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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

FORM 10-Q

(Mark One)


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

For the quarterly period ended June 30, 2025


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

For the transition period from ___________________ to ___________________

Commission File Number: 001-41199

Amylyx Pharmaceuticals, Inc.

(Exact name of registrant as specified in its charter)


Delaware	46-4600503
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)
43 Thorndike St. Cambridge, Massachusetts	02141
(Address of principal executive offices)	(Zip Code)

(617) 682-0917

(Registrant’s telephone number, including area code)

Not Applicable

(Former name, former address and former fiscal year, if changed since last report)

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

     Title of each class

     Trading
Symbol(s)

     Name of each exchange on which registered

     Common Stock, $0.0001 par value per share

     AMLX

     Nasdaq Global Select Stock Market

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

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

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


Large accelerated filer	☐	Accelerated filer	☒
Non-accelerated filer	☐	Smaller reporting company	☒
		Emerging growth company	☐

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

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

As of July 28, 2025, the registrant had 89,167,432 shares of common stock, $0.0001 par value per share, outstanding.

AMYLYX PHARMACEUTICALS, INC.

QUARTERLY REPORT ON FORM 10-Q

FOR THE QUARTERLY PERIOD ENDED JUNE 30, 2025

Table of Contents


		Page

PART I.	FINANCIAL INFORMATION	3

Item 1.	Financial Statements (Unaudited)	3
	Condensed Consolidated Balance Sheets	3
	Condensed Consolidated Statements of Operations	4
	Condensed Consolidated Statements of Comprehensive Loss	5
	Condensed Consolidated Statements of Stockholders’ Equity	6
	Condensed Consolidated Statements of Cash Flows	7
	Notes to Condensed Consolidated Financial Statements	8
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	16
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	27
Item 4.	Controls and Procedures	27

PART II.	OTHER INFORMATION	28

Item 1.	Legal Proceedings	28
Item 1A.	Risk Factors	28
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	86
Item 3.	Defaults Upon Senior Securities	86
Item 4.	Mine Safety Disclosures	86
Item 5.	Other Information	87
Item 6.	Exhibits	88
Signatures		89

From time to time, we may use our website or our LinkedIn profile at www.linkedin.com/company/amylyx to distribute material information. Our financial and other material information is routinely posted to and accessible on the Investors section of our website, available at www.amylyx.com. Investors are encouraged to review the Investors section of our website because we may post material information on that site that is not otherwise disseminated by us. Information that is contained in and can be accessed through our website or our LinkedIn page is not incorporated into, and does not form a part of, this Quarterly Report on Form 10-Q.

SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q, or Quarterly Report, contains forward-looking statements which are made pursuant to the safe harbor provisions of Section 27A of the Securities Act of 1933, as amended, or the Securities Act, and Section 21E of the Securities Exchange Act of 1934, as amended, or the Exchange Act. All statements other than statements of historical facts contained in this Quarterly Report are forward-looking statements. In some cases, you can identify forward-looking statements by terminology such as “anticipate,” “believe,” “continue,” “could,” “estimate,” “expect,” “intend,” “may,” “plan,” “potential,” “predict,” “project,” “should,” “target,” “would” or the negative of these terms or other comparable terminology. These statements are not guarantees of future results or performance and involve substantial risks and uncertainties. Forward-looking statements in this Quarterly Report include, but are not limited to, express or implied statements about:

•

our ability to obtain regulatory approvals of avexitide in post-bariatric hypoglycemia, or PBH, or any other indications, or AMX0035 in Wolfram syndrome, progressive supranuclear palsy, or PSP, or any other indications, or any other current or future product candidates;

•

the timing, progress and results of our research and development activities, preclinical studies and clinical trials, including the Phase 3 clinical program for avexitide in PBH, known as the LUCIDITY trial, our Phase 2b/3 global clinical trial of AMX0035 for the treatment of PSP known as the ORION trial, our Phase 1 clinical trial of AMX0114 for the treatment of amyotrophic lateral sclerosis, or ALS, known as the LUMINA trial, as well as any other development efforts, preclinical studies and clinical trials for our current and any future product candidates;

•

our ability to successfully commercialize and market our product candidates, if approved, and the timing of any commercialization and marketing efforts;

•

our ability to contract with third-party suppliers, manufacturers and other service providers and their ability to perform adequately and to produce sufficient quantities of clinical and, if needed, commercial supplies;

•

the market size, opportunity, demand and growth potential for our current and any future product candidates, if approved;

•

our ability to build and maintain our own sales and marketing capabilities, or seek collaborative partners, to commercialize our current and any future product candidates, if approved;

•

our ability to obtain funding for our operations;

•

our ability to retain the continued service of our key executives and to identify, hire and retain additional qualified professionals;

•

our ability to successfully complete our ongoing or planned clinical trials of avexitide, AMX0035 and AMX0114 and to advance any other current or future product candidates into, and successfully complete, preclinical studies and clinical trials;

•

our ability to successfully recruit and enroll suitable patients in our clinical trials;

•

the timing or likelihood of the accomplishment of various scientific, clinical, regulatory filings and approvals and other product development objectives;

•

the rate and degree of market acceptance of avexitide, AMX0035, and any other current or future product candidates, if approved, by physicians, patients, third-party payors and others in the medical community;

•

the implementation of our business model and strategic plans for our business, products, product candidates and technology;

•

our ability to identify, evaluate, in-license and develop additional products or product candidates to complement our existing pipeline and our ability to successfully incorporate acquired assets into our existing pipeline;

•

the scope of protection we are able to establish and maintain for intellectual property rights covering our products, product candidates and technology;

•

developments relating to our competitors and our industry, including any regulatory developments;

•

our estimates regarding expenses, potential future revenue, capital requirements, cash runway and future needs for additional financing;

•

fluctuations of our quarterly and annual operating results and the related effects on our stock price;

•

the effect of unfavorable macroeconomic conditions or market volatility resulting from global economic conditions or geopolitical developments, including heightened and fluctuating interest rates and inflation and capital market disruptions,

changes in governmental agencies, international tariffs, trade protection measures, economic sanctions and potential economic slowdowns or recessions, or similar events, on our business; and

•

other statements about future events, including those listed under the section titled “Risk Factors.”

Any forward-looking statements in this Quarterly Report reflect our current views with respect to future events and with respect to our future financial performance, and involve known and unknown risks, uncertainties and other factors that may cause our actual results, performance or achievements to be materially different from any future results, performance or achievements expressed or implied by these forward-looking statements. Factors that may cause actual results to differ materially from current expectations include, among other things, those described under the section titled “Risk Factors” and elsewhere in this Quarterly Report. Given these uncertainties, you should not place undue reliance on these forward-looking statements. Except as required by law, we assume no obligation to update or revise these forward-looking statements for any reason, even if new information becomes available in the future.

All of our forward-looking statements are as of the date of this Quarterly Report only. In each case, actual results may differ materially from such forward-looking information. We can give no assurance that such expectations or forward-looking statements will prove to be correct. An occurrence of or any material adverse change in one or more of the risk factors or risks and uncertainties referred to in this Quarterly Report or included in our other public disclosures or our other periodic reports or other documents or filings filed with or furnished to the Securities and Exchange Commission, or the SEC, could materially and adversely affect our business, prospects, financial condition and results of operations. Except as required by law, we do not undertake or plan to update or revise any such forward-looking statements to reflect actual results, changes in plans, assumptions, estimates or projections or other circumstances affecting such forward-looking statements occurring after the date of this Quarterly Report, even if such results, changes or circumstances make it clear that any forward-looking information will not be realized. Any public statements or disclosures by us following this Quarterly Report that modify or impact any of the forward-looking statements contained in this Quarterly Report will be deemed to modify or supersede such statements in this Quarterly Report.

We may from time to time provide estimates, projections and other information concerning our industry, the general business environment, and the markets for certain diseases, including estimates regarding the potential size of those markets and the estimated incidence and prevalence of certain medical conditions. Information that is based on estimates, forecasts, projections, market research or similar methodologies is inherently subject to uncertainties, and actual events, circumstances or numbers, including actual disease prevalence rates and market size, may differ materially from the information reflected in this Quarterly Report. Unless otherwise expressly stated, we obtained this industry, business information, market data, prevalence information and other data from reports, research surveys, studies and similar data prepared by market research firms and other third parties, industry, medical and general publications, government data, and similar sources, in some cases applying our own assumptions and analysis that may, in the future, prove not to have been accurate.

TRADEMARKS

Solely for convenience, our trademarks and trade names in this report are referred to without the ® and ™ symbols, but such references should not be construed as any indicator that we will not assert, to the fullest extent under applicable law, our rights thereto.

Unless otherwise indicated, the terms “Amylyx,” “the Company,” “we,” “us,” and “our” refer to Amylyx Pharmaceuticals, Inc. and its consolidated subsidiaries, unless the context otherwise requires

PART I—FINANCIAL INFORMATION

Item 1. Financial Statements.

AMYLYX PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(in thousands, except share and per share data)

(Unaudited)


	June 30, 2025			December 31, 2024
Assets
Current assets:
Cash and cash equivalents	$	58,085		$	77,391
Marketable securities		122,741			99,110
Accounts receivable, net		103			447
Prepaid expenses and other current assets		5,961			12,484
Total current assets		186,890			189,432
Property and equipment, net		445			961
Restricted cash equivalents		1,451			1,446
Operating lease right-of-use assets		5,812			1,771
Other assets		—			24
Total assets	$	194,598		$	193,634
Liabilities and Stockholders’ Equity
Current liabilities:
Accounts payable	$	3,294		$	2,939
Accrued expenses		17,465			23,949
Operating lease liabilities, current portion		665			1,518
Total current liabilities		21,424			28,406
Operating lease liabilities, net of current portion		5,297			463
Total liabilities		26,721			28,869
Commitments and contingencies (Note 9)
Stockholders’ equity:
Preferred stock, $0.0001 par value; 10,000,000 shares authorized		—			—
Common stock, $0.0001 par value; 300,000,000 shares authorized; 89,156,350 and 68,629,738 shares issued and outstanding as of June 30, 2025 and December 31, 2024, respectively		9			7
Additional paid-in capital		851,359			771,542
Accumulated deficit		(684,042	)		(606,692	)
Accumulated other comprehensive income		551			(92	)
Total stockholders’ equity		167,877			164,765
Total liabilities and stockholders’ equity	$	194,598		$	193,634

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

AMYLYX PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(in thousands, except share and per share data)

(Unaudited)


	Three Months Ended June 30,						Six Months Ended June 30,
	2025			2024			2025			2024
Product revenue, net	$	—		$	(1,023	)	$	—		$	87,620
Operating expenses:
Cost of sales		—			8			—			5,953
Cost of sales - inventory impairment and loss on firm purchase commitments		—			7,410			—			117,871
Research and development		27,217			23,347			49,336			59,955
Selling, general and administrative		15,640			21,647			31,324			79,406
Restructuring expenses		—			22,851			—			22,851
Total operating expenses		42,857			75,263			80,660			286,036
Loss from operations		(42,857	)		(76,286	)		(80,660	)		(198,416	)
Other income, net:
Interest income		1,960			4,069			4,191			8,395
Other expense, net		(546	)		(483	)		(881	)		(1,230	)
Total other income, net		1,414			3,586			3,310			7,165
Loss before income taxes		(41,443	)		(72,700	)		(77,350	)		(191,251	)
Provision for income taxes		—			—			—			242
Net loss	$	(41,443	)	$	(72,700	)	$	(77,350	)	$	(191,493	)

Net loss per share — basic and diluted	$	(0.46	)	$	(1.07	)	$	(0.88	)	$	(2.82	)
Weighted-average shares used in computing net loss per share — basic and diluted		89,138,568			68,024,929			87,427,345			67,939,642

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

AMYLYX PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS

(in thousands)

(Unaudited)


	Three Months Ended June 30,						Six Months Ended June 30,
	2025			2024			2025			2024
Net loss	$	(41,443	)	$	(72,700	)	$	(77,350	)	$	(191,493	)
Other comprehensive income (loss)
Foreign currency translation gain (loss)		627			(43	)		876			(201	)
Net unrealized (loss) gain on available-for-sale securities		(76	)		23			(233	)		(93	)
Other comprehensive income (loss)		551			(20	)		643			(294	)
Comprehensive loss	$	(40,892	)	$	(72,720	)	$	(76,707	)	$	(191,787	)

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

AMYLYX PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY

(in thousands, except share data)

(Unaudited)


	Common Stock				Additional Paid-In		Accumulated Other Comprehensive			Accumulated			Total Stockholders’
	Shares		Amount		Capital		Income (Loss)			Deficit			Equity
Balance as of December 31, 2024		68,629,738	$	7	$	771,542	$	(92	)	$	(606,692	)	$	164,765
Issuance of common stock upon financing, net of issuance costs		19,714,285		2		65,575		—			—			65,577
Issuance of common stock upon exercise of stock options		36,310		—		57		—			—			57
Issuance of common stock upon vesting of RSUs		700,488		—		—		—			—			—
Stock-based compensation expense		—		—		6,833		—			—			6,833
Other comprehensive income (loss)		—		—		—		92			—			92
Net loss		—		—		—		—			(35,907	)		(35,907	)
Balance as of March 31, 2025		89,080,821	$	9	$	844,007	$	—		$	(642,599	)	$	201,417
Issuance of common stock upon exercise of stock options		855		—		2		—			—			2
Issuance of common stock upon vesting of RSUs		74,674		—		—		—			—			—
Stock-based compensation expense		—		—		7,350		—			—			7,350
Other comprehensive income (loss)		—		—		—		551			—			551
Net loss		—		—		—		—			(41,443	)		(41,443	)
Balance as of June 30, 2025		89,156,350	$	9	$	851,359	$	551		$	(684,042	)	$	167,877


	Common Stock				Additional Paid-In		Accumulated Other Comprehensive			Accumulated			Total Stockholders’
	Shares		Amount		Capital		Income (Loss)			Deficit			Equity
Balance as of December 31, 2023		67,707,432	$	7	$	738,177	$	197		$	(304,949	)	$	433,432
Issuance of common stock upon exercise of stock options		49,618		—		147		—			—			147
Issuance of common stock upon vesting of RSUs		218,537		—		—		—			—			—
Stock-based compensation expense		—		—		9,924		—			—			9,924
Other comprehensive income (loss)		—		—		—		(274	)		—			(274	)
Net loss		—		—		—		—			(118,793	)		(118,793	)
Balance as of March 31, 2024		67,975,587	$	7	$	748,248	$	(77	)	$	(423,742	)	$	324,436
Issuance of common stock upon exercise of stock options		59,981		—		23		—			—			23
Issuance of common stock upon vesting of RSUs		43,489		—		—		—			—			—
Stock-based compensation expense		—		—		9,570		—			—			9,570
Other comprehensive income (loss)		—		—		—		(20	)		—			(20	)
Net loss		—		—		—		—			(72,700	)		(72,700	)
Balance as of June 30, 2024	$	68,079,057	$	7	$	757,841	$	(97	)	$	(496,442	)	$	261,309

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

AMYLYX PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(in thousands)

(Unaudited)


	Six Months Ended June 30,
	2025			2024
Cash flows used in operating activities:
Net loss	$	(77,350	)	$	(191,493	)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation expense		14,183			19,494
Depreciation expense		297			523
Accretion of investment discounts, net		(3,226	)		(5,760	)
Inventory impairment and loss on firm purchase commitments		—			117,871
Other non-cash items		264			827
Changes in operating assets and liabilities:
Accounts receivable, net		345			35,958
Inventories		—			(9,253	)
Interest receivable		73			421
Prepaid expenses and other current assets		6,523			1,657
Operating lease right-of-use assets		1,099			957
Other assets		24			217
Accounts payable		338			(17,087	)
Accrued expenses		(6,484	)		(20,305	)
Operating lease liabilities		(1,158	)		(1,096	)
Net cash used in operating activities		(65,072	)		(67,069	)
Cash flows used in investing activities:
Purchases of property and equipment		(28	)		(156	)
Purchases of investments		(142,637	)		(231,986	)
Proceeds from maturities of marketable securities		122,000			204,000
Net cash used in investing activities		(20,665	)		(28,142	)
Cash flows provided by financing activities:
Proceeds from financing, net of issuance costs		65,577			—
Proceeds from exercise of stock options and RSUs vesting		1,042			1,493
Withholding taxes paid on stock-based awards		(988	)		(1,335	)
Net cash provided by financing activities		65,631			158
Effect of exchange rate changes on cash, cash equivalents and restricted cash equivalents		805			(149	)
Net decrease in cash, cash equivalents and restricted cash equivalents		(19,301	)		(95,202	)
Cash, cash equivalents and restricted cash equivalents, beginning of period		78,837			170,920
Cash, cash equivalents and restricted cash equivalents, end of period	$	59,536		$	75,718
Reconciliation of cash, cash equivalents and restricted cash equivalents:
Cash and cash equivalents	$	58,085		$	74,999
Restricted cash equivalents		1,451			719
Total cash, cash equivalents and restricted cash equivalents:	$	59,536		$	75,718
Supplemental disclosure of cash flow information:
Taxes withheld on stock-based awards included in accrued expenses	$	(3	)	$	12
Purchases of property and equipment included in accounts payable	$	17		$	—
Income taxes paid	$	60		$	281
Right-of-use assets obtained in exchange for new operating lease liabilities	$	5,140		$	—

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

AMYLYX PHARMACEUTICALS, INC.

NOTES TO CONDENSED Consolidated FINANCIAL STATEMENTS

(unaudited)

1. Nature of the Business

Amylyx Pharmaceuticals, Inc., together with its wholly-owned subsidiaries, known as Amylyx or the Company, is a clinical-stage pharmaceutical company with a mission to develop novel therapies for communities with high unmet medical needs. The Company has preclinical and clinical development programs underway in neurodegenerative diseases and endocrine conditions. The Company is currently developing three investigational therapies for potential impact across several diseases: avexitide in PBH, AMX0035 in Wolfram syndrome and PSP, and AMX0114 in ALS.

Risks and Uncertainties

The Company is subject to risks and uncertainties common to companies in the biotechnology industry, including, but not limited to, the outcome of preclinical studies and clinical trials, potential difficulties with or delays in timing with respect to regulatory approval processes, development by competitors of new technological innovations, dependence on key personnel, protection of proprietary technology, compliance with government regulations, ability to secure additional capital to fund operations, and risks associated with the economic challenges caused by economic uncertainty in various global markets caused by geopolitical instability and conflict. The Company and its contractors may experience disruptions in supply of items that are essential for its research and development activities, including, for example, raw materials and bulk drug substances that the Company imports from Europe and Canada used in the manufacturing of AMX0035 and any additional or future product candidates.

The accompanying consolidated financial statements have been prepared on the basis of continuity of operations, realization of assets and the satisfaction of liabilities and commitments in the ordinary course of business. The Company expects to continue to generate operating losses for the foreseeable future. The Company expects that its cash, cash equivalents and marketable securities will be sufficient to fund its operating expenses and capital expenditure requirements for at least 12 months from the issuance of these consolidated financial statements.

To continue its development efforts, the Company will need to obtain substantial additional funding through public or private equity offerings, debt financings, collaborations, strategic alliances and/or licensing arrangements in order to fund its research and development and ongoing operating expenses. The Company may not be able to obtain financing on acceptable terms, when needed or at all, and the Company may not be able to enter into collaborations, strategic alliances or licensing arrangements. The terms of any financing may adversely affect the holdings or the rights of the Company’s stockholders. Any collaborations, strategic alliances or licensing arrangements may require the Company to relinquish rights to certain of its technologies, future revenue streams, research programs or product candidates or grant licenses on terms that may not be favorable to the Company. If the Company is unable to obtain funding, the Company could be forced to delay, limit, reduce or eliminate some or all of its research and development programs, pipeline expansion or future commercialization efforts or grant rights to develop and market product candidates, which could adversely affect its business prospects. Although management will continue to pursue these plans, there is no assurance that the Company will be successful in obtaining sufficient funding on terms acceptable to the Company to fund continuing operations when needed or at all.

2. Summary of Significant Accounting Policies

Significant Accounting Policies

The Company’s significant accounting policies are disclosed in the audited consolidated financial statements for the year ended December 31, 2024 and the notes thereto, which are included in the Company’s most recent Annual Report on Form 10-K. There have been no material changes to its significant accounting policies since the date of those consolidated financial statements.

Basis of Presentation and Consolidation

The accompanying condensed consolidated financial statements and the related interim disclosures are unaudited and have been prepared in conformity with accounting principles generally accepted in the U.S., or GAAP, and pursuant to the rules and regulations of the SEC for the interim financial information. These unaudited condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted as permitted by the SEC’s rules and regulations for interim reporting. Interim period results

are not necessarily indicative of results of operations or cash flows for a full year or any subsequent interim period. The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024.

In the opinion of the Company’s management, all normal and recurring adjustments necessary for a fair presentation have been reflected. Any reference in these notes to applicable guidance is meant to refer to the authoritative GAAP as found in the ASC, and Accounting Standards Update, or ASU, of the Financial Accounting Standards Board, or FASB.

Use of Estimates

The preparation of the condensed consolidated financial statements in conformity with GAAP requires the Company’s management to make estimates and assumptions that affect the reported amounts of assets and liabilities at the date of the financial statements and the reported amount of expenses during the reporting period. Actual results could differ from those estimates. Management considers many factors in selecting appropriate financial accounting policies in developing the estimates and assumptions that are used in the preparation of the financial statements. Management must apply significant judgment in this process. Management’s estimation process often may yield a range of potentially reasonable estimates and management must select an amount that falls within that range of reasonable estimates.

Product Revenue

In 2024, the Company voluntarily discontinued the marketing authorizations for RELYVRIO®/ALBRIOZA™ and removed the product from the market in the U.S. and Canada based on topline results from the Phase 3 PHOENIX trial, or the RELYVRIO®/ALBRIOZA™ Discontinuation. As a result, we do not expect to generate revenue from the sale of RELYVRIO®/ALBRIOZA™ in future periods.

New Accounting Pronouncements Not Yet Adopted

In November 2024, the FASB issued ASU No. 2024-03, Income Statement – Reporting Comprehensive Income – Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses, which requires new financial statement disclosures in tabular format, in the notes to financial statements, of specified information about certain costs and expenses. The amendments in this update do not change or remove current expense disclosure requirements. The amendments in this update are effective for the Company's annual financial statement disclosure beginning December 31, 2027, and interim periods within the years beginning January 1, 2028. Early adoption is permitted. The Company is currently evaluating the impact of this ASU on its consolidated financial statements and related disclosures.

Recent Accounting Pronouncements

In December 2023, the FASB issued ASU No. 2023-09, Income Taxes (Topic 740): Improvement to Income Tax Disclosures, or ASU 2023-09, to enhance the transparency and decision usefulness of income tax disclosures. ASU 2023-09 is effective for the Company beginning with its 2025 annual report on a prospective basis. The impact of this ASU on the tax disclosures in the Company’s 2025 annual report is not expected to be material.

3. MARKETABLE SECURITIES

The Company has classified all of its marketable securities at June 30, 2025 as “available-for-sale”. The Company records available-for-sale securities at fair value, with the unrealized gains and losses included as a separate component of other accumulated comprehensive loss. There were no realized gains or losses recognized during the three and six months ended June 30, 2025 and 2024.

The Company adjusts the cost of available-for-sale debt securities for amortization of premiums and accretion of discounts to maturity. Such amortization and accretion are included in interest income. The cost of securities sold is based on the specific identification method. The Company includes interest and dividends on securities classified as available-for-sale in interest income. Accrued interest receivable relating to the Company’s available-for-sale securities is presented within prepaid expenses and other current assets in the accompanying condensed consolidated balance sheets, and amounted to less than $0.1 million and $0.1 million at June 30, 2025 and December 31, 2024, respectively.

As of June 30, 2025, there were no securities in an unrealized loss position for greater than 12 months. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases. The Company did not record an allowance for credit losses as of June 30, 2025.

Marketable securities, which are classified as available-for-sale, consisted of the following (in thousands):


Balance at June 30, 2025:	Amortized Cost Basis		Unrealized Gain		Unrealized Loss			Fair Value
Treasury bills	$	122,803	$	—	$	(62	)	$	122,741
Total marketable securities	$	122,803	$	—	$	(62	)	$	122,741


Balance at December 31, 2024:	Amortized Cost Basis		Unrealized Gain		Unrealized Loss		Fair Value
Treasury bills	$	98,939	$	171	$	—	$	99,110
Total marketable securities	$	98,939	$	171	$	—	$	99,110

4. Accrued Expenses

Accrued expenses consisted of the following (in thousands):


	June 30, 2025		December 31, 2024
Accrued external research and development	$	6,770	$	4,353
Accrued employee compensation and benefits		6,950		9,992
Accrued manufacturing		—		500
Accrued consulting and other professional fees		1,101		1,974
Accrued rebates		2,452		5,334
Accrued loss on future purchase commitments		—		1,538
Other accrued expenses		192		258
Total accrued expenses	$	17,465	$	23,949

5. FAIR VALUE MEASUREMENTS

The following tables present information about the Company’s financial assets and liabilities measured at fair value on a recurring basis and indicates the level of the fair value hierarchy utilized to determine such fair values (in thousands):


	June 30, 2025
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents	$	21,462	$	—	$	—	$	21,462
Restricted cash equivalents		1,451		—		—		1,451
Treasury bills		122,741		—		—		122,741
Total financial assets	$	145,654	$	—	$	—	$	145,654


	December 31, 2024
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents	$	37,550	$	—	$	—	$	37,550
Restricted cash equivalents		1,446		—		—		1,446
Treasury bills		99,110		—		—		99,110
Total financial assets	$	138,106	$	—	$	—	$	138,106

The Company classifies its money market funds, including restricted cash equivalents, and treasury bills as Level 1 assets under the fair value hierarchy, as these assets have been valued using quoted market prices for identical assets in active markets without any valuation adjustment.

6. Stock Option and Grant Plan

Stock Incentive Plan

General Option Information

A summary of option activity for the six months ended June 30, 2025 is as follows:


	Number of Options			Weighted- Average Exercise Price		Weighted- Average Remaining Contractual Term (in years)		Aggregate Intrinsic Value (in thousands)
Outstanding at December 31, 2024		7,728,707		$	14.34		7.5	$	3,584
Granted		2,317,846		$	3.73
Exercised		(37,165	)	$	1.58			$	80
Cancelled or forfeited		(193,448	)	$	17.37
Outstanding at June 30, 2025		9,815,940		$	11.82		7.7	$	13,879
Options exercisable as of June 30, 2025		4,870,345		$	14.67		6.4	$	3,331
Options unvested as of June 30, 2025		4,945,595		$	9.02		9.0	$	10,548
Weighted average grant-date fair value of options granted during the period	$	3.12

The aggregate intrinsic value of options exercised during the six months ended June 30, 2025 and 2024 was $0.1 million and $0.7 million, respectively.

The total fair value of stock options vested during the six months ended June 30, 2025 and 2024 was $10.6 million and $23.7 million, respectively.

Restricted Stock Unit Activity

A summary of restricted stock unit, or RSU, activity for the six months ended June 30, 2025 is as follows:


	Number of Shares			Weighted Average Grant Date Fair Value
Nonvested as of December 31, 2024		2,212,905		$	10.96
Granted		1,821,306		$	3.65
Vested		(775,162	)	$	9.43
Forfeited		(119,247	)	$	6.57
Nonvested as of June 30, 2025		3,139,802		$	7.26

Performance-Based Restricted Stock Unit Activity

In 2025, the Company granted performance-based restricted stock units, or PSUs, whereby vesting depends upon the occurrence of certain milestone events, or the 2025 PSUs. When achievement of a milestone event becomes probable, compensation cost will be recognized from the grant date over the requisite service period and a cumulative catch-up adjustment will be recorded to reflect the portion of the employees' requisite service that has been provided to date. As of June 30, 2025, none of the milestone events related to the 2025 PSUs had been deemed probable of being achieved.

A summary of PSU activity for the six months ended June 30, 2025, is as follows:


	Number of Shares			Weighted Average Grant Date Fair Value
Nonvested as of December 31, 2024		—		$	—
Granted		1,438,732		$	3.80
Vested		—		$	—
Forfeited		(46,100	)	$	3.91
Nonvested as of June 30, 2025		1,392,632		$	3.80

Summary of Stock-Based Compensation Expense

Stock-based compensation expense for the three and six months ended June 30, 2025 and 2024, is as follows (in thousands):


	Three Months Ended June 30,				Six Months Ended June 30,
	2025		2024		2025		2024
Research and development	$	1,960	$	2,449	$	3,782	$	5,161
Selling, general and administrative		5,390		7,121		10,401		14,333
Total stock-based compensation expense	$	7,350	$	9,570	$	14,183	$	19,494

The following table summarizes unrecognized stock-based compensation expense as of June 30, 2025, by type of awards (in thousands), and the weighted-average period over which that expense is expected to be recognized (in years). The total unrecognized stock-based compensation expense will be adjusted for actual forfeitures as they occur.


	June 30, 2025
	Unrecognized Expense		Weighted-average Recognition Period
Stock options	$	28,678		2.12
Restricted stock units	$	19,095		2.62
Performance-based restricted stock units	$	5,291		—

7. STOCKHOLDERS’ EQUITY

Common Stock

Under the Company’s Fourth Amended and Restated Certificate of Incorporation, or the certificate of incorporation, each share of common stock entitles the holder to one vote on all matters submitted to the stockholders for a vote provided, however, that, except as otherwise required by law, holders of common stock shall not be entitled to vote on any amendment to the Company’s certificate of incorporation that relates solely to the terms of one or more outstanding series of preferred stock if the holders of such affected series are entitled, either separately or together with the holders of one or more other such series, to vote thereon pursuant to the certificate of incorporation or pursuant to the Delaware General Corporation Law. Holders of common stock are entitled to receive dividends, as may be declared by the Company’s Board of Directors, if any, subject to the preferential dividend rights of the preferred stock. No dividends were declared or paid during the six months ended June 30, 2025 and 2024.

On January 13, 2025, the Company closed an underwritten public offering of 19,714,285 shares of its common stock at a public offering price of $3.50 per share. The net proceeds from this offering were approximately $65.5 million, after deducting underwriting discounts and commissions and offering expenses.

8. NET LOSS PER SHARE

Net Loss per Share

Basic earnings per share is computed by dividing net loss by the weighted average number of common shares outstanding during the period. Diluted earnings per share is calculated based on the combined weighted average number of common shares and

potentially dilutive shares, which include the assumed exercise of employee stock options, unvested RSUs and unvested PSUs. In computing diluted earnings per share, the Company utilizes the treasury stock method.

Because the Company reports a net loss attributable to common stockholders, basic and diluted net loss per share attributable to common stockholders are the same for both periods presented. All stock options, RSUs and PSUs units were excluded from the computation of diluted weighted-average shares outstanding because such securities would have an antidilutive impact for the three and six months ended June 30, 2025. The following stock options, RSUs and PSUs outstanding at each period end have been excluded from the calculation of diluted net loss per share because their inclusion would have been antidilutive:


	Three Months Ended June 30,				Six Months Ended June 30,
	2025		2024		2025		2024
Options to purchase common stock		9,815,940		10,742,139		9,815,940		10,742,139
Restricted stock units		3,139,802		2,910,900		3,139,802		2,910,900
Performance-based restricted stock units		1,392,632		—		1,392,632		—
Total excluded common stock equivalents		14,348,374		13,653,039		14,348,374		13,653,039

9. Commitments and Contingencies

Letter of Credit

Restricted cash equivalents consist of $0.9 million of cash serving as collateral for a letter of credit issued for the Company’s office spaces, and $0.5 million as collateral for a corporate credit card program. As of June 30, 2025 and December 31, 2024, the Company’s restricted cash equivalents balance was $1.4 million on its condensed consolidated balance sheets.

Legal Proceedings

On February 9, 2024, a putative class action lawsuit was filed in the U.S. District Court for the Southern District of New York against us and certain of our current and former officers (Shih v. Amylyx Pharmaceuticals, Inc., et al., Case Number 1:24-CV-00988, or the Shih Complaint). Plaintiff filed an amended complaint on June 24, 2024. The Shih Complaint asserts a claim against all defendants for alleged violations of Section 10(b) of the Exchange Act and Rule 10b-5 promulgated thereunder and a claim under Section 20(a) against certain current and former officers as alleged controlling persons. The Shih Complaint alleges that defendants made materially false and misleading statements related to the commercial results and prospects for RELYVRIO. The Shih Complaint seeks unspecified damages, interest, costs and attorneys’ fees, and other unspecified relief that the court deems appropriate.

On August 12, 2024, the case was transferred from the U.S. District Court for the Southern District of New York to the U.S. District Court for the District of Massachusetts, or the Court, and assigned docket number 1:24-CV-12068. Following the transfer, on September 6, 2024, defendants moved to dismiss the Shih Complaint. The fully briefed motion to dismiss is pending before the Court.

In addition to the Shih Complaint, on October 2, 2024, a derivative complaint was filed in the U.S. District Court for the District of Massachusetts against certain current and former director and officer defendants, or the Individual Defendants, naming the Company as a nominal defendant (Jones v. Cohen, et al., 1:24-CV-12527, or the Jones Derivative Complaint). The substantive allegations mirror those of the Shih Complaint but also include claims for alleged violations of Section 14(a) of the Exchange Act, breach of fiduciary duty, insider trading, and unjust enrichment against the Individual Defendants. The Jones Derivative Complaint seeks unspecified damages to be awarded to the Company along with interest, restitution, unspecified corporate governance and internal procedural reforms and improvements, and plaintiff's attorneys' fees and costs. On October 31, 2024, the Court entered an order staying the action until the earlier of the dismissal of the Shih Complaint with prejudice, including the exhaustion of all appeals, or defendants file an answer to the Shih Complaint.

On July 2, 2025, a second derivative complaint was filed in the Court against certain current and former directors and officer defendants, naming the Company as nominal defendant (Hassine v. Cohen, et al., 1:25-CV-11879, or the Hassine Derivative Complaint and, together with the Jones Derivative Complaint, the Derivative Complaints”). The substantive allegations mirror those of the Shih Complaint but also include claims for alleged violations of Sections 14(a), 10(b), and 21D of the Exchange Act, breach of fiduciary duty, and certain other common law claims. The Hassine Derivative Complaint seeks unspecified damages to be awarded to the Company along with interest, costs, and attorneys’ fees, restitution, and certain corporate governance and internal procedural reforms and improvements. On July 16, 2025, the parties to both derivative cases moved the Court to consolidate the Hassine Derivative Complaint with the Jones Derivative Complaint and stay the action according to the terms of the previously entered stay of the Jones Derivative Complaint. The Court approved the motion on July 22, 2025.

We intend to defend against the Shih Complaint and Derivative Complaints vigorously. At this time, an estimate of the impact, if any, of the claims made in the Shih Complaint and Derivative Complaints cannot be made.

Royalty Payments

The Company entered into grant agreements and royalty arrangements pursuant to which the Company has certain payment obligations that are contingent upon future events, such as the achievement of commercialization or the receipt of proceeds from a revenue generating transaction resulting from the technologies subject to the grants and royalties. As the conditions that would trigger royalty payments under the agreements have not occurred, no amounts have been recorded in the consolidated financial statements.

Purchase Commitments

The Company enters into agreements in the normal course of business with contract manufacturing organizations, or CMOs, for raw material purchases and manufacturing services. As of June 30, 2025, the amounts committed under these agreements are not material.

Facility Leases

In September 2024, the Company entered into a lease agreement for the lease of approximately 15,000 square feet of office space in Cambridge, Massachusetts, which will be used as the Company's new headquarters facility. The accounting lease commencement occurred on June 1, 2025, at which time the Company recognized a right-of-use, or ROU, asset and corresponding lease liability of $5.1 million. The contractual term of the lease commenced on June 1, 2025, with an initial term of approximately 67 months. The Company’s obligation for the payment of rent for the new lease begins seven months after the lease commencement. In addition to base rent, the Company has agreed to reimburse the landlord for certain operating expenses under the terms of the lease. The Company has the option to extend the new lease one time for an additional five-year period, subject to the terms therein; however, the exercise of the option to extend the lease term was not determined to be reasonably certain, and the Company will therefore recognize lease expense through the expiration of the initial lease term in December 2030.

10. Segments

The Company views its operations and manages its business as one operating segment and reporting unit. Our operating segments are determined based on how our Co-Chief Executive Officers, who collectively serve as our chief operating decision makers, or CODM, manage our business, regularly access discrete financial information, and evaluate performance for operating decision-making purposes, including allocation of resources or capital to specific compounds or projects in line with the Company’s overall strategies and goals. The Company’s entire business is managed by a single management team, which reports to the CODM.

The CODM assess segment performance and decide how to allocate resources based on consolidated net loss. The CODM use net loss to monitor budget and forecast versus actual results in assessing segment performance and to determine how to allocate resources. The measure of segment assets used in determining how to manage and allocate resources is reported on the consolidated balance sheets as total assets. All of the Company's long-lived assets were held within the U.S.

The following table reconciles segment revenue and expenses to consolidated net loss for the three and six months ended June 30, 2025 and 2024 (in thousands):


	Three Months Ended June 30,						Six Months Ended June 30,
	2025			2024			2025			2024
Product revenue, net	$	—		$	(1,023	)	$	—		$	87,620

Less1,5:
Cost of sales2		—			7,418			—			123,824
Direct research and development expenses by program:
Avexitide		7,105			—			12,531			—
AMX0035 - PSP		7,146			3,546			11,709			7,734
AMX0035 - ALS		794			9,408			1,264			23,818
Other programs		3,965			2,221			7,267			4,771
Personnel-related research and development3		8,207			8,172			16,565			23,632
Selling, general and administrative		15,640			21,647			31,324			79,406
Restructuring expenses		—			22,851			—			22,851
Provision for income taxes		—			—			—			242
Interest income		(1,960	)		(4,069	)		(4,191	)		(8,395	)
Other segment items4		546			483			881			1,230
Net loss	$	(41,443	)	$	(72,700	)	$	(77,350	)	$	(191,493	)

1. The significant expense categories and amounts align with the segment-level information that is regularly provided to the CODM. As the Company has one reportable segment, there were no intersegment eliminations for the three and six months ended June 30, 2025 and 2024.

2. Includes inventory impairment and loss on firm purchase commitments of $7.4 million and $117.9 million during the three and six months ended June 30, 2024, respectively.

3. The Company does not allocate personnel and other similar costs to specific programs because these costs are deployed across multiple programs.

4. Other segment items primarily consists of net realized and unrealized losses on foreign exchange transactions.

5. Depreciation and amortization expense of $0.1 million and $0.3 million during the three and six months ended June 30, 2025, respectively, and $0.2 million and $0.5 million during the three and six months ended June 30, 2024, respectively, are allocated across the significant expense captions.

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

The following information should be read in conjunction with the condensed consolidated financial information and the notes thereto appearing elsewhere in this Quarterly Report.

This discussion and other parts of this Quarterly Report contain forward-looking statements that involve risks and uncertainties, such as statements of our plans, objectives, expectations and intentions. As a result of many factors, including those risk factors set forth in our most recent Annual Report on Form 10-K, or 2024 Annual Report, and in our subsequent Quarterly Reports, our actual results could differ materially from the results described in or implied by the forward-looking statements contained in the following discussion and analysis.

Overview

We are a clinical-stage pharmaceutical company with a mission to develop novel therapies for communities with high unmet medical needs. We have preclinical and clinical development programs underway in neurodegenerative diseases and endocrine conditions. We are advancing a pipeline in which we have matched investigational therapies with diseases where we believe they can make the greatest impact, based on well-defined mechanistic rationale, clear clinical outcomes and biomarkers, and rigorous preclinical data, agnostic of modality. We are currently developing three investigational therapies for potential impact across several diseases: avexitide in PBH, AMX0035 in Wolfram syndrome and PSP, and AMX0114 in ALS.

Our lead investigational asset is avexitide, a first-in-class glucagon-like peptide-1, or GLP-1 receptor antagonist. Avexitide has been evaluated as a treatment for PBH and congenital hyperinsulinism, or HI, two indications characterized by hyperinsulinemic hypoglycemia. The U.S. Food and Drug Administration, or the FDA, has granted avexitide Breakthrough Therapy Designation for both PBH and congenital HI, Rare Pediatric Disease Designation in congenital HI, and Orphan Drug Designation for the treatment of hyperinsulinemic hypoglycemia (which includes PBH and congenital HI).

PBH is a condition that affects about 160,000 people in the U.S., or approximately 8% of those in the U.S. who have undergone the two most common types of bariatric surgery: sleeve gastrectomy and Roux-en-Y gastric bypass, or RYGB surgery. Currently, there are no FDA-approved therapies for PBH. PBH is thought to be caused by an excessive GLP-1 response, leading to hypoglycemia and impaired quality of life. Clinical manifestations can include impaired cognition, loss of consciousness, and seizures. Avexitide is designed to bind to the GLP-1 receptor on pancreatic islet beta cells and inhibit the effects of excessive GLP-1 in PBH, mitigating hypoglycemia by decreasing insulin secretion and stabilizing blood glucose levels.

In April 2025, we dosed the first participant for the pivotal Phase 3 LUCIDITY clinical trial for avexitide in PBH following RYGB surgery. LUCIDITY (NCT06747468) is a multicenter, randomized, double-blind, placebo-controlled, 16-week clinical trial evaluating the efficacy and safety of avexitide in participants with PBH following RYGB surgery. The Phase 3 trial is being conducted at approximately 20 sites in the U.S. Approximately 75 participants will be randomized 3:2 to receive either 90 mg of avexitide subcutaneously once daily or placebo. Participants who complete the 16-week double-blind period of the ongoing study will be eligible to enter an open-label extension, or OLE, period with a duration of 32 weeks. The primary efficacy objective of LUCIDITY is to evaluate the FDA-agreed primary endpoint of reduction in the composite of Level 2 and Level 3 hypoglycemic events through Week 16. Safety and tolerability will also be evaluated. Completion of recruitment is expected in 2025, with topline data anticipated in the first half of 2026 and, if approved, commercial launch is anticipated in 2027.

LUCIDITY was informed by data from five clinical trials of avexitide in people with PBH showing consistent, dose-dependent effects across studies. The five clinical trials include a Phase 1 trial, a single ascending dose trial, a multiple ascending dose trial, and two Phase 2 trials:

•

In the Phase 2 (PREVENT), 28-day, randomized, blinded, placebo-controlled crossover trial (N=18), results showed a significant reduction in rates of Level 2 and 3 hypoglycemic events in participants with PBH after RYGB surgery following treatment with 30 mg twice daily and 60 mg once daily of avexitide compared with placebo. PREVENT’s primary endpoint was met with statistical significance, showing both avexitide dosing regimens improved the lowest glucose level (nadir) after a meal as measured during formal mixed meal tolerance testing, or MMTT. Mean plasma glucose nadir was increased by 21% (p=0.001) and 26% (p=0.0002) following avexitide 30 mg twice daily and 60 mg once daily dosing, respectively, compared to placebo. Avexitide was generally well-tolerated. The most common adverse events, or AEs, were injection site bruising, headache, and nausea; these occurred more often with placebo than either avexitide dose. No participants withdrew due to AEs.

•

In the Phase 2b, 28-day, open-label, investigator-initiated, crossover trial (N=16), 90 mg once daily and 45 mg twice daily of avexitide met its primary endpoint and significantly reduced rates of hypoglycemic events in participants following

RYGB surgery and other upper-gastrointestinal surgeries. Participants in the Phase 2b trial receiving 90 mg once daily of avexitide, the dose Amylyx is evaluating in LUCIDITY, saw a statistically significant 53% reduction in Level 2 hypoglycemic events (p=0.004) and a statistically significant 66% reduction in Level 3 hypoglycemic events (p=0.0003). There were no reported serious AEs, and AEs were mostly mild to moderate and resolved without medical treatment. The most common AEs included diarrhea, headache, bloating, and injection site reaction/bruising. No participant withdrew due to AEs. In the Phase 2b trial, 90 mg once daily of avexitide has also demonstrated a favorable pharmacokinetic, or PK, profile maintaining exposure in the therapeutic range through 24 hours, supporting once daily dosing.

•

In addition, new exploratory analyses from the Phase 2 PREVENT and Phase 2b clinical trials of avexitide were presented at the Endocrine Society’s annual meeting in July 2025. In the Phase 2b trial, avexitide 90 mg once daily, the dose being evaluated in the pivotal Phase 3 LUCIDITY trial, led to a 64% least-squares mean reduction (p=0.0031) vs. baseline in the composite rate of Level 2 and Level 3 hypoglycemic events in PBH, with more than half of the participants experiencing no events during the treatment period. Consistent reductions in composite rate of Level 2 and Level 3 hypoglycemic events also were seen with avexitide 45 mg twice daily studied in the Phase 2b trial and avexitide 30 mg twice daily and 60 mg once daily studied in the Phase 2 PREVENT trial. New PK and pharmacodynamic, or PD, data were also presented, demonstrating continuous pharmacologic activity of the 90 mg once daily dose regimen for a 24-hour period.

Avexitide was generally well-tolerated, with a favorable safety profile replicated across five clinical trials in people with PBH. In healthy volunteers, avexitide demonstrated a clear GLP-1 antagonist PD effect, including lowering insulin and raising the glucose nadir.

In congenital HI, we are actively engaging in discussions with the broader congenital HI community to develop a path forward.

In December 2024, we announced a collaboration with Gubra A/S for the development of a potential novel long-acting GLP-1 receptor antagonist. As part of this collaboration, we anticipate identifying a lead development candidate to enter Investigational New Drug, or IND-enabling studies.

In addition to avexitide, we are investigating AMX0035, an oral, fixed-dose combination of sodium phenylbutyrate and taurursodiol in Wolfram syndrome and PSP, and AMX0114, an antisense oligonucleotide targeting calpain-2 in ALS.

AMX0035 is designed to slow or mitigate neurodegeneration by targeting endoplasmic reticulum, or ER stress, and mitochondrial dysfunction, two connected central pathways that lead to cell death and neurodegeneration. We are investigating AMX0035 in neurodegenerative diseases and endocrine conditions where ER stress and mitochondrial dysfunction are implicated, including Wolfram syndrome and PSP.

Wolfram syndrome is a rare, monogenic, progressive neurodegenerative disorder that progressively impacts multiple organs and systems. Wolfram syndrome is characterized by childhood-onset diabetes mellitus, optic nerve atrophy, and neurodegeneration. Common manifestations of Wolfram syndrome include diabetes mellitus and diabetes insipidus, gradual vision loss leading to blindness, hearing loss, neurogenic bladder, difficulties with balance and coordination, and difficulty breathing that can lead to respiratory failure. There are currently no approved therapies for the approximately 3,000 people in the U.S., and more around the world, living with Wolfram syndrome.

The majority of people with Wolfram syndrome carry mutations in the WFS1 gene, which encodes a protein called wolframin that spans the membrane of the ER. Loss of wolframin function leads to ER stress and impaired mitochondrial dynamics, which lead to multi-organ cell dysfunction and death – starting with beta cells in the pancreas, then neurons in the visual system, auditory system, and throughout the body. Because of the clear link between WFS1 mutations and ER stress, Wolfram syndrome is considered a prototypical ER stress disorder. AMX0035 is hypothesized to mitigate cell death in Wolfram syndrome by reducing ER stress and mitochondrial dysfunction. In preclinical models, treatment with AMX0035 improved WFS1 protein expression, increased insulin secretion, and inhibited beta cell death in cells derived from people with Wolfram syndrome. AMX0035 also prevented cell death in neuronal cells derived from people with Wolfram syndrome and significantly delayed progression of the diabetes phenotype in a WFS1-knock-out preclinical model.

In October 2024, we announced positive topline data, including the primary efficacy outcome of the trial, from the Phase 2 open-label HELIOS clinical trial of AMX0035 in 12 adults living with Wolfram syndrome, and in May 2025, we announced positive long-term data from the HELIOS trial of AMX0035 in Wolfram syndrome through Week 48. HELIOS (NCT05676034) is a single-site, single-arm, open-label, Phase 2 trial designed to evaluate the safety and tolerability of AMX0035, as well as its effects on various measures of endocrinological, neurological, and ophthalmologic function in adult participants living with Wolfram syndrome. Consistent with the HELIOS trial’s previously presented primary efficacy outcome of improvement in pancreatic function, as

measured by C-peptide response to a mixed-meal tolerance test at Week 24, treatment with AMX0035 through Week 48 demonstrated continued and sustained improvement in pancreatic beta cell function, in contrast to the expected decrease in pancreatic function with disease progression.

Treatment with AMX0035 at Week 24 and at Week 48 also showed sustained improvements or stabilization in glycemic control, as measured by hemoglobin A1c (HbA1c) and time in target glucose range assessed by continuous glucose monitoring, as well as visual acuity. All participants with available measurements met the responder criteria, defined as either improvement or no change, on both the Patient Global Impression of Change and Clinician Global Impression of Change at Weeks 24 and 48, indicating stability or improvement in their Wolfram syndrome-related symptoms. Results from qualitative on-study interviews further supported the potential positive impact of AMX0035 on symptom burden. Safety data were consistent with safety data from prior studies of AMX0035. All AEs were mild or moderate, and there were no serious AEs related to AMX0035 treatment. The analysis performed at Week 24 included 11 participants in the Per Protocol population with genetically confirmed Wolfram syndrome (one participant was excluded from the Per Protocol population due to not meeting the study inclusion criteria of genetically confirmed Wolfram syndrome) and 12 participants in the Intent-to-Treat population. Long-term data at Week 48 included 10 participants in the Per Protocol population with genetically confirmed Wolfram syndrome and 11 participants in the Intent-to-Treat population. One participant discontinued between Week 24 and Week 48 for reasons unrelated to safety. These data and discussions with the FDA will inform the design of a Phase 3 trial of AMX0035 in Wolfram syndrome.

PSP is a rare, progressive, and fatal neurodegenerative disease that can affect movement, gait, balance, cognition, eye movements, swallowing, and speech and is estimated to affect 23,000 people in the U.S. People living with PSP have a life expectancy of six to eight years after symptom onset. There are no approved therapies for PSP. PSP is a tauopathy, which is defined by the buildup of tau protein in the brain. Based on its prior effect from a Phase 2 trial of AMX0035 in reducing tau in cerebrospinal fluid, or CSF, in people with Alzheimer’s disease, we believe AM00X35 is the first brain- and cell-penetrant agent that has demonstrated a significant tau reduction in CSF to be tested in PSP.

In December 2023, we initiated the Phase 2b/3 ORION (NCT06122662) clinical trial, a global, randomized, double-blind, placebo-controlled trial of AMX0035 for the treatment of PSP. ORION is a Phase 2b/3 clinical trial designed to assess the efficacy and safety of AMX0035 compared to placebo. The primary objective of the ORION trial is to assess the impact of AMX0035 compared to placebo on disease progression rate as measured by the Progressive Supranuclear Palsy Rating Scale, an established and validated endpoint in PSP clinical trials. Safety and tolerability will also be evaluated. We completed enrollment in the Phase 2b portion of the ORION trial in January 2025, with a total of 139 participants randomized. Efficacy and safety data from an unblinded interim analysis of the Phase 2b portion of the Phase 2b/3 ORION trial of AMX0035 in PSP is anticipated in the third quarter of 2025, which will be used to inform a go/no-go decision on the Phase 3 portion of the trial.

AMX0114 is an investigational antisense oligonucleotide designed to target calpain-2, a calcium-activated protease. The FDA has granted AMX0114 Fast Track designation for the treatment of ALS. Peer-reviewed research has demonstrated that overactive calpain-2 activity may be an important driver of disease progression in ALS and other neurodegenerative diseases by executing the degeneration of axons, the long tubular neuronal segments which carry signals from neurons to the muscle or other neurons. ALS is a relentlessly progressive and fatal neurodegenerative disorder caused by motor neuron death in the brain and spinal cord. Motor neuron loss in ALS leads to deteriorating muscle function, the inability to move and speak, respiratory paralysis, and eventually, death. ALS is defined as a rare disease, but it affects as many as 30,000 adults in the U.S. and 3,000 in Canada. The most common form of the disease is sporadic ALS, with more than 90% of people with ALS showing no clear family history.

In preclinical studies, treatment with AMX0114 resulted in potent, dose-dependent, and durable reduction in CAPN2 mRNA and calpain-2 protein levels in disease-relevant cell models of axonal degeneration. This translated to improved neuronal survival and reductions in extracellular neurofilament light chain, or NfL levels, a broadly researched biomarker for axonal degeneration in ALS, across multiple disease models and paradigms of neuronal injury. AMX0114 was generally well-tolerated in in vivo preclinical safety studies.

In April 2025, we dosed the first participant in Canada for the Phase 1 LUMINA clinical trial (NCT06665165), a multicenter, randomized, double-blind, placebo-controlled, multiple ascending dose trial designed to evaluate the safety and biological activity of AMX0114 in people living with ALS. LUMINA will also assess ALS biomarkers, including change from baseline in NfL levels. In addition to the activated sites in Canada, we are continuing to open U.S. sites for screening, enrollment, and dosing. Approximately 48 participants will be randomized 3:1 to receive AMX0114 or placebo by intrathecal administration once every four weeks, for up to four doses. Early cohort data from LUMINA are expected in 2025.

Components of Our Results of Operations

Operating Expenses

Research and Development Expenses

Research and development expenses consist primarily of costs incurred in connection with the research and development of avexitide, AMX0035, AMX0114 and other potential future product candidates. We expense research and development costs as incurred. These expenses include:

•

expenses incurred under agreements with CROs, CMOs, as well as investigative sites and consultants that conduct our clinical trials, preclinical studies and other scientific development services;

•

manufacturing scale-up expenses and the cost of acquiring and manufacturing drug product for our preclinical studies and clinical trials, including manufacturing registration and validation batches, as well as pre-commercial manufacturing activities;

•

expenses to acquire technologies to be used in research and development;

•

employee-related expenses, including salaries, payroll taxes, related benefits and stock-based compensation expense for employees engaged in research and development functions; and

•

costs related to compliance with quality and regulatory requirements.

Advance payments that we make for goods or services to be received in the future for use in research and development activities are recorded as prepaid expenses. Such amounts are recognized as an expense as the goods are delivered or the related services are performed, or until it is no longer expected that the goods will be delivered, or the services rendered.

Certain of our indirect research and development expenses are not tracked on an indication-by-indication basis. We do not allocate employee costs and facilities, including depreciation or other indirect costs, to specific indications because these costs are deployed across multiple indications and, as such, are not separately classified. We use internal resources to oversee the research and discovery as well as to manage our preclinical development, process development, manufacturing and clinical development activities. These employees work across multiple indications and, therefore, we do not track their costs by indication.

Research and development activities are central to our business model. Product candidates such as avexitide and AMX0035 in later stages of clinical development generally have higher development costs than those in earlier stages of clinical development, such as AMX0114, primarily due to the increased size and duration of later-stage clinical trials and related product manufacturing expenses. Despite a decline in research and development expenses in 2024 and in the first quarter of 2025 compared to prior respective periods, research and development expenses increased in the second quarter of 2025 compared to the prior year period and we expect that our research and development expenses will continue to increase in connection with our planned clinical development activities in the near term and in the future. At this time, we cannot accurately estimate or know the nature, timing and costs of the efforts that will be necessary to complete the clinical development of avexitide, AMX0035, AMX0114 and any future product candidates. Our clinical development costs may vary significantly based on factors such as:

•

per patient trial costs;

•

the number of trials required for approval;

•

the number of sites included in the trials;

•

the countries in which the trials are conducted;

•

the length of time required to enroll eligible patients;

•

the number of patients that participate in the trials;

•

the number of doses that patients receive;

•

the drop-out or discontinuation rates of patients;

•

potential additional safety monitoring requested by regulatory agencies;

•

the duration of patient participation in the trials and follow-up periods;

•

the cost and timing of manufacturing our current or future product candidates;

•

the phase of development of our current or future product candidates;

•

the efficacy and safety profile from clinical trials and preclinical studies of our current or future product candidates; and

•

the number of product candidates we are developing.

The successful development and commercialization of avexitide, AMX0035 and any other current or future product candidates is highly uncertain, due to the numerous risks and uncertainties associated with product development and commercialization, including the following:

•

the timing and progress of preclinical and clinical development activities;

•

the number and scope of preclinical and clinical trials for separate indications we decide to pursue;

•

raising additional funds, if necessary;

•

the progress of the development efforts of parties with whom we may enter into collaboration arrangements;

•

our ability to maintain our current development activities and to establish new ones;

•

our ability to establish new licensing or collaboration arrangements;

•

the successful initiation and completion of clinical trials with safety, tolerability and efficacy profiles that are satisfactory to the FDA or any other comparable foreign regulatory authority;

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the availability of drug substance and drug product for use in production of avexitide, AMX0035 or other product candidates;

•

establishing and maintaining agreements with third-party manufacturers for clinical supply for our clinical trials;

•

our ability to obtain and maintain patents, trade secret protection and regulatory exclusivity, both in the U.S. and internationally;

•

our ability to protect our rights in our intellectual property portfolio;

•

obtaining and maintaining third-party insurance coverage and adequate reimbursement in the future for any approved products;

•

the acceptance of our products and product candidates, if approved, by patients, the medical community and third-party payors;

•

competition with other products; and

•

a continued acceptable safety profile of our therapies in pre-approval market access programs or in commercial access following approval.

A change in the outcome of any of these variables with respect to the development of avexitide, AMX0035, AMX0114 or any other current or future product candidates could have a significant impact on the cost and timing associated with the development of our product candidates. We may never succeed in obtaining or maintaining, as applicable, regulatory approval for avexitide, AMX0035, AMX0114 or any other current or future product candidates.

Selling, General and Administrative Expenses

Selling, general and administrative expenses consist primarily of salaries and related costs for personnel in executive, finance, sales, marketing, as well as administrative functions. Selling, general and administrative expenses also include legal fees relating to patent and corporate matters; professional fees for accounting, auditing, tax and administrative consulting services; corporate insurance costs; administrative travel expenses; sales and marketing expenses; information technology; charitable donations to independent charitable foundations; facility-related and other operating costs. In April 2024, we announced a restructuring plan, or the Restructuring Plan, designed to focus our resources on key clinical and preclinical programs. The restructuring included a reduction in force which reduced our workforce by approximately 70% and a decrease in external financial commitments outside our priority areas. As a result, our selling, general and administrative expenses decreased during the three and six months ended June 30, 2025 as compared to the three and six months ended June 30, 2024. However, we expect that general and administrative expenses will increase in future periods as we advance our clinical pipeline.

Income Taxes

We have historically not incurred significant income taxes. We continue to maintain a full valuation allowance against all of our deferred tax assets based on management’s evaluation of all available evidence, including our history of incurring significant losses from operations. As a result, we don’t expect to incur material income taxes for the foreseeable future.

Results of Operations

Comparison of the three months ended June 30, 2025 and 2024

The following table summarizes our results of operations for the periods presented (in thousands):


	Three Months Ended June 30,
	2025			2024			$ Change			% Change
Product revenue, net	$	—		$	(1,023	)	$	1,023			(100	)%
Operating expenses:
Cost of sales		—			8			(8	)		(100	)%
Cost of sales - inventory impairment and loss on firm purchase commitments		—			7,410			(7,410	)		(100	)%
Research and development		27,217			23,347			3,870			17	%
Selling, general and administrative		15,640			21,647			(6,007	)		(28	)%
Restructuring expenses		—			22,851			(22,851	)		(100	)%
Total operating expenses		42,857			75,263			(32,406	)		(43	)%
Loss from operations		(42,857	)		(76,286	)		33,429			(44	)%
Other income, net:
Interest income		1,960			4,069			(2,109	)		(52	)%
Other expense, net		(546	)		(483	)		(63	)		13	%
Total other income, net		1,414			3,586			(2,172	)		(61	)%
Loss before income taxes		(41,443	)		(72,700	)		31,257			(43	)%
Provision for income taxes		—			—			—		*NM
Net loss	$	(41,443	)	$	(72,700	)	$	31,257			(43	)%

* NM - not meaningful

Product Revenue, Net and Cost of Sales

As a result of the RELYVRIO®/ALBRIOZA™ Discontinuation, we did not generate revenue from product sales for the three months ended June 30, 2025. For the three months ended June 30, 2024, product revenue, net was primarily related to gross-to-net adjustments reflecting actual rebate and return activity during the period.

As a result of the RELYVRIO®/ALBRIOZA™ Discontinuation, we did not generate cost of sales for the three months ended June 30, 2025. Cost of sales for the three months ended June 30, 2024 consisted of costs to procure, manufacture and distribute our marketed products, RELYVRIO and ALBRIOZA. As a result of the RELYVRIO®/ALBRIOZA™ Discontinuation, we recorded approximately $7.4 million of charges associated with the write-down of inventory and losses on firm purchase commitments for the three months ended June 30, 2024.

Research and Development Expenses

The following table summarizes our research and development expenses for the three months ended June 30, 2025 and 2024 (in thousands):


	Three Months Ended June 30,
	2025		2024		$ Change			% Change
Direct research and development expenses by program:
Avexitide	$	7,105	$	—	$	7,105		*NM
AMX0035 - PSP		7,146		3,546		3,600			102	%
AMX0035 - ALS		794		9,408		(8,614	)		(92	)%
Other programs		3,965		2,221		1,744			79	%
Total direct research and development expenses by program		19,010		15,175		3,835			25	%
Payroll and personnel-related		8,207		8,172		35			0	%
	$	27,217	$	23,347	$	3,870			17	%

* NM - not meaningful

Research and development expenses were $27.2 million for the three months ended June 30, 2025, compared to $23.3 million for the three months ended June 30, 2024. The increase was primarily due to a $7.1 million increase in expenses related to the pivotal Phase 3 LUCIDITY clinical trial for avexitide in PBH, a $3.6 million increase in expenses related to AMX0035 for the treatment of PSP and a $1.7 million increase in expenses related to other research and development activities. The increase was partially offset by a $8.6 million decrease in spending on AMX0035 for the treatment of ALS following the topline data from the PHOENIX trial.

Selling, General and Administrative Expenses

Selling, general and administrative expenses were $15.6 million for the three months ended June 30, 2025 compared to $21.6 million for the three months ended June 30, 2024. The decrease was primarily due to a decrease of $0.8 million in payroll and personnel-related costs, a decrease of $2.0 million in consulting and professional services and a decrease of $3.2 million in other expenses. The decrease in payroll and personnel-related costs was primarily related to a decrease in the number of employees as a result of the Restructuring Plan. The decrease in consulting and professional services is primarily due to a decrease in commercial sales and marketing activity as a result of the RELYVRIO®/ALBRIOZA™ Discontinuation. The decrease in other expenses is primarily due to a decrease in facilities and IT-related expenses.

Restructuring Expenses

We did not recognize restructuring expenses for the three months ended June 30, 2025. During the three months ended June 30, 2024, restructuring expenses were approximately $22.9 million which includes employee severance and termination benefits of approximately $21.8 million, contract termination costs, impairment of long-lived assets and other costs of $1.0 million. We substantially completed the Restructuring Plan in the second quarter of 2024.

Comparison of the six months ended June 30, 2025 and 2024

The following table summarizes our results of operations for the periods presented (in thousands):


	Six Months Ended June 30,
	2025		2024		$ Change			% Change
Product revenue, net	$	—	$	87,620	$	(87,620	)		(100	)%
Operating expenses:
Cost of sales		—		5,953		(5,953	)		(100	)%
Cost of sales - inventory impairment and loss on firm purchase commitments		—		117,871		(117,871	)		(100	)%
Research and development		49,336		59,955		(10,619	)		(18	)%
Selling, general and administrative		31,324

Amylyx Pharmaceuticals, Inc. 10-Q