[10-Q] Septerna, Inc. Quarterly Earnings Report

Rhea-AI Filing Summary

Septerna, Inc. reported a profitable Q3 2025 as collaboration revenue ramped and interest income increased. Revenue was $21,495 thousand for the three months ended September 30, 2025, up from $176 thousand a year ago, reflecting recognition under its Novo Nordisk collaboration. The company recorded net income of $8,173 thousand in Q3 2025, compared to a net loss of $20,523 thousand in Q3 2024. Results also included a $12,500 thousand gain on sale of a non‑financial asset tied to a Vertex milestone.

Liquidity strengthened with cash, cash equivalents and marketable securities of $561,600 thousand as of September 30, 2025. Deferred revenue was $182,250 thousand (current $61,603 thousand; non‑current $120,647 thousand) from the $195,000 thousand Novo upfront received in July 2025, of which $12,750 thousand was recognized year‑to‑date. R&D expense was $24,264 thousand and G&A was $7,117 thousand in Q3 2025. Shares outstanding were 44,774,192 as of November 4, 2025.

Positive

• Q3 2025 profitability with $8,173 thousand net income and liquidity of $561,600 thousand in cash and marketable securities, supported by the $195,000 thousand Novo upfront and deferred revenue of $182,250 thousand.

Negative

• None.

Insights

Biopharma equity analyst

Q3 turns profitable on Novo revenue and Vertex gain; cash strong.

Septerna posted Q3 2025 revenue of $21,495 thousand primarily from its Novo collaboration, shifting to net income of $8,173 thousand. The quarter also included a $12,500 thousand gain from a Vertex milestone. Operating lines grew with R&D at $24,264 thousand and G&A at $7,117 thousand.

Balance sheet capacity is notable: cash, cash equivalents and marketable securities totaled $561,600 thousand, aided by the $195,000 thousand Novo upfront, with $182,250 thousand recorded as deferred revenue. Interest income of $5,565 thousand contributed to profitability.

Future revenue recognition will track progress under ASC 606, with $61,603 thousand current and $120,647 thousand non‑current deferred revenue. Actual impact depends on execution of the four R&D programs under the Novo agreement and timing of service delivery and cost accruals.

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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 September 30, 2025

OR

☐ 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: 001-42382

Septerna, Inc.

(Exact Name of Registrant as Specified in its Charter)

Delaware	84-3891440
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)
250 East Grand Avenue South San Francisco, CA	94080
(Address of principal executive offices)	(Zip Code)

Registrant’s telephone number, including area code: (650) 338-3533

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, par value $0.001 per share		SEPN		The Nasdaq Global 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 November 4, 2025 the registrant had 44,774,192 shares of common stock, $0.001 par value per share, outstanding.

1

TABLE OF CONTENTS

		Page
PART I.	FINANCIAL INFORMATION	1
Item 1.	Financial Statements (unaudited)	1
	Condensed Balance Sheets	1
	Condensed Statements of Operations and Comprehensive Income (Loss)	2
	Condensed Statements of Convertible Preferred Stock and Stockholders’ Equity (Deficit)	3
	Condensed Statements of Cash Flows	5
	Notes to Unaudited Condensed Financial Statements	7
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	23
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	35
Item 4.	Controls and Procedures	35
PART II.	OTHER INFORMATION	37
Item 1.	Legal Proceedings	37
Item 1A.	Risk Factors	37
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	41
Item 3.	Defaults Upon Senior Securities	42
Item 4.	Mine Safety Disclosures	42
Item 5.	Other Information	42
Item 6.	Exhibits	42
Signatures		44

We own various U.S. federal trademark applications and unregistered trademarks, including our company name and logo, that we use in connection with the operation of our business. This Quarterly Report on Form 10-Q (this “Quarterly Report”) includes our trademarks and trade names which are protected under applicable intellectual property laws and are our property. This Quarterly Report also contains trademarks, trade names and service marks of other companies, which are the property of their respective owners. Solely for convenience, trademarks, trade names and service marks referred to in this Quarterly Report may appear without the ®, ™ or SM symbols, but such references are not intended to indicate, in any way, that we will not assert, to the fullest extent permitted under applicable law, our rights or the right of the applicable licensor to these trademarks, trade names and service marks. We do not intend our use or display of other parties’ trademarks, trade names or service marks to imply, and such use or display should not be construed to imply, a relationship with, or endorsement or sponsorship of us by, these other parties.

From time to time, we may use our website as well as social media, including our X (formerly known as Twitter) account at Septerna_Inc and our LinkedIn account at https://www.linkedin.com/company/septernainc/ to distribute material information about us and for complying with our disclosure obligations under Regulation FD. Our financial and other material information is routinely posted to and accessible on the Investors section of our website, available at www.Septerna.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 social media are not incorporated into, and does not form a part of, this Quarterly Report.

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SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report contains express or implied forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, Section 27A of the Securities Act of 1933, as amended (the “Securities Act”), and Section 21E of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). These statements are based on our management’s belief and assumptions and on information currently available to our management. Although we believe that the expectations reflected in these forward-looking statements are reasonable, these statements relate to future events or our future operational or 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. Forward-looking statements in this Quarterly Report include, but are not limited to, statements about:

•the initiation, timing, progress, results and costs of conducting our research and development programs and our current and future preclinical studies and clinical trials, including statements regarding the timing of initiation and completion of studies or trials and related preparatory work, the period during which the results of the trials will become available, and our current and future programs;

•the potential therapeutic benefits of our product candidates, including our PTH1R agonist and SEP-631 programs;

•our ability to demonstrate, and the timing of, preclinical proof-of-concept in vivo and ex vivo for multiple programs;

•our ability to replicate positive results achieved in our preclinical studies or clinical trials in current or future clinical trials;

•our ability to obtain and maintain regulatory approval for our current and future product candidates and research and development programs, including our PTH1R agonist and SEP-631 programs, and to advance any product candidates that we may identify and successfully complete any clinical studies, including the manufacture of any such product candidates;

•the timing, scope and likelihood of regulatory filings and approvals, including timing of Investigational New Drug (“IND”) applications or comparable foreign applications, and final U.S. Food and Drug Administration (the “FDA”) approval of our product candidates;

•the timing, scope or likelihood of foreign regulatory filings and approvals;

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

•the scope of protection we are able to establish and maintain for intellectual property rights covering our product candidates and other product candidates we may develop, including the extensions of existing patent terms where available, the validity of intellectual property rights held by third parties, and our ability not to infringe, misappropriate or otherwise violate any third-party intellectual property rights;

•developments relating to our competitors and our industry;

•our ability to leverage programs within our initial target indications and to progress additional programs to further develop our pipeline;

•our ability of our preclinical studies and clinical trials to demonstrate safety and efficacy of our product candidates, and other positive results;

•the partnership with Novo Nordisk A/S (“Novo”) and the intended and potential benefits thereof, including the receipt of potential milestone payments and royalty payments from commercial product sales, along with tiered royalties based on global net sales, if any;

•Novo's ability to develop and commercialize potential oral small molecule therapies for metabolic-related diseases and the potential of G protein-coupled receptors, including the GLP-1, GIP, and glucagon receptors, to address the unmet medical need for treating obesity, type 2 diabetes and other related conditions;

•our ability to maintain existing collaborations and strategic partnerships, to identify and enter into future license agreements and collaborations, and to realize the intended and potential benefits of such agreements and collaborations;

•our ability to rely on third-party manufacturers and successfully manufacture product candidates for preclinical use, clinical trials and on a larger scale for commercial use, if approved;

•our ability to realize the benefits of collaborations for the development and commercialization of our product candidates;

•our ability to commercialize any of our product candidates;

•developments related to our proprietary Native Complex Platform™;

•regulatory developments in the U.S. and foreign countries;

ii

•our ability to obtain funding for our operations necessary to complete further development and commercialization of our product candidates;

•the size and growth potential of the markets for our product candidates and our ability to serve those markets;

•our need for and ability to attract and retain key scientific, management and other personnel and to identify, hire, and retain additional qualified professionals;

•our expectations regarding the period during which we will remain an emerging growth company under the Jumpstart Our Business Startups Act of 2012 (“JOBS Act”);

•the period over which we expect our existing cash, cash equivalents and investments will be sufficient to fund our operating expenses and capital expenditure requirements;

•our anticipated use of our existing resources;

•our financial performance and estimates of our future expenses, capital requirements, and our needs for additional financing;

•the impact of macroeconomic and geopolitical developments on our business, including rising inflation and capital market disruptions, changes in or disruptions of U.S. governmental agencies, whether from a continued U.S. federal government shutdown or reduced resources, new or increased international tariffs and retaliatory tariffs, trade protection measures, economic sanctions and economic slowdowns or recessions that may result from such developments which could harm our research and development efforts as well as the value of our common stock and our ability to access capital markets; and

•other risks and uncertainties, including those listed under the section titled “Risk Factors” in Part II, Item 1A.

In some cases, you can identify forward-looking statements by terminology such as “may,” “might,” “will,” “could,” “would,” “should,” “expect,” “plan,” “anticipate,” “intend,” “believe,” “estimate,” “seek,” “predict,” “future,” “project,” “potential,” “continue,” “target,” “contemplate,” “possible,” “can,” or the negative of these terms or other comparable terminology, and similar expressions, although not all forward-looking statements contain these identifying words. These statements are only predictions. You should not place undue reliance on forward-looking statements because they involve known and unknown risks, uncertainties, and other factors, which are, in some cases, beyond our control and which could materially affect results. Factors that may cause actual results to differ materially from current expectations include, among other things, those listed under the section titled “Risk Factors” and elsewhere in this Quarterly Report. If one or more of these risks or uncertainties occur, or if our underlying assumptions prove to be incorrect, actual events or results may vary significantly from those implied or projected by the forward-looking statements. No forward-looking statement is a guarantee of future performance. You should read this Quarterly Report and the documents that we reference in this Quarterly Report and have filed with the Securities and Exchange Commission (the “SEC”) thereto completely and with the understanding that our actual future results may be materially different from any future results expressed or implied by these forward-looking statements.

The forward-looking statements in this Quarterly Report represent our views as of the date of this Quarterly Report. We do not undertake any obligation to publicly update any forward-looking statement except to the extent required by applicable law. You should therefore not rely on these forward-looking statements as representing our views as of any date subsequent to the date of this Quarterly Report.

This Quarterly Report also contains estimates, projections and other information concerning our industry, our business and the markets for our product candidates. Information that is based on estimates, forecasts, projections, market research or similar methodologies is inherently subject to uncertainties and actual events or circumstances may differ materially from events and circumstances that are assumed in this information. Unless otherwise expressly stated, we obtained this industry, business, market, and other data from our own internal estimates and research as well as 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. All of the market data used in this Quarterly Report involves a number of assumptions and limitations, and you are cautioned not to give undue weight to such data. Industry publications and third-party research, surveys, and studies generally indicate that their information has been obtained from sources believed to be reliable, although they do not guarantee the accuracy or completeness of such information. Our estimates of the potential market opportunities for our product candidates include several key assumptions based on our industry knowledge, industry publications, third-party research, and other surveys, which may be based on a small sample size and may fail to accurately reflect market opportunities. While we believe that our internal assumptions are reasonable, no independent source has verified such assumptions.

This Quarterly Report contains summaries of certain provisions contained in some of the documents described herein, but reference is made to the actual documents for complete information. All of the summaries are qualified in their entirety by the actual documents. Copies of some of the documents referred to herein have been filed as exhibits to this Quarterly Report. Unless the context

iii

otherwise requires, reference in this Quarterly Report to the terms “Septerna,” “the Company,” “we,” “us,” “our,” and similar designations refer to Septerna, Inc.

iv

PART I—FINANCIAL INFORMATION

Item 1. Condensed Financial Statements.

SEPTERNA, INC.

Condensed Balance Sheets

(In thousands, except for share and per share data)

(Unaudited)

		September 30,				December 31,
		2025				2024
Assets
Current assets:
Cash and cash equivalents		$	319,989			$	238,196
Marketable securities			154,357				112,727
Accounts receivable			8,645				171
Prepaid expenses and other current assets			8,690				5,730
Total current assets			491,681				356,824
Marketable securities, non-current			87,212				69,866
Property and equipment, net			4,316				5,090
Operating lease right-of-use assets			22,038				23,602
Restricted cash			905				905
Other non-current assets			501				267
Total assets		$	606,653			$	456,554
Liabilities and Stockholders' Equity
Current liabilities:
Accounts payable		$	3,729			$	3,200
Accrued expenses and other current liabilities			7,833				7,798
Operating lease liabilities, current			2,117				1,851
Deferred revenue, current			61,603				—
Total current liabilities			75,282				12,849
Operating lease liabilities, non-current			21,993				23,625
Deferred revenue, non-current			120,647				—
Other non-current liabilities			—				33
Total liabilities			217,922				36,507
Commitments and contingencies (Note 5)
Stockholders' equity:
Preferred stock, $0.001 par value per share; 10,000,000 shares authorized as of    September 30, 2025 and December 31, 2024; no shares issued and outstanding as    of September 30, 2025 and December 31, 2024			—				—
Common stock, $0.001 par value per share, 500,000,000 shares authorized at    September 30, 2025 and December 31, 2024; 44,638,703 and 44,422,505 shares    issued and outstanding at September 30, 2025 and December 31, 2024, respectively;    228,020 and 576,829 shares subject to repurchase as of September 30, 2025 and    December 31, 2024, respectively			45				44
Additional paid-in capital			544,826				538,321
Accumulated other comprehensive income			375				56
Accumulated deficit			(156,515	)			(118,374	)
Total stockholders' equity			388,731				420,047
Total liabilities and stockholders' equity		$	606,653			$	456,554

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

1

SEPTERNA, INC.

Condensed Statements of Operations and Comprehensive Income (Loss)

(In thousands, except for share and per share data)

(Unaudited)

		Three Months Ended September 30,								Nine Months Ended September 30,
		2025				2024				2025				2024
Revenue		$	21,495			$	176			$	21,833			$	863
Operating (income) expenses:
Research and development			24,264				17,832				65,723				46,020
General and administrative			7,117				4,894				20,884				10,948
Gain on sale of non-financial asset			(12,500	)			—				(12,500	)			—
Total operating expenses			18,881				22,726				74,107				56,968
Income (loss) from operations			2,614				(22,550	)			(52,274	)			(56,105	)
Other income, net:
Interest income			5,565				1,900				14,192				4,709
Other expense, net			(6	)			(9	)			(59	)			(72	)
Total other income, net			5,559				1,891				14,133				4,637
Income (loss) before benefit for income taxes			8,173				(20,659	)			(38,141	)			(51,468	)
Benefit for income taxes			—				136				—				338
Net income (loss) attributable to common stockholders		$	8,173			$	(20,523	)		$	(38,141	)		$	(51,130	)
Net income (loss) per share attributable to common stockholders:
Basic		$	0.18			$	(8.40	)		$	(0.86	)		$	(21.87	)
Diluted		$	0.18			$	(8.40	)		$	(0.86	)		$	(21.87	)
Weighted-average shares outstanding used in computing net income per share attributable to common stockholders:
Basic			44,343,085				2,443,678				44,150,041				2,337,891
Diluted			45,602,099				2,443,678				44,150,041				2,337,891
Comprehensive income (loss):
Net income (loss)		$	8,173			$	(20,523	)		$	(38,141	)		$	(51,130	)
Net unrealized gain on marketable securities			199				184				319				176
Total other comprehensive income			199				184				319				176
Comprehensive income (loss)		$	8,372			$	(20,339	)		$	(37,822	)		$	(50,954	)

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

2

SEPTERNA, INC.

Condensed Statements of Convertible Preferred Stock and Stockholders’ Equity (Deficit)

(In thousands, except for share data)

(Unaudited)

										Additional				Accumulated Other								Total
		Common Stock								Paid-In				Comprehensive				Accumulated				Stockholders'
		Shares				Amount				Capital				Income				Deficit				Equity
Balance at December 31, 2024			44,422,505			$	44			$	538,321			$	56			$	(118,374	)		$	420,047
Issuance of common stock upon exercise of stock    options			25,930				—				66				—				—				66
Vesting of restricted common stock			—				—				5				—				—				5
Stock-based compensation expense			—				—				1,482				—				—				1,482
Net unrealized gain on marketable securities			—				—				—				142				—				142
Net loss			—				—				—				—				(21,476	)			(21,476	)
Balance at March 31, 2025			44,448,435				44				539,874				198				(139,850	)			400,266
Issuance of common stock upon exercise of stock    options			119,456				1				338				—				—				339
Vesting of restricted common stock			—				—				6				—				—				6
Stock-based compensation expense			—				—				1,806				—				—				1,806
Net unrealized loss on marketable securities			—				—				—				(22	)			—				(22	)
Net loss			—				—				—				—				(24,838	)			(24,838	)
Balance at June 30, 2025			44,567,891				45				542,024				176				(164,688	)			377,557
Issuance of common stock upon exercise of stock    options			73,424				—				264				—				—				264
Vesting of restricted common stock			—				—				6				—				—				6
Repurchase of unvested restricted common stock			(2,612	)			—				—				—				—				—
Stock-based compensation expense			—				—				2,532				—				—				2,532
Net unrealized gain on marketable securities			—				—				—				199				—				199
Net income			—				—				—				—				8,173				8,173
Balance at September 30, 2025			44,638,703			$	45			$	544,826			$	375			$	(156,515	)		$	388,731

3

		Convertible Preferred Stock																									Additional				Accumulated Other								Total
		Series A								Series B									Common Stock								Paid-In				Comprehensive				Accumulated				Stockholders'
		Shares				Amount				Shares				Amount					Shares				Amount				Capital				Loss				Deficit				Deficit
Balance at December 31, 2023			75,000,000			$	74,694				60,828,720			$	74,521					3,168,134			$	3			$	8,199			$	—			$	(46,576	)		$	(38,374	)
Issuance of common stock    upon exercise of stock options			—				—				—				—					217				—				1				—				—				1
Vesting of restricted common    stock			—				—				—				—					—				—				6				—				—				6
Repurchase of unvested restricted    common stock			—				—				—				—					(11,517	)			—				—				—				—				—
Stock-based compensation    expense			—				—				—				—					—				—				577				—				—				577
Net unrealized loss on    marketable securities			—				—				—				—					—				—				—				(7	)			—				(7	)
Net loss			—				—				—				—					—				—				—				—				(14,097	)			(14,097	)
Balance at March 31, 2024			75,000,000				74,694				60,828,720				74,521					3,156,834				3				8,783				(7	)			(60,673	)			(51,894	)
Issuance of Series B Convertible    Preferred Stock, net of issuance    costs of $479			—				—				60,828,732				74,942					—				—				—				—				—				—
Issuance of common stock    upon exercise of stock options			—				—				—				—					6,186				—				10				—				—				10
Vesting of restricted common    stock			—				—				—				—					—				—				4				—				—				4
Stock-based compensation    expense			—				—				—				—					—				—				628				—				—				628
Net unrealized loss on    marketable securities			—				—				—				—					—				—				—				(1	)			—				(1	)
Net loss			—				—				—				—					—				—				—				—				(16,510	)			(16,510	)
Balance at June 30, 2024			75,000,000				74,694				121,657,452				149,463					3,163,020				3				9,425				(8	)			(77,183	)			(67,763	)
Issuance of common stock    upon exercise of stock options			—				—				—				—					2,730				—				5				—				—				5
Vesting of restricted common    stock			—				—				—				—					—				—				6				—				—				6
Repurchase of unvested    restricted common stock			—				—				—				—					(2,782	)			—				—				—				—				—
Stock-based compensation    expense			—				—				—				—					—				—				683				—				—				683
Net unrealized gain on    marketable securities			—				—				—				—					—				—				—				184				—				184
Net loss			—				—				—				—					—				—				—				—				(20,523	)			(20,523	)
Balance at September 30, 2024			75,000,000			$	74,694				121,657,452			$	149,463					3,162,968			$	3			$	10,119			$	176			$	(97,706	)		$	(87,408	)

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

4

SEPTERNA, INC.

Condensed Statements of Cash Flows

(In thousands)

(Unaudited)

		Nine Months Ended September 30,
		2025				2024
Cash flows from operating activities:
Net loss		$	(38,141	)		$	(51,130	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization			1,203				1,013
Gain on sale of non-financial asset			(12,500	)			—
Non-cash operating lease expense			1,564				890
Stock-based compensation			5,820				1,888
Accretion of premiums (discounts), net			(2,561	)			(601	)
Deferred income tax			—				(338	)
Other			26				52
Changes in operating assets and liabilities:
Prepaid expenses and other current assets			(2,956	)			(1,249	)
Accounts receivable			(8,474	)			(60	)
Other non-current assets			(238	)			(173	)
Accounts payable			530				2,419
Accrued expenses and other current liabilities			20				579
Operating lease, net			(1,366	)			198
Deferred revenue			182,250				—
Net cash provided by (used in) operating activities			125,177				(46,512	)
Cash flows from investing activities:
Purchases of property and equipment			(453	)			(1,491	)
Proceeds from sale of non-financial asset			12,500				22,625
Purchases of marketable securities			(223,515	)			(65,828	)
Maturities of marketable securities			167,416				17,335
Net cash used in investing activities			(44,052	)			(27,359	)
Cash flows from financing activities:
Proceeds from issuance of Series B Convertible Preferred stock, net of issuance costs			—				74,942
Repurchases of unvested restricted common stock			(1	)			(1	)
Proceeds from exercise of stock options			669				16
Payments of deferred offering costs			—				(1,327	)
Net cash provided by financing activities			668				73,630
Net increase (decrease) in cash, cash equivalents and restricted cash			81,793				(241	)
Cash, cash equivalents and restricted cash, beginning of period			239,101				89,388
Cash, cash equivalents and restricted cash, end of period		$	320,894			$	89,147
Supplemental cash flow information:
Cash paid for income taxes		$	—			$	232
Supplemental disclosure for noncash investing and financing activities:
Right-of-use asset recognized in exchange for operating lease liability		$	—			$	(12,462	)
Unpaid deferred offering costs included in accounts payable and accrued expenses and    other current liabilities		$	—			$	1,882
Property and equipment included in accounts payable and accrued expenses and other    current liabilities		$	—			$	321

5

Cash, Cash Equivalents and Restricted Cash:

		As of September 30,
		2025				2024
Cash and cash equivalents		$	319,989			$	88,242
Restricted cash			905				905
Total cash, cash equivalents and restricted cash		$	320,894			$	89,147

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

6

SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements

Note 1. Organization and Basis of Presentation

Description of the Business

Septerna, Inc. (“Septerna” or the “Company”) is a clinical-stage biotechnology company with a world-class team of G protein-coupled receptor (“GPCR”) experts and drug developers advancing cutting-edge science to unlock the full potential of GPCR therapies for patients with significant unmet needs. The Company’s proprietary Native Complex Platform™ is designed to enable new approaches to GPCR drug discovery and has led to the development of a diverse pipeline of novel oral small molecule drug candidates. The Company is advancing programs in endocrinology, immunology and inflammation, metabolic diseases and additional therapeutic areas, both independently and with partners.

The Company’s proprietary Native Complex Platform™ replicates the natural structure, function, and dynamics of GPCRs outside of cells at an industrial scale. The Company’s foundational technologies enable it to isolate, purify, and reconstitute full-length, properly folded GPCR proteins within ternary complexes with ligands and transducer proteins in a lipid bilayer that mimics the cell membrane. The Company then applies state-of-the-art discovery tools and technologies to these defined and tunable protein complexes to structurally design, screen for, and optimize potential product candidates. Leveraging its platform, the Company has transformed GPCR oral small molecule drug discovery to an industrialized and iterative structure-based drug design approach to expand the landscape of druggable GPCR targets with novel oral small molecule medicines for patients. The Company’s Native Complex Platform™ is designed to enable it to target certain GPCRs for the first time, uncover novel binding pockets for validated receptors, and pursue a wide spectrum of pharmacologies, including agonists, antagonists, and allosteric modulators, to affect GPCR signaling in different ways to achieve desired therapeutic effects.

The Company was incorporated in Delaware in December 2019, under the name GPCR NewCo, Inc. In June 2021, the Company changed its name to Septerna, Inc. The Company is headquartered in South San Francisco, California.

Reverse Stock Split

On October 18, 2024, the Company effected a 1-for-8.6103 reverse stock split of its issued and outstanding shares of common stock. Upon the effectiveness of the reverse stock split, (i) all shares of outstanding common stock were adjusted; (ii) the conversion ratio of the convertible preferred stock was adjusted; (iii) the number of shares of common stock for which each outstanding option to purchase common stock is exercisable were adjusted; and (iv) the exercise price of each outstanding option to purchase common stock was adjusted. All of the outstanding common stock (including shares of common stock subject to the Company’s options and as converted for the outstanding convertible preferred stock), share prices, exercise prices and per share amounts contained in the condensed financial statements have been retroactively adjusted to reflect this reverse stock split for all periods presented. The par value per share and the authorized number of shares of common stock and preferred stock were not adjusted as a result of the reverse stock split. The number of authorized shares did not change.

Initial Public Offering

In October 2024, the Company completed its initial public offering (“IPO”), pursuant to which it issued and sold an aggregate of 18.4 million shares of its common stock at the IPO price of $18.00 per share, including 2.4 million shares that were issued to the underwriters pursuant to the full exercise of their option to purchase additional shares, resulting in net proceeds of $302.8 million, net of total offering costs of $28.4 million. Immediately prior to the closing of the IPO, the Company’s then outstanding convertible preferred stock automatically converted into 22,839,774 shares of common stock.

Following the closing of the IPO, no shares of convertible preferred stock were authorized or outstanding. In connection with the completion of the IPO, on October 28, 2024, the Company’s certificate of incorporation was amended and restated to (i) authorize 500.0 million shares of common stock, par value $0.001 per share, which eliminates all references to the previously existing series of convertible preferred stock; and (ii) authorize 10.0 million shares of undesignated preferred stock, par value $0.001 per share, that may be issued from time to time by the Company’s board of directors in one or more series.

Liquidity and Capital Resources

The accompanying unaudited condensed financial statements have been prepared assuming the Company will continue as a going concern, which assumes that the Company will realize its assets and satisfies its liabilities in the normal course of business. The Company is subject to risks inherent in operating an early-stage biotechnology business. These risks include, but are not limited to, dependence

7

SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

on the development of marketable products, the ability to attract, retain, and motivate qualified personnel, rapid technological changes and the rapidly evolving nature of the biotechnology industry.

The Company has incurred significant losses and negative cash flows from operations since its inception and expects to incur losses as a result of its continued research and development activities. To date, none of the Company’s product candidates have been approved by the U.S. Food and Drug Administration (the “FDA”) for commercial sale and, therefore, the Company has not generated any revenue from product sales.

The Company historically financed its operations primarily through the issuance of convertible promissory notes, convertible preferred stock, the sale of its common stock in an IPO, and most recently, through a one-time, non-refundable upfront payment upon commencement of its collaboration agreement with Novo Nordisk A/S (“Novo”) and achievement of a milestone event pursuant to its agreement with Vertex Pharmaceuticals Incorporated ("Vertex"). The Company will need additional financing to support its continuing operations and pursue its growth strategy. Until such time as the Company can generate significant revenue from product sales, if ever, it expects to finance its operations through equity offerings, debt financings or other capital sources, including collaborations with other companies or other strategic transactions. The Company may not be able to obtain funding on acceptable terms, or at all. The terms of any financing may adversely affect the holdings or the rights of the Company’s stockholders.

For the nine months ended September 30, 2025 and 2024, the Company incurred net losses of $38.1 million and $51.1 million, respectively. The Company had an accumulated deficit of $156.5 million as of September 30, 2025. The Company believes its cash, cash equivalents, and marketable securities of $561.6 million as of September 30, 2025 will be sufficient to fund its operations for at least 12 months from the date of issuance of the unaudited condensed financial statements.

Basis of Presentation

The accompanying unaudited interim condensed financial statements have been prepared in conformity with generally accepted accounting principles in the U.S. (“U.S. GAAP”) for interim financial information. Accordingly, they do not include all of the information and footnotes required by U.S. GAAP for complete financial statements. In the opinion of management, all adjustments (consisting only of normal recurring adjustments) that are necessary for the fair presentation of the unaudited interim condensed financial statements for the periods presented have been included. Any reference in these notes to applicable guidance is meant to refer to the authoritative GAAP as found in the Accounting Standards Codification and Accounting Standards Updates (“ASUs”), of the Financial Accounting Standards Board (“FASB”). The interim condensed financial statements are unaudited. The operating results presented in these unaudited interim condensed financial statements are not necessarily indicative of the results that may be expected for the full year or for any other future annual or interim period. Actual results could differ materially from estimates and assumptions. As appropriate, the Company assesses estimates each period and updates them to reflect current information, and generally reflect any changes in estimates in the period first identified.

The balance sheet data at December 31, 2024 was derived from the audited financial statements included in Septerna’s Annual Report on Form 10-K for the year ended December 31, 2024 as filed with the SEC on March 27, 2025. These interim unaudited condensed financial statements should be read in conjunction with the audited financial statements and related notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024.

Significant Accounting Policies

During the nine months ended September 30, 2025, there were no changes to the Company’s significant accounting policies as described in Note 2 of the audited financial statements for the year ended December 31, 2024, except as described below.

Revenue Recognition

The Company accounts for revenue in accordance with ASC 606, “Revenue from Contracts with Customers” (“ASC 606”). Under ASC 606, the Company recognizes revenue when the customer obtains control of the promised goods or services at an amount that reflects the consideration the Company expects to receive in exchange for those goods or services. To determine revenue recognition for arrangements that the Company determines are within the scope of ASC 606, the Company performs the following four steps: (i) confirm it has a contract with a customer that creates enforceable rights and obligations; (ii) identify promised products or services to be transferred to a customer; (iii) determine the transaction price, or the amount it expects to receive, including an estimate of uncertain amounts subject to a constraint to ensure revenue is not recognized in an amount that would result in a significant reversal upon resolution

8

SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

of the uncertainty, is determinable and allocated to the performance obligations; and (iv) recognize revenue when or as performance obligations are satisfied.

Performance obligations promised in a contract are identified based on the goods and services that will be transferred to the customer that are both capable of being distinct and are distinct in the context of the contract. To the extent a contract includes multiple promised goods and services, the Company applies judgment to determine whether promised goods and services are both capable of being distinct and are distinct in the context of the contract. If these criteria are not met, the promised goods and services are accounted for as a combined performance obligation. For arrangements that include multiple performance obligations, the Company allocates the transaction price to the identified performance obligations based on the standalone selling price of each distinct performance obligation. In instances where standalone selling price is not directly observable, the Company develops assumptions that require judgment to determine the standalone selling price for each performance obligation identified in the contract using a cost plus margin approach, which is an estimation method used when standalone selling price is not directly observable. Key assumptions used within this estimation method may include full-time equivalent personnel effort and estimated external costs associated with the performance obligation.

The transaction price is determined based on the consideration to which the Company will be entitled in exchange for transferring goods and services to the customer. To the extent the transaction price includes variable consideration, the Company estimates the amount of variable consideration that should be included in the transaction price utilizing either the expected value method or the most likely amount method, depending on the nature of the variable consideration. Variable consideration is included in the transaction price if, in management’s judgment, it is probable that a significant future reversal of cumulative revenue under the contract will not occur. Any estimates, including the effect of the constraint on variable consideration, are evaluated at each reporting period for any changes.

If the contract contains a single performance obligation, the entire transaction price is allocated to the single performance obligation. Contracts that contain multiple performance obligations require an allocation of the transaction price to each performance obligation on a relative standalone selling price basis unless the transaction price is variable and meets the criteria to be allocated entirely to a performance obligation or to a distinct service that forms part of a single performance obligation.

The Company satisfies performance obligations either over time or at a point in time. Revenue is recognized over time if either (i) the customer simultaneously receives and consumes the benefits provided by the entity’s performance, (ii) the entity’s performance creates or enhances an asset that the customer controls as the asset is created or enhanced, or (iii) the entity’s performance does not create an asset with an alternative use to the entity and the entity has an enforceable right to payment for performance completed to date. If the entity does not satisfy a performance obligation over time, the related performance obligation is satisfied at a point in time by transferring the control of a promised good or service to a customer.

The Company’s revenues are primarily derived through its license and research and development service arrangements. Payments to the Company under these arrangements typically include one or more of the following: one-time, non-refundable upfront payment, research and development service funding, milestone and other contingent payments to the Company for the achievement of defined collaboration objectives and certain collaboration, research and development and commercial milestones, as well as royalties based on net sales of approved drugs.

Consideration received prior to revenue recognition is recorded as deferred revenue in the condensed balance sheets. Amounts expected to be recognized as revenue within the 12 months following the balance sheet date are classified as current portion of deferred revenue in the accompanying condensed balance sheets. Amounts not expected to be recognized as revenue within the 12 months following the balance sheet date are classified as deferred revenue, non-current. Contract assets represent research and development services which have been performed but have not yet been billed and are reduced when they are subsequently billed. Such contract assets include accounts receivable when the Company’s right to consideration is unconditional. For its current contracts, the Company recognizes revenue as the amount of the transaction price that is allocated to the respective performance obligation when (or as) each performance obligation is satisfied at a point in time or over time, and, if over time, revenue recognized is based on the use of an input method.

When no remaining performance obligations are required of the Company, or following the completion of the performance obligation period, such amounts are recognized as revenue upon transfer of control of the goods or services to the customer.

The terms of the Company’s collaborative arrangements include one or more of the following:

(i)Licenses of intellectual property, or IP - If the license to the Company’s IP is determined to be distinct from the other performance obligations identified in the arrangement, the Company recognizes revenue from consideration allocated to the license when the license is transferred to the customer and the customer can use and benefit from the licenses. For a license that is determined not to be distinct, it is combined with other promises and the Company utilizes judgment to assess the

9

SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. The Company generally recognizes revenue using the cost incurred to date as compared to the total estimated cost of each performance obligation. The impact on revenue of changes in total estimated costs are recognized on a cumulative basis in the period that the change occurs. If estimates of the total cost change, or if contract amendments change the scope of the performance obligation, the required adjustments to revenue could be material.

(ii)Customer options - The Company evaluates the customer options for material rights or options to acquire additional goods or services at no incremental consideration or at a discount. If the customer options are determined to represent a material right, the material right is recognized as a separate performance obligation at the outset of the arrangement. The Company allocates the transaction price to material rights based on the relative standalone selling price, which is determined based on the identified discount and the probability that the customer will exercise the option. Amounts allocated to a material right are not recognized as revenue until the option is exercised and performance obligations are satisfied. If an option is not exercised before the option right expires, the Company will accelerate and recognize all remaining revenue related to the material right performance obligation.

(iii)Research and development services - The promises under the Company's collaboration agreement include research and development services to be performed by the Company for or on behalf of the customer. Payments or reimbursements resulting from the Company's research and development efforts are recognized as the services are performed and presented on a gross basis because the Company is the principal for such efforts. Reimbursements are recognized in revenue in the Company’s condensed statements of operations and comprehensive loss. Expenses incurred as part of the Company’s efforts to perform the research and development services are recognized in research and development expense in the Company’s condensed statements of operations and comprehensive loss.

(iv)Manufacturing services - The promises under the Company's collaboration agreement include manufacturing services to be performed by the Company. Payments or reimbursements resulting from the Company's manufacturing services are recognized as the services are performed and presented on a gross basis because the Company is the principal for such efforts. Reimbursements are recognized in revenue in the Company’s condensed statements of operations and comprehensive loss. Expenses incurred to perform the manufacturing services are recognized in research and development expense in the Company’s condensed statements of operations and comprehensive loss.

(v)Milestone payments - At the inception of each arrangement that includes development or regulatory milestone payments, the Company evaluates the probability of reaching the milestones and estimates the amount to be included in the transaction price using the most likely amount method. If it is probable that a significant revenue reversal would not occur in the future, the associated milestone value is included in the transaction price. Milestone payments that are not within the Company’s control or the licensee’s, such as regulatory approvals, are not considered probable of being achieved until those approvals are received, and therefore, consideration included in the transaction price is constrained. The Company applied the variable consideration allocation exception under ASC 606 whereby variable milestone payments are not estimated and included in the transaction price at inception. The transaction price is then allocated to each performance obligation on a relative standalone selling price basis, for which the Company recognizes revenue as or when the performance obligations under the contract are satisfied. At the end of each subsequent reporting period, the Company re-evaluates the probability of achievement of such development milestones and any related constraint, and if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenues and earnings in the period of adjustment.

(vi)Commercial milestone payments and royalties - For arrangements that include sales-based royalties, including milestone payments based on levels of sales, if the license is deemed to be the predominant item to which the royalties relate, the Company recognizes revenue at the later of (i) when the related sales occur, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied (or partially satisfied).

Accounting Pronouncements Not Yet Adopted

From time to time, new accounting pronouncements are issued by the FASB, under its Accounting Standards Codification (“ASC”) or other standard setting bodies, and adopted by the Company as of the specified date.

In July 2025, the FASB issued ASU No. 2025-05, Financial Instruments—Credit Losses (Topic 326): Measurement of Credit Losses for Accounts Receivable and Contract Assets, which provides a practical expedient that assumes that current conditions as of the balance sheet date do not change for the remaining life of the asset in developing reasonable and supportable forecasts during the application of the current expected credit loss model for current accounts receivable and current contract assets arising from transactions

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

under ASC 606. ASU 2025-05 is effective for fiscal years beginning after December 15, 2025 and interim reporting periods within those annual reporting periods. Early adoption is permitted. The Company is currently evaluating the impact of adopting ASU 2025-05.

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, an accounting standard update that requires the Company to disclose more detailed information about the types of expenses (including employee compensation, depreciation, and amortization) included in each relevant income statement expense caption. In January 2025, the FASB issued ASU 2025-0, "Income Statement—Reporting Comprehensive Income—Expense Disaggregation Disclosures (Subtopic 220-40): Clarifying the Effective Date", to clarify the effective date of ASU 2024-03. These amendments are effective for fiscal years beginning after December 15, 2026 and interim reporting periods beginning after December 15, 2027. Early adoption is permitted. The Company is currently evaluating the impact that these updates will have on its disclosures.

In December 2023, the FASB issued ASU No. 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures, which enhances the transparency and decision usefulness of income tax disclosures. The standard is intended to improve income tax disclosures primarily related to the rate reconciliation and income taxes paid information. This update also includes certain other amendments to improve the effectiveness of income tax disclosures. The ASU is effective for fiscal years beginning after December 15, 2024 on a prospective basis. Early adoption and retrospective reporting are permitted. The Company is currently evaluating the impact of ASU 2023-09 on its interim condensed financial statements.

Note 2. Balance Sheet Components

Restricted Cash

Restricted cash is comprised of cash that is restricted as to withdrawal or use under the terms of certain contractual agreements. In connection with the Company’s lease agreement, the Company is required to maintain a collateral account to secure a letter of credit issued to its landlord. The collateral account is classified as restricted cash on the Company’s condensed balance sheets.

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets consist of the following (in thousands):

		As of September 30,				As of December 31,
		2025				2024
Prepaid expenses		$	3,973			$	3,114
Interest receivable			1,928				953
Prepaid clinical trial costs			1,250				1,164
Other receivable			1,152				174
Other current assets			387				325
Prepaid expenses and other current assets		$	8,690			$	5,730

Property and Equipment, Net

Property and equipment, net consist of the following (in thousands):

		As of September 30,				As of December 31,
		2025				2024
Lab equipment		$	6,036			$	5,679
Furniture, fixtures, and office equipment			1,222				1,222
Leasehold improvements			717				717
Computer equipment			401				401
Total property and equipment			8,376				8,019
Less: Accumulated depreciation and amortization			(4,060	)			(2,929	)
Property and equipment, net		$	4,316			$	5,090

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

Depreciation and amortization expense was $0.4 million and $1.2 million for the three and nine months ended September 30, 2025, respectively. Depreciation and amortization expense was $0.4 million and $1.0 million for the three and nine months ended September 30, 2024 respectively.

Deferred Revenue

Deferred revenue consists of amounts received prior to satisfying revenue recognition criteria (see Note 3).

Accrued Expenses and Other Current Liabilities

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

		As of September 30,				As of December 31,
		2025				2024
Accrued employee compensation expense		$	3,533			$	4,129
Accrued research and development expense			2,859				2,888
Accrued general and administrative expense			725				703
Employee stock purchase plan liability			604				—
Other current liabilities			112				78
Accrued expenses and other current liabilities		$	7,833			$	7,798

Note 3. Collaboration and Research Service Arrangements

For the nine months ended September 30, 2025, the Company's revenue is comprised solely of arrangements with Novo and Vertex. For the nine months ended September 30, 2024, the Company's revenue was solely comprised of arrangements with Vertex.

Novo Collaboration Agreement

On May 13, 2025, the Company entered into a Collaboration and License Agreement with Novo (the “Novo Collaboration Agreement”). Under the Novo Collaboration Agreement, the Company and Novo are exclusively collaborating to leverage the Company’s proprietary Native Complex Platform™ to discover, develop and commercialize multiple potential oral small molecule therapies for metabolic-related diseases based on certain specified molecular targets.

Upon effectiveness of the Novo Collaboration Agreement on July 1, 2025, the Company and Novo have commenced four simultaneous research and development programs (each an “R&D Program”), each pursuing one or more Collaboration Targets (as defined in the Novo Collaboration Agreement) from discovery through development candidate selection. Subject to certain limitations, Novo also has a right to modify the research plan with the option to commence additional R&D Programs. Novo will reimburse the Company for 100% of the fully burdened costs arising from all research and development activities undertaken by the Company under the Novo Collaboration Agreement. After development candidate selection, beginning with investigational new drug-enabling activities, Novo will be responsible for all further global development and commercialization for each product candidate at its sole cost and expense unless the profit share option described below is exercised. Novo is also responsible for all commercialization costs subject to the Company’s profit share option for up to one program under the Novo Collaboration Agreement. Pursuant to the terms of the Novo Collaboration Agreement, the Company will provide Novo with exclusive licenses to enable Novo to develop and commercialize products directed at the Collaboration Targets. The Company retains all other rights to its Native Complex Platform™ and all of the Company’s other research and development programs.

Upon effectiveness of the Novo Collaboration Agreement, the Company received a one-time, non-refundable upfront payment of $195.0 million in July 2025, which was recorded as deferred revenue in its condensed balance sheet. The Company is also eligible to receive up to $498.0 million in research, development, regulatory, and commercial milestone payments for each R&D Program. In addition, the Company is entitled to escalating, tiered royalties ranging from mid to high single-digits based on global product sales on a country-by-country and product-by-product basis with respect to a R&D Program until the later of ten years after the date of first commercial sale of the first product in such R&D Program in such country, expiration of specified patent rights covering such product in such country or the expiration of specified regulatory exclusivity for the first product in such R&D Program in such country.

Under the Novo Collaboration Agreement, the Company has a one-time option to share in the global development costs and operating profits or losses (in lieu of milestones and royalties) with respect to one licensed product (the "Profit Share Option"), subject

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

to certain terms, conditions and limitations. In the event that the Company chooses to exercise the Profit Share Option, it will be required to pay Novo all previously reimbursed developmental costs pertaining to that program and reimburse Novo for a portion of the R&D costs incurred under the selected licensed product and will share in the profits resulting from the commercialization of the licensed product.

Unless earlier terminated, the term of the Novo Collaboration Agreement continues until expiration of the last royalty term for the applicable product in the applicable country. The Novo Collaboration Agreement is subject to customary termination provisions, including termination by a party for the other party’s uncured, material breach. The Novo Collaboration Agreement also includes customary representations and warranties, covenants and indemnification obligations.

The Company concluded the Agreement is not within the scope of Accounting Standards Codification 808, Collaborative Arrangements as the Company does not share equally in the exposure to significant risk. Accordingly, the Company assessed this arrangement in accordance with ASC 606 and concluded that the contract counterparty, Novo, is a customer.

At commencement, the Company identified several potential performance obligations within the Novo Collaboration Agreement, including research and development services on research targets, option rights held by Novo, license to use the Company’s intellectual property to conduct research and development activities, and participation on the joint steering committee (“JSC”). At inception of the Novo Collaboration Agreement, the Company identified the following performance obligations:

(i)Four combined performance obligations comprised of the license, related research services, and participation of the JSC for the four R&D Programs;

(ii)Manufacturing services related to one of the R&D Programs; and

(iii)A material R&D Program modification right held by Novo.

The Company concluded that the license granted at contract inception is not distinct from the research services as the research services significantly modify the intellectual property underlying the license. As a result, for each R&D Program, the license has been combined with the research services and JSC participation into a single performance obligation, which is the combined performance obligation comprised of the license, related research services, and JSC participation.

In assessing whether the various options under the Novo Collaboration Agreement represent material rights, the Company considered the additional consideration the Company would be entitled to upon option exercise and the standalone selling price of the underlying goods and services. For the material rights identified above, the Company concluded that each of the options provided Novo with a discount that it otherwise would not have received.

The Company recognizes revenue related to the combined license and research services performance obligation and the manufacturing performance obligation over time using the input method. Under the input method, the extent of progress towards completion is measured based on the ratio of actual cost incurred to date to the total estimated cost at completion of the performance obligations, which the Company believes best measures its progress towards satisfying the performance obligations. A cost-based input method of revenue recognition requires management to make estimates of cost to complete the performance obligation. Judgment is required to evaluate assumptions related to cost estimates. The estimated standalone selling prices for the material rights were determined based on the estimated discount provided to Novo and the probability that Novo would exercise the options.

The following table presents revenue recognized, unrecognized transaction price, and estimated revenue expected to be recognized in the future as of September 30, 2025 (in thousands):

		Transaction Price
Combined license, research and manufacturing services		$	247,846
Material right			41,190
Total transaction price(1)		$	289,036
Revenue recognized(2)			(21,258	)
Unrecognized transaction price as of September 30, 2025		$	267,778

_____________________

(1)Comprised of the allocation of the $195.0 million one-time, non-refundable upfront payment, $153.8 million to the four R&D programs and manufacturing services and $41.2 million to the material right, and $94.0 million of variable consideration related to estimated research and manufacturing services for the four R&D Programs.

(2)Recorded within revenue in the condensed statement of operations for the three and nine months ended September 30, 2025,

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

comprised of $12.8 million of the one-time, non-refundable upfront payment and $8.5 million variable considerations related to estimated research services for the four R&D Programs.

Amounts due to the Company for satisfying the revenue recognition criteria or that are contractually due based upon the terms of the Novo Collaboration Agreement are recorded as accounts receivable in the Company’s balance sheets. Contract liabilities consist of amounts received prior to satisfying the revenue recognition criteria, which are recorded as deferred revenue in the Company’s balance sheets.

The following table summarizes the changes in deferred revenue for the nine months ended September 30, 2025 (in thousands):

Balance at January 1, 2025		$	—
Deferred revenue			195,000
Recognized revenue			(12,750	)
Balance at September 30, 2025(1)		$	182,250

_____________________

(1)Comprised of $61.6 million of deferred revenue, current and $120.6 million of deferred revenue, non-current, which is expected to be recognized over the next 3.8 years. As of September 30, 2025, all of the Company's performance obligations are outstanding.

The Company periodically assesses the probability of receiving payments from achieving the research and development, collaboration target, and regulatory milestones and includes the payment in the transaction price when they are deemed probable. Royalties and commercial sale milestones will be recognized when the subsequent sales occur based on the sales or usage-based royalty exception. The Company also periodically reassesses the Profit Share Option. As of September 30, 2025, none of the milestones were deemed probable and no royalty revenue has been recognized, and the Profit Share Option was deemed improbable with no expense recognized for repayment of reimbursements to Novo.

As of September 30, 2025, $8.5 million of the Company’s accounts receivable was attributed to the Novo Collaboration Agreement.

As of September 30, 2025 and December 31, 2024, no allowance for credit loss was recorded related to accounts receivable.

Vertex Asset Purchase and Research Service Agreement

Vertex Asset Purchase Agreement

In September 2023, the Company entered into an asset purchase agreement with Vertex, under which Vertex acquired an in-process research and development ("IPR&D") asset related to a GPCR program, including all intellectual property, materials, and compounds associated with the program (the “Vertex Asset Purchase Agreement”). The Vertex Asset Purchase Agreement also provides for a potential milestone payment payable to the Company contingent upon the achievement of a milestone event.

In July 2025, this milestone event was determined to have been achieved and, as a result, the Company received a payment of $12.5 million in August 2025, which was recorded as a gain on sale of non-financial asset within total operating expenses in the Company’s condensed statements of operations and comprehensive income (loss) for the three and nine months ended September 30, 2025. The Company will not receive any other payments related to this IPR&D asset.

Vertex Research Service Agreement

In conjunction with the Vertex Asset Purchase Agreement in September 2023, the Company entered into research service agreement with Vertex under which the Company agreed to perform certain exploratory research activities for Vertex (the "Vertex Research Service Agreement"). The Company recognized service revenue associated with the Vertex Research Service Agreement over the performance period of the research services as the services are provided in accordance with ASC 606. The Vertex Research Service Agreement expired in September 2025.

During the three and nine months ended September 30, 2025, the Company recorded service revenue of $0.2 million and $0.5 million, respectively, related to research activities performed in connection with the Vertex Research Service Agreement. During the

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

three and nine months ended September 30, 2024, the Company recorded service revenue of $0.2 million and $0.9 million, respectively, related to research activities performed in connection with the Vertex Research Service Agreement. As of September 30, 2025 and December 31, 2024, $0.2 million of the Company’s accounts receivable was attributed to the Vertex Research Service Agreement.

Note 4. Marketable Securities and Fair Value Measurements

The Company records marketable securities and cash equivalents at their estimated fair values, which are based on market prices from a variety of industry standard data providers and generally represent quoted prices for similar assets in active markets or have been derived from observable market data.

Fair value is determined based on a three-tier hierarchy under the authoritative guidance for fair value measurements and disclosures that prioritizes the inputs used in measuring fair value as follows:

Level 1: Unadjusted quoted prices in active markets that are accessible at the measurement date for identical, unrestricted assets or liabilities;

Level 2: Quoted prices in markets that are not active or inputs which are observable, either directly or indirectly, for substantially the full term of the asset or liability; and

Level 3: Prices or valuation techniques that require inputs that are both significant to the fair value measurements and unobservable (i.e., supported by little or no market activity).

Money market funds are highly liquid investments and are classified as Level 1. The pricing information for these assets is readily available and can be independently validated as of the measurement date. Marketable securities, including U.S. Treasury securities, U.S. government agency securities, commercial paper, and corporate debt securities, are classified as Level 2. These securities are valued using fair value from third-party pricing services, which may use observable inputs based on real-time trade data for similar assets, broker/dealer quotes, bids and/or offers and other observable inputs.

The carrying amounts of the Company’s prepaid and other current assets, accounts payable, and accrued and other current liabilities approximate fair value due to their short maturities.

The fair value measurements of the Company’s cash equivalents and marketable securities are identified at the following levels within the fair value hierarchy (in thousands):

	September 30, 2025
					Fair Value Measurement
	Total				Level 1				Level 2				Level 3
Cash equivalents:
Money market funds	$	272,696			$	272,696			$	—			$	—
Commercial paper		39,862				—				39,862				—
U.S. treasury securities		—				—				—				—
Marketable securities, current:
U.S. treasury securities		108,095				—				108,095				—
U.S. government agency    securities		18,631				—				18,631				—
Commercial paper		24,174				—				24,174				—
Corporate debt securities		3,457				—				3,457				—
Marketable securities, non-current:
U.S. treasury securities		79,899				—				79,899				—
U.S. government agency    securities		4,835				—				4,835				—
Corporate securities		2,478				—				2,478				—
Total measured at fair value	$	554,127			$	272,696			$	281,431			$	—

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

	As of December 31, 2024
					Fair Value Measurement
	Total				Level 1				Level 2				Level 3
Cash equivalents:
Money market funds	$	141,779			$	141,779			$	—			$	—
Commercial paper		82,527				—				82,527				—
U.S. government agency    securities		8,059				—				8,059				—
Marketable securities, current:
U.S. treasury securities		73,555				—				73,555				—
Commercial paper		23,487				—				23,487				—
U.S. government agency    securities		14,193				—				14,193				—
Corporate debt securities		1,492				—				1,492				—
Marketable securities, non-current:
U.S. treasury securities		65,406				—				65,406				—
U.S. government agency    securities		2,514				—				2,514				—
Corporate debt securities		1,946				—				1,946				—
Total measured at fair value	$	414,958			$	141,779			$	273,179			$	—

Marketable Securities

As of September 30, 2025 and December 31, 2024, the Company’s marketable securities consist of debt securities, including U.S. Treasury and agency securities, corporate debt securities and commercial paper. These marketable securities are carried at fair value and are included in the tables above. The Company records an allowance for credit losses when unrealized losses are due to credit-related factors. At each reporting date, the Company evaluates securities with unrealized losses to determine whether such losses, if any, are due to credit-related factors. The Company evaluates, among others, whether the Company has the intention to sell any of these marketable securities and whether it is not more likely than not that the Company will be required to sell any of them before recovery of the amortized cost basis. Neither of these criteria were met at September 30, 2025 or December 31, 2024. The credit ratings of the securities held remain of the highest quality. Moreover, the Company continues to receive payments of interest and principal as they become due, and the Company's expectation is that those payments will continue to be received timely. Based on this evaluation, as of September 30, 2025 and December 31, 2024, the Company determined that unrealized losses of its marketable securities were primarily attributable to changes in interest rates and non-credit related factors. As such, no allowances for credit losses were recorded at September 30, 2025 or December 31, 2024.

Interest receivable as of September 30, 2025 and December 31, 2024 was $1.9 million and $1.0 million, respectively, and is recorded as a component of prepaid expenses and other current assets on the Company’s condensed balance sheets.

As of September 30, 2025 and December 31, 2024, all marketable securities in an unrealized loss position had been in an unrealized loss position for less than 12 months. As of September 30, 2025, the Company held 31 marketable securities in an unrealized loss position. As of December 31, 2024, the Company held 36 marketable securities in an unrealized loss position.

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

As of September 30, 2025, the following table summarizes the amortized cost and the unrealized gains (losses) of the marketable securities presented within marketable securities and cash equivalents (in thousands):

		Remaining														Aggregate
		Contractual														Estimated Fair
		Maturity (in years)		Amortized Cost				Unrealized Gains				Unrealized Losses				Value
Commercial paper		Less than 1		$	64,041			$	1			$	(6	)		$	64,036
U.S. treasury securities		Less than 1			107,913				185				(3	)			108,095
U.S. government agency     securities		Less than 1			18,603				28				—				18,631
Corporate debt securities		Less than 1			3,451				6				—				3,457
Total maturity less than 1 year					194,008				220				(9	)			194,219
U.S. treasury securities		1 to 2			79,742				175				(18	)			79,899
U.S. government agency     securities		1 to 2			4,830				8				(3	)			4,835
Corporate debt securities		1 to 2			2,476				2				—				2,478
Total				$	281,056			$	405			$	(30	)		$	281,431

As of December 31, 2024, the following table summarizes the amortized cost and the unrealized gains (losses) of the marketable securities presented within marketable securities and cash equivalents (in thousands):

		Remaining Contractual Maturity (in years)		Amortized Cost				Unrealized Gains				Unrealized Losses				Aggregate Estimated Fair Value
Commercial paper		Less than 1		$	106,017			$	6			$	(9	)		$	106,014
U.S. treasury securities		Less than 1			73,511				44				—				73,555
U.S. government agency     securities		Less than 1			22,245				10				(3	)			22,252
Corporate debt securities		Less than 1			1,491				1				—				1,492
Total maturity less than 1 year					203,264				61				(12	)			203,313
U.S. treasury securities		1 to 2			65,427				37				(58	)			65,406
U.S. government agency     securities		1 to 2			2,492				22				—				2,514
Corporate debt securities		1 to 2			1,940				7				(1	)			1,946
Total				$	273,123			$	127			$	(71	)		$	273,179

As of September 30, 2025, the following table summarizes marketable securities in an unrealized loss position (in thousands):

		Contractual
		Maturity (in years)		Fair Value				Gross Unrealized Loss
Commercial paper		Less than 1		$	48,126			$	(6	)
U.S. treasury securities		Less than 1			9,523				(3	)
Total maturity less than 1 year					57,649				(9	)
U.S. treasury securities		1 to 2			15,596				(18	)
U.S. government agency securities		1 to 2			1,350				(3	)
Total				$	74,595			$	(30	)

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

As of December 31, 2024, the following table summarizes marketable securities in an unrealized loss position (in thousands):

		Less than 12 Months
		Fair Value				Gross Unrealized Loss
Corporate debt securities		$	987			$	(1	)
Commercial paper			70,172				(9	)
U.S. government agency securities			6,469				(3	)
U.S. treasury securities			52,508				(58	)
Total		$	130,136			$	(71	)

Note 5. Commitments and Contingencies

Legal Proceedings

In the ordinary course of business, the Company may be subject to legal proceedings, claims and litigation, as the Company operates in an industry susceptible to patent or other legal claims. The Company is not currently a party to any legal proceeding that, if determined adversely to the Company, in management’s opinion, is expected to individually or in the aggregate have a material adverse effect on its business, financial condition or liquidity and results of operations.

Indemnifications

In the ordinary course of business, the Company enters into agreements that may include indemnification provisions. As permitted under Delaware law and in accordance with its bylaws, the Company indemnifies its officers and directors for certain events or occurrences while the officer or director is or was serving in such capacity. The Company is also party to indemnification agreements with its officers and directors.

The maximum potential amount of future payments that the Company could be required to make under these provisions is not determinable; however, the Company currently holds director and officer liability insurance. This insurance limits the Company’s exposure and may enable it to recover a portion of any future amounts paid. The Company believes that the fair value of these indemnification obligations is minimal. In addition, the Company is not currently aware of any indemnification claims that could have a material effect on its condensed financial statements.

Note 6. Common Stock

As of September 30, 2025 and December 31, 2024, the Company was authorized to issue 500.0 million shares of common stock, par value $0.001 per share.

The Company reserved the following shares of common stock, on an as-converted basis, for future issuance:

		As of September 30,				As of December 31,
		2025				2024
Options issued and outstanding			4,317,824				2,938,982
Shares reserved for future grants under 2024 Stock Option    and Incentive Plan			4,367,678				3,743,915
Shares reserved for issuance under 2024 Employee Stock    Purchase Plan			369,402				369,402
Total common stock reserved for future issuance			9,054,904				7,052,299

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

Note 7. Stock-Based Compensation

Stock Plans

In October 2024, the Company’s board of directors adopted, and its stockholders approved, the 2024 Stock Option and Incentive Plan (the “2024 Plan”), which superseded the Company’s 2021 Stock Option and Grant Plan, as amended (the “2021 Plan”) (together, the “Stock Plans”).

On January 1, 2025, 2.2 million shares of common stock, representing 5% of the Company’s outstanding shares of common stock as of December 31, 2024, were added to the 2024 Plan. As of September 30, 2025, there were 4.4 million shares available for issuance under the 2024 Plan.

Restricted Stock Awards

The following summarizes restricted stock award activity:

		Number of Shares Outstanding				Weighted-Average Grant Date Fair Value Per Share
Balance at December 31, 2024			576,829			$	2.62
Restricted stock awards vested			(346,197	)			2.89
Restricted stock awards repurchased			(2,612	)			3.30
Balance at September 30, 2025			228,020			$	2.18

Restricted stock awards of 228,020 and 576,829 shares were subject to repurchase as of September 30, 2025 and December 31, 2024, respectively. The aggregate grant date fair value of shares vested during the three and nine months ended September 30, 2025 was $0.3 million and $1.0 million, respectively.

Stock Options

The following summarizes stock option activity:

		Stock Options Outstanding
		Total Stock Options Outstanding				Weighted-Average Exercise Price				Weighted-Average Remaining Contractual Life				Aggregate Intrinsic Value
										(in years)				(in thousands)
Outstanding as of December 31, 2024			2,938,982			$	4.64				9.11			$	53,706
Granted			1,706,714				11.51
Exercised			(218,810	)			3.06
Cancelled/forfeited			(109,062	)			4.62
Outstanding as of September 30, 2025			4,317,824				7.44				9.02				49,202
Exercisable as of September 30, 2025			904,814				4.06				8.44				13,342

The aggregate fair value of stock options that vested for the three and nine months ended September 30, 2025 was $1.6 million and $3.3 million, respectively. The stock options granted in the three months ended September 30, 2025 had a weighted-average grant-date fair value per share of $9.23 and a total grant-date fair value of $10.3 million. The stock options granted in the nine months ended September 30, 2025 had a weighted-average grant-date fair value per share of $8.83 and a total grant-date fair value of $15.1 million. The total intrinsic value of stock options exercised during three and nine months ended September 30, 2025 was $0.6 million and $1.3 million, respectively.

Of the total stock options granted during the nine months ended September 30, 2025, options to purchase 0.2 million shares granted to one of the Company's officers include accelerated vesting provisions associated with certain change of control events.

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

Stock Option Valuation

The weighted-average assumptions used to value employee and non-employee stock option awards granted under the Stock Plans using the Black Scholes option pricing model, were as follows:

		Nine Months Ended September 30,
		2025				2024
Fair value of common stock		$	8.83			$	6.46
Risk-free interest rate			4.00	%			3.83	%
Expected volatility			91.7	%			91.2	%
Expected term (years)			5.96				6.03
Expected dividend yield		—%				—%

2024 ESPP

In October 2024, the Company’s board of directors adopted, and its stockholders approved, the 2024 Employee Stock Purchase Plan (the “2024 ESPP”), which became effective immediately prior to the effective date of the Company's IPO. As of September 30, 2025, there were 0.4 million shares available for issuance under the 2024 ESPP.

As of September 30, 2025, no shares under the 2024 ESPP were issued as no purchases had taken place yet. For the three and nine months ended September 30, 2025, the Company recorded approximately $0.4 million and $0.7 million, respectively, of compensation expense associated with the 2024 ESPP.

Stock-based Compensation Expense

Stock-based compensation expense for restricted stock awards, stock options and the 2024 ESPP recognized in the Company’s condensed statements of operations and comprehensive loss is presented as follows (in thousands):

		Three Months Ended September 30,								Nine Months Ended September 30,
		2025				2024				2025				2024
Research and development expense		$	1,489			$	356			$	3,134			$	968
General and administrative expense			1,043				327				2,686				920
Total stock-based compensation expense		$	2,532			$	683			$	5,820			$	1,888

As of September 30, 2025, total unrecognized stock-based compensation expense related to unvested restricted stock awards and unvested stock options was $25.1 million, which is expected to be recognized over a weighted-average period of 2.8 years. As of September 30, 2025, total unrecognized stock-based compensation expense related to the 2024 ESPP was $0.9 million, which is expected to be recognized over a weighted average period of 1.1 years.

Note 8. Related Parties

Third Rock Ventures

In August 2021, the Company entered into a service agreement (the “TRV service agreement”) with Third Rock Ventures, LLC (“TRV”), a holder of more than 5% of the Company’s outstanding capital stock, under which TRV provides consulting services to the Company. For the three and nine months ended September 30, 2025, the Company incurred no fees under the TRV service agreement. For the three and nine months ended September 30, 2024, under the TRV service agreement, the Company incurred fees of $0.1 million and $0.2 million, respectively, which were recorded within general and administrative expenses in the Company’s condensed statements of operations and comprehensive loss. As of December 31, 2024, $0.1 million of expense related to TRV was recorded in accrued expenses and other current liabilities. There were no expenses related to TRV in accrued expenses and other current liabilities on the Company’s condensed balance sheets at September 30, 2025.

The Company’s former interim Chief Medical Officer, and also a member of the Company’s board of directors, is affiliated with TRV (the “TRV Board Member”). The TRV Board Member did not receive any cash compensation from the Company for his service as its interim Chief Medical Officer, as his services were provided to the Company through the TRV service agreement. The TRV Board

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

Member ceased serving as interim Chief Medical Officer in September 2024. In December 2024, the Company entered into a separate consulting agreement with the TRV Board Member, which includes cash compensation to be paid directly to the TRV Board member.

During the three and nine months ended September 30, 2025, total fees incurred related to the TRV Board Member’s consulting services were immaterial and $0.1 million, respectively. As of September 30, 2025, outstanding accounts payable to the TRV Board Member for consulting services was immaterial.

For the three and nine months ended September 30, 2024, the fees attributed to consulting services provided by the TRV Board Member as the interim Chief Medical Officer were $0.1 million and $0.2 million, respectively. Additionally, as compensation for his services as the Company's interim Chief Medical Officer, the Company granted him options to purchase 23,227 shares of common stock during the nine months ended September 30, 2024 at an exercise price of $2.76 per share.

Note 9. Net Income (Loss) Per Share

The following table sets forth the computation of the basic and diluted net income (loss) per share (in thousands, except for share and per share data):

		Three Months Ended September 30,								Nine Months Ended September 30,
		2025				2024				2025				2024
Numerator, basic and diluted:
Net income (loss)		$	8,173			$	(20,523	)		$	(38,141	)		$	(51,130	)
Net income (loss) applicable to common stockholders		$	8,173			$	(20,523	)		$	(38,141	)		$	(51,130	)
Denominator, basic:
Weighted average shares outstanding, basic			44,343,085				2,443,678				44,150,041				2,337,891
Denominator, diluted:
Weighted-average shares outstanding, basic			44,343,085				2,443,678				44,150,041				2,337,891
Effect of dilutive securities			1,259,014				—				—				—
Weighted-average shares outstanding, diluted			45,602,099				2,443,678				44,150,041				2,337,891
Net income (loss) per share, basic		$	0.18			$	(8.40	)		$	(0.86	)		$	(21.87	)
Net income (loss) per share, diluted		$	0.18			$	(8.40	)		$	(0.86	)		$	(21.87	)

The Company had 4,645,443 shares of potentially dilutive securities, comprised of outstanding stock options, restricted stock awards, and ESPP shares, not included in the calculation of diluted net loss per share for the nine months ended September 30, 2025 and 2,986,349 shares for the three and nine months ended September 30, 2024 because to do so would be anti-dilutive.

Note 10. Segment Information

The Company operates in one segment, which is GPCR oral small molecule drug discovery. The Company’s Chief Operating Decision Maker (“CODM”) is its Chief Executive Officer. The measure of segment profit or loss is net income (loss), which is also reported on the condensed statements of operations and comprehensive income (loss) as net income (loss).

The measure of segment assets is reported on the balance sheet as total assets. The CODM uses segment net loss to monitor spending, assess performance for the Company and management, evaluate the progress of completing corporate goals, decide how to allocate resources among the Company’s clinical and pre-clinical portfolios, and make strategic decisions about business development opportunities.

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SEPTERNA, INC.

Notes to UNAUDITED Condensed Financial Statements (CONTINUED)

The CODM is regularly provided with the following significant segment expenses:

		Three Months Ended September 30,								Nine Months Ended September 30,
		2025				2024				2025				2024
Revenue		$	21,495			$	176			$	21,833			$	863
Employee-related expenses, excluding stock-based compensation			8,939				5,384				23,339				14,967
Stock-based compensation			2,532				683				5,820				1,888
External research and development expenses			12,160				9,701				34,286				23,328
External general and administrative expenses			2,016				2,436				7,160				4,753
Other segment expenses1			5,734				4,522				16,002				12,032
Gain on sale of non-financial asset			(12,500	)			—				(12,500	)			—
Total operating expenses			18,881				22,726				74,107				56,968
Income (loss) from operations			2,614				(22,550	)			(52,274	)			(56,105	)
Other income, net			5,559				1,891				14,133				4,637
Income (loss) before benefit for income taxes			8,173				(20,659	)			(38,141	)			(51,468	)
Benefit for income taxes			—				136				—				338
Net income (loss)		$	8,173			$	(20,523	)		$	(38,141	)		$	(51,130	)

_____________________

(1)Other segment expenses include facility-related and office-related costs, information technology costs, general laboratory costs, and other operating expenses.

As of September 30, 2025 and December 31, 2024, all of the Company’s property and equipment was maintained in the U.S. For the three and nine months ended September 30, 2025 and 2024, the Company’s revenue was generated from providing research services and was earned in the U.S.

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

You should read the following discussion and analysis of our financial condition and results of operations together with our unaudited interim condensed financial statements and related notes included elsewhere in this Quarterly Report and audited financial statements and notes thereto as of and for the year ended December 31, 2024 and the related Management’s Discussion and Analysis of Financial Condition and Results of Operations, both of which are contained in our Annual Report on Form 10-K for the year ended December 31, 2024 (“Annual Report”), filed with the Securities and Exchange Commission (the “SEC”) on March 27, 2025. This discussion and other parts of this Quarterly Report contain forward-looking statements based upon current beliefs, plans, and expectations related to future events and our future financial performance that involve risks, uncertainties and assumptions, such as statements of our plans, objectives, expectations, intentions, forecasts and projections. Our actual results and the timing of selected events could differ materially from those discussed in these forward-looking statements as a result of several factors including, but not limited to, those set forth under the section titled “Risk Factors” and elsewhere in this Quarterly Report. Our historical results are not necessarily indicative of the results that may be expected for any period in the future, and you should carefully read the section titled “Risk Factors” to gain an understanding of the important factors that could cause actual results to differ materially from our forward-looking statements. Please also see the section titled “Special Note Regarding Forward-Looking Statements.”

Overview

We are a clinical-stage biotechnology company with a world-class team of G protein-coupled receptor (“GPCR”) experts and drug developers advancing cutting-edge science to unlock the full potential of GPCR therapies for patients with significant unmet needs. Our proprietary Native Complex Platform™ is designed to enable new approaches to GPCR drug discovery and has led to the development of a diverse pipeline of novel oral small molecule drug candidates.

Our proprietary Native Complex Platform™ replicates the natural structure, function, and dynamics of GPCRs outside of cells at an industrial scale for, as we believe it, the first time. Our foundational technologies enable us to isolate, purify, and reconstitute full-length, properly folded GPCR proteins within ternary complexes with ligands and transducer proteins in a lipid bilayer that mimics the cell membrane. We then apply state-of-the-art discovery tools and technologies to these defined and tunable protein complexes to structurally design, screen for, and optimize potential product candidates. Leveraging our platform, we conduct GPCR oral small molecule drug discovery using an industrialized and iterative structure-based drug design approach for a diverse collection of GPCR targets. Our Native Complex Platform™ is designed to enable us to target specific GPCRs, uncover novel binding pockets for validated receptors, and pursue a wide spectrum of pharmacologies, including agonists (which activate GPCR signaling), antagonists (which inhibit GPCR signaling), and allosteric modulators (which either increase or decrease the degree of GPCR activation by endogenous ligands), to affect GPCR signaling in different ways to achieve desired therapeutic effects.

We are advancing a deep portfolio of oral small molecule GPCR-targeted programs with novel mechanistic approaches to treat diseases across multiple therapeutic areas for patients with significant unmet needs. Our wholly-owned pipeline is summarized in the figure below.

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Recent Developments

•SEP-479 PTH1R Agonist Program:

oIn September 2025, we provided an update on SEP-479, our oral small molecule parathyroid hormone 1 receptor (“PTH1R”) agonist program for hypoparathyroidism. In February 2025, we discontinued the Phase 1 clinical trial for SEP-786 as a result of observations of hyperbilirubinemia. The findings from our post-discontinuation investigation found that SEP-786 is a potent UGT1A1 inhibitor, which is a mechanism known to be associated with increases in unconjugated bilirubin. In a follow-up cynomolgus monkey study of SEP-786, conducted after clinical discontinuation, we also observed elevated unconjugated bilirubin levels.

oWe announced in September 2025 that we had selected a new PTH1R development candidate, SEP-479. We presented preclinical data for SEP-479 from a translational rat thyroparathyroidectomy model demonstrating that SEP-479 achieved sustained normalization of serum calcium and phosphate levels over a 28-day dosing period. We also conducted a seven-day pharmacokinetic (“PK”) / pharmacodynamic (“PD”) study of SEP-479 in healthy cynomolgus monkeys, which showed robust, dose-dependent increases in serum calcium and decreases in endogenous parathyroid hormone levels across multiple dose levels of SEP-479.

oWe observed no significant inhibition of UGT1A1 or other transporters for SEP-479 and no hyperbilirubinemia in any of the non-clinical studies to date for SEP-479, including the 7-day cynomolgus monkey study at supratherapeutic doses. SEP-479 was generally well-tolerated in the completed 28-day GLP toxicology studies in rats and dogs. Prior to the planned Phase 1 clinical trial initiation for SEP-479, we are also completing a 28-day GLP toxicology study in cynomolgus monkeys as an additional safety species. We plan to initiate a Phase 1 clinical trial for SEP-479 in the first half of 2026, pending the successful completion of all remaining preclinical studies, drug product manufacturing, and regulatory submissions.

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•SEP-631 MRGPRX2 NAM Program:

oIn August 2025, we announced the dosing of the first participants in our Phase 1 clinical trial of SEP-631, a selective oral small molecule Mas-related G protein-coupled receptor X2 (“MRGPRX2”) negative allosteric modulator being developed for the treatment of chronic spontaneous urticaria and other mast cell-driven diseases. The Phase 1 single-ascending dose (“SAD”) and multiple-ascending dose (“MAD”) clinical trial will evaluate the safety, tolerability, PK and PD of SEP-631 in healthy adult volunteers. The randomized, placebo-controlled Phase 1 SAD / MAD clinical trial is expected to enroll up to approximately 150 healthy adult volunteers. The SAD portion of the trial will evaluate the safety and tolerability of SEP-631 at escalating oral doses. The MAD portion of the trial will evaluate the safety and tolerability of oral doses of SEP-631 over the treatment period, and PD will be assessed through an icatibant skin challenge. We anticipate initial SAD/MAD data to be announced in the first half of 2026.

•TSHR NAM Program:

oWe continue to make progress on our TSHR NAM program, advancing several lead compounds closer to development candidate selection with the goal of delivering a potential disease-modifying oral treatment for Graves’ disease and thyroid eye disease.

•Discovery Programs:

oWe continue to advance discovery-stage programs utilizing our Native Complex Platform™ across multiple therapeutic areas.

Financial Overview

We were incorporated in Delaware in December 2019 under the name GPCR NewCo, Inc. In June 2021, we changed our name to Septerna, Inc. We are headquartered in South San Francisco, California.

We have incurred significant operating losses since our inception, except for the year ended December 31, 2023, when we recorded net income of $4.2 million, resulting from the gain on sale of non-financial asset of $47.6 million for the sale of an in-progress research and development (“IPR&D”) asset related to a GPCR program and the three months ended September 30, 2025 when we recorded net income of $8.2 million, resulting from the $21.5 million of revenue and $12.5 million of gain on sale of a non-financial asset. Our revenue to date has been generated solely from research services and the recognition of the one-time, non-refundable upfront payment of $195.0 million from our collaboration agreement. Since our founding, we have devoted substantially all of our resources to organizing and staffing our company, business planning, raising capital, developing our proprietary and structure-based drug discovery platform, identifying and discovering our product candidates, establishing our intellectual property portfolio, conducting research and preclinical studies, including investigational new drug (“IND”)-enabling studies, initiating and conducting clinical trials, establishing arrangements with third parties for the manufacture of our product candidates and related raw materials, and providing general and administrative support for these operations. We have not had any products approved for sale and have not generated any revenue from product sales. Further, we do not expect to generate revenue from commercial product sales until such time, if ever, that we are able to successfully complete the development and obtain marketing approval for one or more of our product candidates. Our ability to generate product revenue will depend on the successful development and eventual commercialization of one or more of our product candidates.

We expect to continue to incur significant and increasing expenditures for the next several years as we:

•continue to advance our product candidates through preclinical studies and into clinical trials;

•attract, hire and retain additional personnel;

•continue to operate as a public company, including expenses related to compliance with the rules and regulations of the SEC and those of any national securities exchange on which our securities are traded, legal, auditing, insurance expenses, investor relations activities, and other administrative and professional services;

•continue our research and development efforts and expand our pipeline of product candidates;

•acquire, discover, validate, and develop additional product candidates;

•manufacture supplies for our preclinical studies and clinical trials;

•obtain, maintain, expand, and protect our intellectual property portfolio;

•implement operational, financial and information management systems;

•make royalty, milestone or other payments under any future, license or collaboration agreements;

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•potentially seek to identify, assess, acquire, or in-license or develop new technologies or additional product candidates;

•potentially experience any delays, challenges, or other issues associated with the clinical development of our product candidates, including with respect to our regulatory strategies;

•pursue regulatory approval of product candidates that successfully complete clinical trials; and

•establish a sales, marketing and distribution infrastructure to commercialize any product candidate for which we may obtain marketing approval and related commercial manufacturing build-out.

Our net losses may fluctuate significantly from period to period, depending upon the timing of our expenditures on research and development activities. Cash used to fund operating expenses is impacted by the timing of when we pay these expenses, as reflected in the change in our accounts payable and accrued expenses and other current liabilities, which includes accrued research and development, in the statements of cash flows in our audited and unaudited interim condensed financial statements included elsewhere in the Quarterly Report. Our net loss was $38.1 million and $51.1 million for the nine months ended September 30, 2025 and 2024, respectively. As of September 30, 2025, we had an accumulated deficit of $156.5 million.

As a result, we will require substantial additional funding to further develop our product candidates and support our continuing operations. Until such time, if ever, as we can generate substantial product revenue, we expect to finance our operations through a combination of equity offerings, debt financings, collaborations, strategic alliances and marketing, distribution or licensing arrangements. See the section titled “Liquidity and Capital Resources - Future Funding Requirements” below for additional information.

We have historically financed our operations primarily through the issuances of convertible promissory notes and convertible preferred stock, and, most recently, through an initial public offering (“IPO”). In October 2024, we completed our IPO, pursuant to which we issued and sold an aggregate of 18.4 million shares of our common stock (inclusive of an additional 2.4 million shares of our common stock issued and sold pursuant to the underwriters' exercise of their option to purchase additional shares in full). The aggregate net proceeds received by us from the IPO was $302.8 million, net of total offering costs of $28.4 million.

We use contract research and development organizations to conduct our preclinical work and clinical trials. Additionally, we utilize third-party contract manufacturing organizations (“CMOs”), to manufacture and supply our preclinical and clinical materials during the development of our product candidates. We expect to use similar contract resources for the commercialization of our products, at least until our resources and operations are at a scale that justifies investment in internal manufacturing capabilities.

We conduct research and manufacturing work outside of the U.S., including China, that may be affected by tariffs, including tariffs that have been or may in the future be imposed by the U.S. or other countries through reciprocal tariffs. While we do not currently believe tariffs will have a material impact on our business or results of operations, we will continue to carefully monitor the situation. Additionally, we continue to actively monitor macroeconomic conditions and market volatility resulting from global and national economic developments, political unrest, high inflation, disruptions in capital markets, changes in international trade relationships, changes in or the disruptions of U.S. governmental agencies, whether from a continued U.S. federal government shutdown or reduced resources, new laws and regulations or amendments to existing laws and regulations in the U.S. and foreign countries, and military conflicts. While we believe such factors have had no significant impact on our business or financial results during the periods presented, future developments and potential impacts on our business are uncertain and cannot be predicted with confidence.

Collaboration, Research Service, and Asset Purchase Agreements

Novo Collaboration Agreement

In May 2025, we entered into a global Collaboration and License Agreement with Novo Nordisk A/S (“Novo”) (the “Novo Collaboration Agreement”). Under the Novo Collaboration Agreement, we and Novo are exclusively collaborating to leverage our proprietary Native Complex Platform™ to discover, develop and commercialize multiple potential oral small molecule therapies for metabolic-related diseases based on certain specified molecular targets. The collaboration objective is to discover and develop several novel mono-, dual-, or triple-acting oral small molecule drug candidates directed across five GPCRs, including the GLP-1, GIP, and glucagon receptors (the “Collaboration Targets”). The collaboration includes our most advanced preclinical metabolic program focused on developing an oral small molecule agonist to the GIP receptor. We and Novo have initially commenced four simultaneous research and development programs (each an “R&D Program”) with each pursuing one or more Collaboration Targets from discovery through development candidate selection.

In July 2025, the Novo Collaboration Agreement became effective and, subsequently, we received a one-time, non-refundable upfront payment of $195.0 million, which was recorded as deferred revenue in our condensed balance sheet. For each R&D Program, we are also eligible to receive up to approximately $498.0 million in research, development, regulatory, and commercial milestone payments. In addition, we are entitled to escalating, tiered royalties ranging from mid-to-high single-digits based on global product sales

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on a country-by-country and product-by-product basis with respect to a R&D Program until the later of ten years after the date of first commercial sale of the first product in such R&D Program in such country, expiration of specified patent rights covering such product in such country or the expiration of specified regulatory exclusivity for the first product in such R&D Program in such country. See Note 3 to the condensed financial statements included elsewhere in this Quarterly Report for additional information.

Vertex Asset Purchase and Research Service Agreement

Vertex Asset Purchase Agreement

In September 2023, we entered into an asset purchase agreement with Vertex Pharmaceuticals Incorporated (“Vertex”) under which Vertex acquired an IPR&D asset related to a GPCR program, including all intellectual property, materials, and compounds associated with the program (“Vertex Asset Purchase Agreement”). The Vertex Asset Purchase Agreement also provided for a potential milestone payment payable to us contingent upon the achievement of a milestone event.

In July 2025, this milestone event was determined to have been achieved and, as a result, we received a payment of $12.5 million in August 2025, which was recorded as a gain on sale of the non-financial asset within our total operating income (expenses) in our condensed statement of operations and comprehensive loss for the three and nine months ended September 30, 2025. We will not receive any other payments related to this IPR&D asset.

Vertex Research Service Agreement

In conjunction with the Vertex Asset Purchase Agreement in September 2023, we entered into a research service agreement with Vertex under which we agreed to perform certain exploratory research activities for Vertex (“Vertex Research Service Agreement”).

The Vertex Research Service Agreement was for a two-year term, which expired in September 2025. We recognized revenue associated with the Vertex Research Service Agreement over the performance period of the research services as the services were provided.

Components of Results of Operations

Revenue

We have not generated any revenue from product sales and do not expect to do so in the foreseeable future. Our ability to generate product revenue, if ever, will depend on the successful development and eventual commercialization of any product candidates that we identify. If we fail to complete the development of any future product candidates in a timely manner or to obtain regulatory approval for such product candidates, our ability to generate future revenue and our results of operations and financial position would be materially adversely affected. Our revenues to date have been exclusively related to license and research and development ("R&D") services. Our license and research service revenue consists of amounts recognized from the portions of the non-refundable upfront payment and R&D services performed by us.

Operating Expenses

Our operating expenses consist of (i) research and development expenses and (ii) general and administrative expenses.

Research and Development

Research and development expenses account for the largest component of our total operating expenses. Research and development expenses consist primarily of direct and unallocated costs incurred for the research and development of our product candidates.

Our research and development expenses consist of:

•direct costs, including:

▪preclinical and research program costs, which include external research and development costs related to (i) the production of preclinical materials, including fees and milestones paid to contract manufacturers and (ii) agreements with contract development organizations, consultants and other third-party contract organizations to conduct our preclinical studies and other research and development activities on our behalf, costs incurred in connection with laboratory operations, materials and supplies, and other preclinical studies;

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▪clinical program costs, which include external costs to conduct clinical trials, including costs paid to contract research organizations (“CROs”), the production of clinical materials and fees paid to contract manufacturers, costs incurred in connection with clinical laboratory operations, materials and supplies; and

•unallocated costs, including:

▪payroll-related costs, including salaries, benefits and stock-based compensation for employees engaged in research and development activities;

▪external research and development costs, including contract research and development and professional service fees for consulting and related services;

▪facility-related and office costs, including lease/rent, building-related expenses, facility-related overhead, and depreciation expense; and

▪other costs, including expenses related to our funded, sponsored research activities and technology licenses, laboratory operations, information technology (“IT”)-related expenses.

We expense all research and development costs in the periods in which they are incurred. Costs for certain development activities are recognized based on an evaluation of the progress to completion of specific tasks using information and data provided to us by our vendors and third-party service providers.

A significant portion of our research and development costs have been external costs, which we track by stage of development. However, we do not track our unallocated costs on a program specific basis because these costs are deployed across multiple projects and, as such, are not separately classified.

At this time, we cannot reasonably estimate or know the nature, timing, and estimated costs of the efforts that will be necessary to complete the development of, and obtain regulatory approval for, any of our product candidates. We expect that our research and development expenses will increase substantially in absolute dollars for the foreseeable future as we continue to invest in research and development activities related to developing our product candidates, as our product candidates advance into later stages of development, as we begin to conduct clinical trials, as we seek regulatory approvals for any product candidates that successfully complete clinical trials, and as we incur expenses associated with hiring additional personnel to support our research and development efforts. The process of conducting the necessary clinical research to obtain regulatory approval is costly and time-consuming, and the successful development of our product candidates is highly uncertain. This is due to the numerous risks and uncertainties associated with developing product candidates, many of which are outside of our control, including the uncertainty of:

•the scope, timing and progress of preclinical and clinical development activities;

•the number and scope of preclinical and clinical programs we decide to pursue;

•our ability to maintain our current research and development programs and to establish new ones;

•establishing an appropriate safety profile with IND-enabling studies;

•the number of sites and patients included in the clinical trials;

•the countries in which the clinical trials are conducted;

•our ability to replicate positive results from a completed clinical study in a future clinical study;

•per patient trial costs;

•successful patient enrollment in, and the initiation of, clinical trials, as well as drop out or discontinuation rates;

•the successful completion of clinical trials with safety, tolerability and efficacy profiles that are satisfactory to the U.S. Food and Drug Administration (the "FDA"), European Medicines Agency (“EMA”), or any other comparable foreign regulatory authorities;

•delays or disruptions in review, approval, inspection, or other actions by the FDA or other applicable U.S. or foreign government regulatory authorities that could impact the timing, initiation, conduct, or completion of our clinical trials or marketing applications;

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•the number of trials required for regulatory approval;

•the timing, receipt and terms of any regulatory approvals from applicable regulatory authorities;

•our ability to maintain existing collaborations and strategic relationships, to identify and establish any future collaboration arrangements on favorable terms, if at all, and to realize the intended and potential benefits of such agreements and collaborations;

•the performance of any current or future collaborators;

•establishing commercial manufacturing capabilities or making arrangements with third-party manufacturers;

•significant and changing government regulation and regulatory guidance;

•the impact of any business interruptions to our operations or to those of the third parties with whom we work;

•obtaining, maintaining, defending and enforcing patent claims and other intellectual property rights;

•launching commercial sales of our product candidates, if approved, whether alone or in collaboration with others; and

•maintaining a continued acceptable safety profile of the product candidates following regulatory approval.

Any changes in the outcome of any of these variables could mean a significant change in the costs and timing associated with the development of our product candidates. For example, if the FDA, EMA or any other comparable foreign regulatory authority were to require us to conduct clinical trials beyond those that we anticipate will be required for the completion of clinical development of a product candidate, or if we experience significant delays in our clinical trials due to patient enrollment or other reasons, we would be required to expend significant additional financial resources and time on the completion of clinical development. We may never obtain regulatory approval for any of our product candidates.

General and Administrative

General and administrative expenses consist primarily of personnel-related costs, costs related to maintenance and filing of intellectual property, legal fees related to corporate matters, professional fees paid for accounting, auditing, consulting, tax and investor relations services, insurance costs, general corporate expenses, and IT-related and facility-related costs not otherwise included in research and development expenses. Personnel-related costs include salaries, benefits, and stock-based compensation for our personnel in executive, legal, finance and accounting, human resources, and other administrative functions.

We expect that our general and administrative expenses will increase substantially in absolute dollars for the foreseeable future as we continue to increase our headcount to support our business growth and to advance our research and development programs.

Other Income, Net

Interest Income

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

Other Expense, Net

Other expense, net consists primarily of changes in the fair value of our cash equivalents held in money market funds, loss on disposal of our fixed assets and foreign currency transaction gain or loss.

Income Taxes

We are subject to corporate U. S. federal and state income taxation. Our benefit for income taxes is recorded in accordance with Accounting Standard Codification 740, Accounting for Income Taxes, which provides for deferred taxes using an asset and liability approach. We establish a valuation allowance against all of our net deferred tax assets. We consider all available evidence, both positive and negative, including but not limited to our historical operating results, income or loss in recent periods, cumulative losses in recent years, forecasted earnings (losses), future taxable income (loss), and significant risk and uncertainty related to forecasts, and concluded the deferred tax assets are not more likely than not to be realized.

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On July 4, 2025, the One Big Beautiful Bill Act (“H.R.1”) was signed into law, which introduced significant changes to the U.S. federal income tax code. Among other changes, H.R.1 makes permanent key elements of the Tax Cuts and Jobs Act, including restoring 100% bonus depreciation, eliminating the capitalization requirement for domestic research and development expenses, and modifying the business interest expense limitation, which now allows depreciation and amortization to be included in the limitation calculation. ASC 740 requires the effects of changes in tax rates and laws on deferred tax balances to be recognized in the period in which the legislation is enacted in the third quarter of 2025. We are still in the process of evaluating H.R.1's impact on our condensed financial statements and an estimate of the financial impact cannot be made at this time. However, we do not expect the impact to be material to our condensed financial statements.

Results of Operations

Comparison of the Three and Nine Months Ended September 30, 2025 and 2024

Our results of operations for each of the periods indicated are summarized in the table below (in thousands):

		Three Months Ended September 30,												Nine Months Ended September 30,
		2025				2024				Change				2025				2024				Change
Revenue		$	21,495			$	176			$	21,319			$	21,833			$	863			$	20,970
Operating (income) expenses:
Research and development			24,264				17,832				6,432				65,723				46,020				19,703
General and administrative			7,117				4,894				2,223				20,884				10,948				9,936
Gain on sale of non-financial asset			(12,500	)			—				(12,500	)			(12,500	)			—				(12,500	)
Total operating expenses			18,881				22,726				(3,845	)			74,107				56,968				17,139
Income (loss) from operations			2,614				(22,550	)			25,164				(52,274	)			(56,105	)			3,831
Other income, net:
Interest income			5,565				1,900				3,665				14,192				4,709				9,483
Other expense, net			(6	)			(9	)			3				(59	)			(72	)			13
Total other income, net			5,559				1,891				3,668				14,133				4,637				9,496
Income (loss) before benefit for income taxes			8,173				(20,659	)			28,832				(38,141	)			(51,468	)			13,327
Benefit for income taxes			—				136				(136	)			—				338				(338	)
Net income (loss)		$	8,173			$	(20,523	)		$	28,696			$	(38,141	)		$	(51,130	)		$	12,989

Revenue

Our revenue was generated from research activities performed for Novo in connection with the Novo Collaboration Agreement and Vertex in connection with the Vertex Research Service Agreement. We recorded revenue of $21.5 million and $0.2 million for the three months ended September 30, 2025 and 2024, respectively. We recorded revenue of $21.8 million and $0.9 million for the nine months ended September 30, 2025 and 2024, respectively.

$21.3 million of our total revenue for the three and nine months ended September 30, 2025 was generated from research activities performed for Novo in connection with the Novo Collaboration Agreement while the remainder was generated from research activities performed for Vertex in connection with the Vertex Research Service Agreement.

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Operating Expenses

Research and Development

The following table summarizes our research and development expenses for the periods indicated by direct and unallocated costs (in thousands):

		Three Months Ended September 30,												Nine Months Ended September 30,
		2025				2024				Change				2025				2024				Change
Direct costs:
SEP-479 (PTH1R)		$	2,595			$	3,560			$	(965	)		$	9,328			$	8,306			$	1,022
SEP-631 (MRGPRX2)			3,073				550				2,523				6,838				1,424				5,414
Other programs			6,604				1,521				5,083				16,600				3,674				12,926
Unallocated costs:
Payroll-related costs			7,886				4,227				3,659				19,619				12,203				7,416
External research and development    costs			651				4,763				(4,112	)			3,124				11,222				(8,098	)
Facility-related and office costs			2,113				1,841				272				6,089				4,276				1,813
Other costs			1,342				1,370				(28	)			4,125				4,915				(790	)
Total research and development    expense		$	24,264			$	17,832			$	6,432			$	65,723			$	46,020			$	19,703

Research and development expenses were $24.3 million and $17.8 million for the three months ended September 30, 2025 and 2024, respectively. The increase was primarily due to (i) $6.6 million of higher direct costs associated with our clinical and preclinical and research programs, (ii) $3.6 million of higher employee-related costs as a result of increased headcount as we continue to grow our business, and (iii) $0.3 million of higher facility-related and office costs as we expanded our office space in July 2024 to accommodate higher occupancy and larger operational activities, partially offset by $4.1 million of lower expenses attributable to unallocated external research and development costs.

Research and development expenses were $65.7 million and $46.0 million for the nine months ended September 30, 2025 and 2024, respectively. The increase was primarily due to (i) $19.3 million of higher direct costs associated with our clinical and preclinical and research programs, including $2.3 million of higher clinical trial expenses, (ii) 7.4 million of higher employee-related costs as a result of increased headcount as we continue to grow our business, and (iii) $1.8 million of higher facility-related and office costs as we expanded our office space in July 2024 to accommodate higher occupancy and larger operational activities, partially offset by $8.1 million of lower expenses attributable to unallocated external research and development costs and $0.8 million of lower other research and development expense.

In February 2025, the SEP-786 clinical study was discontinued and, as a result, we do not anticipate incurring significant additional clinical trial costs associated with this study. In September 2025, we announced the selection of SEP-479 as our next-generation oral small molecule PTH1R agonist development candidate and are now advancing SEP-479 through the completion of the remaining preclinical studies, manufacturing of clinical drug supply, and preparation of regulatory submissions in support of our plan to initiate a Phase 1 clinical trial for SEP-479 in the first half of 2026. We expect to continue to incur increased research and development expenses as we advance the ongoing clinical trial for SEP-631 towards completion, progress SEP-479 towards clinical development, continue to advance our TSHR NAM preclinical program and multiple discovery-stage programs in our pipeline, and continue to invest in our Native Complex PlatformTM.

General and Administrative

General and administrative expenses were $7.1 million and $4.9 million for the three months ended September 30, 2025 and 2024, respectively. The increase was primarily due to (i) $1.5 million of higher employee-related costs as a result of increased headcount to support our growing operations, (ii) $0.5 million of higher IT-related expenses, (iii) $0.3 million of higher legal and consulting fees, and (iv) $0.2 million of higher facility-related and office costs as a result of increased operational activities and operating as a public company.

General and administrative expenses were $20.9 million and $10.9 million for the nine months ended September 30, 2025 and 2024, respectively. The increase was primarily due to (i) $4.4 million of higher employee-related costs as a result of increased headcount, (ii) $2.2 million of higher legal and consulting fees, (iii) $1.0 million of accounting and consulting fees, (iv) $1.3 million of higher

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IT-related expenses, (v) $0.4 million of higher facility-related and office costs as a result of increased operational activities and operating as a public company and (vi) $0.6 million of other general and administrative expenses.

Gain on Sale of Non-Financial Asset

Gain on sale of non-financial asset of $12.5 million during the three and nine months ended September 30, 2025 was attributable to a milestone payment under the Vertex Asset Purchase Agreement during the year ended December 31, 2023. No gain on sale of non-financial asset was recorded during the three and nine months ended September 30, 2024.

Other Income, Net

Interest Income

Interest income was $5.6 million and $1.9 million for the three months ended September 30, 2025 and 2024, respectively. Interest income was $14.2 million and $4.7 million for the nine months ended September 30, 2025 and 2024, respectively. The increases in interest income for the three and nine months ended September 30, 2025 as compared to the three and nine months ended September 30, 2024, respectively, were due to higher interest rates and higher balances of invested cash in cash equivalents and marketable securities.

Benefit for Income Taxes

We recognized $0.1 million and $0.3 million of benefit for income taxes for the three and nine months ended September 30, 2024, respectively. We did not record a benefit or provision for income taxes for the three and nine months ended September 30, 2025.

Liquidity and Capital Resources

Sources of Liquidity

Our net losses were $38.1 million and $51.1 million for the nine months ended September 30, 2025 and 2024, respectively. As of September 30, 2025, we had an accumulated deficit of $156.5 million. Since our founding, we have devoted substantially all of our resources to organizing and staffing our company, business planning, raising capital, developing our proprietary and structure-based drug discovery platform, identifying and discovering our product candidates, establishing our intellectual property portfolio, conducting research and preclinical studies, including IND-enabling studies, initiating and conducting clinical trials, establishing arrangements with third parties for the manufacture of our product candidates and related raw materials, and providing general and administrative support for these operations. We expect to continue to incur substantial expenditures for our research and development programs.

We have historically financed our operations primarily through the issuances of convertible promissory notes and convertible preferred stock, and most recently, through an IPO. In October 2024, we completed our IPO, pursuant to which we issued and sold an aggregate of 18.4 million shares of common stock (inclusive of 2.4 million shares of common stock sold pursuant to the underwriters' exercise of their option to purchase additional shares in full). The aggregate net proceeds received by us from the IPO was $302.8 million, net of total offering costs of $28.4 million.

In July 2025, upon the effectiveness of the Novo Collaboration Agreement, we received a one-time, non-refundable upfront payment of $195.0 million. In August 2025, we received a $12.5 million milestone payment from the Vertex Asset Purchase Agreement. We believe our cash, cash equivalents and marketable securities of $561.6 million as of September 30, 2025 will be sufficient to fund our operations and capital expenditure requirements at least into 2029.

Cash Flows

The following table summarizes our cash flows for the periods indicated (in thousands):

		Nine Months Ended September 30,
		2025				2024
Net cash provided by (used in) operating activities		$	125,177			$	(46,512	)
Net cash used in investing activities			(44,052	)			(27,359	)
Net cash provided by financing activities			668				73,630
Net increase (decrease) in cash, cash equivalents and restricted cash		$	81,793			$	(241	)

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Net Cash Provided by (Used in) Operating Activities

Net cash provided by operating activities was $125.2 million for the nine months ended September 30, 2025. The net cash provided by operating activities for the nine months ended September 30, 2025 was due to $169.8 million of net change in operating assets and liabilities, partially offset by $38.1 million of net loss, net non-cash charges of $6.5 million primarily attributable to gain on sale of non-financial asset and amortization of premiums (discounts), net.

Net cash used in operating activities was $46.5 million for the nine months ended September 30, 2024. The net cash used in operating activities for the nine months ended September 30, 2024 was due to our net loss of $51.1 million, partially offset by $1.7 million of net change in operating assets and liabilities, $2.9 million of non-cash charges for depreciation and amortization, stock-based compensation, non-cash operating lease expense, deferred income tax and accretion of discounts, net, on marketable securities.

Net Cash Used in Investing Activities

Net cash used in investing activities of $44.1 million for the nine months ended September 30, 2025 was attributable to $223.5 million of purchases of marketable securities and $0.5 million of purchases of property and equipment, partially offset by the maturity of $167.4 million of marketable securities and the receipt of the $12.5 million milestone payment related to the Vertex Asset Purchase Agreement.

Net cash used in investing activities of $27.4 million for the nine months ended September 30, 2024 was attributable to $65.8 million of purchases of available-for-sale marketable securities and $1.5 million of purchases of property and equipment, partially offset by the receipt of the remaining $22.6 million from the sale of non-financial asset during the year ended December 31, 2023 and the maturity of $17.3 million of available-for-sale marketable securities.

Net Cash Provided by Financing Activities

Net cash provided by financing activities of $0.7 million for the nine months ended September 30, 2025 was primarily attributable to the proceeds from the exercise of stock options.

Net cash provided by financing activities of $73.6 million for the nine months ended September 30, 2024 was primarily attributable to the net proceeds from the sale and issuance of our Series B convertible preferred stock.

Future Funding Requirements

Our primary use of cash is to fund our operations, primarily research and development expenditures. Cash used for operating expenses is impacted by the timing of when we pay these expenses, as reflected in the change in our outstanding accounts payable, accrued expenses and prepaid expenses.

Because of the numerous risks and uncertainties associated with research, development and commercialization of pharmaceutical products, we are unable to estimate the exact amount of our operating capital requirements. Our future funding requirements will depend on many factors, including, but not limited to:

•the scope, timing, progress and results of discovery, preclinical development, laboratory testing and clinical trials for our product candidates;

•our ability to successfully develop, obtain regulatory and marketing approvals of our product candidates for the expected indications and patient populations;

•the expenses of manufacturing our product candidates for clinical trials and in preparation for marketing approval and commercialization;

•our ability to maintain existing collaborations or strategic relationships and the extent to which we identify and enter into future collaborations or other arrangements with additional third parties in order to further develop our product candidates, as well as our ability to realize the intended and potential benefits of such agreements and collaborations;

•regulatory or legal developments in the United States and other countries;

•the expenses of preparing, filing and prosecuting patent applications, maintaining and enforcing our intellectual property rights and defending intellectual property-related claims;

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•the expenses and fees associated with the discovery, acquisition or in-license of additional product candidates or technologies;

•our ability to establish additional collaborations on favorable terms, if at all;

•the expenses required to scale up our clinical, regulatory and manufacturing capabilities;

•the expenses of future commercialization activities, if any, including establishing sales, marketing, manufacturing and distribution capabilities, for any of our product candidates for which we receive marketing approval; and

•revenue, if any, received from commercial sales of our product candidates, should any of our product candidates receive marketing approval.

We will need additional funds to meet operational needs and capital requirements for clinical trials, other research and development expenditures, and business development activities. Because of the numerous risks and uncertainties associated with the development and commercialization of our product candidates, we are unable to estimate the amounts of increased capital outlays and operating expenditures associated with our current and anticipated clinical studies.

Until such time, if ever, as we can generate substantial product revenue, we expect to finance our operations through a combination of private and public equity offerings, debt financings, collaborations, strategic alliances and marketing, distribution or licensing arrangements. However, the trading prices for our common stock and for other biopharmaceutical companies have been highly volatile. As a result, we may face difficulties raising capital through sales of our common stock, and such sales may be on unfavorable terms. Similarly, adverse macroeconomic conditions and market volatility resulting from global and national economic developments, political unrest, high inflation, disruptions in capital markets, changes in international trade relationships, changes in or the disruptions of U.S. governmental agencies, whether from a continued U.S. federal government shutdown or reduced resources, global health crises, or other factors could materially and adversely affect our ability to consummate an equity or debt financing on favorable terms or at all. We may be unable to raise additional funds or enter into such other agreements or arrangements when needed on favorable terms, or at all. To the extent that we raise additional capital through the sale of equity or convertible debt securities, existing stockholders’ ownership interests will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect existing stockholders’ rights as common stockholders. Debt financing and preferred equity financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making acquisitions or capital expenditures or declaring dividends. If we raise additional funds through collaborations, strategic alliances or marketing, distribution or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs or product candidates, or grant licenses on terms that may not be favorable to us. If we are unable to raise additional funds through equity or debt financings or other arrangements when needed, we may be required to delay, limit, reduce or terminate our research, product development or future commercialization efforts, or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves.

We historically financed our operations primarily through the issuances of convertible promissory notes and convertible preferred stock, and most recently, through an IPO. In October 2024, we completed our IPO, which resulted in net proceeds of $302.8 million, net of total offering costs of $28.4 million. Since our inception, we have devoted substantially all of our resources to raising capital, organizing and staffing our company, business and scientific planning, conducting discovery and research and development activities, establishing, maintaining, and protecting our intellectual property portfolio, developing and progressing our product candidates and preparing for clinical trials, establishing arrangements with third parties for the manufacture of our product candidates and component materials, engaging in collaboration activities, and providing general and administrative support for these operations.

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Critical Accounting Policies and Use of Estimates

Management’s discussion and analysis of our financial condition and results of operations is based on our condensed financial statements, which have been prepared in accordance with generally accepted accounting principles in the U.S. (“U.S. GAAP”). The preparation of these condensed financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the condensed financial statements, as well as the reported revenue generated and expenses incurred during the reporting periods. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions and any such differences may be material. We believe that the accounting policies discussed below are critical to understanding our historical and future performance, as these policies relate to the more significant areas involving management’s judgments and estimates.

During the nine months ended September 30, 2025, there have been no material changes to our critical accounting policies and estimates as described in our Annual Report, except as described below.

Revenue Recognition

We account for revenue in accordance with ASC 606, “Revenue from Contracts with Customers” (“ASC 606”). Under ASC 606, we recognize revenue when the customer obtains control of the promised goods or services at an amount that reflects the consideration we expect to receive in exchange for those goods or services. See Note 1, Significant Accounting Policies, to our condensed financial statements included elsewhere in this Quarterly Report for additional information.

Recent Accounting Pronouncements

A description of recently issued accounting pronouncements that may potentially impact our financial position and results of operations is disclosed in Note 1 to our condensed financial statements included elsewhere in this Quarterly Report.

Emerging Growth Company and Smaller Reporting Company Status

We qualify as “emerging growth company” under the JOBS Act, which permits us to take advantage of an extended transition period to comply with new or revised accounting standards. This provision allows an emerging growth company to delay the adoption of accounting standards that have different effective dates for public and private companies until those standards would otherwise apply to private companies. We have elected to use this extended transition period under the JOBS Act until the earlier of the date we (i) are no longer an emerging growth company or (ii) affirmatively and irrevocably opt out of the extended transition period provided in the JOBS Act. As a result, our financial statements may not be comparable to companies that comply with new or revised accounting pronouncements as of public company effective dates. We could be an emerging growth company until the earliest to occur: (i) the last day of the fiscal year in which we have more than $1.235 billion in annual gross revenue; (ii) the date we qualify as a “large accelerated filers” as defined in Rule 12b-2 under the Exchange Act, with at least $700.0 million of equity securities held by non-affiliates; (iii) the issuance, in any three-year period, by us of more than $1.0 billion in non-convertible debt securities; or (iv) the last day of the fiscal year ending after the fifth anniversary of our IPO. Even after we no longer qualify as an emerging growth company, we may continue to qualify as a “smaller reporting company,” which would allow us to take advantage of many of the same exemptions from disclosure requirements including reduced disclosure obligations regarding executive compensation in our periodic reports and proxy statements, if either (i) the market value of our stock held by non-affiliates is less than $250.0 million or (ii) our annual revenue is less than $100.0 million during the most recently completed fiscal year and the market value of our stock held by non-affiliates is less than $700.0 million.

Item 3. Quantitative and Qualitative Disclosures About Market Risk.

We are a smaller reporting company as defined by Rule 12b-2 of the Exchange Act and are not required to provide the information required under this item.

Item 4. Controls and Procedures.

Evaluation of Disclosure Controls and Procedures

Our management, with the participation of our Principal Executive Officer and Principal Financial Officer, has evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act), as of the end of the period covered by this Quarterly Report.

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Based on such evaluation, our Principal Executive Officer and Principal Financial Officer have concluded that these disclosures controls were effective at a reasonable assurance level as of September 30, 2025.

Changes in Internal Control Over Financial Reporting

There have been no changes in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) during the fiscal quarter ended September 30, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Limitations on Effectiveness of Controls and Procedures

Our management, including our Principal Executive Officer and Principal Financial Officer, believes that our disclosure controls and procedures and internal control over financial reporting are designed to provide reasonable assurance of achieving their objectives and are effective at the reasonable assurance level. However, the effectiveness of any internal control over financial reporting is subject to inherent limitations, including the exercise of judgment in designing, implementing, operating, and evaluating the controls and procedures, and the inability to eliminate misconduct completely. Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, have been detected. The design of any system of controls is based in part on certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Over time, controls may become inadequate because of changes in conditions or deterioration in the degree of compliance with policies or procedures. Because of the inherent limitations in a cost-effective control system, misstatements due to error or fraud may occur and not be detected.

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PART II—OTHER INFORMATION

Item 1. Legal Proceedings.

The information required with respect to this item can be found under “Legal Proceedings” in Note 5 to our condensed financial statements included elsewhere in this Quarterly Report on Form 10-Q (this “Quarterly Report”) and is incorporated by reference into this Item 1. From time to time, we may become involved in litigation or other legal proceedings. We are not currently a party to any litigation or legal proceedings that, in the opinion of our management, are probable to have a material adverse effect on our business. Regardless of outcome, litigation can have an adverse impact on our business, financial condition, results of operations and prospects because of defense and settlement costs, diversion of management resources and other factors.

Item 1A. Risk Factors.

Investing in our common stock involves a high degree of risk. For a detailed discussion of the risks and uncertainties related to our business, please refer to the section titled “Risk Factors” in our Annual Report on Form 10-K for the year ended December 31, 2024. There have been no material changes from the risk factors set forth in our Annual Report on Form 10-K for the year ended December 31, 2024, except as set forth below. You should carefully consider the risks and uncertainties described below and in our Annual Report on Form 10-K for the year ended December 31, 2024, together with all of the other information contained in or incorporated by reference into this Quarterly Report, including our condensed financial statements and the related notes appearing at the end of this Quarterly Report and the section titled “Management’s Discussion and Analysis of Financial Condition and Results of Operations,” before deciding to invest in our common stock. If any of the events or developments described below were to occur, our business, prospects, operating results and financial condition could suffer materially, the trading price of our common stock could decline and you could lose all or part of your investment. The risks and uncertainties described below are not the only ones we face. Additional risks and uncertainties not presently known to us or that we currently believe to be immaterial may also adversely affect our business. This Quarterly Report also contains forward-looking statements that involve risks and uncertainties. Our actual results could differ materially from those anticipated in the forward-looking statements as a result of a number of factors, including the risks described below. See the section titled “Special Note Regarding Forward-Looking Statements.”

Disruptions at the FDA, the SEC and other U.S. government agencies caused by reduction in staffing, funding shortages or global health concerns could hinder their ability to hire, retain or deploy key leadership and other personnel, or otherwise prevent new or modified products from being developed, approved or commercialized in a timely manner or at all, or otherwise prevent those agencies from performing normal business functions on which the operation of our business may rely, which could negatively impact our business.

Currently, federal agencies in the U.S. are operating under a federal government shutdown due to expiration of the continuing resolution on September 30, 2025 and the current U.S. administration is focused on reducing costs of the federal government generally, including significantly reducing the number of government employees. The duration of the current government shutdown is unknown. Without appropriation of additional funding to federal agencies, our business operations related to our product development activities for the U.S. market could be impacted. The ability of the FDA, EMA, and other comparable foreign regulatory authorities to review and approve new products can be affected by a variety of factors, including government budget and funding levels, ability to hire and retain key personnel and accept the payment of user fees, availability of personnel and other resources, and statutory, regulatory, and policy changes, and other events that may otherwise affect the FDA’s ability to perform routine functions. Average review times at the FDA have fluctuated in recent years as a result. In addition, government funding of the SEC and other government agencies on which our operations may rely, including those that fund research and development activities is subject to the political process, which is inherently fluid and unpredictable. The current U.S. administration has issued executive orders seeking to greatly reduce the size of the federal workforce, including through layoffs and severance packages offered to employees of federal agencies within the executive branch and independent agencies, including the FDA, SEC and U.S. Patent and Trademark Office (“USPTO”). Any such reduction in personnel may result in longer review times by the FDA and other agencies.

Disruptions and personnel turnover, as a result of leadership changes, staff reductions or otherwise, at the FDA and other agencies may also slow the time necessary for new drugs to be reviewed and/or approved by necessary government agencies, which would adversely affect our business. Changes and cuts in FDA staffing have been reported by some within the pharmaceutical industry as creating instances of delays in the FDA’s responsiveness or in its ability to review IND submissions or applications, issue regulations or guidance, or implement or enforce regulatory requirements in a timely fashion or at all. There is also substantial uncertainty as to how regulatory reform measures being implemented by the current U.S. administration, and other political developments, such as government shutdowns or work stoppages, would impact other U.S. regulatory agencies, such as the FDA, SEC and USPTO, on which our operations rely. For example, in March 2025, the Department of Health and Human Services announced a broad-scale restructuring effort designed to significantly reduce FDA headcount. In April 2025, FDA employees began to receive reduction in force notices. In addition, over the last several years, including beginning on October 1, 2025, the U.S. government has shut down several times and certain regulatory agencies, such as the FDA and the SEC, furloughed critical employees and ceased critical activities. Specifically, on

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October 1, 2025, the U.S. federal government entered a shutdown suspending services deemed non-essential as a result of the failure by Congress to enact regular appropriations for the 2026 fiscal year. If a prolonged government shutdown occurs or a widespread freeze on federal funding continues or occurs in the future, or if staffing changes prevent the FDA, USPTO or other regulatory authorities from conducting their regular inspections, reviews, or other regulatory activities, including formal and informal interactions with product developers, it could significantly impact the ability of such regulatory agencies to timely review and process our regulatory submissions, which could have a material adverse effect on our business. Further, in our operations as a public company, current and future government shutdowns and/or substantial leadership, personnel, and policy changes at the SEC could impact our ability to access the public markets and obtain necessary capital in order to properly capitalize and continue our operations.

Unfavorable macroeconomic conditions, political instability and geopolitical events could adversely affect our business, financial condition, stock price, and results of operations.

Our business could be adversely affected by unstable economic and political conditions within the U.S. and foreign jurisdictions, including as a result of an economic downturn and geopolitical events, such as the potential for significant changes in the U.S. federal policies or regulatory environment that affect the geopolitical landscape, changes in or the disruptions of U.S. governmental agencies, whether from a continued U.S. federal government shutdown or reduced resources, disruptions in capital markets, changes in international trade relationships and military conflicts. The global credit and financial markets have also generally experienced extreme volatility and disruptions (including as a result of actual or perceived changes in interest rates, inflation, international tariffs and macroeconomic uncertainties), which has included severely diminished liquidity and credit availability, declines in consumer confidence, declines in economic growth, high inflation, uncertainty about economic stability, global supply chain disruptions, and increases in unemployment rates. There can be no assurance that further deterioration in credit and financial markets and confidence in economic conditions will not occur. A severe or prolonged economic downturn could result in a variety of risks to our business, including a decrease in the demand for our product candidates and in our ability to raise additional capital when needed on acceptable terms, if at all.

The financial markets and the global economy may also be adversely affected by the current or anticipated impact of military conflicts, such as the ongoing conflicts between Russia and Ukraine, Israel and Iran, and Israel and Hamas, terrorism, or other geopolitical events. Sanctions imposed by the U.S. and other countries in response to such conflicts, including the one in Ukraine, may also continue to adversely impact the financial markets and the global economy, and any economic countermeasures by the affected countries or others could exacerbate market and economic instability. Additionally, changes to policy implemented by the U.S. Congress, the current U.S. administration or any new U.S. administration have impacted and may in the future impact, among other things, the U.S. and global economy, international trade relations, unemployment, immigration, healthcare, taxation, the U.S. regulatory environment, inflation and other areas. For example, in 2018 and 2019, increased tariffs were implemented on goods imported into the U.S., particularly from China, Canada, and Mexico. Additionally, in early 2025, the U.S. imposed significant tariffs on imports from other countries, including a baseline tariff of 10% on imports into the U.S. and higher tariffs on multiple designated countries (including the EU Member States, China, Canada, and Mexico), such as "reciprocal" tariffs at varying rates. Such tariffs have prompted retaliatory measures from several countries, which may further escalate.

On April 9, 2025, the U.S. announced that the imposition of most "reciprocal" tariffs would be paused for 90 days pending negotiations with the relevant countries. On September 25, 2025, the current U.S. administration announced a 100% tariff on brand-name or patented drugs unless pharmaceutical companies expand their manufacturing operations in the U.S., and may impose more restrictions on goods. While pharmaceutical products are currently excluded from the baseline and "reciprocal" tariffs imposed by the U.S., such tariffs still apply to the raw materials and other products necessary for the manufacture and formulation of our product candidates. In addition, the current U.S. administration has expressed an intent to impose tariffs on pharmaceutical imports, with the stated policy objective of reshoring pharmaceutical manufacturing to the U.S. Among other means, such tariffs may be imposed by the U.S. under Section 232 of the Trade Expansion Act of 1962, as amended, pursuant to which the U.S. Department of Commerce recently initiated an investigation to determine the effects of importing pharmaceuticals and pharmaceutical ingredients on national security. While certain tariffs have subsequently been suspended, modified or temporarily reduced, we cannot predict the results of the U.S. government’s trade negotiations or the outcome of ongoing legal challenges to specific tariff policies. In response to tariffs, other countries have implemented retaliatory tariffs on U.S. goods. Political tensions as a result of trade policies could reduce trade volume, investment, technological exchange and other economic activities between major international economies, resulting in a material adverse effect on global economic conditions and the stability of global financial markets. There has also been proposed U.S. legislation, such as the bill titled the BIOSECURE Act introduced in 2024, that may restrict the ability of U.S. pharmaceutical companies to purchase services or products from, or otherwise collaborate with, certain Chinese biotechnology companies of concern without losing the ability to contract with, or otherwise receive funding from, the U.S. government. Although the BIOSECURE Act was not passed, in October 2025, versions of the National Defense Authorization Act of 2026 passed each respective chamber of Congress and both included an amendment that will effectively implement federal government contracting, loan, and grant restrictions similar to the 2024 BIOSECURE Act. This 2025 version of the BIOSECURE Act does not identify any specific companies by name in the legislative text. If the BIOSECURE Act or similar legislation is passed in the future, we may not be able to engage a backup or alternative supplier or service provider in a timely manner or at all. We continue to assess the legislation as it develops to determine whether it could have an effect

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on our contractual relationships. Any changes in political, trade, regulatory, and economic conditions, including U.S. trade policies, could have a material adverse effect on our financial condition or results of operations. Until we know what policy changes are made, whether those policy changes are challenged and subsequently upheld by the court system and how those changes impact our business and the business of our competitors over the long term, we will not know if, overall, we will benefit from them or be negatively affected by them.

Furthermore, any disruptions to our supply chain as a result of unfavorable global economic conditions, including due to geopolitical conflicts, could negatively impact the timely execution of our ongoing and future clinical trials. In addition, current inflationary trends in the global economy may impact salaries and wages, costs of goods and transportation expenses, among other things, and recent and potential future disruptions in access to bank deposits or lending commitments due to bank failures may create market and economic instability. We cannot anticipate all of the ways in which the foregoing, and the current economic climate and financial market conditions generally, could adversely impact our business.

Healthcare legislative reform measures may have a negative impact on our business and results of operations.

In the U.S. and some foreign jurisdictions, there have been, and continue to be, several legislative and regulatory changes and proposed changes regarding the healthcare system that could prevent or delay marketing approval of product candidates, restrict or regulate post-approval activities, and affect our ability to profitably sell any product candidates for which we obtain marketing approval. For more information, see the section titled “Business-Government Regulation-Current and Future U.S. Healthcare Reform.”

Among policy makers and payors in the U.S. and elsewhere, there is significant interest in promoting changes in healthcare systems with the stated goals of containing healthcare costs, improving quality and/or expanding access. In the U.S., the pharmaceutical industry has been a particular focus of these efforts and has been significantly affected by major legislative initiatives. In 2010, the Patient Protection and Affordable Care Act, as amended by the Health Care and Education Reconciliation Act was passed, which substantially changed the way healthcare is financed by both the government and private insurers, and significantly impacts the U.S. pharmaceutical industry.

The continuing efforts of the government, insurance companies, managed care organizations and other payors of healthcare services to contain or reduce costs of healthcare may adversely affect:

•the demand for any of our product candidates, if approved;

•the ability to set a price that we believe is fair for any of our product candidates, if approved;

•our ability to generate revenues and achieve or maintain profitability;

•the level of taxes that we are required to pay; and

•the availability of capital.

Legislative and regulatory proposals have been made to expand post-approval requirements and restrict sales and promotional activities for pharmaceutical and biologic products. In addition, there has been increasing legislative and enforcement interest in the U.S. with respect to specialty drug pricing practices. Specifically, there have been several recent U.S. Congressional inquiries and proposed and enacted federal and state legislation designed to, among other things, bring more transparency to drug pricing, reduce the cost of prescription drugs under Medicare, review the relationship between pricing and manufacturer patient programs, and reform government program reimbursement methodologies for drugs.

In August 2022, the Inflation Reduction Act of 2022 (“IRA”) was signed into law. The IRA includes several provisions that may impact our business, depending on how various aspects of the IRA are implemented. Provisions that may impact our business include a $2,000 out-of-pocket cap for Medicare Part D beneficiaries, the imposition of new manufacturer financial liability on most drugs in Medicare Part D, permitting the U.S. government to negotiate Medicare Part B and Part D pricing for certain high-cost drugs and biologics without generic or biosimilar competition, requiring companies to pay rebates to Medicare for drug prices that increase faster than inflation, and delay until January 1, 2032 the implementation of the HHS rebate rule that would have limited the fees that pharmacy benefit managers can charge. Further, under the IRA, orphan drugs are exempted from the Medicare drug price negotiation program, but only if they have one orphan designation and for which the only approved indication is for that disease or condition. If a product receives multiple orphan designations or has multiple approved indications, it may not qualify for the orphan drug exemption. The implementation of the IRA is currently subject to ongoing litigation challenging the constitutionality of the IRA’s Medicare drug price negotiation program. The effects of the IRA on our business and the healthcare industry in general is not yet known.

On April 15, 2025, the current U.S. administration published Executive Order 14273, “Lowering Drug Prices by Once Again Putting Americans First,” which generally directs the federal government to take measures to reduce drug prices, including eliminating the so-called “pill penalty” under the IRA that creates a distinction between small molecule and large molecule products for purposes

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of determining when a drug may be eligible for drug price negotiation. On May 12, 2025, the current U.S. administration published Executive Order 14297, “Delivering Most-Favored-Nation Prescription Drug Pricing to American Patients” which generally, among other things, directs the federal government to establish and communicate most-favored-nation price targets to pharmaceutical manufacturers to bring prices for American patients in line with comparably developed nations. Further, the Executive Order directs the federal government to support regulatory paths to allow direct-to-patient sales for companies that meet these targets. It also states that the current U.S. administration will take additional aggressive action (for example, examining whether marketing approvals should be modified or rescinded or opening the door for individual drug importation waivers) should manufacturers fail to offer American consumers the most-favored-nation lowest price. It also directs the Secretary of Commerce and the U.S. Trade Representative to “take all necessary and appropriate action to ensure foreign countries are not engaged in any act, policy, or practice that may be unreasonable or discriminatory or that may impair U.S. national security. including by suppressing the price of pharmaceutical products below fair market value in foreign countries.” Notably, a similar “Most Favored Nation” pricing rule enacted in 2020 was subject to an injunction resulting from judicial challenges to the rule, which was formally rescinded in August 2021.

In addition, at the state level, legislatures have increasingly passed legislation and implemented regulations similar to those under consideration at the federal level, as well as laws designed to control pharmaceutical and biotherapeutic product pricing, including restrictions on pricing or reimbursement at the state government level, limitations on discounts to patients, marketing cost disclosure and transparency measures, restrictions or other limitations on patient assistance, and, in some cases, policies to encourage importation from other countries (subject to federal approval) and bulk purchasing. Certain states are also pursuing cost containment efforts through Prescription Drug Affordability Boards and similar entities.

We cannot be sure whether additional legislative changes will be enacted, or whether FDA regulations, guidance or interpretations will be changed, or what the impact of such changes on the marketing approvals of our product candidates, if any, may be. In addition, increased scrutiny by Congress of the FDA’s approval process may significantly delay or prevent marketing approval, as well as subject us to more stringent product labeling and post-marketing testing and other requirements.

We cannot predict what healthcare reform initiatives may be adopted in the future. We expect that these and other healthcare reform measures that may be adopted in the future, may result in more rigorous coverage criteria and additional downward pressure on the price that we receive for any approved drug. Any reduction in reimbursement from Medicare or other government programs may result in a similar reduction in payments from private payors. The implementation of cost containment measures or other healthcare reforms may prevent us from being able to generate revenue, attain profitability, or commercialize our drugs.

The U.S. Congress, the current U.S. administration, or any new U.S. administration may make substantial changes to fiscal, tax, and other federal policies that may adversely affect our business

Since the start of the current U.S. administration in 2025, U.S. policy changes have been implemented at a rapid pace and additional changes are likely. For example, the U.S. government has adopted new approaches to trade policy and in some cases may renegotiate, or potentially terminate, certain existing bilateral or multi-lateral trade agreements. The U.S. government has also imposed substantial tariffs on most countries throughout the world and has further threatened to continue to broadly impose tariffs, which could lead to corresponding punitive actions by the countries with which the U.S. trades. Changes to U.S. policy implemented by the U.S. Congress, the current U.S. administration or any new U.S. administration have impacted and may in the future impact, among other things, the U.S. and global economy, international trade relations, unemployment, immigration, healthcare, taxation, the U.S. regulatory environment, inflation and other areas. Although we cannot predict the impact, if any, of these changes to our business, they could adversely affect our business. Until we know what policy changes are made, whether those policy changes are challenged and subsequently upheld by the court system and how those changes impact our business and the business of our competitors over the long term, we will not know if, overall, we will benefit from them or be negatively affected by them.

Legislation or other changes in U.S. tax law may have a material adverse effect on our business, cash flow, financial condition, or results of operations.

The rules dealing with U.S. federal, state, and local income taxation are constantly under review by persons involved in the legislative process and by the Internal Revenue Service and the U.S. Treasury Department. For example, the One Big Beautiful Bill Act (“H.R.1”) was signed into law on July 4, 2025 and made significant changes to U.S. federal tax law. Changes to tax laws (which changes may have retroactive application) could adversely affect us or holders of our common stock. For example, under Section 174 of the Internal Revenue Code of 1986, as amended (the “IRC”), in taxable years beginning after December 31, 2021, expenses that are incurred for research and development performed outside the U.S. will be capitalized and amortized, which may have an adverse effect on our cash flow. H.R.1 provides that for taxable years beginning after December 31, 2024, expenses that are incurred for research and development performed in the U.S. may, at the taxpayer’s election, be immediately deducted or capitalized and amortized. In addition, H.R.1 provides that for taxable years beginning after December 31, 2021 and before January 1, 2025, certain eligible taxpayers generally may elect to retroactively deduct expenses for research and development performed in the U.S. in such taxable years by filing amended tax returns for such taxable years, and all other taxpayers that are not eligible to make such an election and that amortized expenses for research and development performed in the U.S. in such taxable years generally may elect to accelerate and deduct the remaining

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unamortized amounts of such research and development expenses (i) in the first taxable year beginning after December 31, 2024, or (ii) ratably over the two-taxable year period beginning with the first taxable year beginning after December 31, 2024. In recent years, many changes have been made to applicable tax laws and changes are likely to continue to occur in the future. For example, under Section 174 of the Code, in taxable years beginning after December 31, 2021, expenses that are incurred for research and development in the U.S. will be capitalized and amortized, which may have an adverse effect on our cash flow. Future changes in tax laws could have a material adverse effect on our business, cash flow, financial condition or results of operations.

It cannot be predicted whether, when, in what form, or with what effective dates, new tax laws may be enacted, or regulations and rulings may be enacted, promulgated or issued under existing or new tax laws, which could result in an increase in our or our stockholders’ tax liability or require changes in the manner in which we operate in order to minimize or mitigate any adverse effects of changes in tax law or in the interpretation thereof. We urge investors to consult with their legal and tax advisers regarding the implications of potential changes in tax laws on an investment in our common stock.

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds

(a) Unregistered Sales of Equity Securities

None.

(b) Use of Proceeds from our IPO

On October 24, 2024, our Registration Statement on Form S-1 (File No. 333-282469), as amended, relating to our IPO was declared effective by the Securities and Exchange Commission (the “SEC”) (the “Registration Statement”). Pursuant to the Registration Statement, we registered the offer and sale of 18,400,000 shares of our common stock. On October 28, 2024, we closed our IPO, pursuant to which we issued and sold 18.4 million shares of common stock at the public offering price of $18.00 per share, which included 2.4 million shares of our common stock issued and sold on October 30, 2024 to the underwriters pursuant to the full exercise of their option to purchase additional shares of our common stock, at the public offering price of $18.00 per share. Pursuant to the IPO, we received gross proceeds of $331.2 million, which resulted in net proceeds to us of $302.8 million, after deducting underwriting discounts and commissions and other offering costs payable by us of $28.4 million. J.P. Morgan Securities LLC, TD Securities (USA) LLC, Cantor Fitzgerald & Co. and Wells Fargo Securities, LLC acted as joint book-running managers for the IPO.

The net proceeds from our IPO have been invested according to our approved investment policy in a mix of money market funds and high-quality, fixed income securities. Our planned use of the net proceeds from the IPO as described in our final prospectus filed with the SEC pursuant to Rule 424(b)(4) under the Securities Act of 1933, as amended (the “Securities Act”) on October 25, 2024 has changed due to the discontinuation of the development of our prior lead product candidate, SEP-786. As a result, we currently expect to use our cash, cash equivalents and marketable securities, which include the net proceeds from the IPO, to advance a next-generation oral small molecule PTH1R agonist from our PTH1R program into clinical development, advance SEP-631 into clinical development, continue to advance the other programs in our pipeline, and the remainder to fund working capital and other general corporate purposes. Except for the reallocation of SEP-786 funds discussed above, there has been no material changes in the planned use of proceeds from our IPO as described in our final prospectus filed with the SEC pursuant to Rule 424(b)(4) under the Securities Act on October 25, 2024.

(c) Issuer Repurchases of Equity Securities

The following table provides stock repurchase activity during each of the months of the three months ended September 30, 2025:

		Total number of shares purchased(1)				Average price paid per share				Total number of shares purchased as part of publicly announced plans or programs				Maximum number of shares that may yet be purchased under the plans or programs
July 1, 2025 - July 31, 2025			—			$	—				—				—
August 1, 2025 - August 31, 2025			2,322				0.09				—				—
September 1, 2025 - September 30, 2025			—				—				—				—
		$	2,322			$	0.09				—				—

_____________________

(1) Represents shares of unvested common stock that were repurchased by us from former employees upon termination of employment in accordance with the terms of the employees’ stock option agreements. We purchased the shares from the former employees at the respective original exercise prices.

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Item 3. Defaults Upon Senior Securities.

Not applicable.

Item 4. Mine Safety Disclosures.

Not applicable.

Item 5. Other Information.

(c) Rule 10b5-1 Trading Plans

None of our directors or officers (as defined in Rule 16a-1(f) of the Exchange Act) adopted or terminated a Rule 10b5-1 trading plan or arrangement or a non-Rule 10b5-1 trading plan or arrangement, as defined in Item 408(c) of Regulation S-K, during the fiscal quarter ended September 30, 2025 covered by this Quarterly Report.

Item 6. Exhibits.

(a) Exhibits.

				Incorporated by Reference
Exhibit Number		Description		Form		File No.		Exhibit		Filing Date
3.1		Amended and Restated Certificate of Incorporation of the Registrant.		8-K		001-42382		3.1		October 28, 2024
3.2		Amended and Restated Bylaws of the Registrant.		8-K		001-42382		3.2		October 28, 2024
4.1†		Amended and Restated Investors’ Rights Agreement, by and among the Registrant and certain of its stockholders, dated as of June 28, 2023.		S-1		333-282469		4.1		October 24, 2024
4.2		Specimen Common Stock Certificate.		S-1		333-282469		4.2		October 24, 2024
10.1*#		Amended and Restated Non-Employee Director Compensation Policy
31.1*		Certification of Principal Executive Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
31.2*		Certification of Principal Financial Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
32.1*+		Certifications of Principal Executive Officer and Principal Financial Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
101.INS*		Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because XBRL tags are embedded within the Inline XBRL document.
101.SCH*		Inline XBRL Taxonomy Extension Schema With Embedded Linkbase Documents
104*		Cover Page formatted as Inline XBRL and contained in Exhibit 101

* Filed herewith.

# Indicates a management contract or any compensatory plan, contract or arrangement.

+ The certifications furnished in Exhibit 32.1 hereto are deemed to be furnished with this Quarterly Report and will not be deemed to be “filed” for purposes of Section 18 of the Exchange Act, except to the extent that the Registrant specifically incorporates it by reference.

† Annexes, schedules and/or exhibits have been omitted pursuant to Item 601(a)(5) of Regulation S-K. The Registrant agrees to furnish supplementally a copy of any omitted attachment to the SEC on a confidential basis upon request.

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(b) Financial Statement Schedules.

None.

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SIGNATURES

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

		Septerna, Inc.
Date: November 10, 2025		By:	/s/ Jeffrey Finer, M.D., Ph.D.
			Jeffrey Finer, M.D., Ph.D.
			Chief Executive Officer
			(Principal Executive Officer)
Date: November 10, 2025		By:	/s/ Gil M. Labrucherie, CFA, J.D.
			Gil M. Labrucherie, CFA, J.D.
			Chief Financial Officer
			(Principal Financial Officer and Principal Accounting Officer)

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FAQ

How did SEPN perform in Q3 2025?

Revenue was $21,495 thousand and net income was $8,173 thousand for the three months ended September 30, 2025.

What drove the revenue increase for Septerna (SEPN)?

Revenue reflected recognition under the Novo collaboration; year‑to‑date recognized was $12,750 thousand from the $195,000 thousand upfront.

What is Septerna’s cash position?

Cash, cash equivalents and marketable securities totaled $561,600 thousand as of September 30, 2025.

How much deferred revenue does SEPN have from the Novo deal?

Deferred revenue was $182,250 thousand, including $61,603 thousand current and $120,647 thousand non‑current.

What were Septerna’s operating expenses in Q3 2025?

R&D expense was $24,264 thousand and G&A was $7,117 thousand.

Did SEPN record any non-operating gains in Q3 2025?

Yes, a $12,500 thousand gain on sale of a non‑financial asset linked to a Vertex milestone.

How many SEPN shares were outstanding?

Shares outstanding were 44,774,192 as of November 4, 2025.