ANNUAL REPORT 2019 © 2020 Assembly Biosciences, Inc. www.assemblybio.com CORPORATE INFORMATION Directors Headquarters 331 Oyster Point Blvd., Fourth Floor Anthony E. Altig South San Francisco, California 94080 Former Chief Financial Officer, Biotix 833.509.4583 Holdings, Inc. Mark Auerbach Website Former Non-Executive Chairman of the Board and Chairman of the Audit Committee for RCS www.assemblybio.com Capital Corporation; Former Lead Independent Director and Chairman of the Audit Committee Stock Listing of Optimer Pharmaceuticals, Inc. Assembly Biosciences, Inc. common stock is listed on the Nasdaq Global Select Market and Richard D. DiMarchi, Ph.D. quoted under the symbol “ASMB” Cox Distinguished Professor of Biochemistry and Gill Chair in Biomolecular Sciences and Executive Officers Myron Z. Holubiak John G. McHutchison, A.O., M.D. President and Chief Executive Officer, Citius Chief Executive Officer and President Pharmaceuticals, Inc. Thomas J. Russo, CFA Helen S. Kim Chief Financial Officer Managing Director, Vida Ventures Luisa M. Stamm, M.D., Ph.D. Alan J. Lewis, Ph.D. Chief Medical Officer Former Chief Executive Officer, DiaVacs, Inc. Richard J. Colonno, Ph.D. Susan Mahony, Ph.D. Executive Vice President and Chief Scientific Former Senior Vice President and President of Officer of Virology Operations Lilly Oncology, Eli Lilly and Company Jacqueline S. Papkoff, Ph.D. John G. McHutchison, A.O., M.D. Chief Scientific Officer, Microbiome Chief Executive Officer and President, Assembly Biosciences, Inc. Jason A. Okazaki Chief Legal and Business Officer William R. Ringo, Jr. Interim Chief Executive Officer and Chairman Transfer Agent of the Board, Five Prime Therapeutics, Inc. VStock Transfer, LLC 18 Lafayette Place Derek A. Small Woodmere, New York 11598 Managing Director, Luson Bioventures 212.828.8436 DEAR FELLOW SHAREHOLDERS, When I was approached in 2019 with the opportunity to lead Assembly Biosciences, I was struck by the exceptional quality of the science, founders, and team, and the tremendous opportunity we have before us. For many years, I have believed in a future with new, curative treatment regimens for individuals with chronic Hepatitis B, of which there are nearly a quarter of a billion worldwide. I embraced this challenge and the opportunity to focus on such an important global problem, having undertaken a similar effort earlier in my career with Hepatitis C, which is fortunately now a curable disease. I’m also pleased that over the course of the past year we have been able to attract a number of highly experienced and talented leaders to augment our senior team. Like me, they recognized the opportunity for Assembly to bring novel, and potentially curative, treatments to patients. Importantly, with the completion of our securities offering this past December, our team also has the financial resources needed to advance our programs, and we expect our current cash to fund operations into 2022. OUR HEPATITIS B CORE INHIBITOR PORTFOLIO: DRIVING TOWARD CURE Assembly’s vision is to lead the advancement of curative, finiteCURE duration regimens for individuals with chronic Hepatitis B virus (HBV) infection. Our HBV portfolio includes three novel, wholly owned small molecule inhibitors of the HBV core protein targeting multiple steps of the HBV life cycle, and all three are clinical-stage candidates. During 2019, we made significant scientific progress with ABI-H0731 (731), our first-generation core inhibitor candidate. Our Phase 2 data set puts us on a path to greater chronic suppression of HBV viral replication (and related consequences of HBV infection), as well as, we believe, toward potential “cures.” With the successful completion of our two Phase 2, 24-week treatment studies (201 and 202), we were encouraged to see that 731 administered with nucleos(t)ide therapy (Nrtl) was well tolerated. 731 also demonstrated both statistically superior antiviral activity in HBV DNA suppression compared to Nrtl alone and significant declines in pgRNA that may indicate decreases in the level of cccDNA, a central component of chronic HBV infection. The vast majority of our Phase 2 patients are continuing in our extension study (Study 211) with 731 and Nrtl treatment for up to 76 weeks, at which point we plan to begin transitioning some patients off therapy. For those meeting a set of response criteria suggesting complete suppression of viral replication as measured by our sensitive assays, all HBV treatment will be withdrawn, and we will be able to observe for sustained virologic response (SVR), another key step towards a potential cure. Given this is the first time the SVR concept has been tested in HBV patients receiving regimens containing core inhibitors, we thoughtfully defined the response criteria, developed a clinical monitoring plan, and have sought input from our study investigators and regulators. We expect to provide details on this plan shortly and to begin implementing it during the remainder of the year. 2020 IS AN IMPORTANT YEAR FOR OUR HBV PORTFOLIO: ABI-H0731—OUR MOST ADVANCED CANDIDATE: – We expect to begin transitioning patients in Study 211 off treatment based on individual virologic response to observe for SVR. – We intend to discuss with the regulatory authority in China our plan to initiate studies to enable registration for chronic suppressive therapy, as the health burden of chronic HBV infection there is widespread and significant. – We continue to explore the potential for collaborative studies combining 731 and Nrtl with other agents that have complementary mechanisms of action, so that we can evaluate triple drug combination regimens in chronic HBV patients. 2020 NEXT-GENERATION CANDIDATES: – ABI-H2158: We plan to initiate a Phase 2 trial. Data from the first dose cohort of our Phase 1b trial were presented at AASLD 2019, showing potent antiviral activity and tolerability, and final results from the dose-ranging cohorts are among our data sets that have been accepted for presentation at EASL 2020. – ABI-H3733: We are conducting our first-in-human study, a Phase 1a trial to evaluate safety, tolerability, and pharmacokinetics in healthy volunteers. PROGRAM UPDATE: Because EASL 2020 has been rescheduled from April to August due to the COVID-19 pandemic, we plan to provide an update on 731 and our HBV core inhibitor portfolio around quarterly reporting in the first half of May. OUR MICROBIOME PLATFORM: CLINICAL DEVELOPMENT UNDERWAY, PROPRIETARY PROGRAMS ADVANCING We are developing novel oral live microbial biotherapeutic candidatesREAL for a range of important diseases. Our fully integrated proprietary platform includes function-based microbial discovery, in-house scalable GMP manufacturing, and targeted oral delivery technology. Using Assembly’s differentiated, scientific approach, individual bacteria and defined consortia are rationally selected for specific biological functions based on our platform of in silico, in vitro, and in vivo capabilities. We achieved a significant milestone in mid-year 2019, when we dosed our first patient with ABI-M201, our first investigational oral live biotherapeutic product (LBP), as part of our gastrointestinal-focused collaboration with Allergan. Our Phase 1b trial is ongoing, evaluating the safety and efficacy of M201 treatment in patients with mildly to moderately active ulcerative colitis (UC). We look forward to presenting preclinical data on the M201 consortium at the upcoming DDW 2020 Virtual Annual Meeting. In parallel, we are expanding the potential of our microbiome platform to develop new proprietary LBP candidates for other disease indications. Preclinical data from our immuno-oncology microbiome program have been selected for presentation at the American Association for Cancer Research 2020 Virtual Annual Meeting. The rescheduled scientific meetings I have mentioned are just one small example of the almost unimaginable impact that the COVID-19 pandemic is having on the lives of people around the world. We have all become acutely aware of how critical health and wellbeing are to our lives. At Assembly, we recognize that the patients we aim to serve face these concerns every day, and this is why we strive to bring them our potentially transformational treatments as rapidly and effectively as we can. We are continually reminded of the crucial nature of our efforts, striving to advance health and, especially, to combat other viral diseases. On an operational level, our highly experienced team was able to quickly organize and implement plans aimed at mitigating issues arising from the pandemic. This included early strategies to minimize on-site work and adapt to social distancing directives as the region around our headquarters near San Francisco became one of the first in the country to “shelter in place.” The situation is fluid and causes a number of uncertainties beyond our direct control, but we continue to monitor and respond to developments in order to maintain business operations to the extent possible. I am proud of the focus and scientific approach we bring to our mission and the commitment our employees continue to show as we adapt the way we work in order to achieve our objectives. Our team has accomplished a great deal since the beginning of 2019, and I believe the Company and its programs are in a strong position. I’m confident that we have the resilience and resources to push toward our goals for 2020 and beyond. On behalf of the Assembly team, we are grateful for the support of shareholders like you, and I look forward to updating you on our continued progress in the coming months. Wishing you good health, John McHutchison, AO, MD Chief Executive Officer and President [This page intentionally left blank.] UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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 Number: 001-35005 ASSEMBLY BIOSCIENCES, INC.