☒QUARTERLY REPORT PURSUANT TO SECTION13 OR 15(d)OF THE SECURITIESEXCHANGE ACT OF 1934For the quarterly period endedMarch 31, 2025or PROTAGONIST THERAPEUTICS,INC. Securities registered pursuant to Section 12(b) of the Act: Indicate by check mark whether the registrant (1)has filed all reports required to be filed by Section13 or 15(d)of theSecurities Exchange Act of 1934 during the preceding 12months (or for such shorter period that the registrant was required to file Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to besubmitted pursuant to Rule405 of Regulation S-T (§232.405 of this chapter) during the preceding 12months (or for such shorter Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, asmaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transitionperiod for complying with any new or revised financial accounting standards provided pursuant to Section13(a)of the Exchange As of April 30, 2025, there were61,981,955shares of the registrant’s Common Stock, par value $0.00001 per share,outstanding. PROTAGONIST THERAPEUTICS, INC.FORM 10-Q PARTI FINANCIAL INFORMATION Item1.Condensed Consolidated Financial Statements (unaudited) Condensed Consolidated Balance SheetsCondensed Consolidated Statements of OperationsCondensed Consolidated Statements of Comprehensive (Loss) IncomeCondensed Consolidated Statements of Stockholders’ EquityCondensed Consolidated Statements of Cash FlowsNotesto Unaudited Condensed Consolidated Financial StatementsItem2.Management’s Discussion and Analysis of Financial Condition and Results ofOperationsItem3.Quantitative and Qualitative Disclosures About Market RiskItem4.Controls and Procedures PARTII OTHER INFORMATION Item 1.Legal Proceedings34Item1A.Risk Factors34Item2.Unregistered Sales of Equity Securities and Use of Proceeds36Item3.Defaults Upon Senior Securities36Item4.Mine Safety Disclosures36Item5.Other Information36Item6.Exhibits36SIGNATURES38 PARTI.– FINANCIAL INFORMATION PROTAGONIST THERAPEUTICS,INC.Condensed Consolidated Balance Sheets PROTAGONIST THERAPEUTICS,INC.Condensed Consolidated Statements of Operations(Unaudited) PROTAGONIST THERAPEUTICS,INC.Condensed Consolidated Statements of Comprehensive (Loss) Income(Unaudited)(In thousands) The accompanying notes are an integral part of these unaudited condensed consolidated financialstatements. PROTAGONIST THERAPEUTICS,INC.Condensed Consolidated Statements of Cash Flows PROTAGONIST THERAPEUTICS, INC.Notes to Unaudited Condensed Consolidated Financial Statements Note1.Organization and Description of Business Protagonist Therapeutics,Inc. (the “Company”) is a discovery through late-stagedevelopment biopharmaceutical company focused on peptide therapeutics.The Company’sclinicalprograms fall into two broad categories of diseases: (i) inflammatory and immunomodulatory (“I&I”)diseases and (ii) hematology and blood disorders. Two novel peptides derived from the Company’s Icotrokinra is a first-in-class investigational targeted oral peptide that selectively blocks theInterleukin-23 receptor (“IL-23R”) and is licensed to J&J Innovative Medicines (“JNJ”), formerlyJanssen Biotech, Inc. Following icotrokinra’s joint discovery by the Company and JNJ scientistspursuant to their IL-23R collaboration, the Company was primarily responsible for the developmentof icotrokinra through Phase 1, with JNJ assuming responsibility for development in Phase 2 andbeyond. Rusfertide, an injectable mimetic of the natural hormone hepcidin, is currently in The Company also has a number of pre-clinical stage oral drug discovery programsaddressing biologically and commercially validated targets, including the IL-17 oral peptide The Company is headquartered in Newark, California and has one wholly owned subsidiary,Protagonist Pty Limited (“Protagonist Australia”), located in Brisbane, Queensland, Australia. Operating Segments Operating segments are components of an enterprise for which separate financialinformation is available and is evaluated regularly by the Chief Executive Officer, the Company’schief operating decision maker (“CODM”), in deciding how to allocate resources and assessingperformance.The Company operates and manages its business asoneoperating segment. TheCompany’s Chief Executive Officer reviews financial information on an aggregate basis for the Liquidity As of March 31, 2025, the Company had cash, cash equivalents and marketable securities of$697.9million. The Company has incurred an accumulated deficit from inception through March 31,2025 of $352.2million. The Company’s ultimate success depends upon the outcome of its researchand development and collaboration activities. The Company may incur addit