Protagonist Therapeutics reported $274.41 million in revenue for Q3 2026.

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For the quarterly period ended June September 30, 2026

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As of July October 31, 2026, there were 64,708,285 65,270,114 shares of the registrant's Common Stock, par value $0.00001 per share, outstanding.

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Financial statements 76 changes

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Income taxes payable

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Common stock, $ 0.00001 par value, 180,000,000 shares authorized; 64,672,032 65,256,152 and 62,577,897 shares issued as of September 30, 2026 and December 31, 2025, respectively, and 65,215,592 and 62,577,897 shares outstanding as of June September 30, 2026 and December 31, 2025, respectively

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Net income (loss) per share, diluted

Weighted-average shares used to compute net income (loss) per share, diluted

Net income (loss) per share: basic

Weighted-average shares used to compute net income (loss) per share: basic

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Balance at March 31, 2026

Issuance of common stock under equity incentive and employee stock purchase plans

Stock-based compensation expense

Other comprehensive loss

Three months ended June September 30, 2026

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Three months ended June 30, 2025

Balance at March 31, 2025

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Repurchase of common stock

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Balance at September 30, 2026

Three months ended September 30, 2025

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Issuance of common stock under equity incentive and employee stock purchase plans

Stock-based compensation expense

Other comprehensive income

Balance at September 30, 2025

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Six months ended June 30, 2026

Nine months ended September 30, 2026

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Repurchase of common stock

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Six months ended June 30, 2025

Balance at June September 30, 2026

Nine months ended September 30, 2025

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Balance at June September 30, 2025

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Proceeds from issuance of common stock upon exercise of stock options and purchases under employee stock purchase plan ( 5,791 )

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Common stock issued for cash not yet received

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Leasehold improvements obtained under tenant improvement allowance

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Rusfertide, a first-in-class investigational injectable mimetic of the natural hormone hepcidin, is currently in development for the treatment of the rare blood disorder polycythemia vera ("PV"). Rusfertide is licensed to Takeda Pharmaceuticals Inc. ("Takeda"). The Company discovered and led development for rusfertide through Phase 3, and Takeda is responsible for further development and commercialization. In August 2025, rusfertide was granted Breakthrough Therapy designation by the U.S. Food and Drug Administration (the "FDA") for the treatment of erythrocytosis in patients with PV. In December 2025, a New Drug Application ("NDA") was submitted to the FDA by Takeda and the Company seeking the first approval of rusfertide for the treatment of adults with PV. The NDA was granted priority review by the FDA, with a Prescription Drug User Fee Act target action date in August 2026.

Protagonist Therapeutics, Inc. (the "Company") is a discovery through late-stage development biopharmaceutical company with built on a proprietary peptide technology platform. that enables de novo discovery of peptide therapeutics. The Company's programs fall into three broad therapeutic areas: (i) inflammation and immunology ("I&I"), (ii) hematology and (iii) metabolic diseases. The Company's aim is to develop medicines for biologically and commercially validated targets which demonstrate a strong differentiation compared to existing therapies.

ICOTYDE ® (icotrokinra) was approved in the United States in March 2026 for the treatment of moderate-to-severe plaque psoriasis in adults and pediatric patients 12 years of age or older who weigh at least 40 kg and are candidates for systemic therapy or phototherapy. ICOTYDE is the first and only targeted oral peptide that precisely blocks the Interleukin-23 receptor ("IL-23R") and is licensed to Janssen Biotech, Inc., a Johnson & Johnson company ("JNJ"). ICOTYDE was jointly discovered by the Company and JNJ scientists, with the Company having primary responsibility for the development of ICOTYDE through Phase 1, and JNJ assuming responsibility for further development and commercialization. In September 2025, JNJ submitted an application to 2026, the European Medicines Agency ("EMA") seeking the first Commission granted approval of JNJ's marketing application for ICOTYDE for the treatment of adults and pediatric patients 12 years of age and older with moderate-to-severe plaque psoriasis. ICOTYDE has also received regulatory approval in Japan and China. ICOTYDE is in Phase 3 development for additional immune-mediated diseases, including psoriatic arthritis, and ulcerative colitis, and in Phase 2b/3 for Crohn's disease.

MIMRYLO™ (rusfertide), a subcutaneously delivered first-in-class hepcidin mimetic, was approved in the United States in August 2026 for the treatment of erythrocytosis in adults with the rare blood disorder polycythemia vera ("PV"). On September 30, 2026, MIMRYLO was also approved in the United Arab Emirates. MIMRYLO is licensed to Takeda Pharmaceuticals, Inc. ("Takeda") and is the first and only hepcidin mimetic approved for PV, a blood cancer characterized by excessive production of red blood cells. The Company discovered and led development for MIMRYLO through its New Drug Application ("NDA") filing in December 2025, and Takeda is responsible for further development and commercialization.

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The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally accepted accounting principles in the United States ("GAAP"), the instructions to Form 10-Q and Rule 10-01 of Regulation S-X and applicable rules and regulations of the Securities and Exchange Commission ("SEC") regarding interim financial reporting. As permitted under those rules, certain footnotes or other financial information that are normally required by GAAP have been condensed or omitted and, accordingly, the condensed consolidated balance sheet as of June September 30, 2026 has been derived from the Company's unaudited consolidated financial statements at that date but does not include all of the information required by GAAP for complete consolidated financial statements. These unaudited interim condensed consolidated financial statements have been prepared on the same basis as the Company's annual consolidated financial statements and, in the opinion of management, reflect all adjustments (consisting of normal recurring adjustments) that are necessary for a fair presentation of the Company's condensed consolidated financial statements. The results of operations for the three and six nine months ended June September 30, 2026 are not necessarily indicative of the results to be expected for the year ending December 31, 2026 or for any future period.

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There has been uncertainty and disruption in the global economy and financial markets due to a number of factors, including but not limited to geopolitical instability and changes in trade policies, including tariffs or other trade restrictions or the threat of such actions and retaliatory actions. The Company's business may also be impacted by changes or disruptions at the U.S. Food and Drug Administration (the "FDA") and other government agencies. The Company has taken into consideration any known impacts to its accounting estimates to date and is not aware of any additional specific events or circumstances that would require any additional updates to its estimates or judgments or a revision of the carrying value of its assets or liabilities as of the filing date of this Quarterly Report on Form 10-Q. These estimates may change as new events occur and additional information is obtained. Actual results could differ materially from these estimates under different assumptions or conditions.

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Restricted cash as of June September 30, 2026 and 2025 consists of a cash deposit held as security in connection with a letter of credit related to the Company's facility lease entered into in March 2017, as subsequently amended, and a cash deposit held as security in connection with the issuance of a bank guarantee in May 2025 to maintain the active status of the Company's value-added tax registration.

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PSUs allow the recipients of such awards to earn fully vested shares of the Company's common stock upon the achievement of pre-established performance objectives. Stock-based compensation expense associated with PSUs is based on the fair value of the Company's common stock on the grant date, which equals the closing market price of the Company's common stock on the grant date and is recognized when the performance objective is expected to be achieved. The Company evaluates the probability of achieving the performance criteria on a quarterly basis. The cumulative effect on current and prior periods of a change in the estimated number of PSUs expected to be earned is recognized as compensation expense or as reduction of previously recognized compensation expense in the period of the revised estimate. No stock-based compensation related to PSUs was recognized for the three and six nine months ended June September 30, 2026 and the three months ended June September 30, 2025. During the nine months ended September 30, 2025, the Company recognized $ 1.8 million of stock-based compensation expense related to 75,500 PSUs for that vested during the six months ended June 30, third quarter of 2025. As of September 30, 2026, 122,100 PSUs were outstanding.

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There have been no material changes to the Company's significant accounting policies during the three and six nine months ended June September 30, 2026, as compared to those disclosed in Note 2. Summary of Significant Accounting Policies included in the Company's Annual Report on Form 10-K for the year ended December 31, 2025.

Recently Issued Accounting Pronouncements Not Yet Adopted as of June September 30, 2026

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In November 2024, The Company entered into an Amended and Restated License and Collaboration Agreement with JNJ which are parties to an Amended and Restated the License and Collaboration Agreement, which was originally effective in July 2017, by and between the Company and JNJ, as amended in May 2019, amended and restated in July 2021 (together, and amended in November 2024 (as amended, the "JNJ License and Collaboration Agreement"). The JNJ License and Collaboration Agreement relates to the development, manufacture and commercialization of oral IL-23R antagonist drug candidates and enables JNJ to develop collaboration compounds for multiple indications. Under the JNJ License and Collaboration Agreement, JNJ is required to use commercially reasonable efforts to develop at least one collaboration compound for at least two indications.

During the first quarter of 2026, the Company earned a $ 50.0 million milestone payment upon FDA approval of ICOTYDE for the treatment of moderate-to-severe plaque psoriasis in adults and pediatric patients 12 years of age or older who weigh at least 40 kg and are candidates for systemic therapy or phototherapy. The Company has earned a total of $ 387.5 million in non-refundable upfront and milestone payments from JNJ under the JNJ License and Collaboration Agreement from inception in 2017 through June September 30, 2026.

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In January 2024, the Company entered into a worldwide license and collaboration agreement for rusfertide MIMRYLO with Takeda, which became effective in March 2024, and was amended in March 2025 (the "Takeda Collaboration Agreement").

Pursuant to the Takeda Collaboration Agreement, the Company and Takeda agreed to jointly develop and commercialize rusfertide MIMRYLO and potentially other specified second-generation injectable hepcidin mimetic compounds (the "Licensed Products") in the United States (the "Profit-Share Territory"). Takeda was solely and exclusively responsible for the development and commercialization of the Licensed Products in all other countries (the "Takeda Territory"). The Company and Takeda shared the costs of the development, manufacture and commercialization activities for the Licensed Products in the Profit-Share Territory, provided that (i) the Company led, and was solely responsible for its costs associated with, completion of the ongoing Phase 3 VERIFY trial evaluating rusfertide MIMRYLO for the treatment of PV; (ii) Takeda led, and was solely responsible for its costs associated with, U.S. regulatory and pre-commercialization activities related to rusfertide MIMRYLO in the Profit-Share Territory; and (iii) Takeda led commercialization of rusfertide MIMRYLO in the Profit-Share Territory, though the Company held an option to co-detail. Takeda was solely responsible for all costs for the development, manufacture and commercialization of the Licensed Products in the Takeda Territory. The Company granted Takeda a non-transferable, sublicensable and, except for certain specified exceptions, exclusive license to certain intellectual property of the Company to exercise its rights and perform its obligations under the Takeda Collaboration Agreement. In March 2025, the Company and Takeda agreed, pursuant to the provisions of the Takeda Collaboration Agreement, as amended, that Takeda would assume responsibility for leading and implementing the regulatory strategy and associated activities for preparation of the NDA related to rusfertide MIMRYLO in PV, which was submitted to the FDA in December 2025 and approved in August 2026. The Company was primarily responsible for clinical development activities through the NDA filing and for conducting ongoing rusfertide MIMRYLO long-term extension studies.

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On April 28, 2026, the Company announced that it exercised its right to opt out of the U.S. profit and loss sharing arrangement ( 50 % to the Company and 50 % to Takeda) under the Takeda Collaboration Agreement. Following the Company's exercise of the opt-out right, the Company has agreed to transition transitioned applicable development and commercial activities to Takeda, and Takeda has the right to assume assumed sole operational and financial responsibility for such activities in the United States. The opt-out election triggered a $ 200.0 million payment, with and the FDA's approval of MIMRYLO in August 2026 triggered an additional $ 200.0 million opt-out fee payment and a separate $ 75.0 million milestone due upon FDA approval of rusfertide. payment. Following the opt-out, the Company is also eligible to receive up to $ 775.0 800.0 million in development and sales milestone payments for MIMRYLO in PV, and tiered royalties ranging from 14 % to 29 % on annual net worldwide sales, with an approximate 21 % weighted-average royalty rate at $ 1.5 billion in annual net sales and a 29 % tier applying to incremental annual net sales above $ 1.5 billion.

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● $ 75.0 million upon FDA approval of an NDA for rusfertide in PV;

● $ 15.0 million upon first regulatory approval for rusfertide MIMRYLO in PV in three European countries, after pricing and reimbursement approval; and

● $ 10.0 million upon first regulatory approval for rusfertide MIMRYLO in PV in Japan.

The Company is was obligated to perform certain wind-down activities during the three-month opt-out wind-down period which includes included transferring the VERIFY trial and other projects to Takeda, overseeing vendors and development activities until such activities are fully transferred to Takeda, and continuing to perform the rusfertide open label MIMRYLO open-label extension. Such costs during the wind-down period (from April 28, 2026 to July 27, 2026) are were shared ( 50 %) with Takeda and the Company aims to transfer transferred the majority of the activities to Takeda by July 27, 2026. As agreed upon with Takeda, Protagonist the Company will continue work for on the rusfertide MIMRYLO open-label extension after the wind-down period until completion, which is expected in the first quarter of 2027. Costs incurred by Protagonist the Company for any remaining wind-down activities and rusfertide MIMRYLO open-label extension after July 27, 2026 will be fully reimbursed by Takeda.

The Company initially evaluated the Takeda Collaboration Agreement and concluded that it had elements that were within the scope of ASC Topic 606 and ASC Topic 808. As of the effective date of the Takeda Collaboration Agreement, the Company identified two distinct performance obligations: (i) the rusfertide MIMRYLO license delivered upon the effectiveness of the Takeda Collaboration Agreement and (ii) certain development services to be provided prior to the opt-out period, including certain of the Company's responsibilities to complete the VERIFY Phase 3 clinical trial in PV and associated manufacturing services. Following the completion of the wind-down period on July 27, 2026, the Takeda Collaboration Agreement will no longer meet meets the definition of a collaborative arrangement under ASC Topic 808.

The Company determined that the initial transaction price totaled $ 300.0 million, which was comprised of the upfront payment. The Company initially excluded any future estimated milestones or royalties from this transaction price, all of which were either constrained or subject to the sales-and sales- and usage-based royalty exception. As part of the Company's evaluation of this variable consideration constraint, it determined that the potential payments were contingent upon developmental and regulatory milestones that were uncertain and were highly susceptible to factors outside of its control. The Company allocated $ 254.1 million of the initial transaction price to the license and $ 45.9 million to the development services based upon the relative standalone selling price of each performance obligation. The estimate of standalone selling price for the license was determined based on discounted cash flows for the expected development and commercialization of rusfertide MIMRYLO and included assumptions for forecasted revenues, development timelines and expenses, discount rates, and probabilities of technical and regulatory success. The estimate of standalone selling price for the development services was determined based on forecasted costs and expenses over the expected development period. For the license of rusfertide, MIMRYLO, the Company determined that Takeda could benefit from the license at the time the license was granted and therefore, the related performance obligation was satisfied at that point in time.

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For the six months ended June 30, 2026, the Company recognized license and collaboration revenue of $269.8 million. This included $ 205.7 million under the Takeda Collaboration Agreement using the cost-based input method for development services, consisting of (i) $ 192.4 million related to the proportional recognition of the $ 200.0 million opt-out payment, (ii) $ 5.7 million related to cost reimbursement for post opt-out wind-down services provided by the Company, $3.4 million of which was recorded as a contract asset, and (iii) $ 7.6 million related to the initial upfront payment and milestones received to date. In addition, the Company recognized a $ 50.0 million milestone payment related to the JNJ License and Collaboration Agreement, which was earned upon FDA approval of ICOTYDE for the treatment of moderate-to-severe plaque psoriasis, and $14.1 million for rusfertide clinical supplies under the Takeda Collaboration Agreement and other revenues.

For the three months ended June September 30, 2026, the Company recognized license and collaboration revenue of $ 213.5 274.4 million. This included $202.5 million under the Takeda Collaboration Agreement using the cost-based input method for development services, consisting of (i) $ 192.4 million related to revenue was primarily driven by the proportional recognition of the $ 200.0 million opt-out payment, (ii) $ 5.7 266.6 million related to cost reimbursement for post opt-out wind-down services provided by the Company, $ 3.4 million of which was recorded as a contract asset, and (iii) $ 4.4 275.0 million related to the initial upfront payment and milestones received to date. in addition, the Company recognized revenue during the period of $ 11.0 million for rusfertide clinical supplies opt-out and milestone payments earned under the Takeda Collaboration Agreement during the period, ongoing development services, and other revenues. The remaining $ 7.6 8.4 million in unrecognized revenue related to the $ 200.0 275.0 million payments in opt-out payment under and milestone payments earned during the Takeda Collaboration Agreement period that was recorded as deferred revenue on the Company's condensed consolidated balance sheet and is expected to be recognized through the conclusion of the development services performance obligation.

For the nine months ended September 30, 2026, the Company recognized license and collaboration revenue of $ 544.3 million. This revenue was primarily driven by proportional recognition of $ 460.5 million related to $ 475.0 million in milestone payments earned under the Takeda Collaboration Agreement during the period, ongoing development services, and other revenues, and (ii) a $ 50.0 million milestone payment related to the JNJ License and Collaboration Agreement, and other revenues.

For the three and six nine months ended June September 30, 2026, the Company recognized $ 4.4 1.8 million and $ 7.6 8.0 million of revenue, respectively, that was included in the deferred revenue balance at the beginning of the period. None of the costs to obtain or fulfill the contracts were capitalized.

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All of the Company's marketable securities are classified as available-for-sale. Current marketable securities of $ 362.5 301.8 million and $ 439.0 million held as of June September 30, 2026 and December 31, 2025, respectively, had contractual maturities of less than one year . Noncurrent marketable securities of $ 66.9 34.6 million and $ 78.6 million held as of June September 30, 2026 and December 31, 2025, respectively, had contractual maturities of at least one year but no more than two years . The Company does not intend to sell its securities that are in an unrealized loss position, and it is not more likely than not that the Company will be required to sell its securities before recovery of their amortized cost basis, which may be at maturity.

During the six nine months ended June September 30, 2026 and 2025, the Company sold $ 3.4 million and $ 7.0 million of marketable securities and realized a net gain of $ 5.0 thousand and a net loss of $ 5.0 thousand, respectively. The Company evaluated securities with unrealized losses to determine whether such losses, if any, were due to credit-related factors and determined that there were no credit-related losses to be recognized as of June September 30, 2026 and December 31, 2025.

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Other current assets as of September 30, 2026 included $ 5.0 million in proceeds from option exercises not yet received.

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Stock Repurchase Program

On September 8, 2026, the Company announced that its board of directors authorized a share repurchase program under which the Company may repurchase up to $ 300.0 million of its outstanding common stock (the "Repurchase Program"). The Repurchase Program has no fixed expiration, does not obligate the Company to repurchase any specific number of shares and may be modified, suspended or discontinued at any time without prior notice. Under the Repurchase Program, stock repurchases may be made from time to time in open market or through privately negotiated transactions, including transactions pursuant to a trading plan adopted in accordance with Rule 10b5-1 under the Securities Exchange Act of 1934, as amended. The Company intends to fund repurchases from its cash, cash equivalents and marketable securities, as well as royalties and other payments received under its collaboration arrangements with Takeda related to MIMRYLO and JNJ related to ICOTYDE. The timing and amount of any repurchases will depend on market conditions, alternative capital deployment opportunities and other factors.

During the three and nine months ended September 30, 2026, the Company repurchased 40,560 shares of its common stock under the Repurchase Program for an aggregate purchase price of $ 5.8 million. As of September 30, 2026, $ 294.2 million remained available and authorized for repurchases. Shares purchased under the Repurchase Plan during the three months ended September 30, 2026 are held as Treasury shares. See Part II, Item 2. Unregistered Sales of Equity Securities and Use of Proceeds elsewhere in this Quarterly Report on Form 10-Q for additional information.

In August 2023, the Company entered into certain agreements with certain accredited investors and their affiliates (the "Investors") under which the Company issued pre-funded warrants with an exercise price of $ 0.001 per share (the "Pre-Funded Warrants"). The Pre-Funded Warrants will expire on the day they are exercised in full. The Pre-Funded Warrants are exercisable at any time prior to expiration except that the Pre-Funded Warrants cannot be exercised by the Investors if, after giving effect thereto, the Investors would beneficially own more than 9.99 % of the Company's common stock, subject to certain exceptions. In accordance with ASC Topic 260, " Earnings Per Share" , outstanding Pre-Funded Warrants are included in the computation of basic net income (loss) per share because the exercise price is negligible, and they are fully vested and exercisable after the original issuance date. No Pre-Funded Warrants were exercised during the three and six nine months ended June September 30, 2026 and 2025. As of June September 30, 2026, Pre-Funded Warrants to purchase 1,500,000 shares of common stock remained outstanding.

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The Company recorded income tax expense of $ 2.3 6.6 million and $ 0.8 7.3 million for the three and six nine months ended June September 30, 2026, respectively. The Company recorded income tax expense of zero and $ 0.2 million for both the three and six nine months ended June September 30, 2025, respectively. The increases in income tax expense were due to pretax income recorded as compared to pretax losses for the prior year periods. The tax provision for the three and six nine months ended June September 30, 2026 was determined using an estimated annual effective tax rate, adjusted for discrete items, if any.

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Basic net income (loss) per share of common stock

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Dilutive effect of common stock equivalents

Weighted-average shares of common stock, dilutive

Net income (loss) per share of common stock

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Weighted-average shares of common stock, basic

Dilutive effect of common stock equivalents

Weighted-average shares of common stock, diluted

Diluted net income (loss) per share of common stock

Approximately 0.9 million potentially dilutive shares of common stock (consisting of shares subject to outstanding stock options, RSUs, PSUs and under the ESPP, as applicable) were excluded from the diluted net income per share of common stock computation for the three and six nine months ended June September 30, 2026 because their effect was anti-dilutive. Approximately 9.5 9.1 million potentially dilutive shares of common stock (consisting of shares subject to outstanding stock options, RSUs, PSUs, and under the ESPP, as applicable) were excluded from the diluted net loss per share of common stock computation for the three and six nine months ended June September 30, 2025 due to the Company's net loss for these periods.

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License and collaboration revenue

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Segment profit (loss)

Reconciliation of profit (loss)

Adjustments and reconciling items

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Forward-looking statements 103 changes

This Quarterly Report contains certain forward-looking statements within the meaning of 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"). All statements other than statements of historical fact, including statements concerning our plans, objectives, goals, strategies, future events, future revenues or performance, financing needs, expectations, plans or intentions relating to clinical development, product candidates, the regulatory approval process, products and markets, and business trends and other information referred to under the sections entitled "Risk Factors" and "Management's Discussion and Analysis of Financial Condition and Results of Operations," are forward-looking statements. These statements are subject to substantial known and unknown risks, uncertainties and other factors that may cause our actual results, outcomes, performance or achievements, or the timing of such results, outcomes, performance or achievements, to be materially different from any results, outcomes, performances or achievements expressed or implied by the forward-looking statements. In some cases, you can identify forward-looking statements by terms such as "anticipates," "assumes," "believes," "commitments," "could," "estimates," "expects," "forecasts," "intends," "may," "plans," "potential," "predicts," "projects," "should," "targets," "will," "would," "seeks" and similar expressions intended to identify forward-looking statements. Forward-looking statements reflect our current views with respect to future events, are based on assumptions, and are subject to risks, uncertainties and other important factors, including, among other things, the commercial acceptance and success of ICOTYDE and MIMRYLO, which depends on the efforts of our collaboration partners; the timing and amount of royalty and milestone payments we receive from our ICOTYDE and MIMRYLO collaborations; the results of ICOTYDE and MIMRYLO clinical trials; the potential for our programs; the timing, initiation, progress and expected results of our clinical trials and research and development programs, including enrollment, data, costs and regulatory submissions and approvals; our cash runway; our ability to advance product candidates into, and successfully complete, non-clinical studies and clinical trials; our eligibility for, and any expected benefits of, any U.S. Food and Drug Administration ("FDA") programs or special designations; the potential for eventual regulatory approval and commercialization of our product candidates; the commercialization of our product candidates, if approved; which for ICOTYDE and rusfertide depends largely on the efforts of our collaboration partners; our ability and the potential to successfully manufacture and supply our product candidates for clinical trials and for commercial use, if approved; the pricing, coverage, and reimbursement of our product candidates, if approved; our potential receipt of milestone payments and royalties under our collaboration agreements; future operating results; our ability and that of our collaboration partners to generate sales, income or cash flow; our estimates regarding expenses, capital requirements, and potential needs for additional financing and our ability to obtain additional capital; our ability to retain the continued service of our key executives and to identify, hire, and retain additional qualified professionals ; developments relating to our competitors and our industry, including competing product candidates and therapies; uncertainty and disruption in the global economy and financial markets due to a number of factors, including but not limited to geopolitical instability, such as the ongoing military conflicts between Russia and Ukraine and in the Middle East and rising tensions between China and Taiwan, elevated and sustained inflation, high oil and other commodity prices and changes in trade policies, including tariffs or other trade restrictions or the threat of such actions and retaliatory actions; the availability of credit; and other factors . Forward-looking statements involve risks, uncertainties and assumptions that are beyond our ability to control or predict, including those risks, uncertainties and assumptions discussed in Part II, Item 1A, of this Quarterly Report, Part 1. Item 1A of our Annual Report on Form 10-K for the year ended December 31, 2025 and in our other filings with the SEC. These statements are based on information available to us as of the date of this Quarterly Report and, while we believe such information provides a reasonable basis for these statements, the information may be limited or incomplete, and our statements should not be read to indicate that we have conducted an exhaustive inquiry into, or review of, all potentially available relevant information. Given these risks, uncertainties and other important factors, you should not place undue reliance on these forward-looking statements. Also, forward-looking statements represent our estimates and assumptions only as of the date of this Quarterly Report. Except as required by law, we assume no obligation to update any forward-looking statements publicly, or to update the reasons actual results or outcomes could differ materially from those anticipated in any forward-looking statements, whether as a result of new information, future developments, changes in assumptions or otherwise. We caution investors that our business and financial performance are subject to substantial risks and uncertainties.

"Protagonist," the Protagonist logo and other trademarks, service marks and trade names of Protagonist are registered and unregistered marks of Protagonist Therapeutics, Inc. in the United States and other jurisdictions. Other registered and unregistered trademarks, service marks and trade names are the property of their respective owners.

We are a discovery through late-stage development biopharmaceutical company with built on a proprietary peptide technology platform. that enables de novo discovery of peptide therapeutics. Our development products and discovery programs fall into three broad therapeutic areas: (i) inflammation and immunology ("I&I"), (ii) hematology and (iii) metabolic diseases. Our aim is to develop medicines for biologically and commercially validated targets which demonstrate a strong differentiation compared to existing therapies.

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Rusfertide is a first-in-class investigational injectable mimetic of the natural hormone hepcidin in development for the treatment of the rare blood disorder polycythemia vera ("PV"). We discovered rusfertide, advanced it into Phase 3 development, and entered into a license and collaboration agreement with Takeda Pharmaceuticals, Inc. ("Takeda") in January 2024 (the "Takeda Collaboration Agreement"). We remained primarily responsible for clinical development activities through rusfertide's New Drug Application ("NDA") filing for the treatment of erythrocytosis in patients with PV, which we and Takeda submitted in December 2025, and Takeda is responsible for further development and commercialization. In March 2026, the FDA accepted the NDA and granted Priority Review status for rusfertide. Rusfertide has also previously received Orphan Drug status, Fast Track designation and, in August 2025, Breakthrough Therapy designation ("BTD"). BTD is a process designed to expedite the development and review of drugs that are intended to treat a serious condition, and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapies. BTD also provides eligibility for priority NDA review, and Orphan Drug status qualifies sponsors for various incentives, including the potential for extended market exclusivity. The NDA for rusfertide is currently under priority review by the FDA, with a Prescription Drug User Fee Act target action date in August 2026. Takeda has disclosed that it expects to launch rusfertide in the second half of 2026, subject to regulatory approval.

ICOTYDE ® (icotrokinra) was approved in the United States in March 2026 for the treatment of moderate-to-severe plaque psoriasis in adults and pediatric patients 12 years of age or older who weigh at least 40 kg and are candidates for systemic therapy or phototherapy. ICOTYDE is the first and only targeted oral peptide that precisely blocks the Interleukin-23 receptor ("IL-23R"), which underpins the inflammatory response in psoriasis and offers potential in other IL-23-mediated diseases. ICOTYDE is licensed to Janssen Biotech, Inc., a Johnson & Johnson company ("JNJ"), under a license and collaboration agreement initially entered into in 2017. Following ICOTYDE's joint discovery by Protagonist and JNJ scientists, we were primarily responsible for the development of ICOTYDE through Phase 1, with JNJ assuming responsibility for further development and commercialization. In September 2025, JNJ submitted an application to 2026, the European Medicines Agency ("EMA") seeking the first Commission granted approval of JNJ's marketing application for ICOTYDE for the treatment of adults and pediatric patients 12 years of age or and older with moderate-to-severe plaque psoriasis. ICOTYDE has also received regulatory approval in Japan and China. ICOTYDE is in Phase 3 development for additional indications immune-mediated diseases, including psoriatic arthritis, ulcerative colitis and Crohn's disease.

In October 2026 JNJ submitted an abstract accepted for presentation at the American College of Rheumatology Convergence 2026 outlining Week 24 results from a Phase 3, randomized, double-blind, placebo-controlled study evaluating icotrokinra in biologic-naïve participants with active psoriatic arthritis. The publicly released abstract reported that in biologic-naïve patients with active psoriatic arthritis, once-daily ICOTYDE 200 mg demonstrated both joint and skin improvements versus placebo at Week 16, with 400 mg showing no additional benefit beyond the 200 mg dose. Continued improvements were observed through Week 24 for both joint and skin responses. Adverse event profiles were comparable across groups with no new safety signals identified.

In November 2026, JNJ disclosed the following results from the Phase 3 ICONIC-ASCEND study evaluating ICOTYDE in adult and pediatric patients 12 years of age and older with moderate-to-severe plaque psoriasis versus placebo and ustekinumab:

● ICOTYDE met both co-primary endpoints, with 70% of adults and adolescents with moderate-to-severe plaque psoriasis achieving clear or almost clear skin (IGA 0/1) and 55% achieving PASI 90 versus placebo at Week 16.

● Results showed ICOTYDE achieved non-inferiority to ustekinumab, with numerically higher skin clearance rates in both systemic-naive and biologic-experienced plaque psoriasis patients, though statistical superiority was not demonstrated. ICOTYDE delivered consistent skin clearance against a comparator that performed at a level well above what has been seen historically.

● ICOTYDE delivered a 17-point improvement in complete skin clearance (PASI 100) versus ustekinumab in systemic-naïve patients at Week 28 (48% versus 31%).

MIMRYLO™ (rusfertide)

MIMRYLO™ (rusfertide), a subcutaneously delivered first-in-class hepcidin mimetic, was approved in the United States in August 2026 for the treatment of erythrocytosis in adults with the rare blood disorder polycythemia vera ("PV"). On September 30, 2026, MIMRYLO was also approved in the United Arab Emirates. MIMRYLO, the first and only hepcidin mimetic approved for PV, a blood cancer characterized by the excessive production of red blood cells, demonstrated key efficacy outcomes of response rate and hematocrit control as well as fatigue improvement. We discovered MIMRYLO, advanced it into Phase 3 development, and entered into a license and collaboration agreement with Takeda Pharmaceuticals, Inc. ("Takeda") in January 2024 (the "Takeda Collaboration Agreement"). We remained primarily responsible for clinical development activities through MIMRYLO's New Drug Application ("NDA") filing for the treatment of erythrocytosis in patients with PV, which we and Takeda submitted in December 2025, and Takeda is responsible for further development and commercialization. In September 2026, MIMRYLO was added as a Category 1 treatment option for both low- and high-risk PV in the National Comprehensive Cancer Network's updated guidelines. MIMRYLO previously received Orphan Drug designation, which qualifies sponsors for various incentives, including the potential for extended market exclusivity.

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In October 2025, the first human subject was dosed in our Phase 1 trial of PN-881 (ClinicalTrials.gov identifier NCT07153146) evaluating its safety, tolerability, pharmacokinetics and pharmacodynamics in healthy adults. We believe data from our completed Phase 1 study supports our decision to advance PN-881 into a comprehensive Phase 2b psoriasis program, with initiation of a dose range-finding study in patients with plaque psoriasis expected in early first quarter 2027. Phase 1 data are expected to be presented at a future medical meeting.

PN-477 . In June 2025, we nominated PN-477, a potential best-in-class novel triple GLP-1, GIP and GCG receptor agonist peptide, with oral ("PN-477o") and subcutaneous ("PN-477sc") routes of administration, as a development candidate for the treatment of obesity. In the subcutaneously administered PN-477sc single ascending dose study, we designed PN-477 to offer an optimal combination of total body weight loss, improved gastrointestinal tolerability observed positive dose-related pharmacokinetic, pharmacodynamic and fat to lean mass ratio, with the dosing convenience of clinical activity. Based on these highly encouraging findings, we have made a once-daily oral agent and strategic decision to prioritize the added optionality of a once-weekly subcutaneous administration. A Phase 1 orally administered PN-477o clinical study for PN-477sc has been initiated, and development program. The initiation of a Phase 1 study for of PN-477o is anticipated in the first half of 2027.

PN-458 . In December 2025, we nominated development candidate PN-458, a potential best-in-class novel dual GLP-1 and GIP receptor agonist peptide, as a development candidate for the treatment of obesity. IND-enabling studies are ongoing, with the initiation of a Phase 1 study for the PN-458 oral formulation anticipated in the second half of 2027.

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PN-8047 . In December 2025, we nominated development candidate PN-8047, an orally administered small molecule hepcidin functional mimetic, which we believe may be complementary to the injectable rusfertide MIMRYLO for offering the best treatment options for PV. IND-enabling studies for PN-8047 are ongoing, with the initiation of a Phase 1 study anticipated in the first quarter of 2027.

We also have pre-clinical stage drug discovery programs addressing biologically and commercially validated targets, including an oral IL-4R alpha antagonist for the treatment of atopic dermatitis and moderate-to-severe asthma, and amylinR-based oral and subcutaneous mono- and poly-agonists for the treatment of obesity.

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We ended the second third quarter of 2026 with cash, cash equivalents and marketable securities of approximately $849.5 $834.6 million, as compared to cash, cash equivalents and marketable securities of approximately $646.0 million as of December 31, 2025. For the remainder of 2026 and beyond, we are eligible to receive significant milestone, royalty and other payments from our collaborations with JNJ and Takeda, as described below.

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We and JNJ are parties to a license and collaboration agreement related to the development and commercialization of ICOTYDE. We entered into the agreement in July 2017, and amended it in May 2019, July 2021 and November 2024 (as amended, the "JNJ License and Collaboration Agreement"). Pursuant to the JNJ License and Collaboration Agreement, we were primarily responsible for the discovery, IND-enabling studies, and the initial Phase 1 study for ICOTYDE, and JNJ is primarily responsible for conducting all further development.

In March 2026, we earned a $50.0 million milestone payment upon FDA approval of ICOTYDE for the treatment of moderate-to-severe plaque psoriasis in adults and pediatric patients 12 years of age or older who weigh at least 40 kg and are candidates for systemic therapy or phototherapy. As of June September 30, 2026, we have earned a total of $387.5 million in non-refundable upfront and milestone payments from JNJ under the agreement. We are eligible to receive up to $580.0 million in future development and sales milestone payments, including the following potential milestones:

ICOTYDE ® Potential Development Milestones

ICOTYDE ® Potential Sales Milestones

NDA filing acceptance

Calendar Year Net Sales

Receipt of marketing approval

NDA filing acceptance

Receipt of marketing approval

Total Potential Development Milestones

Total Potential Sales Milestones

We will are also eligible to receive upward tiered royalties on net worldwide ICOTYDE product sales at percentages ranging from 6% to 10%. Our weighted-average royalty rate on the first $4.0 billion in annual net sales is 7.25%, and the rate on net sales over $4.0 billion is 10%. The ultimate magnitude of our royalty stream, along with the achievement of development and commercial milestones, will depend upon ICOTYDE's commercial launch success and market trajectory, which depends on the efforts of our collaboration partner, as well as the successful clinical development, regulatory approval, and commercialization of ICOTYDE in the additional indications currently being studied.

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In January 2024, we entered into the Takeda Collaboration Agreement related to rusfertide MIMRYLO (and specified second-generation injectable hepcidin mimetic compounds developed and commercialized under the agreement that are not currently in development). In December 2025, we and Takeda submitted an NDA to the FDA for rusfertide MIMRYLO in PV, which is currently under priority review. was approved in August 2026. We were primarily responsible for the clinical development of rusfertide MIMRYLO through NDA filing and remain primarily responsible for the conduct of conducting ongoing rusfertide MIMRYLO long-term extension studies. Under the terms of the agreement, we received an upfront payment of $300.0 million in April 2024 and a $25.0 million milestone payment in September 2025 upon completion of the Phase 3 VERIFY clinical trial (NCT05210790) report.

Effective April 28, 2026, we exercised our right to opt-out opt out of the U.S. profit and loss sharing arrangement (50% to us and 50% to Takeda) under the Takeda Collaboration Agreement. The opt-out election triggered a $200.0 million payment to us, which we received in the second quarter of 2026. and In August 2026, we also became eligible to receive earned an additional $200.0 million opt-out fee payment and a separate $75.0 million milestone both of which are due upon FDA approval of rusfertide. MIMRYLO, which were received in October 2026. Following the opt-out, Takeda has an exclusive worldwide license to develop and commercialize rusfertide, MIMRYLO, and we are eligible to receive tiered royalties ranging from 14% to 29% on annual worldwide net sales, with an approximate weighted-average royalty rate of 21% at $1.5 billion in annual net sales and a rate of 29% for incremental annual net sales over $1.5 billion. In addition, under the agreement, we are eligible to receive up to $775.0 $800.0 million in sales milestones. Upcoming potential development milestones and potential sales milestones under the agreement include the following: for MIMRYLO in PV as follows:

MIMRYLO™ Selected Upcoming Potential Development Milestones

MIMRYLO™ Potential Sales Milestones

First regulatory approval in three European countries

Calendar Year Net Sales

First regulatory approval in Japan

Total Upcoming Potential Development Milestones

Total Potential Sales Milestones

The receipt of future royalties and commercial milestones is contingent upon the relevant products receiving FDA approval and achieving a successful commercial launch, which depends on the efforts of our collaboration partner.

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We describe the respective risks, uncertainties and assumptions that could affect our business, financial condition or results of operations in Part II, Item 1A. "Risk Factors" herein, Part II, Item 1A. "Risk Factors" in our Quarterly Report on Form 10-Q for the quarter ended June 30, 2026 and in Part 1, I, Item 1A. "Risk Factors" in our Annual Report on Form 10-K for the year ended December 31, 2025.

We have incurred cumulative net losses from inception through June September 30, 2026 of $304.0 $84.0 million. Substantially all of our net losses have resulted from costs incurred in connection with our research and development programs and from general and administrative costs associated with our operations. We expect to continue to incur significant research and development expenses, and other expenses related to our ongoing operations, clinical development and pre-clinical discovery programs.

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There have been no material changes to our critical accounting policies during the three and six nine months ended June September 30, 2026, as compared to those disclosed in "Management's Discussion and Analysis of Financial Condition and Results of Operations—Critical Accounting Policies and Estimates" in our Annual Report for the year ended December 31, 2025 filed with the SEC on February 25, 2026.

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Our license and collaboration revenue is derived from payments we receive from our collaboration partners under the JNJ License and Collaboration Agreement and the Takeda Collaboration Agreement. We expect our revenue to increase significantly in future periods due to the receipt of milestone payments, including payments related to NDA approvals and the exercise of our opt-out right under the Takeda Collaboration Agreement and royalties for sales of ICOTYDE for moderate-to-severe plaque psoriasis, and in other indications if approved. We also expect to receive royalties for rusfertide in PV if NDA approval is received and the product is successfully commercialized. See Note 3 to the condensed consolidated financial statements included elsewhere in this Quarterly Report for additional information.

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Cost of revenue represents costs incurred pursuant to a collaboration agreement entered into in June 2012 and a related arbitration resolution agreement entered into in August 2021 between us and Zealand Pharma A/S ("Zealand"). We are obligated to pay Zealand certain milestone and royalty payments for MIMRYLO. These payments are recorded as cost of revenue in the period in which they are incurred. As of September 30, 2026, remaining potential payments under the agreement include: (i) up to $1.65 million in development milestone payments; (ii) a 1% royalty on worldwide net sales of MIMRYLO; and (iii) sales milestone payments on achievement of specified annual net sales amounts in specified geographies.

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● license fees and certain milestone payments under license and collaboration agreements; and

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Comparison of the Three Months Ended June September 30, 2026 and 2025

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License and Collaboration Revenue

License and collaboration revenue was comprised of the following for the periods presented:

(Dollars in thousands)

(1) Includes $7.5 $7.7 million and $6.3 $6.0 million of non-cash stock-based compensation expense for the three months ended June September 30, 2026 and 2025, respectively.

(2) Includes $6.5 $6.6 million and $4.6 million of non-cash stock-based compensation expense for the three months ended June September 30, 2026 and 2025, respectively.

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Takeda Collaboration Agreement and other

Total license and collaboration revenue

*Percentage not meaningful.

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License and collaboration revenue for the three months ended June 30, 2026, was $213.5 million, which consisted of (i) $192.4 million related to the proportional recognition of the $200.0 million opt-out payment received from Takeda, and (ii) $21.1 million for ongoing development services, including post opt-out wind down services, rusfertide clinical supplies provided by us under the Takeda Collaboration Agreement and other revenues.

As described above, we opted out of the U.S. profit and loss sharing arrangement under the Takeda Collaboration Agreement in April 2026 and are eligible to receive both an additional $200.0 million opt-out payment and an enhanced milestone payment of $75.0 million upon FDA approval of rusfertide, which is expected in August 2026. In addition, we may receive royalties and sales milestones from rusfertide , pending potential FDA approval and commercial launch.

For the three months ended September 30, 2026, we recognized license and collaboration revenue of $274.4 million. This revenue was primarily driven by the proportional recognition of $266.6 million related to the $275.0 million in total opt-out and milestone payments earned under the Takeda Collaboration Agreement during the period, ongoing development services, and other revenues.

License and collaboration revenue for the three months ended June September 30, 2025 was $5.5 million, which consisted of (i) $5.0 $4.7 million and was related to the Takeda Collaboration Agreement for development services provided by us during the period under the Takeda Collaboration Agreement based on the cost-based input method. and (ii) $0.5 million related to the proportional recognition of the $25.0 million milestone from Takeda deemed probable of being achieved due to the Phase 3 VERIFY trial meeting its primary endpoint.

For the three months ended September 30, 2026, we recorded cost of revenue of $1.1 million for a milestone payment due to Zealand upon the FDA's approval and the commercial launch of MIMRYLO. No expense was recorded for cost of revenue for the three months ended September 30, 2025.

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Research and development expenses increased $1.3 million, as detailed in the table below:

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Clinical and development expense — rusfertide

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Clinical and development expense — MIMRYLO

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Research and development expenses increased $5.0 million, or 14%, from $37.0 million for the three months ended June 30, 2025 to $42.1 million for the three months ended June 30, 2026. The increase was primarily due to an increase of $8.6 million in costs related to our Phase 1 study for development candidate PN-881 initiated in the third quarter of 2025 and an $8.4 million increase in pre-clinical and drug discovery research program expense, partially offset by a decrease of $12.0 million in rusfertide expenses primarily related to the completion of our Phase 3 VERIFY trial during the first quarter of 2025.

We had 108 111 and 100 99 full-time equivalent research and development headcount as of June September 30, 2026 and 2025, respectively. Research and development personnel-related expenses for the three months ended June September 30, 2026 increased by $1.9 $0.6 million as compared to the three months ended June September 30, 2025, primarily driven by increases in wages, benefits and stock-based compensation.

We expect research and development expenses to increase significantly in for the second half remainder of 2026 the year as compared to the first half of prior quarters in 2026. The increase is expected to be driven primarily by the advancement of PN-881 into a comprehensive Phase 2b psoriasis program, planned investments in clinical manufacturing and related activities, including at-risk expenditures to ensure readiness for other programs as they advance to clinical development (PN-477sc, (PN-477o, PN-458, PN-8047), additional pre-clinical discovery programs, and increases in headcount and stock-based compensation expense. The timing and magnitude of these expenses will vary depending on the progress of our programs, including the initiation and pace of clinical trials and related development activities.

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General and administrative expenses increased $2.1 $2.6 million, or 20%, 23%, from $10.6 $11.1 million for the three months ended June September 30, 2025 to $12.6 $13.7 million for the three months ended June September 30, 2026. The increase was primarily due to an increase in personnel-related expenses driven by increases in wages, benefits and stock-based compensation.

We had 33 38 and 30 29 full-time equivalent general and administrative headcount as of June September 30, 2026 and 2025, respectively.

Interest income decreased increased by $1.0 $1.2 million, or 13%, 17%, from $7.4 $7.0 million for the three months ended June September 30, 2025 to $6.4 $8.2 million for the three months ended June September 30, 2026 primarily due to lower yields and lower higher average investment balance balances as compared to the prior period.

Income tax expense was $2.3 $6.6 million and $0.2 million zero for the three months ended June September 30, 2026 and 2025, respectively. The increase in income tax expense for the three months ended June September 30, 2026 was primarily due to pretax income recorded as compared to a pretax loss for the prior year period. The effective tax rate was 1.4% 2.9% and 0% for the three months ended June September 30, 2026 and 2025, respectively.

Comparison of the Six Nine Months Ended June September 30, 2026 and 2025

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License and Collaboration Revenue

License and collaboration revenue was comprised of the following for the periods presented:

(Dollars in thousands)

(1) Includes $15.3 $23.1 million and $14.3 $20.3 million of non-cash stock-based compensation expense for the six nine months ended June September 30, 2026 and 2025, respectively.

(2) Includes $13.2 $19.9 million and $10.4 $15.0 million of non-cash stock-based compensation expense for the six nine months ended June September 30, 2026 and 2025, respectively.

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Takeda Collaboration Agreement and other

JNJ License and Collaboration Agreement milestone

Total license and collaboration revenue

*Percentage not meaningful.

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and 23 more changes in the filing

Market risk 3 changes

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We had $849.5 $834.6 million and $646.0 million in cash, cash equivalents and marketable securities at June September 30, 2026 and December 31, 2025, respectively. Our cash and cash equivalents consist of cash, money market funds, certificates of deposit and commercial paper. Marketable securities consist of government and agency bonds, commercial paper and corporate bonds. A portion of our investments may be subject to interest rate risk and could decline in value if market interest rates increase. Based on our interest rate sensitivity analysis, an immediate 100 basis point increase in interest rates would increase our annual interest income by approximately $5.4 $6.2 million, while an immediate 100 basis point decrease in interest rates would decrease our annual interest income by approximately $5.4 $6.2 million.

Approximately $2.5 $1.0 million and $2.8 million of our cash balance was located in Australia at June September 30, 2026 and December 31, 2025, respectively. Our expenses, except those related to our Australian operations, are generally denominated in U.S. dollars. For our operations in Australia, the majority of our expenses are denominated in Australian dollars. To date, we have not had a formal hedging program with respect to foreign currency, but we may do so in the future if our exposure to foreign currency becomes more significant. A 10% increase or decrease in current exchange rates would not have a material effect on the results of our operations.

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Inflation generally affects us by increasing our costs, such as the cost of labor and research and development contract costs. We do not believe inflation has had a material adverse effect on the results of our operations during the six nine months ended June September 30, 2026.

Risk factors 10 changes

We are dependent on Takeda for the commercialization of rusfertide. Failure by Takeda to commercialize rusfertide could result in a material adverse effect on our business and operating results.

Pursuant to the terms of the Takeda Collaboration Agreement, following our exercise of our right to opt out of the U.S. profit and loss sharing arrangement in April 2026, Takeda has an exclusive worldwide license to develop and commercialize rusfertide, and we are eligible to receive tiered royalties ranging from 14% to 29% on annual worldwide net sales, with an approximate weighted-average royalty rate of 21% at $1.5 billion in annual net sales and a rate of 29% for incremental annual net sales over $1.5 billion. In addition, under the agreement, we are eligible to receive up to $775.0 million in sales milestone payments.

A substantial portion of our total revenue may be based on royalties and milestones received from Takeda. The commercial success of rusfertide, if approved, including our potential royalties, depends on, among other things, the efforts and allocation of resources of Takeda, which we do not control. Our partnership with Takeda may not be successful, and we may not realize the expected benefits from such partnership, due to a number of important factors, including but not limited to the following:

• Takeda may change the focus of its commercialization efforts or pursue higher priority programs;

• Takeda may fail to manufacture or supply sufficient drug product of rusfertide in compliance with applicable laws and regulations, which could result in program delays or lost revenue; and

• We may disagree with Takeda regarding the development or commercialization of rusfertide, or other matters under the Takeda Collaboration Agreement, or Takeda could breach or terminate the Takeda Collaboration Agreement.

Unstable market and macroeconomic conditions, including geopolitical instability and tariffs or trade policy, may have serious adverse consequences on our business, financial condition and stock price.

As has been widely reported, we are currently operating in a period of macroeconomic uncertainty and capital markets disruption, which has been significantly impacted by domestic and global monetary and fiscal policy, trade regulations, including changes in trade policies, tariffs or other trade restrictions or the threat of such actions, geopolitical instability, including ongoing military conflicts in the Middle East and between Russia and Ukraine, rising tensions between China and Taiwan, and high interest rates. In particular, the conflicts in the Middle East and Ukraine have exacerbated market disruptions, including significant volatility in commodity prices, as well as supply chain interruptions, and have contributed to inflation globally. The U.S. Federal Reserve and other central banks may be unable to contain inflation through more restrictive monetary policy and inflation may increase or continue for a prolonged period of time. Inflationary factors, such as increases in the cost of clinical supplies, interest rates, overhead costs and transportation costs may adversely affect our operating results. In addition, in September 2025, the United States announced the imposition of up to 100% tariffs on imported branded or patented pharmaceuticals, subject to certain exceptions. In early April 2026, the current administration issued a proclamation under Section 232 of the Trade Expansion Act of 1962 determining that imports of certain pharmaceutical products, including patented pharmaceuticals, associated active pharmaceutical ingredients and related materials could threaten U.S. national security and authorized the imposition of tariffs of up to 100% on covered imports, effective July 31, 2026. Imports of certain listed products from specific partner countries, including South Korea and the European Union, may be subject to reduced tariff rates. Certain tariff exemptions or zero-rate treatment may be available for products where all approved indications are designated as orphan, subject to applicable determinations, conditions and implementation guidance. There remains substantial uncertainty as to whether such tariffs would apply to the importation of active pharmaceutical ingredients or bulk drug products that are intended for use in clinical trials and, more generally, about the duration of existing tariffs, tariff levels, implementation of announced tariffs, litigation challenging tariffs and whether additional tariffs or retaliatory actions may be imposed, modified or suspended. Although we do not believe that the macroeconomic factors discussed above have had a material impact on our financial position or results of operations to date, our financial position or results of operations may be adversely affected in the future due to these factors, and such factors may lead to increases in the cost of manufacturing our product candidates and delays in initiating trials. In addition, global credit and financial markets have experienced extreme volatility and disruption in the past several years and the foregoing factors have led to and may continue to cause diminished liquidity and credit availability, declines in consumer confidence, declines in economic growth, uncertainty about economic stability and continued inflation.

There can be no assurance that further deterioration in credit and financial markets and confidence in economic conditions will not occur. A future recession or market correction or other significant geopolitical events could materially affect our business and the value of our common stock. Our general business strategy may be adversely affected by any such economic downturn, volatile business environment or continued unpredictable and unstable market conditions. If the current equity and credit markets deteriorate, or do not improve, it may make any necessary debt or equity financing more difficult, more costly, and more dilutive. Failure to secure any necessary financing in a timely manner and on favorable terms could have a material adverse effect on our growth strategy, financial performance and stock price and could require us to delay or abandon clinical development plans. In addition, there is a risk that one or more of our current service providers, manufacturers and other partners may not survive these difficult economic times, which could directly affect our ability to attain our operating goals.

Our business, results of operations and financial condition are subject to various risks. These risks are described elsewhere in this Quarterly Report on Form 10-Q and in our other filings with the SEC, including our Annual Report on Form 10-K for the year ended December 31, 2025 and our Quarterly Report on Form 10-Q for the quarter ended June 30, 2026. Except as disclosed below, set forth in our Quarterly Report on Form 10-Q for the quarter ended June 30, 2026, there have been no material changes from the risk factors identified in the Company's Annual Report on Form 10-K for the year ended December 31, 2025.

Unregistered sales of stock 10 changes

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The following table summarizes our stock repurchase activity for the three months ended September 30, 2026:

Approximate Dollar Value of

Total Number of Shares

Total Number of Shares Purchased as

Shares that May Yet Be Purchased

Part of Publicly Announced Program (2)

Under the Program (2)

September 1 - 30, 2026

(1) Average price paid per share includes cost associated with the repurchases.

(2) On September 8, 2026, we announced that our board of directors authorized a $300.0 million stock repurchase program. The repurchase program has no fixed expiration, does not obligate us to repurchase any specific number of shares and may be modified, suspended or discontinued at any time without prior notice. Under the repurchase program, stock repurchases may be made from time to time in open market or through privately negotiated transactions, including transactions pursuant to a trading plan adopted in accordance with Rule 10b5-1 under the Exchange Act. See Note 7 to the condensed consolidated financial statements included elsewhere in this Quarterly Report for additional information.

Other information 2 changes

On June 30, 2026 , Asif Ali , our Chief Financial Officer , adopted a trading plan intended to satisfy Rule 10b5-1(c) to sell up to (i) 73,214 shares of the Company's common stock, (ii) 50% of the net shares issued to Mr. Ali after withholding taxes upon the vesting of restricted stock unit awards representing 21,346 shares of the Company's common stock, and (iii) 50% of the net shares issued to Mr. Ali after withholding taxes upon the vesting of performance stock unit awards representing 12,800 shares of the Company's common stock (assuming that such shares underlying performance stock units vest at target amounts) through September 30, 2027 , or such earlier date when all transactions under the trading plan are completed, subject to certain conditions.

Except as discussed above, During the fiscal quarter ended June September 30, 2026, no director or Section 16 officer adopted or terminated any Rule 10b5-1 10 b5-1 trading arrangement or a non-Rule 10b5-1 10 b5-1 trading arrangement (in each case as defined in Item 408(a) of Regulation S-K).

Exhibits 7 changes

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Protagonist Therapeutics, Inc. 2026 Equity Incentive Plan

Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

Certification of Chief Executive Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

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Date: August 5, 2026

Date: November 6, 2026

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Date: August 5, 2026

Date: November 6, 2026

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