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, 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) (State or other jurisdiction of ...

Financial Data and Key Metrics Changes - Protagonist reported a net loss of $77.2 million for the full year of 2019, compared to a net loss of $38.9 million for 2018, and a net loss of $17.5 million for Q4 2019, compared to a net loss of $13.9 million for Q4 2018 [32] - License and collaboration revenue for the full year of 2019 was $0.2 million, significantly down from $30.9 million in 2018, primarily due to a one-time cumulative adjustment related to revenue recognition principles [33] - Research and development expenses were $65 million for the full year of 2019, up from $59.5 million in 2018, while general and administrative expenses increased to $15.7 million from $13.7 million in the previous year [34][35] - Protagonist ended 2019 with $133 million in cash, cash equivalents, and marketable securities, with access to a debt facility of $10 million, sufficient to fund operations through the end of 2021 [36] Business Line Data and Key Metrics Changes - The company has three clinical assets in development: PTG-300 for blood disorders, and PTG-200 and PN-943 for inflammatory bowel diseases (IBD) [11] - PTG-300 is being pursued in four different indications, with ongoing studies expected to yield data-driven decisions in 2020 [13][20] - PTG-200 has progressed into a Phase II clinical proof-of-concept study in Crohn's disease, with results expected in the first half of 2021 [22] - PN-943 is set to initiate a Phase II study in ulcerative colitis in Q2 2020, with topline efficacy results anticipated in the second half of 2021 [25] Market Data and Key Metrics Changes - The company has expanded its collaboration with Janssen, resulting in milestone payments and the nomination of a second-generation development candidate [22][23] - The competitive landscape for ulcerative colitis trials is noted, with Protagonist confident in the advantages of its drug offerings [54] Company Strategy and Development Direction - The company aims to evaluate PTG-300 in multiple indications and select the first indication for a pivotal study in 2021 [28] - Continued collaboration with Janssen for the development of PTG-200 and exploration of second-generation oral IL-23 receptor antagonists is a priority [28] - Advancing PN-943 in a Phase II study is also a key focus, with the potential for significant impact in the IBD treatment paradigm [26][28] Management's Comments on Operating Environment and Future Outlook - Management expressed confidence in the ongoing studies and the potential impact of the coronavirus outbreak on operations, stating that guidance on objectives and timelines remains unchanged [30] - The company is encouraged by progress made in 2019 and looks forward to multiple data-driven decisions in 2020 [87] Other Important Information - The company has strengthened its team and extended its cash runway through the end of 2021, allowing for continued clinical development [9][27] Q&A Session Summary Question: Update on PTG-300 and exploration in non-transfusion-dependent patients - Management confirmed that both transfusion-dependent and non-transfusion-dependent populations are being pursued, though enrollment in the latter is slow [39] Question: Potential for multiple indications for PTG-300 - The focus is currently on selecting the first indication for a pivotal study, with the possibility of pursuing multiple indications in the future [42] Question: Timing for TRANSCEND data announcement - Management indicated that definitive data, including clinical responders, would be shared in 2020 as conclusions are reached [49] Question: Improvement of PN-943 over PTG-100 - PN-943 was found to be roughly threefold more effective than PTG-100 based on preclinical and Phase I studies [50] Question: Competition for ulcerative colitis trials - Management acknowledged competition but expressed confidence in the advantages of their drug, including proven targets and a GI-restricted approach [54] Question: Dosing strategy for PTG-300 - Management stated that while the current focus is on 40 mg twice-weekly dosing, there is flexibility to explore higher doses if necessary [58][61] Question: Lessons learned from PTG-100 study for PN-943 - Management highlighted the importance of addressing high placebo effects and maintaining close communication with key opinion leaders in the IBD community [64] Question: Future Phase II study design for PN-943 - The upcoming Phase II study will be designed to gather sufficient information for potential pivotal study preparation [68]

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, 2019 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 ...

PTG-200 PTG-300 PN-943 COMPANY OVERVIEW Dinesh V. Patel, PhD President & CEO 1 February 2020 Forward Looking Statements This presentation contains forward-looking statements of Protagonist Therapeutics, Inc. (Protagonist) that involve substantial risks and uncertainties. All statements other than statements of historical facts contained in this presentation, including statements regarding our future results of operations and financial position, our capital resources, business strategy, prospective products, ...

PTG-200 PTG-300 PN-943 COMPANY OVERVIEW Dinesh V. Patel, PhD President & CEO 1 January 2020 Forward Looking Statements This presentation contains forward-looking statements of Protagonist Therapeutics, Inc. (Protagonist) that involve substantial risks and uncertainties. All statements other than statements of historical facts contained in this presentation, including statements regarding our future results of operations and financial position, our capital resources, business strategy, prospective products, ...

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, 2019 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 o ...

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, 2019 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Table of Contents Commission File No. 001‑37852 PROTAGONIST THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) (State or other jurisdiction of i ...

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, 2019 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) (Address, including zip code, of ...

Protagonist Therapeutics, Inc. (NASDAQ:PTGX) Q4 2018 Earnings Conference Call March 12, 2019 4:30 PM ET Company Participants Rich Allan - IR Dinesh Patel - President and CEO Don Kalkofen - Senior Advisor, Finance and Accounting Richard Shames - CMO David Liu - CSO and Head, Research & Development Conference Call Participants George Farmer - BMO Capital Markets Joseph Schwartz - SVB Leerink Jackson Harvey - Nomura Instinet Timothy Chiang - BTIG Adam Walsh - Stifel Operator Good day and welcome to the Protago ...

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, 2018 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 incor ...