liability related to the sale of future royalties was $ 1.31 billion, net of closing costs of $ 10.6 million. The carrying value of the liability related to the sale of future royalties approximates fair value as of March 31, 2023 and is based on our current estimates of future royalties and commercial milestones expected to be paid to Blackstone Royalties over the life of the arrangement, which are considered Level 3 inputs. The following table shows the activity with respect to the liability related to the sale of future royalties, in thousands: Carrying value as of December 31, 2022 $ 1,292,304 Interest expense recognized 25,275 Payments ( 8,673 ) Carrying value as of March 31, 2023 $ 1,308,906 6. FAIR VALUE MEASUREMENTS The following tables present information about our financial assets and liabilities that are measured at fair value on a recurring basis and indicate the fair value hierarchy of the valuation techniques we utilized to determine such fair value: (In thousands) As of March 31, 2023 Quoted Prices in Active Markets (Level 1) Significant Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) Financial assets Cash equivalents: Money market funds $ 214,257 $ 214,257 $ — $ — Corporate notes 2,494 — 2,494 — Commercial paper 1,694 — 1,694 — Marketable debt securities: U.S. treasury securities 742,312 — 742,312 — U.S. government-sponsored enterprise securities 335,557 — 335,557 — Corporate notes 190,651 — 190,651 — Commercial paper 90,556 — 90,556 — Certificates of deposit 13,498 — 13,498 — Marketable equity securities 25,856 25,856 — — Restricted cash (money market funds) 1,200 1,200 — — Total financial assets $ 1,618,075 $ 241,313 $ 1,376,762 $ — Financial liabilities Development derivative liability $ 219,748 $ — $ — $ 219,748 16 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) (In thousands) As of December 31, 2022 Quoted Prices in Active Markets (Level 1) Significant Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) Financial assets Cash equivalents: Money market funds $ 270,394 $ 270,394 $ — $ — U.S. treasury securities 44,817 — 44,817 — U.S. government-sponsored enterprise securities 41,763 — 41,763 — Commercial paper 22,350 — 22,350 — Certificates of deposit 3,289 — 3,289 — Corporate notes 1,024 — 1,024 — Marketable debt securities: U.S. treasury securities 820,913 — 820,913 — Corporate notes 208,284 — 208,284 — U.S. government-sponsored enterprise securities 230,770 — 230,770 — Commercial paper 36,793 — 36,793 — Certificates of deposit 1,130 — 1,130 — Marketable equity securities 28,122 28,122 — — Restricted cash (money market funds) 1,197 1,197 — — Total financial assets $ 1,710,846 $ 299,713 $ 1,411,133 $ — Financial liabilities Development derivative liability $ 209,277 $ — $ — $ 209,277 The carrying amounts reflected on our condensed consolidated balance sheets for cash, accounts receivable, net, other current assets, accounts payable and accrued expenses approximate fair value due to their short-term maturities. 7. MARKETABLE DEBT SECURITIES We invest our excess cash balances in marketable debt securities and at each balance sheet date presented, we classify all of our investments in debt securities as available-for-sale and as current assets as they represent the investment of funds available for current operations. We did not record any impairment charges related to our marketable debt securities during the three months ended March 31, 2023 or 2022. The following tables summarize our marketable debt securities: As of March 31, 2023 (In thousands) Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Fair Value U.S. treasury securities $ 744,326 $ 377 $ ( 2,391 ) $ 742,312 U.S. government-sponsored enterprise securities 337,614 194 ( 2,251 ) 335,557 Corporate notes 194,419 50 ( 1,324 ) 193,145 Commercial paper 92,250 — — 92,250 Certificates of deposit 13,498 — — 13,498 Total $ 1,382,107 $ 621 $ ( 5,966 ) $ 1,376,762 17 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) As of December 31, 2022 (In thousands) Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Fair Value U.S. treasury securities $ 870,033 $ 79 $ ( 4,382 ) $ 865,730 U.S. government-sponsored enterprise securities 275,610 24 ( 3,101 ) 272,533 Corporate notes 211,398 16 ( 2,106 ) 209,308 Commercial paper 59,143 — — 59,143 Certificates of deposit 4,419 — — 4,419 Total $ 1,420,603 $ 119 $ ( 9,589 ) $ 1,411,133 The fair values of our marketable debt securities by classification in the condensed consolidated balance sheets were as follows: (In thousands) As of March 31, 2023 As of December 31, 2022 Marketable debt securities $ 1,372,574 $ 1,297,890 Cash and cash equivalents 4,188 113,243 Total $ 1,376,762 $ 1,411,133 8. OTHER BALANCE SHEET DETAILS Inventory The components of inventory are summarized as follows: (In thousands) As of March 31, 2023 As of December 31, 2022 Raw materials $ 22,875 $ 22,315 Work in progress 110,976 113,783 Finished goods 29,534 25,606 Total $ 163,385 $ 161,704 As of March 31, 2023 and December 31, 2022, we had $ 31.5 million and $ 32.7 million of long-term inventory, respectively, included within other assets in our condensed consolidated balance sheet as we anticipate it being consumed beyond our normal operating cycle. Cash, Cash Equivalents and Restricted Cash The following table provides a reconciliation of cash, cash equivalents and restricted cash reported within our condensed consolidated balance sheets that sum to the total of these amounts shown in the condensed consolidated statements of cash flows: As of March 31, (In thousands) 2023 2022 Cash and cash equivalents $ 672,245 $ 534,081 Total restricted cash included in other assets 2,166 2,178 Total cash, cash equivalents, and restricted cash shown in the condensed consolidated statements of cash flows $ 674,411 $ 536,259 18 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) Accumulated Other Comprehensive (Loss) Income The following tables summarize the changes in accumulated other comprehensive (loss) income, by component: (In thousands) Loss on Investment in Joint Venture Defined Benefit Pension Plans Unrealized (Losses) Gains from Debt Securities Foreign Currency Translation Adjustment Total Accumulated Other Comprehensive (Loss) Income Balance as of December 31, 2022 $ ( 32,792 ) $ ( 1,092 ) $ ( 9,470 ) $ ( 1,300 ) $ ( 44,654 ) Other comprehensive (loss) income before reclassifications — — ( 9 ) 1,410 1,401 Amounts reclassified from other comprehensive income (loss) — ( 5 ) 4,134 — 4,129 Net other comprehensive (loss) income — ( 5 ) 4,125 1,410 5,530 Balance as of March 31, 2023 $ ( 32,792 ) $ ( 1,097 ) $ ( 5,345 ) $ 110 $ ( 39,124 ) (In thousands) Loss on Investment in Joint Venture Defined Benefit Pension Plans Unrealized (Losses) Gains from Debt Securities Foreign Currency Translation Adjustment Total Accumulated Other Comprehensive (Loss) Income Balance as of December 31, 2021 $ ( 32,792 ) $ ( 2,811 ) $ ( 1,630 ) $ 3,974 $ ( 33,259 ) Other comprehensive income before reclassifications — — 1 2,376 2,377 Amounts reclassified from other comprehensive income (loss) — 35 ( 7,218 ) — ( 7,183 ) Net other comprehensive income (loss) — 35 ( 7,217 ) 2,376 ( 4,806 ) Balance as of March 31, 2022 $ ( 32,792 ) $ ( 2,776 ) $ ( 8,847 ) $ 6,350 $ ( 38,065 ) Amounts reclassified out of accumulated other comprehensive loss relate to settlements of marketable equity securities and amortization of our pension obligation which are recorded as other income in the condensed consolidated statements of operations and comprehensive loss. 9. CONVERTIBLE DEBT Convertible Senior Notes Due 2027 On September 12, 2022, we commenced a private offering of $ 900.0 million in aggregate principal amount of 1 % Convertible Senior Notes due 2027, or the Initial Notes. On September 13, 2022, the initial purchasers in such offering exercised their option to purchase an additional $ 135.0 million in aggregate principal amount of our 1 % Convertible Senior Notes due 2027, or the Additional Notes, and together with the Initial Notes collectively referred to as the Notes, bringing the total aggregate principal amount of the Notes to $ 1.04 billion. The Notes were issued pursuant to an indenture, dated September 15, 2022, or the Indenture. The Indenture includes customary covenants and sets forth certain events of default after which the Notes may be declared immediately due and payable and sets forth certain types of bankruptcy or insolvency events of default involving the Company after which the Notes become automatically due and payable. The Notes will mature on September 15, 2027, unless earlier converted, redeemed or repurchased. The Notes will bear interest from September 15, 2022 at a rate of 1 % per year payable semiannually in arrears on March 15 and September 15 of each year, beginning on March 15, 2023. The Notes are convertible at the option of the noteholder on or after June 15, 2027. Prior to June 15, 2027, the Notes are convertible only under the following circumstances: (1) During any calendar quarter commencing after the calendar quarter ending on December 31, 2022 (and only during such calendar quarter), if the last reported sale price of our common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on, and including, the last trading day of the immediately preceding calendar quarter is greater than or equal to 130 % of the conversion price on each applicable trading day; (2) During the five business day period after any ten consecutive trading day period in which the trading price per $1,000 principal amount of the Notes for each trading day of that ten consecutive trading day period was less than 98 % of the product of the last reported sale price of our common stock and the conversion rate of the Notes on such trading day; (3) If we call any or all of the Notes for redemption; or (4) Upon the occurrence of specific corporate events as set forth in the Indenture governing the Notes. We will settle any conversions of Notes by paying or delivering, as applicable, cash, shares of our common stock, or a combination of cash and shares of common stock, at our election. 19 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) The conversion rate for the Notes will initially be 3.4941 shares of common stock per $1,000 principal amount of Notes, which is equivalent to an initial conversion price of approximately $ 286.20 per share of common stock. The initial conversion price of the Notes represents a premium of approximately 35 % over the $ 212.00 per share last reported sale price of common stock on September 12, 2022. The conversion rate is subject to adjustment under certain circumstances in accordance with the terms of the Indenture. We may not redeem the Notes prior to September 20, 2025. We may redeem for cash equal to 100% of the principal amount of the Notes being redeemed plus accrued and unpaid interest of all or any portion of the Notes, at our option, on or after September 20, 2025, if the last reported sales price of our common stock has been at least 130 % of the conversion price then in effect for at least 20 trading days (whether or not consecutive) during any 30 consecutive trading day period. No sinking fund is provided for the Notes and therefore we are not required to redeem or retire the Notes periodically. If we undergo a fundamental change, as defined in the indenture agreement, then subject to certain conditions, holders may require us to repurchase for cash all or any portion of their Notes at a fundamental change repurchase price equal to 100% of the principal amount of the Notes to be repurchased plus accrued and unpaid interest. In addition, if specific corporate events occur prior to the maturity date or if we issue a notice of redemption, we will increase the conversion rate by pre-defined amounts for holders who elect to convert their notes in connection with such corporate event. The conditions allowing holders of the Notes to convert were not met this quarter. As of March 31, 2023, the Notes are classified as a long-term liability, net of issuance costs of $ 19.2 million, on the condensed consolidated balance sheets. As of March 31, 2023, the estimated fair value of the Notes was approximately $ 1.03 billion. The fair value was determined based on the last actively traded price per $100 of the Notes for the three months ended March 31, 2023 (Level 2). The Notes were issued at par and costs associated with the issuance of the Notes are amortized to interest expense over the contractual term of the Notes. As of March 31, 2023, the effective interest rate of the Notes is 1 %. Capped Call Transactions In September 2022, in connection with the pricing of the Initial Notes and the initial purchasers’ exercise of their option to purchase the Additional Notes, we entered into privately negotiated capped call transactions, or Capped Call Transactions. The Capped Call Transactions initially cover, subject to customary anti-dilution adjustments, the number of shares of common stock that underlie the Notes. The cap price of the Capped Call Transactions is initially $ 424.00 per share, which represents a premium of 100 % over the last reported sale price of common stock of $ 212.00 per share on September 12, 2022, and is subject to certain adjustments under the terms of the Capped Call Transactions. We used approximately $ 118.6 million of the proceeds from the offering of Notes to pay the cost of the Capped Call Transactions. We evaluated the Capped Call Transactions and determined that they should be accounted for separately from the Notes. The cost of $ 118.6 million to purchase the Capped Call Transactions was recorded as a reduction to additional paid-in capital in the condensed consolidated balance sheet as of March 31, 2023 as the Capped Call Transactions are indexed to our own stock and met the criteria to be classified in stockholders' equity. 10. DEVELOPMENT DERIVATIVE LIABILITY In August 2020, we entered into a co-development agreement, referred to as the Funding Agreement, with BXLS V Bodyguard – PCP L.P. and BXLS Family Investment Partnership V – ESC L.P., collectively referred to as Blackstone Life Sciences, pursuant to which Blackstone Life Sciences will provide up to $ 150.0 million in funding for the clinical development of vutrisiran and zilebesiran, two of our cardiometabolic programs. With respect to vutrisiran, Blackstone Life Sciences has committed to provide up to $ 70.0 million to fund development costs related to the HELIOS-B Phase 3 clinical trial. In November 2021, Blackstone Life Sciences opted in to Phase 2 clinical trial funding of zilebesiran, committing to fund, upon meeting certain patient enrollment thresholds, up to $ 26.0 million. Furthermore, Blackstone Life Sciences has the right, but is not obligated, to fund up to $ 54.0 million for development costs related to a Phase 3 clinical trial of zilebesiran. The amount of funding ultimately provided by Blackstone Life Sciences is dependent on us achieving specified development milestones with respect to each clinical trial. We retain sole responsibility for the development and commercialization of both vutrisiran and zilebesiran. As consideration for Blackstone Life Sciences’ funding for vutrisiran clinical development costs, we have agreed to pay Blackstone Life Sciences a 1 % royalty on net sales of AMVUTTRA (vutrisiran) for a 10 -year term beginning upon the first commercial sale following regulatory approval of vutrisiran for ATTR-cardiomyopathy, as well as fixed payments of up to 2.5 times their investment over a two-year period upon regulatory approval of vutrisiran for ATTR-cardiomyopathy in specified countries, unless it is later withdrawn from the market following a mandatory recall. As consideration for Blackstone Life Sciences’ funding for Phase 2 clinical development costs of zilebesiran, we have agreed to pay Blackstone Life Sciences fixed payments of up to 3.25 times their Phase 2 investment over a four-year period upon the successful completion of the zilebesiran Phase 2 clinical trial, unless certain regulatory events affecting the continued development of zilebesiran occur. As 20 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) consideration for Blackstone Life Sciences’ funding for Phase 3 clinical development costs of zilebesiran, we have agreed to pay Blackstone Life Sciences fixed payments of up to 4.5 times their Phase 3 investment over a four-year period upon regulatory approval of zilebesiran in specified countries, unless it is later withdrawn from the market following a mandatory recall. Our payment obligations under the Funding Agreement will be secured, subject to certain exceptions, by security interests in intellectual property owned by us relating to vutrisiran and zilebesiran, as well as in our bank account in which the funding deposits will be made. We and Blackstone Life Sciences each have the right to terminate the Funding Agreement in its entirety in the event of the other party’s bankruptcy or similar proceedings. We and Blackstone Life Sciences may each terminate the Funding Agreement in its entirety or with respect to either product in the event of an uncured material breach by the other party, or with respect to a product for certain patient health and safety reasons, or if regulatory approval in specified major market countries is not obtained for the product following the completion of clinical trials for the product. In addition, Blackstone Life Sciences has the right to terminate the Funding Agreement in its entirety upon the occurrence of certain events affecting our ability to make payments under the agreement or to develop or commercialize the products, or upon a change of control of us. Blackstone Life Sciences may also terminate the Funding Agreement with respect to a product if the joint steering committee elects to terminate the development program for that product in its entirety, if certain clinical endpoints are not achieved for that product or, with respect to vutrisiran only, if our right to develop or commercialize vutrisiran is enjoined in a specified major market as a result of an alleged patent infringement. In certain termination circumstances, we will be obligated to pay Blackstone Life Sciences an amount that is equal to, or a multiplier of, the development funding received from Blackstone Life Sciences, and we may remain obligated under certain circumstances to make the payments to Blackstone Life Sciences described above, or the royalty described above in the case of AMVUTTRA, should we obtain regulatory approval for zilebesiran or vutrisiran for ATTR-cardiomyopathy following termination. We account for the Funding Agreement under ASC Topic 815, Derivatives and Hedging, as a derivative liability, measured at fair value, within other liabilities on our condensed consolidated balance sheets. The change in fair value due to the remeasurement of the development derivative liability is recorded as other expense on our condensed consolidated statements of operations and comprehensive loss. As of March 31, 2023, the derivative liability is classified as a Level 3 financial liability in the fair value hierarchy. The valuation method incorporates certain unobservable Level 3 key inputs including (i) the probability and timing of achieving stated development milestones to receive payments from Blackstone Life Sciences, (ii) the probability and timing of achieving regulatory approval and payments to Blackstone Life Sciences, (iii) an estimate of the amount and timing of the royalty payable on net sales of AMVUTTRA, assuming regulatory approval for ATTR-cardiomyopathy, (iv) our cost of borrowing ( 12 %), and (v) Blackstone Life Sciences' cost of borrowing ( 4 %). The following table presents the activity with respect to the development derivative liability, in thousands: Carrying value as of December 31, 2022 $ 209,277 Amount received under the Funding Agreement 4,000 Loss recorded from remeasurement 6,471 Carrying value as of March 31, 2023 $ 219,748 11. STOCK-BASED COMPENSATION The following table summarizes stock-based compensation expenses included in operating costs and expenses: Three Months Ended March 31, (In thousands) 2023 2022 Research and development $ 16,232 $ 11,617 Selling, general and administrative 23,715 17,676 Total $ 39,947 $ 29,293 12. NET LOSS PER COMMON SHARE We compute basic net loss per common share by dividing net loss by the weighted-average number of common shares outstanding. We compute diluted net loss per common share by dividing net loss by the weighted-average number of common 21 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) shares and dilutive potential common share equivalents then outstanding during the period. In the diluted net loss per share calculation, net loss would be adjusted for the elimination of interest expense on the Convertible debt. Potential common shares consist of shares issuable upon the vesting of restricted stock units, the exercise of stock options (the proceeds of which are then assumed to have been used to repurchase outstanding shares using the treasury stock method) and upon conversion of the convertible debt outstanding during the period (calculated using the if-converted method assuming the conversion of the convertible debt as of the earliest period reported or at the date of issuance, if later). Because the inclusion of potential common shares would be anti-dilutive for all periods presented, diluted net loss per common share is the same as basic net loss per common share. The following table sets forth the potential common shares (prior to consideration of the treasury stock or if-converted methods) excluded from the calculation of net loss per common share because their inclusion would be anti-dilutive: As of March 31, (In thousands) 2023 2022 Options to purchase common stock, inclusive of performance-based stock options 8,428 12,785 Unvested restricted stock units, inclusive of performance-based restricted stock units 2,547 1,918 Convertible debt 3,616 — Total 14,591 14,703 13. COMMITMENTS AND CONTINGENCIES Technology License and Other Commitments We have licensed from third parties the rights to use certain technologies and information in our research processes as well as in any other products we may develop. In accordance with the related license or technology agreements, we are required to make certain fixed payments to the licensor or a designee of the licensor over various agreement terms. Many of these agreement terms are consistent with the remaining lives of the underlying intellectual property that we have licensed. As of March 31, 2023, our commitments over the next five years to make fixed and cancellable payments under existing license agreements were not material. Legal Matters From time to time, we may be a party to litigation, arbitration or other legal proceedings in the course of our business, including the matters described below. The claims and legal proceedings in which we could be involved include challenges to the scope, validity or enforceability of patents relating to our products or product candidates, and challenges by us to the scope, validity or enforceability of the patents held by others. These include claims by third parties that we infringe their patents or breach our license or other agreements with such third parties. The outcome of any such legal proceedings, regardless of the merits, is inherently uncertain. In addition, litigation and related matters are costly and may divert the attention of our management and other resources that would otherwise be engaged in other activities. If we were unable to prevail in any such legal proceedings, our business, results of operations, liquidity and financial condition could be adversely affected. Our accounting policy for accrual of legal costs is to recognize such expenses as incurred. Government Investigation We have previously disclosed that, on or about April 9, 2021, we received a subpoena from the U.S. Department of Justice, U.S. Attorney’s Office for the District of Massachusetts, requiring production of documents pertaining to our marketing and promotion of ONPATTRO (patisiran) in the U.S. We are cooperating with the U.S. Attorney’s Office and producing documents in response to the subpoena. Current and former officers and employees also have received subpoenas in connection with the preservation and production of related materials. Given the ongoing nature of the investigation, it is possible that the U.S. Attorney’s Office for the District of Massachusetts or other government entities may request other information from, or issue other subpoenas, findings or similar documents to, us, our related entities and their respective directors, officers and employees. In light of the ongoing nature of the investigation, no determination has been made that a loss, if any, arising from this matter is probable or that the amount of any such loss, or range of loss, is reasonably estimable. We also previously disclosed that since learning of this federal government investigation, our nominating and corporate governance committee is directing our review of and response to the matter. Patent Infringement Lawsuits In March 2022, we filed separate lawsuits in the U.S. District Court for the District of Delaware against (1) Pfizer, Inc. and its subsidiary Pharmacia & Upjohn Co. LLC, collectively referred to as Pfizer, and (2) Moderna, Inc., and its subsidiaries 22 Table of Contents ALNYLAM PHARMACEUTICALS, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) ModernaTX, Inc., and Moderna US, Inc., collectively referred to as Moderna. The lawsuits seek damages for infringement of U.S. Patent No. 11,246,933, or ‘933 Patent, in Pfizer’s and Moderna’s manufacture and sale of their messenger RNA, or mRNA, COVID-19 vaccines. The patent relates to the Company’s biodegradable cationic lipids that are foundational to the success of the mRNA COVID-19 vaccines. We are seeking judgment that each of Pfizer and Moderna is infringing the ‘933 Patent, as well as damages adequate to compensate for the infringement, but in no event less than a reasonable royalty for the unlicensed uses made of our patented lipids by Pfizer and Moderna, together with interest and costs as may be awarded by the court. As stated in the filed complaints, we are not seeking injunctive relief in these lawsuits. On May 23, 2022, Moderna filed a partial motion to dismiss, asserting an affirmative defense under Section 1498(a). We responded on May 27, 2022, opposing their motion arguing Moderna had significant non-government sales and the government contract ended in April 2022. Moderna responded on June 13, 2022, requesting a partial motion to dismiss those claims for sales under 1498(a). On May 27, 2022, Pfizer filed an answer to our complaint, denying the allegations, and asserting invalidity and non-infringement defenses. In addition, Pfizer added BioNTech SE to the suit and added counter-claims seeking a declaratory judgment that our patent is invalid and a second claim alleging that our patent is invalid due to patent misuse. We believe their defenses and counter-claims have no merit and responded on June 10, 2022, with substantive arguments as to the validity of our claims and the lack of merit of their patent misuse claim. On July 12, 2022, we filed a new lawsuit against each of Pfizer and Moderna seeking damages for infringing our newly granted U.S. Patent No. 11,382,979 in Pfizer’s and Moderna’s manufacture and sale of their mRNA COVID-19 vaccines. The parties agreed to combine the two patents in one lawsuit, separately against each of Moderna and Pfizer/BioNTech. On February 8, 2023, we received notification from the U.S. Patent Office that a third patent would issue on February 28, 2023, as U.S. Patent No. 11,590,229, which we also believe Pfizer and Moderna’s COVID-19 vaccines infringe upon. On February 15, 2023, we filed a motion with the court to add this patent to the existing cases against Pfizer and Moderna. On April 26, 2023, the court held a hearing and denied Moderna’s partial motion to dismiss those claims for sales under 1498(2), our motion to add the 11,590,229 patent to the current lawsuits as well as a motion filed by Moderna to add certain invalidity arguments made by Pfizer in our case to supplement Moderna’s invalidity arguments previously made. The court has set a trial date of November 12, 2024, for Alnylam v. Moderna and November 18, 2024, for Alnylam v. Pfizer/BioNTech. Indemnifications In connection with license agreements we may enter with companies to obtain rights to intellectual property, we may be required to indemnify such companies for certain damages arising in connection with the intellectual property rights licensed under the agreements. Under such agreements, we may be responsible for paying the costs of any litigation relating to the license agreements or the underlying intellectual property rights, including the costs associated with certain litigation regarding the licensed intellectual property. We are also a party to a number of agreements entered into in the ordinary course of business, which contain typical provisions that obligate us to indemnify the other parties to such agreements upon the occurrence of certain events, including litigation or other legal proceedings. In addition, we have agreed to indemnify our officers and directors for expenses, judgments, fines, penalties, excise taxes, and settlement amounts paid in connection with any threatened, pending or completed litigation proceedings, including, for example, the current government investigation, in which an officer or director was, is or will be involved as a party, on account of such person’s status as an officer or director, or by reason of any action taken by the officer or director while acting in such capacity, subject to certain limitations. These indemnification costs are charged to selling, general and administrative expense. Our maximum potential future liability under any such indemnification provisions is uncertain. We have determined that the estimated aggregate fair value of our potential liabilities under all such indemnification provisions is minimal and had not recorded any liability related to such indemnification provisions as of March 31, 2023. 23 Table of Contents