RHYTHM PHARMACEUTICALS, INC. 10-Q

Item 1. Financial Statements Rhythm Pharmaceuticals, Inc. Condensed Consolidated Balance Sheets (in thousands, except share and per share data) (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ 2024 2023 ​ ​ ​ ​ ​ ​ ​ Assets ​ ​ ​ ​ ​ ​ Current assets: ​ ​ Cash and cash equivalents ​ $ 53,428 ​ $ 60,081 Short-term investments ​ 147,771 ​ 215,765 Accounts receivable, net ​ ​ 14,695 ​ ​ 14,867 Inventory ​ ​ 8,507 ​ ​ 8,624 Prepaid expenses and other current assets ​ 11,352 ​ 8,931 Total current assets ​ 235,753 ​ 308,268 Property and equipment, net ​ 1,149 ​ 1,341 Right-of-use asset ​ ​ 670 ​ ​ 781 Intangible assets, net ​ ​ 6,815 ​ ​ 7,028 Restricted cash ​ 460 ​ 328 Other long-term assets ​ ​ 13,804 ​ ​ 14,999 Total assets ​ $ 258,651 ​ $ 332,745 Liabilities and stockholders’ equity ​ ​ Current liabilities: ​ ​ Accounts payable ​ $ 7,550 ​ $ 4,885 Accrued expenses and other current liabilities ​ 44,531 ​ 48,262 Deferred revenue ​ ​ 1,286 ​ ​ 1,286 Lease liability ​ 793 ​ 770 Total current liabilities ​ 54,160 ​ 55,203 Long-term liabilities: ​ ​ Deferred royalty obligation ​ ​ 107,368 ​ ​ 106,143 Lease liability, non-current ​ 284 ​ 490 Derivative liability ​ ​ 660 ​ ​ 1,150 Other long-term liabilities ​ ​ 34,598 ​ ​ — Total liabilities ​ 197,070 ​ 162,986 Commitments and contingencies (Note 14) ​ ​ ​ ​ ​ ​ Stockholders’ equity: ​ ​ Preferred Stock, $ 0.001 par value: 10,000,000 shares authorized; no shares issued and outstanding at March 31, 2024 and December 31, 2023 ​ — ​ — Common stock, $ 0.001 par value: 120,000,000 shares authorized; 60,964,468 and 59,426,559 shares issued and outstanding at March 31, 2024 and December 31, 2023, respectively ​ 60 ​ 59 Additional paid-in capital ​ ​ 1,097,810 ​ ​ 1,064,302 Accumulated other comprehensive income (loss) ​ ​ ( 181 ) ​ ​ 134 Accumulated deficit ​ ( 1,036,108 ) ​ ( 894,736 ) Total stockholders’ equity ​ 61,581 ​ 169,759 Total liabilities and stockholders’ equity ​ $ 258,651 ​ $ 332,745 ​ ​ ​ ​ ​ ​ ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ 3 Table of Contents Rhythm Pharmaceuticals, Inc. Condensed Consolidated Statements of Operations and Comprehensive Loss (in thousands, except share and per share data) (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ 2024 2023 Revenues: ​ ​ ​ ​ ​ ​ ​ Product revenue, net ​ ​ $ 25,967 ​ $ 11,469 Total revenues ​ ​ ​ 25,967 ​ ​ 11,469 Costs and expenses: ​ ​ ​ ​ ​ ​ ​ Cost of sales ​ ​ ​ 2,807 ​ ​ 1,421 Research and development ​ ​ ​ 128,665 ​ ​ 37,945 Selling, general, and administrative ​ ​ 34,382 ​ 24,634 Total costs and expenses ​ ​ 165,854 ​ 64,000 Loss from operations ​ ​ ( 139,887 ) ​ ( 52,531 ) Other (expense) income: ​ ​ ​ Other income (expense), net ​ ​ 524 ​ ( 27 ) Interest expense ​ ​ ​ ( 4,755 ) ​ ​ ( 3,061 ) Interest income ​ ​ 3,046 ​ 3,440 Total other (expense) income, net ​ ​ ( 1,185 ) ​ 352 Loss before income taxes ​ ​ ​ ( 141,072 ) ​ ​ ( 52,179 ) Provision for income taxes ​ ​ ​ 300 ​ ​ — Net loss ​ ​ $ ( 141,372 ) ​ $ ( 52,179 ) Net loss per share, basic and diluted ​ ​ $ ( 2.35 ) ​ $ ( 0.92 ) Weighted-average common shares outstanding, basic and diluted ​ ​ ​ 60,143,558 ​ ​ 56,708,975 ​ ​ ​ ​ ​ ​ ​ ​ Other comprehensive loss: ​ ​ ​ ​ ​ ​ ​ Net loss ​ ​ $ ( 141,372 ) ​ $ ( 52,179 ) Foreign currency translation adjustment ​ ​ ​ ( 71 ) ​ ​ 21 Unrealized gain (loss), net on marketable securities ​ ​ ( 244 ) ​ 65 Comprehensive loss ​ ​ $ ( 141,687 ) ​ $ ( 52,093 ) The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ ​ 4 Table of Contents Rhythm Pharmaceuticals, Inc. Condensed Consolidated Statements of Stockholders’ Equity (in thousands, except share data) (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ Other ​ ​ ​ ​ Total ​ ​ Common Stock ​ Paid-In ​ Comprehensive ​ Accumulated ​ Stockholders’ ​ Shares Amount Capital Income (Loss) ​ Deficit Equity Balance at December 31, 2023 59,426,559 ​ $ 59 $ 1,064,302 $ 134 ​ $ ( 894,736 ) $ 169,759 Stock-based compensation expense ​ — ​ ​ — ​ ​ 7,767 ​ ​ — ​ ​ — ​ ​ 7,767 Issuance of common stock in connection with ESPP ​ 28,495 ​ ​ — ​ ​ 673 ​ ​ — ​ ​ — ​ ​ 673 Issuance of common stock in connection with exercise of stock options and vesting of restricted stock units ​ 1,077,271 ​ ​ 1 ​ ​ 6,352 ​ ​ — ​ ​ — ​ ​ 6,353 Issuance of common stock as consideration for LGC license ​ 432,143 ​ ​ — ​ ​ 18,716 ​ ​ — ​ ​ — ​ ​ 18,716 Foreign currency translation adjustment ​ — ​ ​ — ​ ​ — ​ ​ ( 71 ) ​ ​ — ​ ​ ( 71 ) Unrealized loss on marketable securities ​ — ​ ​ — ​ ​ — ​ ​ ( 244 ) ​ ​ — ​ ​ ( 244 ) Net loss ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 141,372 ) ​ ​ ( 141,372 ) Balance at March 31, 2024 ​ 60,964,468 ​ $ 60 $ 1,097,810 $ ( 181 ) ​ $ ( 1,036,108 ) $ 61,581 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2022 56,612,429 ​ $ 56 $ 974,356 $ ( 92 ) ​ $ ( 710,058 ) $ 264,262 Stock-based compensation expense ​ — ​ — ​ ​ 6,376 ​ ​ — ​ ​ — ​ 6,376 Issuance of common stock in connection with ESPP ​ 32,169 ​ ​ — ​ ​ 665 ​ ​ — ​ ​ — ​ ​ 665 Issuance of common stock in connection with exercise of stock options and vesting of restricted stock units ​ 207,806 ​ ​ — ​ ​ 553 ​ ​ — ​ ​ — ​ ​ 553 Foreign currency translation adjustment ​ — ​ ​ — ​ ​ — ​ ​ 21 ​ ​ — ​ ​ 21 Net unrealized gains on short-term investments — ​ ​ — ​ ​ — ​ ​ 65 ​ ​ — ​ 65 Net loss — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 52,179 ) ​ ( 52,179 ) Balance at March 31, 2023 ​ 56,852,404 ​ $ 56 ​ $ 981,950 ​ $ ( 6 ) ​ $ ( 762,237 ) ​ $ 219,763 The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. 5 Table of Contents Rhythm Pharmaceuticals, Inc. Condensed Consolidated Statements of Cash Flows (in thousands) (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ 2024 2023 Operating activities ​ ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 141,372 ) ​ $ ( 52,179 ) ​ Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ Stock-based compensation expense ​ 7,767 ​ 6,376 ​ Depreciation and amortization ​ 405 ​ 457 ​ Non-cash interest expense and amortization of debt issuance costs ​ ​ 4,009 ​ ​ 3,061 ​ Non-cash accretion & amortization of short-term investments ​ ​ ( 2,055 ) ​ ​ ( 2,341 ) ​ Unrealized loss on short-term investments ​ ​ ( 244 ) ​ ​ — ​ Non-cash accretion of non-current liability ​ ​ 929 ​ ​ — ​ Non-cash rent expense ​ 111 ​ 94 ​ Change in fair value of embedded derivative liability ​ ​ ( 490 ) ​ ​ ( 50 ) ​ Acquired IPR&D assets classified as investing activities ​ ​ 92,385 ​ ​ 5,395 ​ Changes in operating assets and liabilities: ​ ​ ​ ​ ​ Accounts receivable ​ ​ 172 ​ ​ ( 1,893 ) ​ Inventory ​ ​ 117 ​ ​ ( 2,570 ) ​ Prepaid expenses and other current assets ​ ( 2,421 ) ​ 2,155 ​ Deferred revenue ​ ​ — ​ ​ ( 6 ) ​ Other long-term assets, net ​ 1,195 ​ ( 99 ) ​ Accounts payable, accrued expenses and other liabilities ​ ( 1,251 ) ​ 5,167 ​ Net cash used in operating activities ​ ( 40,743 ) ​ ( 36,433 ) ​ Investing activities ​ ​ ​ Purchases of short-term investments ​ — ​ ( 69,644 ) ​ Maturities of short-term investments ​ 70,050 ​ 92,675 ​ Acquisition of IPR&D assets ​ ​ ( 40,000 ) ​ ​ ( 4,520 ) ​ Purchases of property and equipment ​ — ​ ( 47 ) ​ Net cash provided by investing activities ​ 30,050 ​ 18,464 ​ Financing activities ​ ​ ​ Repayment of deferred royalty obligation ​ ​ ( 2,783 ) ​ ​ ( 1,351 ) ​ Proceeds from the exercise of stock options ​ 6,353 ​ 553 ​ Proceeds from issuance of common stock from ESPP ​ 673 ​ 665 ​ Net cash provided by (used in) financing activities ​ 4,243 ​ ( 133 ) ​ Effect of exchange rates on cash ​ ​ ( 71 ) ​ ​ 86 ​ Net decrease in cash, cash equivalents and restricted cash ​ ( 6,521 ) ​ ( 18,016 ) ​ Cash, cash equivalents and restricted cash at beginning of period ​ 60,409 ​ 128,005 ​ Cash, cash equivalents and restricted cash at end of period ​ $ 53,888 ​ $ 109,989 ​ Supplemental disclosure of non-cash investing activities: ​ ​ ​ ​ ​ ​ ​ Non-current liability issued in exchange for the acquisition of IPR&D ​ $ 33,669 ​ $ — ​ Issuance of common stock in exchange for IPR&D ​ $ 18,716 ​ $ — ​ ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ 6 Table of Contents Rhythm Pharmaceuticals, Inc. Notes to Unaudited Condensed Consolidated Financial Statements (In thousands, except share and per share information) 1. Nature of Business Rhythm Pharmaceuticals, Inc. (the “Company” or “we”) is a global, commercial-stage biopharmaceutical company dedicated to transforming the lives of patients and their families living with rare neuroendocrine diseases. We are focused on advancing our melanocortin-4 receptor agonists, including our lead asset, IMCIVREE ® (setmelanotide), as a precision medicine designed to treat hyperphagia and severe obesity caused by MC4R pathway diseases. While obesity affects hundreds of millions of people worldwide, we are developing therapies for a subset of individuals who have hyperphagia, a pathological hunger that leads to abnormal food-seeking behaviors, and severe obesity due to an impaired MC4R pathway, which may be caused by traumatic injury or genetic variants. The MC4R pathway is an endocrine pathway in the brain that is responsible for regulating hunger, caloric intake and energy expenditure, which consequently affect body weight. IMCIVREE, an MC4R agonist for which we hold worldwide rights, is the first-ever therapy developed for patients with certain rare diseases that is approved or authorized in the United States, European Union, and Great Britain, Canada, and other countries and regions. The Company is a Delaware corporation organized in February 2013 under the name Rhythm Metabolic, Inc., and as of October 2015, under the name Rhythm Pharmaceuticals, Inc. The Company has wholly owned subsidiaries in the US, Ireland, the United Kingdom, the Netherlands, France, Germany, Italy, Spain and Canada. The Company is subject to risks and uncertainties common to commercial-stage companies in the biotechnology industry, including but not limited to, risks associated with the commercialization of approved products, completing preclinical studies and clinical trials, receiving regulatory approvals for product candidates, development by competitors of new biopharmaceutical products, dependence on key personnel, protection of proprietary technology, compliance with government regulations and the ability to secure additional capital to fund operations. Commercialization of approved products will require significant resources and in order to market IMCIVREE, the Company must continue to build its sales, marketing, managerial and other non-technical capabilities or make arrangements with third parties to perform these services. Product candidates currently under development will require significant additional research and development efforts, including preclinical and clinical testing and regulatory approval, prior to commercialization. These efforts require significant amounts of additional capital, adequate personnel and infrastructure and extensive compliance-reporting capabilities. Even though the Company has an approved product, and even if the Company’s further product development efforts are successful, it is uncertain when, if ever, the Company will realize sufficient revenue from product sales to fund operations. Liquidity The Company has incurred operating losses and negative cash flows from operations since inception. As of March 31, 2024, the Company had an accumulated deficit of $ 1,036,108 . The Company has primarily funded these losses through the proceeds from the sales of common and preferred stock, asset sales, royalty financing, out-license arrangements, as well as capital contributions received from the former parent company, Rhythm Holdings LLC. While the Company is generating product revenue, management expects operating losses to continue for the foreseeable future. The Company has devoted substantially all of its resources to its drug development efforts, comprising of research and development, the acquisition of in process research and development assets, manufacturing, conducting clinical trials for its product candidates, protecting its intellectual property, commercialization activities and general and administrative functions relating to these operations. The future success of the Company is dependent on its ability to develop its product candidates and ultimately upon its ability to attain profitable operations. At March 31, 2024, the Company had $ 201,199 of cash and cash equivalents and short-term investments on hand. On April 1, 2024, the Company entered into an Investment Agreement (the “Investment Agreement”) with certain affiliates of Perceptive Advisors LLC (“Perceptive”) and certain other investors (each, an “Investor” and collectively, the 7 Table of Contents “Investors”), relating to the issuance and sale of 150,000 shares of a new series of the Company’s Series A Convertible Preferred Stock, par value $ 0.001 per share, titled the “Series A Convertible Preferred Stock” (the “Convertible Preferred Stock”), for an aggregate purchase price of $ 150,000 , or $ 1,000 per share (the “Issuance”). The Issuance closed on April 15, 2024. In the future, the Company will be dependent on obtaining funding from third parties, such as proceeds from the issuance of debt, sale of equity, proceeds from out license arrangements, product sales and funded research and development programs to maintain the Company's operations and meet the Company's obligations. There is no guarantee that additional equity or other financings will be available to the Company on acceptable terms, or at all. If the Company fails to obtain additional funding when needed, the Company would be forced to scale back, terminate its operations or seek to merge with or be acquired by another company. Management believes that the Company's existing cash resources, together with the proceeds received from the sale of preferred stock in April 2024, will be sufficient to fund the Company’s operations through at least the next twelve months from the filing of this Quarterly Report on Form 10-Q with the SEC . 2. Summary of Significant Accounting Policies Basis of Presentation The Company's unaudited condensed consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States, or GAAP, and the applicable rules and regulations of the Securities and Exchange Commission, or SEC, regarding interim financial reporting. Any reference in these notes to applicable guidance is meant to refer to the authoritative United States generally accepted accounting principles as found in the Accounting Standards Codification, or ASC, and Accounting Standards Updates, or ASU, of the Financial Accounting Standards Board, or FASB. As permitted under these rules, certain footnotes or other financial information that are normally required by GAAP have been condensed or omitted. The accompanying condensed consolidated balance sheet as of March 31, 2024, the condensed consolidated statements of operations and comprehensive loss for the three months ended March 31, 2024 and 2023, the condensed consolidated statements of stockholders’ equity for the three months ended March 31, 2024 and 2023 and the condensed consolidated statements of cash flows for the three months ended March 31, 2024 and 2023 and the related footnote disclosures are unaudited. In management's opinion, the unaudited condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements as of and for the year ended December 31, 2023 and include all adjustments, which are all normal recurring adjustments, necessary for the fair presentation of the interim financial statements. The results for the three months ended March 31, 2024 are not necessarily indicative of the results expected for the full fiscal year, any other interim periods, or any future year or period. The accompanying unaudited condensed consolidated financial statements reflect the application of certain significant accounting policies as described below and elsewhere in these notes to the unaudited condensed consolidated financial statements. As of March 31, 2024, there have been no material changes in the Company's significant accounting policies from those that were disclosed in the Company’s Annual Report on Form 10-K for the year ended December 31, 2023. Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent liabilities at the date of the financial statements and the reported amounts of revenue and expenses during the reporting period. The Company bases its estimates on historical experience and other market-specific or other relevant assumptions that it believes to be reasonable under the circumstances. This process may result in actual results differing materially from those estimated amounts used in the preparation of the financial statements if these results differ from historical experience, or other assumptions do not turn out to be substantially accurate, even if such assumptions are reasonable when made. Significant estimates relied upon in preparing these financial statements include estimates related to determining our net product revenue, license revenue, accruals related to research and development expenses, assumptions used to record stock-based compensation expense, interest expense on our deferred royalty obligation, and the valuation allowance on the Company's 8 Table of Contents deferred tax assets. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Changes in estimates are recorded in the period in which they become known. Actual results could differ materially from those estimates. Principles of Consolidation The consolidated financial statements include the accounts of Rhythm Pharmaceuticals, Inc. and its wholly-owned subsidiaries. All significant intercompany balances and transactions have been eliminated in consolidation. Reclassification of Prior Year Balances Certain prior year amounts have been reclassified to conform to the current period presentation. These reclassifications had no effect on the reported results of operations or cash flows. In the condensed consolidated statements of cash flows, the Company reclassified $ 2,341 to non-cash accretion and amortization of short-term investments from prepaid expenses and other current assets for the three months ended March 31, 2023. The reason for the reclassification was to conform with the current year’s presentation. Segment Information Operating segments are defined as components of an entity about which separate discrete information is available for evaluation by the chief operating decision maker, or decision-making group, in deciding how to allocate resources and in assessing performance. The Company currently operates in one business segment, which is the development and commercialization of therapies for patients with rare diseases. A single management team that reports to the Chief Executive Officer comprehensively manages the entire business. The Company does not operate separate lines of business with respect to its product or product candidates. Accordingly, the Company has one reportable segment. Off-Balance Sheet Risk and Concentrations of Credit Risk Financial instruments, which potentially subject the Company to significant concentration of credit risk, consist primarily of cash and cash equivalents and short-term investments, which are maintained at two federally insured financial institutions. The deposits held at these two institutions are in excess of federally insured limits. The Company has not experienced any losses in such accounts and management believes that the Company is not exposed to significant credit risk due to the financial position of the depository institutions in which those deposits are held. The Company has no off-balance sheet risk, such as foreign exchange contracts, option contracts, or other foreign hedging arrangements. The Company is exposed to risks associated with extending credit to customers related to the sale of products. The Company does not require collateral to secure amounts due from its customers. For the three months ended March 31, 2024 and 2023, approximately 74 % and 83 %, respectively, of all of the Company’s revenue was generated from a single customer in the United States. As of March 31, 2024 and December 31, 2023, approximately 72 % and 67 %, respectively, of the Company’s accounts receivable was outstanding from a single customer in the United States. The Company relies on third-party manufacturers and suppliers for the manufacture and supply of its product. The inability of the suppliers or manufacturers to fulfill supply requirements of the Company could materially impact future operating results. A change in the relationship with the suppliers or manufacturer, or an adverse change in their business, could materially impact future operating results. The Company relies on separate third parties to perform genetic testing in the United States and Europe, respectively. The inability of the vendor to fulfill testing services for the Company could materially impact future operating results and adversely impact our ability to further develop setmelanotide. A change in the relationship with the genetic testing service providers, or an adverse change in their business, could materially impact future operating results. 9 Table of Contents Accounts Receivable, net Accounts receivable consists of amounts due from customers, net of customer allowances for cash discounts and any estimated expected credit losses. The Company's measurement of expected credit losses is based on relevant information about past events, including historical experience, current conditions, and reasonable and supportable forecasts that affect the collectability of the reported amount. To date, the Company has not experienced any credit losses. The Company's contracts with its customers have customary payment terms that generally require payment within 90 days. The Company analyzes amounts that are past due for collectability, and periodically evaluates the creditworthiness of its customers. As of March 31, 2024 and December 31, 2023, the Company determined an allowance for doubtful accounts was not required based upon our review of contractual payments and our customers’ circumstances. Revenue Recognition The Company recognizes revenue in accordance with ASC Topic 606, Revenue from Contracts with Customers , or ASC 606. Under ASC 606, an entity recognizes revenue when its customer obtains control of promised goods or services in an amount that reflects the consideration which the entity expects to receive in exchange for those goods or services. Product Revenue, net In the United States (the “U.S.”), which accounts for the largest portion of our total revenues, the Company sells its product to a limited number of specialty pharmacies. The product is distributed through third-party logistics, or 3PL, distribution agent that does not take title to the product. Once the product is delivered to the Company’s specialty pharmacy provider, our customer in the U.S., the customer (or “wholesaler”) takes title to the product. The wholesaler then distributes the product to patients. In our distribution agreement with the 3PL company, the Company acts as principal because we retain control of the product. Internationally, we make sales primarily to specialty distributors and retail pharmacy chains, as well as hospitals, many of which are government-owned or supported. The Company offers returns of product sold to the customer on a limited basis. Revenue from product sales is recognized when the customer obtains control of our product, which occurs at a point in time, upon transfer of title to the customer because at that point in time we have no ongoing obligations to the customer. There are no other performance obligations besides the sale of product. We classify payments to our customers or other parties in the distribution channel for services that are distinct and priced at fair value as selling, general and administrative expenses in our consolidated statements of operations and comprehensive loss. Otherwise, payments to a customer or other parties in the distribution channel that do not meet those criteria are classified as a reduction of revenue, as discussed further below. Taxes collected from the customer relating to product sales and remitted to governmental authorities are excluded from revenue. Because our payment terms are generally ninety days or less, the Company concluded there is not a significant financing component because the period between the transfer of a promised good or service to the customer and when the customer pays for that good or service will be one year or less. The Company expenses incremental costs of obtaining a contract as and when incurred since the expected amortization period of the asset that we would have recognized is one year or less. Reserves for Variable Consideration Revenues from product sales are recorded at the net sales price, or the transaction price, which includes estimates of variable consideration for which reserves are established and which result from discounts, rebates, and co-pay assistance that are offered within contracts between us and our customers, health care providers and other indirect customers relating to the sale of IMCIVREE. These reserves are based on the amounts earned or to be claimed on the related sales and are classified as reductions of accounts receivable (if the amount is payable to the customer) or a current liability (if the amount is payable to a party other than a customer). Where appropriate, these estimates take into consideration a range of possible outcomes that are probability-weighted for relevant factors such as our historical experience, current contractual and statutory requirements, specific known market events and trends, industry data and forecasted customer buying and payment patterns. Overall, these reserves reflect our best estimates of the amount of consideration to which we are entitled based on the terms of the contract. The amount of variable consideration that is included in the transaction price may be constrained and is included in the net sales price only to the extent that it is considered probable that a significant reversal 10 Table of Contents in the amount of the cumulative revenue recognized will not occur in a future period. Actual amounts of consideration ultimately received may differ from our estimates. If actual results in the future vary from our estimates, we will adjust these estimates, which would affect net product revenue and earnings in the period such variances become known. The following are the components of variable consideration related to product revenue: Chargebacks: The Company estimates obligations resulting from contractual commitments with the government and other entities to sell products to qualified healthcare providers and patients at prices lower than the list prices charged to our customers. The government and other entities charge us for the difference between what they pay for the product and the selling price to our customers. Government rebates: The Company is subject to discount obligations under government programs, including Medicaid programs, Medicare and Tricare in the United States as well as certain government rebates and pricing adjustments in certain international markets that we operate. We estimate Medicaid, Medicare and Tricare rebates based upon a range of possible outcomes that are probability-weighted for the estimated payer mix. These reserves are recorded in the same period the related revenue is recognized, resulting in a reduction of product revenue and the establishment of a liability that is included in accrued expenses and other current liabilities on our condensed consolidated balance sheets. On a quarterly basis, we update our estimates and record any adjustments in the period that we identify the adjustments. Trade discounts and allowances: The Company provides customary invoice discounts on IMCIVREE sales to certain of our customers for prompt payment that are recorded as a reduction of revenue in the period the related product revenue is recognized. In addition, we receive and pay for various distribution services from our customers in the distribution channel. For services that are not distinct from the sale of our product, such fees are classified as a reduction of product revenue. Product returns: Our customers have limited return rights related to the product’s damage or defect. The Company estimates the amount of product sales that may be returned and records the estimate as a reduction of revenue and a refund liability in the period the related product revenue is recognized. Based on the distribution model for IMCIVREE, the Company believes there will be minimal returns. Other incentives: Other incentives include co-payment assistance the Company provides to patients with commercial insurance that have coverage and reside in states that allow co-payment assistance. The calculation of the accrual for co-pay assistance is based on an estimate of claims and the cost per claim that we expect to receive associated with product that has been recognized as revenue. The estimate is recorded as a reduction of revenue in the same period the related revenue is recognized. Provisions for cash discounts are recorded as reductions of accounts receivable, and fees, rebates, and other incentives are recorded as a component of accrued expenses. License Agreements LG Chem In January 2024, we entered into a license agreement and share issuance agreement with LG Chem, Ltd. (“LGC”). Under the terms of the license agreement, we obtained worldwide rights to develop LGC’s proprietary compound LB54640 and will assume sponsorship of two ongoing LGC Phase 2 studies designed to evaluate safety, tolerability, pharmacokinetics and weight loss efficacy of LB54640. The SIGNAL trial is a randomized, placebo-controlled, double-blind study designed to enroll and evaluate approximately 28 patients with acquired hypothalamic obesity. Participants will receive one of three doses of LB54640 by oral administration once daily for up to 52 weeks, and the primary endpoint of the study is the change from baseline in body mass index after 14 weeks of treatment. The open-label, single-arm, 16 -week ROUTE trial is designed to enroll five patients with POMC or LEPR deficiency obesity. We paid LGC $ 40.0 million in cash and issued shares of our common stock with an aggregate fair value of $ 18.7 million. The shares were issued at a per share price equal to the ten-day volume weighted-average closing price for our 11 Table of Contents common stock, calculated as of the trading day immediately prior to January 4, 2024. We also agreed to make a $ 40.0 million payment in cash 18 months after the effective date of the license agreement. This payment has been recorded at its present value and reflected in other long-term liabilities on our unaudited condensed consolidated balance sheet. In addition, and subject to the completion of Phase 2 development of LB54640, the Company has agreed to pay LGC royalties of between low-to-mid single digit percent of net revenues from its MC4R portfolio, including LB54640, commencing in 2029 and dependent upon achievement of various regulatory and indication approvals, and subject to customary deductions and anti-stacking. Royalties may further increase to a low double digit percent royalty, though such royalty would only be applicable on net sales of LB54640 in a region if LB54640 is covered by a composition of matter or method of use patent controlled by LGC in such region and the Company’s MC4R portfolio is not covered by any composition of matter or method of use patents controlled by the Company in such region. Such increased rate would only apply on net sales of LB54640 for the limited remainder of the royalty term in the relevant region. RareStone Group Ltd. ​ In December 2021, the Company entered into an Exclusive License Agreement with RareStone Group Ltd., or the RareStone License. Pursuant to the RareStone License, we granted to RareStone an exclusive, sublicensable, royalty-bearing license under certain patent rights and know-how to develop, manufacture, commercialize and otherwise exploit any pharmaceutical product that contains setmelanotide in the diagnosis, treatment or prevention of conditions and diseases in humans in China, including mainland China, Hong Kong and Macao. RareStone has a right of first negotiation in the event that the Company chooses to grant a license to develop or commercialize the licensed product in Taiwan. The arrangement includes a license and an additional performance obligation to supply product upon the request of RareStone. ​ According to the terms of the RareStone License , RareStone has agreed to seek local approvals to commercialize IMCIVREE for the treatment of obesity and hyperphagia due to biallelic POMC, PCSK1 or LEPR deficiency, as well as Bardet-Biedl and Alström syndromes. Additionally, RareStone has agreed to fund efforts to identify and enroll patients from China in the Company’s global EMANATE trial, a Phase 3, randomized, double-blind, placebo-controlled trial to evaluate setmelanotide in four independent sub-studies in patients with obesity due to a heterozygous variant of POMC/PCSK1 or LEPR; certain variants of the SRCI gene, and certain variants of the SH2B1 gene. In accordance with the terms of the RareStone License , RareStone made an upfront payment to Rhythm of $ 7,000 and issued Rhythm 1,077,586 ordinary shares. The Company is eligible to receive development and commercialization milestones of up to $ 62,500 , as well as tiered royalty payments on annual net sales of IMCIVREE. The Company initially estimated the fair value of the RareStone equity to be $ 2,440 based on a preliminary valuation during the first quarter of 2022. Upon completion of the valuation procedures during the second quarter of 2022, the Company concluded the initial fair value of the RareStone equity to be $ 1,040 . During the third quarter of 2022, the Company estimated the fair value of the RareStone equity to be de minimis based upon the results of an updated valuation and recorded an other-than-temporary impairment of $ 1,040 related to the decline in fair value as a component of other expense in our consolidated statements of operations and other comprehensive loss for the year ended December 31, 2022. The other-than-temporary impairment of $ 1,040 included the reclassification of a $ 300 unrealized loss previously recorded as a component of accumulated other comprehensive income (loss) in our condensed consolidated statement of stockholders’ equity during the second quarter of 2022. The Company received total upfront consideration of $ 8,040 comprised of an upfront payment of $ 7,000 , and the estimated fair value of the RareStone equity of $ 1,040 . The Company determined that the RareStone License contains two performance obligations, the delivery of the license and the supply of clinical and commercial product. The Company further determined the supply of commercial product to RareStone contains a significant future discount and estimates the discount to be $ 1,286 , which is recorded as a component of deferred revenue on the consolidated balance sheet at December 31, 2023. Based on a relative fair-value allocation between the license and the manufacture of clinical and commercial product, the Company recognized $ 6,754 of license revenue in the consolidated statements of operations and comprehensive loss during the year ended December 31, 2022. The discount related to commercial manufacturing supply 12 Table of Contents will be deferred and recognized over the commercial supply period or upon termination of the agreement. No license revenue was recognized during the years ended December 31, 2023 or 2021. On October 28, 2022, we delivered written notice, or the October Notice, to RareStone that we have terminated the RareStone License for cause. In accordance with the Notice, we maintain that RareStone has materially breached its obligations under the RareStone License to fund, perform or seek certain key clinical studies and waivers, including with respect to our global EMANATE trial, among other obligations. On December 21, 2022, RareStone provided written notice to us that it objects to the claims in the Notice, including our termination of the RareStone License for cause. On March 16, 2023, we provided written notice, or the March Notice, to RareStone reaffirming our position that RareStone has materially breached its obligations under the RareStone License and that we have terminated the RareStone License for cause, and also requested documentation supporting RareStone’s purported dispute notice objecting to the claims in the Notice. On May 10, 2023, RareStone provided written notice to the Company reaffirming its objections to the claims in our October Notice and March Notice, including to the Company’s termination of the RareStone License for cause. On November 29, 2023, RareStone wrote to us seeking to negotiate and execute a commercial supply agreement as contemplated under the Exclusive License Agreement, and on January 19, 2024, we responded in writing again reaffirming our position that RareStone has materially breached its obligations under the RareStone License and that we have terminated the RareStone License for cause. Deferred Royalty Obligation The Company treats the debt obligation to HealthCare Royalty Management, LLC as discussed further in Note 12, “Long-Term Obligations”, as a deferred royalty obligation, amortized using the effective interest rate method over the estimated life of the revenue streams. The Company recognizes interest expense thereon using the effective rate, which is based on our current estimates of future revenues over the life of the arrangement. In connection therewith, the Company periodically assesses its expected revenues using internal projections, imputes interest on the carrying value of the deferred royalty obligation, and records interest expense using the imputed effective interest rate. To the extent the Company’s estimates of future revenues are greater or less than previous estimates or the estimated timing of such payments is materially different than previous estimates, the Company will account for any such changes by adjusting the effective interest rate on a prospective basis, with a corresponding impact to the reclassification of our deferred royalty obligation. The assumptions used in determining the expected repayment term of the deferred royalty obligation and amortization period of the issuance costs requires the Company to make estimates that could impact the classification of such costs, as well as the period over which such costs will be amortized. Inventory Prior to receiving approval from the FDA in November 2020 to sell IMCIVREE in the United States, the Company expensed all costs incurred related to the manufacture of IMCIVREE as research and development expense because of the inherent risks associated with the development of a drug candidate, the uncertainty about the regulatory approval process and the lack of history for the Company of regulatory approval of drug candidates. The Company values inventories at the lower of cost or estimated net realizable value. The Company determines the cost of inventories, which includes amounts related to materials and manufacturing overhead, on a first-in, first-out basis. Raw materials and work in process includes all inventory costs prior to packaging and labelling, including raw materials, active pharmaceutical ingredient, and drug product. Finished goods include packaged and labelled products. Raw materials and work in process that may be used for either research and development or commercial sale are classified as inventory until the material is consumed or otherwise allocated for research and development. If the material is intended to be used for research and development, it is expensed as research and development once that determination is made. Cost of Product Sales Cost of product sales consists of manufacturing costs, transportation and freight, amortization of capitalized intangibles, royalty payments and indirect overhead costs associated with the manufacturing and distribution of IMCIVREE. Cost of product sales may also include periodic costs related to certain manufacturing services and inventory 13 Table of Contents adjustment charges. Finally, cost of sales may also include costs related to excess or obsolete inventory adjustment charges, abnormal costs, unabsorbed manufacturing and overhead costs, and manufacturing variances. Intangible Assets, Net Definite-lived intangible assets related to capitalized milestones under license agreements are amortized on a straight-line basis over their remaining useful lives, which are estimated to be the remaining patent life. If our estimate of the product’s useful life is shorter than the remaining patent life, then a shorter period is used. Amortization expense is recorded as a component of cost of sales on the consolidated statements of operations and comprehensive loss. Impairment of Long-Lived Assets The Company evaluates its long-lived assets, which consist primarily of property and equipment and finite lived intangible assets, for impairment whenever events or changes in circumstances indicate that the carrying amount of such assets may not be recoverable. Factors that the Company considers in deciding when to perform an impairment review include significant underperformance of the business in relation to expectations, significant negative industry or economic trends and significant changes or planned changes in the use of the assets. The Company measures recoverability of assets to be held and used by comparing the carrying amount of an asset to the future undiscounted net cash flows expected to be generated by the asset. If such assets are considered to be impaired, the Company measures the impairment to be recognized by the amount by which the carrying amount of the asset exceeds the fair value of the asset, less the cost to sell. No events or changes in circumstances existed to require an impairment assessment during the three months ended March 31, 2024 and 2023, respectively. Acquired IPR&D and Milestone Expenses ​ In an asset acquisition, payments incurred prior to regulatory approval to acquire rights to in-process research and development projects are expensed as acquired IPR&D and recorded as a component of research and development expense in the condensed consolidated statements of operations and comprehensive net loss unless the project has an alternative future use. These costs include upfront and development milestone payments related to licensing arrangements, or other asset acquisitions that provide rights to develop, manufacture and/or sell pharmaceutical products. Where contingent development milestone payments are due to third parties, prior to regulatory approval, the payment obligations are expensed when the achievement of the underlying milestone becomes probable. Regulatory and commercial milestone payments made to third parties subsequent to regulatory approval are capitalized as intangible assets and amortized to cost of products sold over the remaining useful life of the related product. Foreign Currency Translation ​ The majority of the Company’s operations occurs in subsidiaries that have the U.S. dollar denominated as its functional currency. The assets and liabilities of the Company’s subsidiaries with functional currencies other than the U.S. dollar are translated into U.S. dollars at exchange rates in effect at the balance sheet date. Revenue and expense amounts for these subsidiaries are translated using the average exchange rates for the period. Changes resulting from foreign currency translation are included in accumulated other comprehensive income (loss) on the Company’s consolidated statement of stockholders’ equity. Net foreign currency exchange transaction gains (losses), which are included in other (expense) income, net on our consolidated statements of operations, were immaterial for the three months ended March 31, 2024 and 2023. Fair Value Measurements Fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. Financial assets and liabilities carried at fair value are classified and disclosed in one of the following three categories: Level 1 — Quoted market prices in active markets for identical assets or liabilities. 14 Table of Contents Level 2 — Observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities. Level 3 — Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities. The Company’s cash equivalents and marketable securities and derivative liability at March 31, 2024 and December 31, 2023 were carried at fair value, determined according to the fair value hierarchy. See Note 6 for further discussion. The carrying amounts reflected in the condensed consolidated balance sheets for accounts payable and accrued expenses and other current liabilities approximate their fair values due to their short-term maturities at March 31, 2024 and December 31, 2023, respectively. ​ Net Loss Per Share Basic net loss per share is computed by dividing the net loss by the weighted average number of common shares outstanding during the period, without consideration of potential dilutive securities. Diluted net loss per common share is computed by adjusting the weighted average shares outstanding for the potential dilutive effects of common stock equivalents outstanding during the period calculated in accordance with the treasury stock method. For purposes of the diluted net loss per share calculation, stock options, performance stock units and restricted stock units are considered to be common stock equivalents but have been excluded from the calculation of diluted net loss per share, as their effect would be anti-dilutive for all periods presented. Therefore, basic and diluted net loss per share is the same for all periods presented. The following table includes the potential common shares that were excluded from the computation of diluted net loss per share as their effect would have been anti-dilutive for the periods indicated: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ ​ ​ March 31, ​ 2024 2023 Stock options ​ ​ ​ 7,029,546 ​ ​ 6,973,369 Restricted stock units ​ ​ 1,775,146 ​ 1,046,232 Performance stock units ​ ​ ​ — ​ ​ 613,191 Potential common shares ​ ​ ​ 8,804,692 ​ ​ 8,632,792 ​ Subsequent Events The Company considers events or transactions that occur after the balance sheet date but prior to the issuance of the financial statements to provide additional evidence for certain estimates or to identify matters that require additional disclosure. Subsequent events have been evaluated as required. Application of New or Revised Accounting Standards From time to time, new accounting pronouncements are issued by the FASB and adopted by the Company as of the specified effective date. Unless otherwise discussed, the Company believes that the impact of recently issued standards that are not yet effective will not have a material impact on its financial position or results of operations upon adoption. In November 2023, the FASB issued ASU 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures. The standard requires disclosure of incremental segment information on an annual and interim basis and allows for multiple measures of a segment’s profit or loss provided that one of those measures is consistent with GAAP. The amendments in this update do not change how a public company identifies its operating segments, aggregates those operating segments, or applies the quantitative thresholds to determine its reportable segments, 15 Table of Contents but rather requires public entities to provide in interim periods all disclosures about a reporting segment’s profit or loss and assets that are currently required annually. ASU 2023-07 becomes effective for the annual period starting on January 1, 2024, and for interim periods starting on January 1, 2025. Early adoption is permitted. The Company is currently evaluating the disclosure requirements related to the new standard but does not anticipate a material impact to its net financial position. 3. Asset Acquisitions LG Chem, Ltd. On January 4, 2024, the Company entered into a license agreement and share issuance agreement with LG Chem, Ltd. (“LGC”). Under the terms of the license agreement, the Company obtained worldwide rights to LGC’s proprietary compound LB54640 and will assume sponsorship of two ongoing LGC Phase 2 studies designed to evaluate safety, tolerability, pharmacokinetics and weight loss efficacy of LB54640. ​ The total purchase consideration of $ 92.4 million was composed of $ 40.0 million of cash paid at closing and issued shares of the Company’s common stock with an aggregate value of $ 20.0 million. The shares were issued at a per share price equal to the ten-day volume weighted average closing price for our common stock, calculated as of the trading day immediately prior to January 4, 2024. As of January 4, 2024, the fair value of common stock issued was $ 18.7 million. The total purchase consideration also includes a $ 40.0 million license fee payable in 18 months , whose present value at closing was $ 33.7 million, and $ 0.8 million of transaction costs which are recorded as selling, general and administrative expenses. ​ In addition, under the terms of the license agreement, we agreed to pay LGC up to $ 205 million in cash upon achieving various regulatory and sales milestones based on net sales of LB54640. In addition and subject to the completion of Phase 2 development of LB54640, the Company has agreed to pay LGC royalties of between low-to-mid single digit percent of net revenues from its MC4R portfolio, including LB54640, commencing in 2029 and dependent upon achievement of various regulatory and indication approvals, and subject to customary deductions and anti-stacking. Royalties may further increase to a low double digit percent royalty, though such royalty would only be applicable on net sales of LB54640 in a region if LB54640 is covered by a composition of matter or method of use patent controlled by LGC in such region and the Company’s MC4R portfolio is not covered by any composition of matter or method of use patents controlled by the Company in such region. Such increased rate would only apply on net sales of LB54640 for the limited remainder of the royalty term in the relevant region. ​ The assets acquired were In-Process Research and Development (IPR&D) assets. However, since the IPR&D assets were determined to have no alternative future use, the Company recognized the $ 92.4 million of purchase consideration as research and development expense in the three months ended March 31, 2024. The Company determined that the additional contingent consideration did not meet the definition of a derivative as of the acquisition date. Therefore, the Company did not record a contingent consideration liability on the acquisition date. The Company will recognize any future contingent consideration payments related to the LG Chem transaction in the period in which the achievement of the underlying milestones becomes probable. ​ Xinvento B.V. On February 27, 2023, the Company, through its wholly-owned Dutch subsidiary, Rhythm Pharmaceuticals Netherlands B.V., a Dutch private limited liability company (“Rhythm BV”), entered into a Share Purchase Agreement (the “Purchase Agreement”) with Xinvento B.V., a Dutch private limited liability company based in the Netherlands (“Xinvento”), and the other parties named therein, pursuant to which, and concurrently with the execution thereof, Rhythm BV acquired all of the issued and outstanding shares of Xinvento. The aggregate consideration at closing was approximately $ 5,667 , inclusive of transaction costs, as adjusted pursuant to the terms of the Purchase Agreement and subject to the distribution and payment terms set forth therein (the “Closing Purchase Price”). 16 Table of Contents In addition to the Closing Purchase Price, the Purchase Agreement provides for the payment of additional contingent consideration totaling up to $ 206,000 upon achievement of certain development, regulatory and commercial milestones by Xinvento, as follows: (i) up to an aggregate of $ 6,000 in clinical development milestones; (ii) up to an aggregate of $ 125,000 in regulatory approval and commercial milestones; and (iii) up to an aggregate of $ 75,000 in sales milestones in the event a second molecule is selected, developed and approved. The total purchase consideration of $ 5,667 was composed of $ 4,520 of cash paid at closing, a $ 500 holdback, paid in the three months ended March 31, 2024, and $ 647 of acquisition-related costs. The Company determined that substantially all of the value as of acquisition date related to Xinvento’s In-Process Research and Development. As a result, the Company determined this transaction should be accounted for as an asset acquisition. The assets acquired were In-Process Research and Development (IPR&D) assets. However, since the IPR&D assets were determined to have no alternative future use, the Company recognized the $ 5,667 of purchase consideration as research and development expense in the year ended December 31, 2023. The Company determined that the additional contingent consideration did not meet the definition of a derivative as of the acquisition date. Therefore, the Company did not record a contingent consideration liability on the acquisition date. The Company will recognize any future contingent consideration payments related to the Xinvento transaction in the period in which the achievement of the underlying milestones becomes probable. ​ Xinvento's results of operations are included in the condensed consolidated financial statements from the date of acquisition. For the three months ended March 31, 2024, the net loss associated with the operations of Xinvento was de minimis in the Company’s condensed consolidated statements of operations. ​ 4. Inventory Inventory consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ 2024 2023 Raw Materials ​ $ 3,226 ​ $ 4,625 WIP ​ 2,541 ​ 1,104 Finished Goods ​ 2,740 ​ 2,895 Total Inventory ​ $ 8,507 ​ $ 8,624 ​ ​ 5. Accrued Expenses and Other Current Liabilities Accrued expenses and other current liabilities consisted of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ 2024 2023 Research and development costs ​ $ 13,193 ​ $ 12,925 Professional fees ​ 3,960 ​ 3,833 Payroll related ​ 7,754 ​ 15,439 Royalties ​ ​ 1,278 ​ ​ 1,180 Sales Allowances ​ ​ 10,144 ​ ​ 9,475 Other ​ 8,202 ​ 5,410 Accrued expenses and other current liabilities ​ $ 44,531 ​ $ 48,262 ​ ​ ​ ​ ​ ​ ​ ​ ​ 6. Fair Value of Financial Assets and Liabilities As of March 31, 2024 and December 31, 2023, the carrying amount of cash and cash equivalents and short-term investments was $ 201,199 and $ 275,846 respectively, which approximates fair value. Cash and cash equivalents and 17 Table of Contents short-term investments includes investments in U.S. treasury securities and money market funds that invest in U.S. government securities that are valued using quoted market prices. Accordingly, money market funds and government funds are categorized as Level 1. The financial assets valued based on Level 2 inputs consist of corporate debt securities and commercial paper, which consist of investments in highly-rated investment-grade corporations. The following tables present information about the Company's financial assets measured at fair value on a recurring basis and indicate the level of the fair value hierarchy utilized to determine such fair value: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements as of ​ ​ March 31, 2024 using: ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents: ​ ​ ​ ​ Money market funds ​ $ 43,028 ​ $ — ​ $ — ​ $ 43,028 Marketable securities: ​ ​ ​ ​ Corporate debt securities and commercial paper ​ ​ — ​ ​ 147,771 ​ ​ — ​ ​ 147,771 Total ​ $ 43,028 ​ $ 147,771 ​ $ — ​ $ 190,799 Liabilities: ​ ​ ​ ​ Derivative liability ​ $ — ​ $ — ​ $ 660 ​ $ 660 Total ​ $ — ​ $ — ​ $ 660 ​ $ 660 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements as of ​ ​ December 31, 2023 using: ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents: ​ ​ ​ ​ Commercial paper ​ $ — ​ $ — ​ $ — ​ $ — Money market funds ​ 40,868 ​ 4,979 ​ — ​ 45,847 Marketable securities: ​ ​ ​ ​ Corporate debt securities and commercial paper ​ ​ — ​ ​ 215,765 ​ ​ — ​ ​ 215,765 Total ​ $ 40,868 ​ $ 220,744 ​ $ — ​ $ 261,612 Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative liability ​ $ — ​ $ — ​ $ 1,150 ​ $ 1,150 Total ​ $ — ​ $ — ​ $ 1,150 ​ $ 1,150 ​ The estimated fair value of the derivative liability related to our Royalty Interest Financing Agreement (RIFA) with HealthCare Royalty Partners was determined using Level 3 inputs. The fair value measurement of the derivative liability is sensitive to changes in the unobservable inputs used to value the financial instrument. Changes in the inputs could result in changes to the fair value of each financial instrument. The embedded derivative liability associated with our deferred royalty obligation, as discussed further in Note 12, “Long-Term Obligations”, is measured at fair value using an option pricing Monte Carlo simulation model and is included as a component of the deferred royalty obligation on the condensed consolidated balance sheets. The embedded derivative liability is subject to remeasurement at the end of each reporting period, with changes in fair value recognized as a component of other (expense) income, net. The assumptions used in the option pricing Monte Carlo simulation model include: (1) our estimates of the probability and timing of related events; (2) the probability-weighted net sales of IMCIVREE, including worldwide net product sales, upfront payments, milestones and royalties; (3) our risk-adjusted discount rate that includes a company specific risk premium; (4) our cost of debt; (5) volatility; and (6) the probability of a change in control occurring during the term of the instrument. ​ 18 Table of Contents ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended ​ ​ March 31, ​ 2024 2023 Beginning aggregate estimated fair value of Level 3 liabilities ​ $ 1,150 ​ $ 1,340 Initial recording of embedded derivative ​ ​ — ​ ​ — Change in fair value of embedded derivative ​ ​ ( 490 ) ​ ​ ( 50 ) Ending aggregate estimated fair value of Level 3 liabilities ​ $ 660 ​ $ 1,290 ​ Marketable Securities The following tables summarize the Company's marketable securities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, 2024 ​ ​ ​ ​ ​ Gross ​ Gross ​ ​ ​ ​ ​ Amortized ​ Unrealized ​ Unrealized ​ Fair ​ Cost Gains Losses Value Assets ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Corporate debt securities and commercial paper (due within 1 year) ​ $ 147,742 ​ $ 51 ​ $ ( 22 ) ​ $ 147,771 ​ ​ $ 147,742 ​ $ 51 ​ $ ( 22 ) ​ $ 147,771 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2023 ​ ​ ​ ​ ​ Gross ​ Gross ​ ​ ​ ​ ​ Amortized ​ Unrealized ​ Unrealized ​ Fair ​ Cost Gains Losses Value Assets ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Corporate debt securities and commercial paper (due within 1 year) ​ $ 215,490 ​ $ 282 ​ $ ( 7 ) ​ $ 215,765 ​ ​ $ 215,490 ​ $ 282 ​ $ ( 7 ) ​ $ 215,765 ​ ​ ​ ​ 7. Right of Use Asset and Lease Liability The Company has a material operating lease for its head office facility and other immaterial operating leases for certain equipment. The Company’s office lease has a remaining lease term of 1.3 years. The Company measured the lease liability associated with the office lease using a discount rate of 10 % at inception. The Company estimated the incremental borrowing rate for the leased asset based on a range of comparable interest rates the Company would incur to borrow an amount equal to the lease payments on a collateralized basis over a similar term in a similar economic environment. As of March 31, 2024, the Company has not entered into any lease arrangements classified as a finance lease. The Company’s corporate headquarters is located in Boston, Massachusetts. This facility houses the Company’s research, clinical, regulatory, commercial and administrative personnel. The Company’s lease agreement commenced May 2019 and has a term of six years with a five-year renewal option to extend the lease. The Company has not included the five-year renewal option to extend the lease in its measurement of the right-of-use asset or lease liability. The following table presents the maturities of the Company’s operating lease liability related to office space as of March 31, 2024, all of which is under a non-cancellable operating lease: ​ ​ ​ ​ ​ ​ Operating Lease 2024 ​ 640 2025 ​ 502 Total operating lease payments ​ ​ 1,142 Add: imputed interest ​ ​ ( 65 ) Total operating lease liability ​ $ 1,077 ​ ​ ​ 19 Table of Contents 8. Intangible Assets ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ As of March 31, 2024 ​ As of December 31, 2023 ​ Estimated life (years) Cost Accumulated Amortization Net Cost Accumulated Amortization Net ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Capitalized Milestones ​ 11 ​ $ 9,000 ​ $ ( 2,185 ) ​ $ 6,815 ​ $ 9,000 ​ $ ( 1,972 ) ​ $ 7,028 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ As of March 31, 2024, the Company’s finite-lived net intangible assets, which totaled $ 6,815 resulted from the capitalization of certain milestone payments made to Ipsen Pharma, S.A.S., or Ipsen, in accordance with the terms of the Company’s license agreement with Ipsen, in connection with the Company’s first commercial sale of IMCIVREE in the U.S. in March 2021 and in France in March 2022. As of March 31, 2024, amortization expense for the next five years and beyond is summarized as follows: ​ ​ ​ ​ ​ 2024 ​ $ 641 2025 ​ ​ 855 2026 ​ ​ 855 2027 ​ ​ 855 2028 ​ ​ 855 Thereafter ​ 2,754 Total ​ $ 6,815 ​ Amortization expense totaled $ 214 and $ 214 for the three months ended March 31, 2024 and 2023, respectively. Amortization expense is included in cost of sales in the condensed consolidated statements of operations and comprehensive loss. 9. Income Taxes The Company recorded an income tax provision of approximately $ 300 for the three months ended March 31, 2024. The income tax provision is a result of taxable income from the Company’s foreign jurisdictions. The Company did not record an income tax provision for the three months ended March 31, 2023, as it generated sufficient tax losses during the period. The Company expects to maintain a full valuation allowance against its net deferred tax assets for the year. 10. Common Stock As of March 31, 2024, an aggregate of 15,285,096 shares of common stock was reserved for future issuance under the Company’s stock plans, including outstanding stock options, restricted stock units, and performance stock units that have been issued totaling 8,804,692 and 1,294,531 shares available for future grants under the Company’s 2017 Equity Employee Stock Purchase Plan. On November 2, 2021, the Company entered into a Sales Agreement with Cowen and Company, LLC (“Cowen”), pursuant to which the Company may issue and sell shares of its common stock, having an aggregate offering price of up to $ 100.0 million, from time to time through an “at the market” equity offering program under which Cowen acts as sales agent (the “ATM Program”). Between August 10, 2023 and August 21, 2023, the Company sold approximately two million shares of its common stock in the ATM Program for net proceeds of approximately $ 48.9 million. The Company intends to use the net proceeds from the ATM Program to support its global commercialization efforts for IMCIVREE® (setmelanotide) and clinical development programs in hypothalamic obesity and other rare MC4R pathway diseases. On February 29, 2024, the Company and Cowen entered into Amendment No. 1 to Sales Agreement (the “Amendment”) to increase the aggregate offering price of the shares of Common Stock that may be issued and sold pursuant to the Sales Agreement to $ 200,000,000 (excluding the aggregate offering price of shares of Common Stock 20 Table of Contents issued and sold pursuant to the Sales Agreement prior to February 29, 2024). In connection with the Amendment, on February 29, 2024, the Company filed with the SEC a prospectus supplement, dated February 29, 2024, which, combined with the Base Prospectus (together, the “New Prospectus”), amended the Prior Prospectus in its entirety. The issuances and sales under the Sales Agreement, as amended by the Amendment, will be made pursuant to the Registration Statement and the New Prospectus. On February 9, 2022, the Company’s board of directors adopted the Rhythm Pharmaceuticals, Inc. 2022 Employment Inducement Plan or the Inducement Plan, without stockholder approval pursuant to Rule 5635(c)(4) of the Nasdaq Stock Market LLC listing rules or Rule 5635(c)(4). In accordance with Rule 5635(c)(4), awards under the Inducement Plan may only be made to a newly hired employee who has not previously been a member of the Company’s board of directors, or an employee who is being rehired following a bona fide period of non-employment by the Company or a subsidiary, as a material inducement to the employee’s entering into employment with the Company or its subsidiary. An aggregate of 1,000,000 shares of the Company’s common stock have been reserved for issuance under the Inducement Plan. The Company will continue to grant awards under the 2017 Plan pursuant to the terms thereof. The exercise price of stock options granted under the Inducement Plan will not be less than the fair market value of a share of the Company’s common stock on the grant date. Other terms of awards, including vesting requirements, are determined by the Company’s board of directors and are subject to the provisions of the Inducement Plan. Stock options granted to employees generally vest over a four-year period but may be granted with different vesting terms. Certain options may provide for accelerated vesting in the event of a change in control. Stock options granted under the Inducement Plan expire no more than 10 years from the date of grant. As of the three months ended March 31, 2024, 553,889 stock option awards have been issued under the Inducement Plan. As of March 31, 2024, 281,196 restricted stock unit awards have been granted under the Inducement Plan. As of March 31, 2024, 164,915 shares of common stock are available for future grant under the Inducement Plan. On January 4, 2024, the Company issued 432,143 shares of common stock as partial consideration for its acquisition of the worldwide rights to LGC’s proprietary compound LB54640. 11. Related-Party Transactions Expenses paid directly to related parties for the three months ended March 31, 2024 and 2023, were $ 135 and $ 322 , respectively. Outstanding payments due to related parties as of March 31, 2024 and December 31, 2023 were $ 5 and $ 1 , respectively. See also Note 13, “Subsequent Events” for disclosure regarding transactions after March 31, 2024. 12. Long-Term Obligations On June 16, 2022, we entered into a RIFA with entities managed by HealthCare Royalty Management, LLC, collectively referred to as the Investors. Pursuant to the RIFA and subject to customary closing conditions, the Investors have agreed to pay the Company an aggregate investment amount of up to $ 100,000 , or the Investment Amount. Under the terms of the RIFA, we received $ 37,500 on June 29, 2022 upon FDA approval of IMCIVREE in BBS, referred to as the Initial Investment Amount, and we received an additional $ 37,500 on September 29, 2022 of the Investment Amount upon EMA approval for BBS. On September 12, 2023, we received the remaining $ 24,370 of the Investment Amount, net of debt issuance costs, following the achievement of a specified amount of cumulative net sales of IMCIVREE between July 1, 2022 and September 30, 2023. As consideration for the Investment Amount and pursuant to the RIFA, we agreed to pay the Investors a tiered royalty on our annual net revenues, or Revenue Interest, including worldwide net product sales and upfront payments and milestones. The applicable tiered percentage will initially be 11.5 % on annual net revenues up to $ 125,000 , 7.5 % on annual net revenues of between $ 125,000 and $ 300,000 and 2.5 % on annual net revenues exceeding $ 300,000 . If the Investors have not received cumulative minimum payments equal to 60 % of the amount funded by the Investors to date by March 31, 2027, or 120 % of the amount funded by the Investors to date by March 31, 2029, we must make a cash payment immediately following each applicable date to the Investors sufficient to gross the Investors up to such minimum amounts after giving full consideration of the cumulative amounts paid by us to the Investors through each date, referred to as the Under Performance Payment. As the repayment of the funded amount is contingent upon worldwide net product sales and upfront payments, milestones, and royalties, the repayment term may be shortened or extended depending on actual 21 Table of Contents worldwide net product sales and upfront payments, milestones, and royalties. We made repayments of $ 2,783 in the three months ended March 31, 2024. As of March 31, 2024 we have made cumulative payments of $ 10,313 . The Investors’ rights to receive the Revenue Interests will terminate on the date on which the Investors have received payments equal to a certain percentage of the funded portion of the Investment Amount including the aggregate of all payments made to the Investors as of such date, each percentage tier referred to as the Hard Cap, unless the RIFA is earlier terminated. The total Revenue Interests payable by us to the Investors is capped between 185 % and 250 % of the Investment Amount paid, dependent on the aggregate royalty paid between 2028 and 2032. If a change of control of occurs, the Investors may accelerate payments due under the RIFA up to the Hard Cap plus any other obligations payable under the RIFA. The repayment period commenced on July 8, 2022 for the Initial Investment Amount, and expires on the earlier of (i) the date at which the Investors received cash payments totaling an aggregate of a Hard Cap ranging from 185 % to 250 % of the Initial Investment Amount or (ii) the legal maturity date of July 8, 2034. If the Investors have not received payments equal to 250 % of the Investment Amount by the twelve-year anniversary of the initial closing date, we will be required to pay an amount equal to the Investment Amount plus a specific annual rate of return less payments previously received by Investors. In the event of a change of control, we are obligated to pay Investors an amount equal to the Hard Cap in effect at the time, ranging from 185 % to 250 % plus any Under Performance Payment of the Investment Amount less payments previously received by Investors. In addition, upon the occurrence of an event of default, including, among others, our failure to pay any amounts due to Investors under the deferred royalty obligation, insolvency, our failure to pay indebtedness when due, the revocation of regulatory approval of IMCIVREE in the U.S. or our breach of any covenant contained in the RIFA and our failure to cure the breach within the prescribed time frame, we are obligated to pay Investors an amount equal to the Hard Cap in effect at the time of default ranging from 185 % to 250 % plus any Under Performance Payment of the Investment Amount less payments previously received by Investors. In addition, upon an event of default, Investors may exercise all other rights and remedies available under the RIFA, including foreclosing on the collateral that was pledged to Investors, which consists of all of our present and future assets relating to IMCIVREE. We have evaluated the terms of the RIFA and concluded that the features are similar to those of a debt instrument. Accordingly, we have accounted for the transaction as long-term debt and presented it as a deferred royalty obligation on our condensed consolidated balance sheets. We have further evaluated the terms of the RIFA and determined that the repayment of the Hard Cap in effect at the time which ranges from 185 % to 250 % of the Investment Amount, less any payments made to date, upon a change of control is an embedded derivative that requires bifurcation from the debt instrument and fair value recognition. We determined the fair value of the derivative using an option pricing Monte Carlo simulation model taking into account the probability of change of control occurring and potential repayment amounts and timing of such payments that would result under various scenarios, as further described in Note 2, “Summary of Significant Accounting Policies” to our condensed consolidated financial statements. The aggregate fair value of the embedded derivative liability was $ 660 and $ 1,150 as of March 31, 2024 and December 31, 2023, respectively. We will remeasure the embedded derivative to fair value each reporting period until the time the features lapse and/or termination of the deferred royalty obligation. For the three months ended March 31, 2024 and 2023, we recognized other income of $ 490 and $ 50 , respectively, due to the remeasurement of the embedded derivative liability. The carrying value of the deferred royalty obligation as of March 31, 2024 was $ 107,368 based on $ 100,000 of proceeds, net of the fair value of the bifurcated embedded derivative liability upon execution of the RIFA, and debt issuance costs incurred. The carrying value of the deferred royalty obligation approximated fair value as of March 31, 2024 and December 31, 2023. The effective interest rate as of March 31, 2024 was 15.15 %. In connection with the deferred royalty obligation, we incurred debt issuance costs totaling $ 3,287 . Debt issuance costs have been netted against the debt and are being amortized over the estimated term of the debt using the effective interest method, adjusted on a prospective basis for changes in the underlying assumptions and inputs. The assumptions used in determining the expected repayment term of the debt and amortization period of the issuance costs requires that we make estimates that could impact the short and long-term classification of these costs, as well as the period over which these costs will be amortized. 13. Subsequent Events On April 1, 2024, the Company entered into an Investment Agreement (the “Investment Agreement”) with certain affiliates of Perceptive Advisors LLC (“Perceptive”) and certain other investors (each, an “Investor” and collectively, the 22 Table of Contents “Investors”), relating to the issuance and sale of 150,000 shares of a new series of the Company’s Series A Convertible Preferred Stock, par value $ 0.001 per share, titled the “Series A Convertible Preferred Stock” (the “Convertible Preferred Stock”), for an aggregate purchase price of $ 150,000 , or $ 1,000 per share (the “Issuance”). The Issuance closed on April 15, 2024. Prior to the closing of the Issuance, certain of the investors and certain of their affiliated entities held over 5 % of the Company’s common stock, par value $ 0.001 per share (the “Common Stock”). On May 7, 2024, the Company filed an Amended and Restated Certificate of Designations in respect of the Convertible Preferred Stock containing certain technical amendments to the terms of the Convertible Preferred Stock. The amendments contained in the Amended and Restated Certificate of Designations (x) limited the voting rights of the Convertible Preferred Stock to 24.9438 shares of the Company’s common stock per $ 1,000 liquidation preference of Convertible Preferred Stock and (y) eliminated a 1 % step up in the interest rate that otherwise would have applied in the unlikely event that the Company was required to obtain and failed to obtain stockholder approval for certain conversion shares underlying the Convertible Preferred Stock. On May 2, 2024, the Company entered into an agreement to amend the current material operating lease agreement for its head office facility located at 222 Berkeley Street in Boston, Massachusetts. Under the amendment, the current lease has been extended for five years through July 31, 2030, with $ 5,694 committed to future lease payments. 14. Commitments and Contingencies Legal Proceedings ​ The Company, from time to time, may be party to various litigation arising in the ordinary course of business. The Company is not presently subject to any pending or threatened litigation that it believes, if determined adversely to the Company, individually, or taken together, would reasonably be expected to have a material adverse effect on its business or financial results. ​ Other ​ The Company is party to various agreements, principally relating to licensed technology, that require future payments relating to milestones whose achievement may become probable in subsequent periods, or royalties on future sales of specified products. Additionally, the Company is party to various contracts with CROs and CMOs that generally provide for termination on notice, with the exact amounts in the event of termination to be based on the timing of the termination and the terms of the agreement. ​ Based on the Company’s current development plans as of March 31, 2024, the Company does not expect to make milestone payments due to third parties during the next 12 months from the filing of this Annual Report on Form 10-K, in connection with our license agreements. These milestones are generally recognized in the period in which the achievement of the underlying milestones becomes probable. When the achievement of these milestones or sales have not occurred, such contingencies are not recorded in the Company’s consolidated financial statements. ​