1 COMPANY OVERVIEW Dinesh V. Patel, PhD | President & CEO January 2022 Forward-looking Statements This presentation and the accompanying oral presentation contain forward-looking statements made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. All statements other than statements of historical facts contained in this presentation, including statements regarding our future results of operations and financial position, business strategy, product candidates, capit ...

8 Protagonist 1 COMPANY OVERVIEW December 2021 Dinesh V. Patel, PhD President & CEO Forward-looking Statements This presentation and the accompanying oral presentation contain forward-looking statements made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. All statements other than statements of historical facts contained in this presentation, including statements regarding our future results of operations and financial position, business strategy, product cand ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2021 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 No. 001-37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) (State or other jurisdiction ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2021 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 No. 001-37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Indicate by check mark whether th ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2021 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 No. 001-37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) (State or other jurisdiction of ...

8 Protagonist 1 PN-943 PTG-200 PN-235 PN-232 rusfertide (PTG-300) PTG-100 March 2021 COMPANY OVERVIEW Dinesh V. Patel, PhD President & CEO Forward-looking Statements This presentation and the accompanying oral presentation contain forward-looking statements made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. All statements other than statements of historical facts contained in this presentation, including statements regarding our future results of operations ...

Protagonist Therapeutics, Inc. (NASDAQ:PTGX) Q4 2020 Earnings Conference Call March 10, 2021 4:30 PM ET Company Participants Dinesh Patel - President and Chief Executive Officer Don Kalkofen - Chief Financial Officer Samuel Saks - Chief Medical Officer David Liu - Chief Scientific Officer Suneel Gupta - Chief Development Officer Conference Call Participants Chris Howerton - Jefferies Anupam Rama - JPMorgan Douglas Tsao - H.C. Wainwright Operator Good afternoon and welcome to Protagonist Therapeutics Fourth ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2020 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 No. 001-37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 98-0505495 (State or other j ...

Table of Contents Commission File No. 001-37852 PROTAGONIST THERAPEUTICS, INC. UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2020 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to (Exact name of registrant as specified in its charter) (State or other jurisdiction ...

Financial Performance - The net loss for the three and six months ended June 30, 2020, was $19.4 million and $39.5 million, respectively, compared to $29.2 million and $43.3 million for the same periods in 2019[137][138]. - The net loss for the six months ended June 30, 2020, was $39.5 million, a decrease of $3.8 million, or 9%, from a net loss of $43.3 million in 2019[186]. - Net loss decreased by $9.8 million, or 33%, from $29.2 million in Q2 2019 to $19.4 million in Q2 2020[161]. - The company does not anticipate achieving sustained profitability in the foreseeable future, continuing to incur significant losses related to ongoing operations and product development[139]. Cash and Capital - As of June 30, 2020, the company had $208.7 million in cash, cash equivalents, and marketable securities, with an accumulated deficit of $257.2 million[186]. - Cash used in operating activities for the six months ended June 30, 2020 was $37.3 million, compared to $13.0 million for the same period in 2019[201][202]. - Cash provided by financing activities for the six months ended June 30, 2020 was $113.0 million, primarily from a public offering of common stock totaling $105.7 million[207]. - The company anticipates needing to raise substantial additional capital to advance product candidates and fund operations[196]. - The company completed a public offering of 7,000,000 shares at $14.00 per share in May 2020, generating net proceeds of $105.3 million[192]. Research and Development - PTG-300, the most advanced clinical asset, is in Phase 2 studies for polycythemia vera and hereditary hemochromatosis, with preliminary results showing the ability to control hematocrit levels below 45%[128]. - PTG-200 is in a global Phase 2 clinical study for moderate-to-severe Crohn's disease, with a milestone payment of $5.0 million received for the nomination of a second-generation development candidate[130][132]. - PN-943, an orally delivered integrin antagonist, completed Phase 1 studies and is expected to initiate a Phase 2 proof of concept study in ulcerative colitis, pending conditions for safe patient accrual[133]. - Research and development expenses increased by $0.9 million, or 5%, from $19.4 million in Q2 2019 to $20.3 million in Q2 2020[165]. - Research and development expenses rose by $7.2 million, or 23%, from $31.8 million in 2019 to $39.0 million in 2020, driven by increased pre-clinical and clinical trial costs[178]. - The proprietary technology platform enables the development of novel peptide-based drugs, addressing significant unmet medical needs in various therapeutic areas[126][134]. - The company is discontinuing the development of PTG-300 for beta-thalassemia and myelodysplastic syndromes, focusing efforts on polycythemia vera and hereditary hemochromatosis[128]. Revenue and Expenses - License and collaboration revenue increased by $14.4 million, or 176%, from a loss of $8.2 million in Q2 2019 to $6.2 million in Q2 2020[163]. - License and collaboration revenue increased by $16.5 million, or 249%, from a loss of $6.6 million in 2019 to $9.9 million in 2020[176]. - Total operating expenses rose by $1.2 million, or 5%, from $23.2 million in Q2 2019 to $24.4 million in Q2 2020[161]. - General and administrative expenses increased by $0.3 million, or 8%, from $3.9 million in Q2 2019 to $4.2 million in Q2 2020[166]. - General and administrative expenses increased by $1.1 million, or 15%, from $7.6 million in 2019 to $8.8 million in 2020, primarily due to higher insurance and salary costs[179]. - Interest income decreased by $0.4 million, or 68%, from $0.6 million in Q2 2019 to $0.2 million in Q2 2020[167]. - Interest income decreased by $0.6 million, or 47%, from $1.4 million in 2019 to $0.7 million in 2020, attributed to a declining interest rate environment[180]. - Income tax expense increased by $2.8 million, or 169%, from a tax benefit of $1.6 million in Q2 2019 to an expense of $1.1 million in Q2 2020[172]. - Income tax expense increased by $2.8 million, or 190%, from a benefit of $1.4 million in 2019 to an expense of $1.3 million in 2020[185]. Impact of COVID-19 - The impact of the COVID-19 pandemic has introduced significant uncertainties, potentially affecting clinical trials, patient recruitment, and overall business operations[135][136]. Collaboration and Agreements - The company has received a total of $75.0 million in non-refundable cash payments from Janssen under the collaboration agreement, including $50.0 million upfront and $25.0 million upon the execution of the First Amendment[140]. - The transaction price of the initial performance obligation under the Janssen License and Collaboration Agreement was $113.9 million as of June 30, 2020, an increase of $0.3 million from March 31, 2020[164]. - The transaction price of the initial performance obligation under the Janssen License and Collaboration Agreement was $113.9 million as of June 30, 2020, an increase of $1.0 million from December 31, 2019[177]. - The company had a decrease of $7.5 million in deferred revenue related to the Janssen License and Collaboration Agreement during the first half of 2020[201]. Debt and Financial Obligations - Loss on early repayment of debt was $0.6 million for Q2 2020, reflecting fees related to the repayment of a term loan[170]. - The company prepaid a $10.0 million term loan in June 2020, incurring a loss of $0.6 million on early repayment[184]. Off-Balance Sheet Arrangements - The company has not entered into any off-balance sheet arrangements as defined under SEC rules[210].