ASSEMBLY BIOSCIENCES, INC. 10-K

Item 9A. Controls and Procedures Evaluation of Disclosure Controls and Procedures We maintain a system of disclosure controls and procedures, as defined in Rule 13a-15(e) promulgated under the Securities and Exchange Act of 1934, as amended (the Exchange Act), that is designed to provide reasonable assurance that information, which is required to be disclosed in our reports filed pursuant to the Exchange Act, is accumulated and communicated to management in a timely manner. At the end of fiscal year ending December 31, 2020, we carried out an evaluation, under the supervision, and with the participation of, our management, including our Chief Executive Officer and our Chief Financial Officer, of the effectiveness of the design and operation of our disclosure controls and procedures pursuant to Exchange Act Rule 13a-15(b). Based upon that evaluation, our Chief Executive Officer and Chief Financial Officer concluded that our disclosure controls and procedures for the fiscal year ending as of December 31, 2020 were effective at reasonable assurance levels. 54 Management’s Annual Report on Internal Control over Financial Reporting Our management is responsible for establishing and maintaining adequate internal control over financial reporting, as such term is defined in Exchange Act Rule 13a-15(f). Our internal control over financial reporting is designed to provide reasonable assurance to our management and Board of Directors regarding the preparation and fair presentation of published financial statements. A control system, no matter how well designed and operated, can only provide reasonable, not absolute, assurance that the objectives of the control system are met. Because of these inherent limitations, management does not expect that our internal controls over financial reporting will prevent all error and all fraud. Under the supervision and with the participation of our management, including our Chief Executive Officer and our Chief Financial Officer, we conducted an evaluation of the effectiveness of our internal control over financial reporting based on the framework in Internal Control-Integrated Framework issued in 2013 by the Committee of Sponsoring Organizations of the Treadway Commission. Based on our evaluation under the framework in Internal Control-Integrated Framework, our management concluded that our internal control over financial reporting was effective as of December 31, 2020. Our independent registered public accounting firm, Ernst & Young LLP has issued an opinion on the effectiveness of our internal control over financial reporting as of December 31, 2020. The report of Ernst & Young LLP is included with the financial statements appended to this Form 10-K pursuant to Item 8. Changes in Internal Control over Financial Reporting There were no changes in our internal control over financial reporting in the fourth quarter of 2020 that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. Item 9B. Other Information Not applicable. 55 PART III ITEM 10. Directors, Executive Officers and Corporate Governance Except as set forth below, the information required by this item will be contained in our definitive proxy statement to be filed with the SEC in connection with the Annual Meeting of Stockholders (Proxy Statement) within 120 days after the conclusion of our fiscal year ended December 31, 2020 and is incorporated in this Annual Report on Form 10-K by reference. Code of Ethics Our Board has adopted a Code of Ethics for our principal executive officer and all senior financial officers and a Code of Conduct applicable to all of our employees and our directors. Both Codes are available under the “Investors—Corporate Governance” section of our website at www.assemblybio.com. If we make any substantive amendments to, or grant any waivers from, the Code of Ethics for our principal executive officer, principal financial officer, principal accounting officer, controller or persons performing similar functions, or any officer or director, we will disclose the nature of such amendment or waiver on our website or in a Current Report on Form 8-K. ITEM 11. Executive Compensation The information required by this item will be contained in the Proxy Statement and is incorporated into this Annual Report on Form 10-K by reference. ITEM 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters Except for the table regarding equity compensation plans, which is included in Part II, Item 5 of this Annual Report on Form 10-K, the information required by this item will be contained in the Proxy Statement and is incorporated into this Annual Report on Form 10-K by reference. ITEM 13. Certain Relationships and Related Party Transactions, and Director Independence The information required by this item will be contained in the Proxy Statement and is incorporated into this Annual Report on Form 10-K by reference. ITEM 14. Principal Accounting Fees and Services The information required by this item will be contained in the Proxy Statement and is incorporated into this Annual Report on Form 10-K by reference. ITEM 15. Exhibits, Financial Statement Schedules (a) Exhibits. The following exhibits are filed as part of this registration statement: Exhibit Number Description of Document Registrant’s Form Dated Exhibit No. Filed Herewith 3.1 Fifth Amended and Restated Certificate of Incorporation dated June 11, 2020. 8-K 06/01/2018 3.1 3.2 Amended and Restated Bylaws as amended through January 22, 2021. 8-K 01/27/2021 3.1 4.1 Specimen of Common Stock Certificate. S-3 12/30/2015 4.1 4.2 Form of Pre-Funded Warrant. 8-K 12/16/2019 4.1 4.3 Description of Securities. X 10.1 Sub-Sublease, dated as of July 18, 2018, between Prothena Biosciences, Inc., as Sub-Sublandlord, and Assembly Biosciences, Inc., as Sub-Subtenant. 10-Q 11/08/2018 10.1 10.2* Exclusive License Agreement dated September 3, 2013 by and between The Indiana University Research and Technology Corporation and Assembly Pharmaceuticals, Inc. 10-Q 11/17/2014 10.29 56 Exhibit Number Description of Document Registrant’s Form Dated Exhibit No. Filed Herewith 10.3 † Amendment No. 1 to Exclusive License Agreement, by and between Assembly Biosciences, Inc. and the Indiana University Research and Technology Corporation. 10-Q 11/05/2020 10.1 10.4 † Amendment No. 2 to Exclusive License Agreement, by and between Assembly Biosciences, Inc. and the Indiana University Research and Technology Corporation. 10-Q 11/05/2020 10.2 10.5 † ‡ Collaboration Agreement, dated as of July 17, 2020, by and between Assembly Biosciences, Inc. and BeiGene, Ltd. 10-Q 11/05/2020 10.3 10.6# Employment Agreement, dated August 6, 2019, between Assembly Biosciences, Inc. and John G. McHutchison, A.O., M.D. 10-Q 11/07/2019 10.1 10.7# Employment Agreement, dated September 30, 2019, between Assembly Biosciences, Inc. and Thomas J. Russo, effective as of October 28, 2019. 10-Q 11/07/2019 10.6 10.8# Amendment No. 1 to Employment Agreement, dated February 26, 2020, between Assembly Biosciences, Inc. and Thomas J. Russo. 10-Q 05/08/2020 10.6 10.9# Employment Agreement, dated October 22, 2019, between Assembly Biosciences, Inc. and Luisa M. Stamm, M.D., Ph.D. effective as of November 6, 2019. 10-K 03/04/2020 10.7 10.10# Amendment No. 1 to Employment Agreement, dated February 26, 2020, between Assembly Biosciences, Inc. and Luisa M. Stamm, M.D., Ph.D. 10-Q 05/08/2020 10.7 10.11# Employment Agreement, dated March 23, 2020, between Assembly Biosciences, Inc. and Jason A. Okazaki, effective as of March 26, 2020. X 10.12# Employment Agreement, dated May 1, 2020, between Assembly Biosciences, Inc. and William E. Delaney IV, Ph.D., effective as of May 27, 2020. X 10.13# 2010 Equity Incentive Plan . S-1/A 10/4/2010 10.14 10.14# Assembly Biosciences, Inc. Amended and Restated 2014 Stock Incentive Plan. 8-K 6/6/2016 10.1 10.15# Omnibus Amendment to Assembly Biosciences, Inc. Stock Incentive Plans. 10-Q 05/08/2020 10.2 10.16# Form of Notice of Stock Option Grant and Stock Option Agreement under Amended and Restated 2014 Stock Incentive Plan. S-8 9/17/2014 10.28 10.17# Form of Restricted Stock Unit Award Notice and Restricted Stock Unit Award Agreement under the Amended and Restated 2014 Stock Incentive Plan. 10-Q 11/01/2017 10.1 10.18# Assembly Biosciences, Inc. 2017 Inducement Award Plan. 10-Q 08/09/2017 10.1 10.19# Form of Notice of Stock Option Grant and Stock Option Agreement under the 2017 Inducement Award Plan. 10-Q 08/09/2017 10.2 10.20# Form of Restricted Stock Unit Award Notice and Restricted Stock Unit Award Agreement under the 2017 Inducement Award Plan. 10-Q 08/09/2017 10.3 10.21# Assembly Biosciences, Inc. 2018 Stock Incentive Plan. 8-K 6/1/2018 10.1 10.22# Amendment No. 1 to Assembly Biosciences, Inc. 2018 Stock Incentive Plan . 8-K 05/21/2019 10.2 10.23# Amendment No. 3 to Assembly Biosciences, Inc. 2018 Stock Incentive Plan. 8-K 06/16/2020 10.1 10.24# Form of Notice of Stock Option Grant and Stock Option Agreement under the 2018 Stock Incentive Plan. 8-K 6/1/2018 10.2 10.25# Form of Restricted Stock Unit Award Notice and Restricted Stock Unit Award Agreement under the 2018 Stock Incentive Plan. 8-K 6/1/2018 10.3 10.26# Form of Stock Appreciation Right Award Agreement for Non-U.S. Grantees under the Assembly Biosciences, Inc. 2018 Stock Incentive Plan. 8-K 10/12/2018 10.4 10.27# Assembly Biosciences, Inc. 2018 Employee Stock Purchase Plan. 8-K 6/1/2018 10.4 57 Exhibit Number Description of Document Registrant’s Form Dated Exhibit No. Filed Herewith 10. 28 # Assembly Biosciences, Inc. 2019 Inducement Award Plan . 10-Q 11/07/2019 10.4 10.29# Form of Notice of Stock Option Grant and Stock Option Agreement under the 2019 Inducement Award Plan. 10-Q 11/07/2019 10.5 10.30# Assembly Biosciences, Inc. 2020 Inducement Award Plan. 10-Q 05/08/2020 10.3 10.31# Form of Notice of Stock Option Grant and Stock Option Agreement under the 2020 Inducement Award Plan. 10-Q 05/08/2020 10.4 10.32# Form of Restricted Stock Unit Award Notice and Restricted Stock Unit Award Agreement under the 2020 Inducement Award Plan. 10-Q 05/08/2020 10.5 10.33# Assembly Biosciences, Inc. 2020 Corporate Bonus Plan. 8-K 02/11/2020 10.1 21.1 List of Subsidiaries of Assembly Biosciences, Inc. X 23.1 Consent of Independent Registered Public Accounting Firm. X 24.1 Power of Attorney (included on signature page) . X 31.1 Certification of the Chief Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. X 31.2 Certification of the Chief Financial Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. X 32.1** Certification of the Chief Executive Officer Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. X 32.2 ** Certification of the Chief Financial Officer Pursuant to 18 U.S.C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. X 101.INS Inline XBRL Instance Document. 101.SCH Inline XBRL Taxonomy Extension Schema Document. 101.CAL Inline XBRL Taxonomy Extension Calculation Linkbase Document. 101.DEF Inline XBRL Taxonomy Extension Definitions Linkbase Document. 101.LAB Inline XBRL Taxonomy Extension Label Linkbase Document. 101.PRE Inline XBRL Taxonomy Extension Presentation Linkbase Document. 104 Cover Page Interactive Data File (embedded within the Inline XBRL document). * Certain information in this exhibit has been omitted and filed separately with the Securities and Exchange Commission pursuant to a confidential treatment request. † The schedules to this exhibit have been omitted pursuant to Item 601(a)(5) of Regulation S-K. ‡ Portions of this exhibit that are both not material and would likely cause competitive harm to the registrant if publicly disclosed have been omitted pursuant to Item 601(b)(10)(iv) of Regulation S-K. # Represents management contracts or compensatory plans or arrangements. ** The certifications attached as Exhibits 32.1 and 32.2 that accompany this Annual Report on Form 10-K are to be deemed furnished and shall not be deemed “filed” with the SEC and are not to be incorporated by reference into any filing of Assembly Biosciences, Inc. under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended, whether made before or after the date of this Annual Report on Form 10-K, irrespective of any general incorporation language contained in such filing. Item 16. Form 10-K Summary. None 58 SIGNA TURES In accordance with Section 13 or 15(d) of the Securities Exchange Act, the Registrant caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. ASSEMBLY BIOSCIENCES, INC. Date: February 25, 2021 By: /s/ John G. McHutchison, A.O., M.D. Name: John G. McHutchison, A.O., M.D. Title: Chief Executive Officer and President POWER OF ATTORNEY KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints John G. McHutchison, A.O., M.D., Thomas J. Russo, CFA and Jason A. Okazaki, jointly and severally, his or her attorneys-in-fact, each with the power of substitution, for him or her in any and all capacities, to sign any amendments to this report, and to file the same, with exhibits thereto and other documents in connection therewith with the Securities and Exchange Commission, hereby ratifying and confirming all that each of said attorneys-in-fact, or his or her substitute or substitutes may do or cause to be done by virtue hereof. Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed by the following persons on behalf of the registrant in the capacities and on the dates indicated. Signature Title Date /s/ John G. McHutchison, A.O., M.D. Chief Executive Officer, President and Director February 25, 2021 John G. McHutchison, A.O., M.D. (Principal Executive Officer) /s/ Thomas J. Russo, CFA Chief Financial Officer February 25, 2021 Thomas J. Russo, CFA (Principal Financial and Principal Accounting Officer) /s/ William R. Ringo, Jr. Chairman of the Board February 25, 2021 William R. Ringo, Jr. /s/ Anthony E. Altig Director February 25, 2021 Anthony E. Altig /s/ Gina Consylman Director February 25, 2021 Gina Consylman /s/ Richard D. DiMarchi, Ph.D. Director February 25, 2021 Richard D. DiMarchi, Ph.D. /s/ Myron Z. Holubiak Director February 25, 2021 Myron Z. Holubiak /s/ Susan Mahony, Ph.D. Director February 25, 2021 Susan Mahony, Ph.D. 59 ASSEMBLY BIOSCIENCES, INC. FINANCIAL STATEMENTS Page Reports of Independent Registered Public Accounting Firm F-2 Consolidated Balance Sheets as of December 31, 2020 and 2019 F-7 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2020, 2019 and 2018 F-8 Consolidated Statements of Changes in Stockholders’ Equity for the Years Ended December 31, 2020, 2019 and 2018 F-9 Consolidated Statements of Cash Flows for the Years Ended December 31, 2020, 2019 and 2018 F-10 Notes to Consolidated Financial Statements F-11 F-1 Report of Independent Registered Public Accounting Firm To the Stockholders and the Board of Directors of Assembly Biosciences, Inc. Opinion on the Financial Statements We have audited the accompanying consolidated balance sheets of Assembly Biosciences, Inc. (the Company) as of December 31, 2020 and 2019, the related consolidated statements of operations and comprehensive loss, changes in stockholders’ equity and cash flows for each of the three years in the period ended December 31, 2020, and the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company at December 31, 2020 and 2019, and the results of its operations and its cash flows for each of the three years in the period ended December 31, 2020, in conformity with U.S. generally accepted accounting principles. We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the Company's internal control over financial reporting as of December 31, 2020, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 Framework) and our report dated February 25, 2021 expressed an unqualified opinion thereon. Basis for Opinion These financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on the Company’s financial statements based on our audits. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion. Critical Audit Matters The critical audit matters communicated below are matters arising from the current period audit of the financial statements that were communicated or required to be communicated to the audit committee and that: (1) relate to accounts or disclosures that are material to the financial statements and (2) involved our especially challenging, subjective or complex judgments. The communication of critical audit matters does not alter in any way our opinion on the consolidated financial statements, taken as a whole, and we are not, by communicating the critical audit matters below, providing separate opinions on the critical audit matters or on the accounts or disclosures to which they relate. F-2 Accrued clinical trial expenses Description of the Matter For the year ended December 31, 2020, the Company incurred $106.8 million of research and development expenses and recorded $4.4 million for accrued clinical trial expenses at December 31, 2020. As described in Note 2 to the consolidated financial statements, the Company’s expense accruals for clinical trials are based on estimates of the services received and efforts expended pursuant to contracts with multiple contract research organizations (CROs) and manufacturing vendors that conduct and manage these activities on its behalf. When billing terms under such contracts do not coincide with the timing of when the work is performed, management is required to make estimates of outstanding obligations to those third parties as of period end. The accrual is based on a number of factors, including the time period over which services will be performed, enrollment of subjects, number of sites activated, and the level of effort to be expended in each period. At period end, accrued clinical trial expenses are recorded based upon estimates of the proportion of work completed over the term of the individual clinical trial and manufacturing activities in accordance with signed agreements with the third parties. If possible, the Company obtains information regarding unbilled services directly from these service providers and performs procedures to challenge these estimates based on their internal understanding of the services provided to date. However, the Company may also be required to estimate these services based on information available to its internal clinical or administrative staff if such information is not able to be obtained timely from its services providers. Auditing accrued clinical trial expenses is complex because of the judgments applied by management to determine the commencement and completion date of vendor tasks and the cost and extent of work performed during the reporting period for services not yet billed by contracted third-party vendors. The testing of the Company’s accrued clinical trial expense models also involves a high level of effort to test the high volume of data used to determine the estimated accrual. How We Addressed the Matter in Our Audit We obtained an understanding, evaluated the design and tested the operating effectiveness of controls over the Company’s process for estimating the accrued clinical trial expenses including controls over management’s assessment and measurement of clinical trial progress and related estimates of accrued clinical trial costs and the completeness and accuracy of underlying data used in the analysis. To test the estimate of accrued clinical trial expenses, we performed audit procedures that included, among others, direct confirmation of contract terms and conditions with a sample of the Company’s third-party vendors. We also confirmed the progress of contracted clinical activities with these third-party vendors and compared such data to the Company’s estimates of progress as reflected in their accrual models. We further tested the accuracy of the calculations, the completeness of the data utilized, and the reasonableness of the assumptions used in management’s accrual models by testing actual invoices paid to date, agreeing inputs back to contractual terms and holding discussions with clinical or administrative staff outside of the finance function. Procedures were performed to evaluate the reliability, completeness and relevance of management’s data by testing actual invoices paid and holding discussions with clinical or administrative staff outside of the finance function to corroborate progress and estimated level of expended effort incurred by the Company’s third-party vendors. Further, we inspected material invoices received from third parties after the balance sheet date and evaluated whether services performed prior to the consolidated balance sheet date had been properly included in the accrual. F-3 Revenue Recognition for the Collaborative Arrangement with BeiGene, Ltd. Description of the Matter As described in Note 9 to the consolidated financial statements, in July 2020, the Company entered into a collaboration agreement with BeiGene, Ltd. (BeiGene) to develop and commercialize the Company’s product candidates in China for the treatment of chronic Hepatitis B virus infection (the BeiGene Agreement). The BeiGene Agreement includes up-front fees, milestones, royalties, expense reimbursement, and potential cost share and profit sharing. Management was required to use judgment to determine what part of the BeiGene Agreement was within the scope of the contract with customers guidance and what part of the agreement was within the scope of the collaborative arrangement guidance. For the year ended December 31, 2020, the Company recognized $31.0 million as collaboration revenue and $9.0 million of long-term deferred revenue from the BeiGene Agreement. Auditing the Company’s accounting for revenues from its BeiGene Agreement was especially challenging due to the complex and highly judgmental nature of evaluating the terms of the agreement, evaluating whether analogies to the revenue accounting or collaborative arrangements guidance are appropriate, and allocating the transaction price to the performance obligations. How We Addressed the Matter in Our Audit We obtained an understanding, evaluated the design and tested the operating effectiveness of controls over management’s assessment of the accounting treatment of the BeiGene Agreement and identification of performance obligations and application of the accounting guidance. To test the accounting for revenue from the BeiGene Agreement, among other procedures, we tested and evaluated, the performance obligations identified and the allocation of transaction price to performance obligations. We also assessed whether management’s evaluation of the portions of the BeiGene Agreement subject to the scope of the contract with customers accounting standard and collaborative arrangements accounting standard, as well as their analogies to the revenue from contracts with customers accounting standard or the portion of the BeiGene Agreement subject to the collaborative arrangements guidance, was an appropriate application of an accounting policy. /s/ Ernst & Young LLP We have served as the Company’s auditor since 2015. Redwood City, California February 25, 2021 F-4 Report of Independent Registered Public Accounting Firm To the Stockholders and the Board of Directors of Assembly Biosciences, Inc. Opinion on Internal Control over Financial Reporting We have audited Assembly Biosciences, Inc.’s internal control over financial reporting as of December 31, 2020, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework) (the COSO criteria). In our opinion, Assembly Biosciences, Inc. (the Company) maintained, in all material respects, effective internal control over financial reporting as of December 31, 2020, based on the COSO criteria. We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the consolidated balance sheets of the Company as of December 31, 2020 and 2019, the related consolidated statements of operations and comprehensive loss, changes in stockholders’ equity and cash flows for each of the three years in the period ended December 31, 2020, and the related notes and our report dated February 25, 2021 expressed an unqualified opinion thereon. Basis for Opinion The Company’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting included in the accompanying Management's Annual Report on Internal Control Over Financial Reporting. Our responsibility is to express an opinion on the Company’s internal control over financial reporting based on our audit. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects. Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion. Definition and Limitations of Internal Control Over Financial Reporting A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements. F-5 Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. /s/ Ernst & Young LLP Redwood City, California February 25, 2021 F-6 ASSEMBLY BIOSCIENCES, INC. CONSOLIDATED BALANCE SHEETS (In thousands except for share amounts and par value) As of December 31, 2020 2019 ASSETS Current assets Cash and cash equivalents $ 59,444 $ 46,732 Marketable securities 156,969 227,311 Accounts receivable from collaborations 1,230 3,374 Prepaid expenses and other current assets 6,850 5,363 Total current assets 224,493 282,780 Property and equipment, net 1,600 1,830 Operating lease right-of-use (ROU) assets 9,131 11,975 Other assets 6,392 1,684 Indefinite-lived intangible asset 29,000 29,000 Goodwill 12,638 12,638 Total assets $ 283,254 $ 339,907 LIABILITIES AND STOCKHOLDERS' EQUITY Current liabilities Accounts payable $ 4,598 $ 1,731 Accrued clinical expenses 4,444 4,826 Other accrued expenses 11,987 8,286 Deferred revenue - short-term — 6,411 Operating lease liabilities - short-term 3,404 3,186 Total current liabilities 24,433 24,440 Deferred tax liabilities 2,531 2,531 Deferred revenue - long-term 8,987 30,637 Operating lease liabilities - long-term 6,725 9,082 Total liabilities 42,676 66,690 Commitments and contingencies Stockholders' equity Preferred stock, $ 0.001 par value; 5,000,000 shares authorized; no shares issued or outstanding — — Common stock, $ 0.001 par value; 100,000,000 shares authorized as of December 31, 2020 and 2019; 34,026,680 and 32,558,307 shares issued and outstanding as of December 31, 2020 and 2019, respectively 34 32 Additional paid-in capital 742,387 712,807 Accumulated other comprehensive loss ( 270 ) ( 201 ) Accumulated deficit ( 501,573 ) ( 439,421 ) Total stockholders' equity 240,578 273,217 Total liabilities and stockholders' equity $ 283,254 $ 339,907 See Accompanying Notes to the Consolidated Financial Statements F-7 ASSEMBLY BIOSCIENCES, INC. CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS (In thousands except for share and per share amounts) Year ended December 31, 2020 2019 2018 Collaboration revenue $ 79,105 $ 15,963 $ 14,804 Operating expenses: Research and development 106,823 85,757 72,741 General and administrative 37,058 32,919 34,798 Total operating expenses 143,881 118,676 107,539 Loss from operations ( 64,776 ) ( 102,713 ) ( 92,735 ) Other income Interest and other income 2,624 4,305 3,083 Total other income 2,624 4,305 3,083 Loss before income taxes ( 62,152 ) ( 98,408 ) ( 89,652 ) Income tax benefit (expense) — 774 ( 1,099 ) Net loss $ ( 62,152 ) $ ( 97,634 ) $ ( 90,751 ) Other comprehensive income Unrealized gain (loss) on marketable securities, net of tax ( 69 ) 146 45 Comprehensive loss $ ( 62,221 ) $ ( 97,488 ) $ ( 90,706 ) Net loss per share, basic and diluted $ ( 1.75 ) $ ( 3.72 ) $ ( 3.98 ) Weighted average common shares outstanding, basic and diluted 35,427,120 26,258,790 22,801,644 See Accompanying Notes to the Consolidated Financial Statements F-8 ASSEMBLY BIOSCIENCES, INC. CONSOLIDATED STATEMENTS OF CHANGES IN STOCKHOLDERS’ EQUITY (In thousands except for share amounts) Common Stock Additional Paid-in Accumulated Other Comprehensive Accumulated Total Stockholders' Shares Amount Capital Loss Deficit Equity Balance as of December 31, 2017 20,137,974 $ 20 $ 364,528 $ ( 392 ) $ ( 251,036 ) $ 113,120 Sale of common stock, net of underwriters' discount and costs 4,600,000 4 155,421 — — 155,425 Issuance of common stock upon exercise of stock options 735,030 1 3,959 — — 3,960 Issuance of common stock under Employee Stock Purchase Plan (ESPP) 21,483 — 408 — — 408 Issuance of shares of common stock for settlement of restricted stock units (RSUs) 938 — — — — — Unrealized gain on marketable securities, net of tax — — — 45 — 45 Stock-based compensation — — 28,446 — — 28,446 Net loss — — — — ( 90,751 ) ( 90,751 ) Balance as of December 31, 2018 25,495,425 $ 25 $ 552,762 $ ( 347 ) $ ( 341,787 ) $ 210,653 Sale of common stock and pre-funded warrants, net of underwriters' discount and costs 6,287,878 6 134,655 — — 134,661 Issuance of common stock upon exercise of stock options 585,292 1 4,237 — — 4,238 Settlement of RSUs for cash — — ( 4 ) — — ( 4 ) Issuance of common stock under ESPP 59,370 — 747 — — 747 Issuance of shares of common stock for settlement of RSUs 130,342 — — — — — Unrealized gain on marketable securities, net of tax — — — 146 — 146 Stock-based compensation — — 20,410 — — 20,410 Net loss — — — — ( 97,634 ) ( 97,634 ) Balance as of December 31, 2019 32,558,307 $ 32 $ 712,807 $ ( 201 ) $ ( 439,421 ) $ 273,217 Sale of common stock, net of commissions and fees 892,840 1 5,451 — — 5,452 Issuance of common stock upon exercise of stock options 175,579 1 1,466 — — 1,467 Issuance of common stock under ESPP 86,812 — 680 — — 680 Issuance of shares of common stock for settlement of RSUs 313,142 — — — — — Unrealized loss on marketable securities — — — ( 69 ) — ( 69 ) Stock-based compensation — — 21,983 — — 21,983 Net loss — — — — ( 62,152 ) ( 62,152 ) Balance as of December 31, 2020 34,026,680 $ 34 $ 742,387 $ ( 270 ) $ ( 501,573 ) $ 240,578 See Accompanying Notes to the Consolidated Financial Statements F-9 ASSEMBLY BIOSCIENCES, INC. CONSOLIDATED STATEMENTS OF CASH FLOWS (In thousands) Year Ended December 31, 2020 2019 2018 Cash flows from operating activities Net loss $ ( 62,152 ) $ ( 97,634 ) $ ( 90,751 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 691 494 643 Non-cash IPR&D expense 1,750 — — Stock-based compensation 21,853 20,558 28,485 Net accretion and amortization of investments in marketable securities ( 13 ) ( 1,735 ) ( 229 ) Non-cash rent expense 5,214 4,454 — Deferred income tax (benefit) expense — ( 774 ) 1,099 Loss on disposal of fixed assets 9 102 — Other — ( 5 ) — Changes in operating assets and liabilities: Accounts receivable from collaborations 2,144 ( 944 ) ( 156 ) Prepaid expenses and other current assets ( 1,487 ) ( 3,685 ) ( 1,094 ) Other assets ( 4,708 ) 1,664 ( 3,008 ) Accounts payable 2,867 ( 1,962 ) 1,569 Accrued clinical expenses ( 382 ) 1,265 3,119 Other accrued expenses 3,831 2,016 382 Deferred revenue ( 28,061 ) ( 3,612 ) ( 5,125 ) Deferred rent — — 108 Operating lease liabilities ( 4,513 ) ( 4,269 ) — Net cash used in operating activities ( 62,957 ) ( 84,067 ) ( 64,958 ) Cash flows from investing activities Purchases of property and equipment ( 470 ) ( 1,554 ) ( 340 ) Purchase of IPR&D ( 1,750 ) — — Purchases of marketable securities ( 193,188 ) ( 281,334 ) ( 183,941 ) Proceeds from maturities of marketable securities 221,617 203,911 48,884 Proceeds from sale of marketable securities 41,861 28,659 — Net cash provided by (used in) investing activities 68,070 ( 50,318 ) ( 135,397 ) Cash flows from financing activities Proceeds from common stock and pre-funded warrants sold, net of underwriters' discount, commissions and costs 5,452 134,661 155,425 Proceeds from the issuance of common stock under ESPP 680 747 408 Proceeds from the exercise of stock options 1,467 4,238 3,960 Net cash provided by financing activities 7,599 139,646 159,793 Net increase (decrease) in cash and cash equivalents 12,712 5,261 ( 40,562 ) Cash and cash equivalents at the beginning of the period 46,732 41,471 82,033 Cash and cash equivalents at the end of the period $ 59,444 $ 46,732 $ 41,471 Supplemental non-cash investing and financing activities Operating lease liabilities arising from obtaining right-of-use assets $ 1,302 $ 15,261 $ — See Accompanying Notes to the Consolidated Financial Statements F-10 ASSEMBLY BIOSCIENCES, INC. Notes to Consolidated Financial Statements Note 1 - Nature of Business Overview Assembly Biosciences, Inc., together with its subsidiaries (Assembly or the Company), incorporated in Delaware in October 2005, is a clinical-stage biotechnology company advancing a novel class of oral therapeutic candidates for the treatment of hepatitis B virus (HBV) infection. The Company operates in one segment and is headquartered in South San Francisco, California with operations in California, Connecticut and China. The Company’s research and development programs are pursuing multiple drug candidates that inhibit the HBV replication cycle and block the generation of covalently closed circular DNA (cccDNA), with the aim of discovering and developing finite and curative therapies for patients with HBV. Assembly has discovered multiple novel core inhibitors, which are small molecules that directly target and allosterically modify the HBV core (HBc) protein. In December 2020, the Company and its Board of Directors approved a plan to wind down its Microbiome program in order to prioritize and focus its resources entirely on discovering and developing finite and curative therapies for HBV. The Microbiome program had been developing a novel class of oral live microbial biotherapeutics candidates designed to treat disorders associated with the microbiome. Liquidity The Company has not derived any revenue from product sales to date and currently has no approved products. Once a product has been developed, it will need to be approved for sale by the U.S. Food and Drug Administration (FDA) or an applicable foreign regulatory agency. Since inception, the Company’s operations have been financed primarily through the sale of equity securities, the proceeds from the exercise of warrants and stock options, the issuance of debt, and upfront payments related to collaboration agreements. The Company has incurred losses from operations since inception and expects to continue to incur substantial losses for the next several years as it continues its product development efforts. Management believes the Company currently has sufficient funds to meet its operating requirements for at least the next twelve months following the date that these consolidated financial statements are issued. If the Company cannot generate significant cash from its operations, it intends to obtain any additional funding it requires through strategic relationships, public or private equity or debt financings, grants or other arrangements (see Note 7 for recent sales of common stock). The Company cannot assure such funding will be available on reasonable terms, if at all. Market volatility resulting from the novel coronavirus disease (COVID-19) pandemic or other factors could also adversely impact the Company’s ability to access capital when and as needed. If the Company is unable to generate enough revenue from its collaborations, secure additional sources of funding or receive full and timely collections of amounts due, it may be necessary to significantly reduce the current rate of spending through reductions in staff and delaying, scaling back, or stopping certain research and development programs, including more costly clinical trials. F-11 Note 2 - Summary of Significant Accounting Policies and Recent Accounting Pronouncements Basis of Presentation These consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States (U.S. GAAP) and include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. Use of Estimates The preparation of consolidated financial statements in conformity with the accounting principles generally accepted in the United States of America (U.S. GAAP) requires management to make estimates and assumptions that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and reported amounts of expenses during the reporting period. Actual results could differ from those estimates. Significant estimates inherent in the preparation of the accompanying consolidated financial statements include estimates for the cost-based input of revenue recognition and standalone selling price estimates for allocation of transaction price to performance obligations revenue recognition, estimates of costs incurred but not yet invoiced for clinical trial accruals, recoverability and useful lives of our long-lived assets, the estimated fair value of our indefinite-lived intangible assets, the estimated fair value of our reporting unit for purposes of evaluating goodwill impairment, provisions for income taxes, amounts receivable under collaboration agreements, measurement of operating lease liabilities, and the fair value of stock options, stock appreciation rights, and RSUs granted to employees, directors, and consultants. The Company’s estimates could be affected by external conditions, including those unique to the Company and general economic conditions. It is reasonably possible that these external factors could have an effect on the Company’s estimates and could cause actual results to differ from those estimates and assumptions. Other Risks and Uncertainties In March 2020, the World Health Organization declared the COVID-19 outbreak a pandemic. To date, the Company’s operations have not been significantly impacted by the COVID-19 pandemic. However, the Company cannot at this time predict the specific extent, duration, or full impact the COVID-19 pandemic will have on its business, operations, strategy, prospects and financial condition and results. The impact of the COVID-19 pandemic on the Company’s financial performance will depend on future developments, including the duration and spread of the outbreak and related governmental advisories and restrictions. These developments and the impact of the COVID-19 pandemic on the financial markets and the overall economy are highly uncertain. If the financial markets and/or the overall economy are impacted for an extended period, the Company’s results may be adversely affected. Cash and Cash Equivalents All highly liquid investments, including money market funds, with original maturities of three months or less at the time of purchase are considered to be cash equivalents. All of the Company’s cash equivalents have liquid markets and high credit ratings. The Company maintains its cash in bank deposits and other accounts, the balances of which, at times and at December 31, 2020 and 2019, exceed federally insured limits. Investments in Marketable Securities The Company invests its excess cash in debt securities with high credit ratings including but not limited to money market funds classified as cash equivalents, asset backed securities, securities issued by the U.S. government and its agencies, corporate debt securities and commercial paper. The Company has designated its investments in marketable securities as available-for-sale and measures these securities at their respective fair values. Marketable securities are classified as short-term or long-term based on the maturity date and their availability to meet current operating requirements. Marketable securities that mature in one year or less are classified as short-term available-for-sale securities and are reported as a component of current assets. F-12 Securities that are classified as available-for-sale are measured at fair value with temporary unrealized gains and losses reported in other comprehensive loss, and as a component of stockholders' equity until their disposition. The Company reviews all available-for-sale securities at each period end to determine if they remain available-for-sale based on their current intent and ability to sell the security if it is required to do so. Realized gains and losses from the sale of marketable securities, if any, are calculated using the specific-identification method. Marketable securities are subject to a periodic impairment review. The Company may recognize an impairment charge when a decline in the fair value of investments below the cost basis is determined to be other-than-temporary. In determining whether a decline in market value is other-than-temporary, various factors are considered, including the cause, duration of time and severity of the impairment, any adverse changes in the investees’ financial condition, and the Company’s intent and ability to hold the security for a period of time sufficient to allow for an anticipated recovery in market value. To date, there have been no declines in value deemed to be other than temporary for any of our investments in marketable securities. Goodwill and Indefinite-Lived Intangible Asset Goodwill and indefinite-lived intangible assets are reviewed for impairment at least annually in the fourth quarter, and more frequently if events or other changes in circumstances indicate that the carrying amount of the assets may not be recoverable. Impairment of goodwill and indefinite-lived intangibles is determined to exist when the fair value is less than the carrying value of the net assets being tested. Goodwill The difference between the purchase price and the fair value of assets acquired and liabilities assumed in a business combination is allocated to goodwill. Goodwill is evaluated for impairment on an annual basis as of October 1, and more frequently if indicators are present or changes in circumstances suggest that impairment may exist. In performing each annual impairment assessment and any interim impairment assessment, the Company determines if it should qualitatively assess whether it is more likely than not that the fair value of goodwill is less than its carrying amount (the qualitative impairment test). If the Company concludes it is more likely than not that the fair value of the reporting unit is less than its carrying amount, or elect not to use the qualitative impairment test, a quantitative impairment test is performed The Company annual or interim quantitative impairment testing is performed by comparing the estimated fair value of the reporting unit to its carrying value. An impairment charge is recognized for the amount by which the carrying amount exceeds the reporting unit’s fair value, not to exceed the carrying value of goodwill. As of October 1, 2020 the Company has determined through its quantitative impairment test that the fair value of its goodwill significantly exceeded the carrying value of its single reporting unit and concluded that goodwill was not impaired. In November 2020, after the Company’s public announcement that it became clear that patients who stopped therapy in Study 211 had not achieved meaningful sustained virologic response rates most of the patients had relapsed, the Company’s stock price declined significantly. Due to a sustained decline in the Company’s stock price during the remainder of the fourth quarter of 2020, the Company determined these factors were an indication of a triggering event of impairment and an interim goodwill impairment test was performed as of December 31, 2020. However, the interim quantitative impairment test still determined the fair value, when considering a control premium based on a range of recent acquisitions of entities similar to the Company which were made on a non-minority basis, exceeded the carrying value of its single reporting unit, and concluded that goodwill was still not impaired. The Company has not recognized any goodwill impairment in any of the periods presented. Indefinite-Lived Intangible Asset The Company’s indefinite-lived intangible asset consists of IPR&D acquired in a business combination that are used in research and development activities but have not yet reached technological feasibility, regardless of whether they have alternative future use. The primary basis for determining the technological feasibility or completion of these projects is obtaining regulatory approval to market the underlying products in an applicable geographic region. The Company classifies IPR&D acquired in a business combination as an indefinite-lived intangible asset until the completion or abandonment of the associated research and development efforts. Upon completion of the associated research and development efforts, the Company performed a final test for impairment and will determine the useful F-13 life of the technology and begin amortizing the assets to reflect their use over their remaining lives. Upon permanent abandonment, the Company would write-off the remaining carrying amount of the associated IPR&D intangible asset. Indefinite-lived intangible assets are not amortized, but instead are reviewed for impairment at least annually, or more frequently if events occur or circumstances change that would indicate the carrying amount may be impaired. In performing each annual impairment assessment and any interim impairment assessment, the Company determines if it should qualitatively assess whether it is more likely than not that the fair value of its IPR&D asset is less than its carrying amount (the qualitative impairment test). If the Company concludes that is the case, or elect not to use qualitative impairment test, the Company would proceed with quantitatively determining the fair value of the IPR&D asset and comparing its fair value to its carrying value to determine the amount of impairment, if any (the quantitative impairment test). When performing the quantitative impairment assessment, the Company uses the income approach to determine the fair value of its IPR&D asset. This approach calculates fair value by estimating the after-tax cash flows attributable to an in-process project over its useful life and then discounting these after-tax cash flows back to a present value. This estimate includes judgmental assumptions regarding the estimates that market participants would make in evaluating the IPR&D asset, including the probability of successfully completing clinical trials and obtaining regulatory approval to market the IPR&D asset, the timing of and the expected costs to complete IPR&D projects, future net cash flows from potential drug sales, which are based on estimates of the sales price of the drug, the size of the patient population and cure rate, our competitive position in the marketplace, and appropriate discount and tax rates. Any impairment to be recorded is calculated as the difference between the fair value of the IPR&D asset as of the date of the assessment with the carrying value of the IPR&D asset on its consolidated balance sheet. In performing the qualitative impairment test, the Company considers the results of the most recent quantitative impairment test and identifies the most relevant drivers of the fair value for the IPR&D asset. The most relevant drivers of fair value identified are consistent with the assumptions used in the quantitative estimate of the IPR&D asset discussed below. Using these drivers of fair value, the Company identifies events and circumstances that may have an effect on the fair value of the IPR&D asset since the last time the IPR&D’s fair value was quantitatively determined. The Company then weighs these factors to determine and conclude if it is not more likely than not that the IPR&D asset is impaired. If it is more likely than not that the IPR&D asset is impaired, the Company proceeds with quantitatively determining the fair value of the IPR&D asset. For the Company’s 2020 impairment test, the Company performed a qualitative test and concluded it was more-likely-than-not that the fair value of its IPR&D asset exceeded its carrying value and no further testing was required. This was based on a decrease in the probability of success based on the impact of the Study 211 and dual combination VBR and NrtI therapy’s ability to serve as a finite and curative therapy for chronic HBV infection offset by an increase in the probability of success of 2158 and 3733 based on their advancement into Phase 2 and Phase 1 trials during 2020, respectively and the significance of the future net cash flows from potential drug sales for a finite and curative therapy for chronic HBV infection as primarily driven by the number of patients who will be diagnosed and treated and the Company’s competitive position in the marketplace. The Company did not recognize any IPR&D impairment in any of the periods presented . Leases All of the Company’s leases are operating leases for facilities and equipment. Prior to January 1, 2019, the Company recognized related rent expense on a straight-line basis over the term of the lease. Incentives granted under the Company’s facilities lease, including allowances for leasehold improvements and rent holidays, were recognized as reductions to rental expense on a straight-line basis over the term of the lease. Deferred rent consisted of the difference between cash payments and the rent expense recognized. Subsequent to the adoption of the new leasing standard on January 1, 2019, the Company recognizes a lease asset for its right to use the underlying asset and a lease liability for the corresponding lease obligation. The Company determines whether an arrangement is or contains a lease at contract inception. Operating leases with a duration greater than one year are included in operating lease right-of-use assets, operating lease liabilities - short-term, and operating lease liabilities - long-term in the Company’s consolidated balance sheets. Operating lease right-of-use assets and liabilities are recognized at the lease commencement date based on the present value of lease payments over the lease term. In determining the net present value of lease payments, the Company uses its incremental borrowing F-14 rate based on the information available at the lease commencement date. The incremental borrowing rate represents the interest rate the Company would incur at lease commencement to borrow an amount equal to the lease payments on a collateralized basis over the term of a lease. The Company considers a lease term to be the noncancelable period that it has the right to use the underlying asset, including any periods where it is reasonably assured the Company will exercise the option to extend the contract. Periods covered by an option to extend are included in the lease term if the lessor controls the exercise of that option. The operating lease right-of-use assets also include any lease payments made and exclude lease incentives. Lease expense is recognized on a straight-line basis over the expected lease term. Variable lease expenses are recorded when incurred. The Company has elected not to separate lease and non-lease components for its leased assets and accounts for all lease and non-lease components of its agreements as a single lease component. Impairment of Long-Lived Assets The Company monitors the carrying value of long-lived assets, including ROU operating lease assets, for potential impairment and tests the recoverability of such assets whenever events or changes in circumstances indicate that the carrying amounts may not be recoverable. If a change in circumstance occurs, the Company performs a test of recoverability by comparing the carrying value of the asset or asset group to its undiscounted expected future cash flows. If cash flows cannot be separately and independently identified for a single asset, the Company will determine whether impairment has occurred for the group of assets for which the Company can identify the projected cash flows. If the carrying values are in excess of undiscounted expected future cash flows, the Company measures any impairment by comparing the fair value of the asset or asset group to its carrying value. In conjunction with the decision to wind down the Microbiome program in December 2020, the Company evaluated its ROU assets and property and equipment used in the Microbiome program for impairment. The Company determined the carrying value was no longer recoverable and, based on a fair value of the assets determined from market quotes, recorded an impairment loss of $ 0.7 million included in research and development expenses. The Company did no t recognize any impairment on its long-lived assets in 2019 or 2018. Property and Equipment, Net Property and equipment are stated at cost and consist of lab and office equipment, leasehold improvements and computer hardware and software. The Company records depreciation under the straight-line method over the estimated useful lives of its property and equipment ranging from three to seven years . Leasehold improvements are amortized over the remaining terms of the respective leases or the estimated useful life of the leasehold improvements, whichever is less. Maintenance and repair costs are expensed as incurred. Fair Value Measurements The Company follows accounting guidance on fair value measurements for financial instruments measured on a recurring basis, as well as for certain assets and liabilities that are initially recorded at their estimated fair values. Fair value is defined as the exit price, or the amount that would be received from selling an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. The Company uses the following three-level hierarchy that maximizes the use of observable inputs and minimizes the use of unobservable inputs to value its financial instruments: Level 1: Observable inputs such as unadjusted quoted prices in active markets for identical instruments. Level 2: Quoted prices for similar instruments that are directly or indirectly observable in the marketplace. Level 3: Significant unobservable inputs which are supported by little or no market activity and that are financial instruments whose values are determined using pricing models, discounted cash flow methodologies, or similar techniques, as well as instruments for which the determination of fair value requires significant judgment or estimation. Financial instruments measured at fair value are classified in their entirety based on the lowest level of input that is significant to the fair value measurement. The assessment of the significance of a particular input to the fair value measurement in its entirety requires us to make judgments and consider factors specific to the asset or liability. The use of different assumptions and/or estimation methodologies may have a material effect on estimated fair values. Accordingly, the fair value estimates disclosed or initial amounts recorded may not be indicative of the amount that the Company or holders of the instruments could realize in a current market exchange. F-15 The carrying amounts of cash equivalents and marketable securities approximate their fair value based upon quoted market prices. Certain of the Company’s financial instruments are not measured at fair value on a recurring basis, but are recorded at amounts that approximate their fair value due to their liquid or short-term nature, such as cash, accounts receivable, accounts payable and accrued expenses. The following tables present the fair value of the Company’s financial assets measured at fair value on a recurring basis using the above input categories (in thousands): December 31, 2020 Level 1 Level 2 Level 3 Estimated Fair Value Cash equivalents Money market funds $ 47,553 $ — $ — $ 47,553 U.S. and foreign commercial paper — 6,498 — 6,498 Total cash equivalents 47,553 6,498 — 54,051 Short-term investments U.S. and foreign corporate debt securities — 16,939 — 16,939 Asset-backed securities — 12,675 — 12,675 U.S. treasury securities — 23,999 — 23,999 U.S. and foreign commercial paper — 103,356 — 103,356 Total short-term investments — 156,969 — 156,969 Total assets measured at fair value $ 47,553 $ 163,467 $ — $ 211,020 December 31, 2019 Level 1 Level 2 Level 3 Estimated Fair Value Cash equivalents Money market fund $ 33,095 $ — $ — $ 33,095 U.S. and foreign corporate debt securities — 4,999 — 4,999 U.S. and foreign commercial paper — 4,484 — 4,484 Total cash equivalents 33,095 9,483 — 42,578 Short-term investments U.S. and foreign corporate debt securities — 72,486 — 72,486 Asset-backed securities — 34,025 — 34,025 U.S. treasury securities — 44,714 — 44,714 U.S. and foreign commercial paper — 76,086 — 76,086 Total short-term investments — 227,311 — 227,311 Total assets measured at fair value $ 33,095 $ 236,794 $ — $ 269,889 Money market funds are highly liquid and actively traded marketable securities that generally transact at a stable $1.00 net asset value representing its estimated fair value. The Company estimates the fair value of its U.S. and foreign corporate debt securities, asset backed securities, U.S. treasury securities and U.S. and foreign commercial paper by taking into consideration valuations obtained from third-party pricing services. The pricing services utilize industry standard valuation models, including both income and market-based approaches, for which all significant inputs are observable, either directly or indirectly, to estimate fair value. These inputs include reported trades of and broker/dealer quotes on the same or similar securities, issuer credit spreads; benchmark securities; prepayment/default projections based on historical data; and other observable inputs. There have been no transfers between Level 1, Level 2 or Level 3 for any of the periods presented. See Note 3 for further information regarding the carrying value of our investments in marketable securities. F-16 Revenue Recognition and Accounts Receivable from Collaborations The Company analyzes its collaboration arrangements to assess whether such arrangements, or transactions between arrangement participants, involve joint operating activities performed by parties that are both active participants in the activities and exposed to significant risks and rewards dependent on the commercial success of such activities or are more akin to a vendor-customer relationship. In making this evaluation, the Company considers whether the activities of the collaboration are considered to be distinct and deemed to be within the scope of the collaborative arrangement accounting standard and those that are more reflective of a vendor-customer relationship and, therefore, within the scope of the revenue with contracts with customers accounting standard. This assessment is performed throughout the life of the arrangement based on changes in the responsibilities of all parties in the arrangement. For elements of collaboration arrangements that are not accounted for pursuant to the revenue from contracts with customers accounting standard, an appropriate recognition method is determined and applied consistently, generally by analogy to the revenue from contracts with customers accounting standard. Amounts related to transactions with a counterparty in a collaborative arrangement that is not a customer are presented as collaboration revenue and on a separate line item from revenue recognized from contracts with customers, if any, in the Company’s consolidated statements of operations and comprehensive loss. Under certain collaborative arrangements, the Company has been reimbursed for a portion of its research and development expenses or participates in the cost-sharing of such research and development expenses. Such reimbursements and cost-sharing arrangements are reflected as a reduction of research and development expense in the Company’s consolidated statements of operations and comprehensive loss, as the Company does not consider performing these activities for reimbursement to be a part of its ongoing major or central operations. For arrangements or transactions between arrangement participants determined to be within the scope of the contracts with customers accounting standard, the Company evaluates the term of the arrangement and recognizes revenue when the customer obtains control of promised goods or services in a contract for an amount that reflects the consideration the Company expects to receive in exchange for those goods or services. For contracts with customers, the Company applies the following five-step model in order to determine this amount: (1) identification of the promised goods or services in the contract; (2) determination of whether the promised goods or services are performance obligations, including whether they are distinct in the context of the contract; (3) measurement of the transaction price, including the constraint on variable consideration; (4) allocation of the transaction price to the performance obligations; and (5) recognition of revenue when (or as) the Company satisfies each performance obligation. The Company has provided standard indemnification and protection of licensed intellectual property for its customer. These provisions are part of assurance that the licenses meet the agreements, representations and are not obligations to provide goods or services. The Company only applies the five-step model to contracts when it is probable the Company will collect the consideration it is entitled to in exchange for the goods or services it transfers to the customer. As part of the accounting for contracts with customers, the Company must develop assumptions that require judgment to determine the standalone selling price of each performance obligation identified in the contract. The Company then allocates the total transaction price to each performance obligation based on the estimated standalone selling prices of each performance obligation. The Company recognizes the amount of the transaction price that is allocated to the respective performance obligation when the performance obligation is satisfied or as it is satisfied as revenue. Upfront License Fees If a license to the Company’s intellectual property is determined to be distinct from the other performance obligations identified in the arrangement, the Company recognizes revenues from nonrefundable, upfront license fees based on the relative value prescribed to the license compared to the total value of the arrangement. The revenue is recognized when the license is transferred to the collaborator and the collaborator is able to use and benefit from the license. For licenses that are not distinct from other obligations identified in the arrangement, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time. If the combined performance obligation is satisfied over time, the Company applies an appropriate method of measuring progress for purposes of recognizing revenue from nonrefundable, upfront license fees. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. F-17 Development and Regulatory Milestone Payments Depending on facts and circumstances, the Company may record revenues from certain milestones in a reporting period before the milestone is achieved if the Company concludes achievement of the milestone is probable and recognition of revenue related to the milestone will not result in a significant reversal in amounts recognized in future periods. The Company records a corresponding contract asset when this conclusion is reached. Milestone payments that have not been included in the transaction price to date are fully constrained. The Company re-evaluates the probability of achievement of such milestones and any related constraint each reporting period. The Company adjusts its estimate of the overall transaction price, including the amount of collaborative revenue that was recorded, if necessary. Research and Development Service Payments Under the Research, Development, Collaboration and License Agreement (Allergan Agreement) with Allergan Pharmaecuticals International Limited (Allergan), the Company was reimbursed at a certain percentage for performing research and development services based on hours worked by the Company’s employees, at a fixed contractual rate per hour, and third-party pass-through costs the Company incurred on a quarterly basis. Research and development service payments were included in the transaction price in the reporting period the Company concluded it was probable that recording revenue in the period would not result in a significant reversal in amounts recognized in future periods. Accounts receivable were recorded when the right to the research and development service payment consideration became unconditional. The Company recorded the full reimbursed portion of these expenses as collaboration revenue associated with the Allergan Agreement in its consolidated statements of operations as the Company consider performing research and development services to be a part of its ongoing and central operations. Sales-based Milestone and Royalty Payments The Company’s customer may be required to pay the Company sales-based milestone payments or royalties on future sales of commercial products. The Company recognizes revenues related to sales-based milestone and royalty payments upon the later to occur of (i) achievement of the collaborator’s underlying sales or (ii) satisfaction of any performance obligation(s) related to these sales, in each case assuming the Company’s licensed intellectual property is deemed to be the predominant item to which the sales-based milestones and/or royalties relate. The Company receives payments from its customer based on billing schedules established in each contract. Upfront payments and fees are recorded as deferred revenue upon receipt or when due until the Company performs its obligations under the arrangement. If the related performance obligation is expected to be satisfied within the next twelve months, these amounts will be classified in current liabilities. The Company recognizes a contract asset relating to its conditional right to consideration that is not subject to a constraint. Amounts are recorded as accounts receivable when the Company’s right to consideration is unconditional. A net contract asset or liability is presented for each contract with a customer. The Company does not assess whether a contract has a significant financing component if the expectation at contract inception is such that the period between payment by the customer and the transfer of the promised goods or services to the customer will be one year or less. At December 31, 2020 and 2019, all accounts receivable are deemed collectible. Stock-Based Compensation The Company measures stock-based compensation to employees, consultants, and Board members at fair value on the grant date of the award. The fair value of RSUs is determined based on the number of shares granted and the quoted market price of the Company’s common stock on the date of grant. Compensation cost is recognized as expense on a straight-line basis over the requisite service period of the award. Stock-based awards with graded vesting schedules are recognized using the accelerated attribution method on a straight-line basis over the requisite service period for each separately vesting portion of the award. For awards that have a performance condition, compensation cost is measured based on the fair value of the award on the grant date, the date performance targets are established, and is expensed over the requisite service period for each separately vesting tranche when achievement of the performance condition becomes probable. The Company assesses the probability of the performance conditions being met on a continuous basis. Forfeitures are recognized when they occur. F-18 The Company estimates the fair value of stock option grants that do not contain market-based vesting conditions using the Black-Scholes option pricing model . T he assumptions used in estimating the fair value of these awards, such as expected term, expected dividend yield , volatility and risk-free interest rate, represent management’s best estimates and involve inherent uncertainties and the application of management’s judgment. The Company is also required to make estimates as to the probability of achieving the specific performance conditions. If actual results are not consistent with the Company’s assumptions and judgments used in making these estimates, the Company may be required to increase or decrease compensation expense, which could be material to the Company’s consolidated results of operations. Prior to January 1, 2019, the Company remeasured the fair value of the non-employee awards at each reporting period prior to vesting and finally at the vesting date of the award. Changes in the estimated fair value of these non-employee awards were recognized as compensation expense in the period of change. After January 1, 2019, the Company recognizes non-employee compensation costs over the requisite service period based on a measurement of fair value for each stock award. Research and Development Expense and Accruals Research and development costs include personnel-related costs, outside contracted services including clinical study costs, facilities costs, fees paid to consultants, milestone payments prior to FDA approval, license fees prior to FDA approval, professional services, travel costs, dues and subscriptions, depreciation and materials used in clinical trials and research and development and costs incurred under the Collaboration Agreement. Research and development costs are expensed as incurred unless there is an alternative future use in other research and development projects. Payments made prior to the receipt of goods or services to be used in research and development are capitalized until the goods or services are received. Such payments are evaluated for current or long-term classification based on when they will be realized or consumed. Assets acquired as part of an asset acquisition that are used in research and development or are IPR&D are immediately expensed as research and development unless there is an alternative future use in other research and development projects. The Company records expenses related to clinical studies and manufacturing development activities based on its estimates of the services received and efforts expended pursuant to contracts with multiple contract research organizations (CROs) and manufacturing vendors that conduct and manage these activities on its behalf. The financial terms of these agreements are subject to negotiation, vary from contract to contract, and may result in uneven payment flows. There may be instances in which payments made to the Company’s vendors will exceed the level of services provided and result in a prepayment of the expense. Payments under some of these contracts depend on factors such as the successful enrollment of subjects and the completion of clinical study milestones. In amortizing or accruing service fees, the Company estimates the time period over which services will be performed, enrollment of subjects, number of sites activated and the level of effort to be expended in each period. If the actual timing of the performance of services or the level of effort varies from the Company’s estimate, the Company will adjust the accrued or prepaid expense balance accordingly. To date, there have been no material differences from the Company’s estimates to the amounts actually incurred. The Company has entered and may continue to enter into license agreements to access and utilize certain technology. In each case, the Company evaluates if the license agreement results in the acquisition of an asset or a business. To date, none of the Company’s license agreements have been considered to be acquisitions of businesses. For asset acquisitions, the upfront payments to acquire such licenses, as well as any future milestone payments, are immediately recognized as research and development expense when paid, provided there is no alternative future use of the rights in other research and development projects. These license agreements may also include contingent consideration in the form of cash payments to be made for future milestone events. The Company assesses whether such contingent consideration meets the definition of a derivative and to date the Company has determined that such contingent consideration are not derivatives. Restructuring Charges The Company recognizes restructuring charges related to reorganization plans that have been committed to by management and when liabilities have been incurred. In connection with these activities, the Company records restructuring charges at fair value for (1) contractual employee termination benefits when obligations are associated to services already rendered, rights to such benefits have vested, and payment of benefits is probable and can be reasonably estimated, (2) one-time employee termination benefits when management has committed to a plan of termination, the plan identifies the employees and their expected termination dates, the details of termination benefits are complete, it is unlikely changes to the plan will be made or the plan will be withdrawn and communication to such employees has occurred, and (3) contract termination costs when a contract is terminated before the end of its term. F-19 One-time employee termination benefits are recognized in their entirety when communication has occurred, and future services are not required. If future services are required, the costs are recorded ratably over the remaining period of service. Contract termination costs to be incurred over the remaining contract term without economic benefit are recorded in their entirety when the contract is canceled. The recognition of restructuring charges requires the Company to make certain judgments and estimates regarding the nature, timing and amount of costs associated with the planned reorganization plan. To the extent the Company’s actual results differ from its estimates and assumptions, the Company may be required to revise the estimates of future accrued restructuring liabilities, requiring the recognition of additional restructuring charges or the reduction of accrued restructuring liabilities already recognized. Such changes to previously estimated amounts may be material to the consolidated financial statements. Changes in the estimates of the restructuring charges are recorded in the period the change is determined. At the end of each reporting period, the Company evaluates the remaining accrued restructuring balances to ensure that no excess accruals are retained, and the utilization of t he provisions are for their intended purpose in accordance with developed restructuring plans. Variable Interest Entities The Company reviews agreements it enters into with third party entities, pursuant to which we may have a variable interest in the entity, in order to determine if the entity is a variable interest entity (VIE). If the entity is a VIE, the Company assesses whether or not it is the primary beneficiary of that entity. In determining whether the Company is the primary beneficiary of an entity, the Company applies a qualitative approach that determines whether it has both (1) the power to direct the economically significant activities of the entity and (2) the obligation to absorb losses of, or the right receive benefits from, the entity that could potentially be significant to that entity. If the Company were to determine it is the primary beneficiary of a VIE, the Company would consolidate the statements of operations and financial condition of the VIE into its consolidated financial statements. The Company’s determination about whether it should consolidate such VIEs is made continuously as changes to existing relationships or future transactions may result in a consolidation event. As of December 31, 2020, the Company did not consolidate any entities it had determined to be VIEs. Income Taxes The Company records income taxes using the asset and liability method. Deferred income tax assets and liabilities are recognized for the future tax effects attributable to temporary differences between the financial statement carrying amounts of existing assets and liabilities and their respective income tax bases, and operating loss and tax credit carryforwards. The effect of a change in tax rates on deferred tax assets and liabilities is recognized in income in the period that includes the enactment date. The Company establishes a valuation allowance if it is more likely than not that the deferred tax assets will not be realized based on an evaluation of objective verifiable evidence. For tax positions that are more likely than not of being sustained upon audit, the Company recognizes the largest amount of the benefit that is greater than 50% likely of being realized. For tax positions that are not more likely than not of being sustained upon audit, the Company does not recognize any portion of the benefit. The Company recognizes and measures uncertain tax positions using a two-step approach set forth in authoritative guidance. The first step is to evaluate the tax position taken or expected to be taken by determining whether the weight of available evidence indicates that it is more likely than not that the tax position will be sustained in an audit, including resolution of any related appeals or litigation processes. The second step is to measure the tax benefit as the largest amount that is more than 50% likely to be realized upon ultimate settlement. Significant judgment is required to evaluate uncertain tax positions. The Company evaluates uncertain tax positions on a regular basis. The evaluations are based on a number of factors, including changes in facts and circumstances, changes in tax law, correspondence with tax authorities during the course of the audit, and effective settlement of audit issues. The provision for income taxes includes the effects of any accruals that the Company believes are appropriate. It is the Company’s policy to recognize interest and penalties related to income tax matters in income tax expense. No interest or penalties related to uncertain tax positions has been incurred or accrued for any periods presented. F-20 In March 2020, the Families First Coronavirus Response Act (FFCR Act) and the Coronavirus Aid, Relief, and Economic Security Act (CARES Act) were each enacted in response to the COVID-19 pandemic. The FFCR Act and the CARES Act contain numerous income tax provisions relating to refundable payroll tax credits, deferment of employer side social security payments, net operating loss carryback periods, alternative minimum tax credit refunds, modifications to the net interest deduction limitations and technical corrections to tax depreciation methods for qualified improvement property. In June 2020, Assembly Bill 85 (A.B. 85) was signed into California law. A.B. 85 provides for a three-year suspension of the use of net operating losses for medium and large businesses and a three-year cap on the use of business incentive tax credits to offset no more than $5.0 million of tax per year. A.B. 85 suspends the use of net operating losses for taxable years 2020, 2021 and 2022 for certain taxpayers with taxable income of $1.0 million or more. The carryover period for any net operating losses that are suspended under this provision will be extended. A.B. 85 also requires that business incentive tax credits including carryovers may not reduce the applicable tax by more than $5.0 million for taxable years 2020, 2021 and 2022. In December 2020, the Consolidated Appropriations Act, 2021 (CAA) was signed into law. The CAA included additional funding through tax credits as part of its economic package for 2021. The FFCR Act, CARES Act, A.B. 85 did and CAA not have a material impact on the Company’s consolidated financial statements; however, the Company continues to examine the impacts the FFCR Act, CARES Act, A.B. 85 and CAA may have on its business, results of operations, financial condition and liquidity. Net Loss per Share Basic net loss per common share excludes dilution and is computed by dividing net loss by the weighted average number of common shares outstanding during the period. Diluted net loss per common share reflects the potential dilution that could occur if securities or other contracts to issue common stock were exercised or converted into common stock or resulted in the issuance of common stock that then shared in the earnings of the entity unless inclusion of such shares would be anti-dilutive. Since the Company has only incurred losses, basic and diluted net loss per share is the same. In December 2019, the Company sold 6,287,878 shares of common stock as well as pre-funded warrants to purchase up to 2,424,242 shares of common stock (see Note 7). The pre-funded warrants are exercisable for shares of common stock at a price of $ 0.001 per share. The shares of common stock into which the pre-funded warrants may be exercised are considered outstanding for the purposes of computing earnings per share because the shares may be issued for little or no consideration, they are fully vested, and are exercisable after the original issuance date. Securities excluded from the computation of diluted loss from per share because including them would have been antidilutive are as follows: Year Ended December 31, 2020 2019 2018 Warrants to purchase common stock — 15,296 15,296 Options to purchase common stock 6,696,592 5,613,353 4,637,145 Common stock subject to purchase under our ESPP 44,223 11,342 21,483 Unvested RSUs 746,868 630,384 568,005 Total 7,487,683 6,270,375 5,241,929 Comprehensive Loss Comprehensive loss is comprised of net loss and adjustments for the change in unrealized gains and losses on investments in available-for-sale marketable securities. The Company displays comprehensive loss and its components in the consolidated statements of operations and comprehensive loss, net of tax effects if any. F-21 Concentrations of Risk Credit Risk Financial instruments which potentially subject the Company to credit risk consist primarily of cash, cash equivalents and marketable securities. The Company holds these investments in highly rated financial institutions, and, by policy, limits the amounts of credit exposure to any one financial institution. These amounts at times may exceed federally insured limits. The Company has not experienced any credit losses in such accounts and does not believe it is exposed to any significant credit risk on these funds. The Company has no off-balance sheet concentrations of credit risk, such as foreign currency exchange contracts, option contracts or other hedging arrangements. Supplier Risk Certain materials and key components the Company utilizes in its operations are obtained through single suppliers. Since the suppliers of key components and materials must be named in a New Drug Application (NDA) filed with the FDA for a product , significant delays can occur if the qualification of a new supplier is required. If delivery of material from the Company’s suppliers were interrupted for any reason, the Company may be unable to supply any of its product candidates for clinical trials. Adoption of Recent Accounting Pronouncements In January 2017, the Financial Accounting Standards Board (FASB) issued ASU 2017-04, Intangibles-Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment (ASU 2017-04), which simplifies how an entity is required to test goodwill for impairment by eliminating Step 2 from the goodwill impairment test. Step 2 measures a goodwill impairment loss by comparing the implied fair value of a reporting unit's goodwill with the carrying amount of that goodwill. Under the amendments in ASU 2017-04, an entity should recognize an impairment charge for the amount by which the carrying amount of a reporting unit exceeds its fair value; however, the loss recognized should not exceed the total amount of goodwill allocated to that reporting unit. The updated accounting standard requires a prospective adoption. In November 2019, the FASB issued ASU 2019-10, Financial Instruments – Credit Losses (Topic 326), Derivatives and Hedging (Topic 815), and Leases (Topic 842): Effective Dates (ASU 2019-10), which deferred the effective date of this standard for all entities except SEC filers that are not smaller reporting companies to fiscal years beginning after December 15, 2022, including interim periods within those fiscal years. Early adoption is permitted for goodwill impairment tests performed on testing dates after January 1, 2017. The Company early adopted ASU 2017-04 effective January 1, 2020 . The adoption of this standard had no material impact on the Company’s consolidated financial statements. On January 1, 2020 , the Company adopted ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework - Changes to the Disclosure Requirements for Fair Value Measurement, which makes a number of changes meant to add, modify or remove certain disclosure requirements associated with the movement amongst or hierarchy associated with Level 1, Level 2 and Level 3 fair value measurements. The adoption of this standard had no material impact on the Company’s consolidated financial statements and related disclosures. On January 1, 2020 , the Company adopted ASU 2018-18, Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606 , which clarifies that certain transactions between collaborative arrangement participants should be accounted for as revenue under Topic 606 when the collaborative arrangement participant is a customer in the context of a unit of account. In those situations, all the guidance in Topic 606 should be applied, including recognition, measurement, presentation, and disclosure requirements. The standard adds unit-of-account guidance in Topic 808 to align with the guidance in Topic 606 (that is, a distinct good or service) when an entity is assessing whether the collaborative arrangement or a part of the arrangement is within the scope of Topic 606 and requires that in a transaction with a collaborative arrangement participant that is not directly related to sales to third parties, presenting the transaction together with revenue recognized under Topic 606 is precluded if the collaborative arrangement participant is not a customer. Amendments in the standard should be applied retrospectively to the date of initial application of Topic 606, but entities may elect to apply the amendments in Topic 808 retrospectively either to all contracts or only to contracts that are not completed at the date of initial application of Topic 606, and should disclose the election. An entity may also elect to apply the practical expedient for contract modifications that is permitted for entities using the modified retrospective transition method in Topic 606. The adoption of this standard had no impact on the Company’s consolidated financial statements and related disclosures. F-22 In December 2019, the FASB issued ASU No. 2019-12, Simplifying the Accounting for Income Taxes (ASU 2019-12), which eliminates certain exceptions to the guidance in Income Taxes (Topic 740) related to the approach for intraperiod tax allocation, the methodology for calculating income taxes in an interim period and the recognition of deferred tax liabilities for outside basis differences. The new accounting standard also simplifies aspects of the accounting for franchise taxes and enacted changes in tax laws or rates and clarifies the accounting for transactions that result in a step-up in the tax basis of goodwill. The standard is effective for fiscal years beginning after December 15, 2020 and interim periods within those fiscal years. Early adoption is permitted in an interim or annual period. Entities that elect to early adopt the amendments in an interim period should reflect any adjustments as of the beginning of the annual period that includes that interim period. Additionally, entities that elect early adoption must adopt all the amendments in the same period. Entities will apply the accounting standard prospectively, except for certain amendments. The Company early adopted ASU 2019-12 effective January 1, 2020 . The adoption of this standard did not have a material impact on the Company’s consolidated financial statements and related disclosures. Accounting Pronouncements to Be Adopted In June 2016, the FASB issued ASU 2016-13, Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments (ASU 2016-13), which requires that expected credit losses relating to financial assets measured on an amortized cost basis and available-for-sale debt securities be recorded through an allowance for credit losses. ASU 2016-13 limits the amount of credit losses to be recognized for available-for-sale debt securities to the amount by which carrying value exceeds fair value and also requires the reversal of previously recognized credit losses if fair value increases. In April, May and November 2019, the FASB issued additional amendments to the new accounting standard related to transition and clarification. In November 2019, the FASB issued ASU 2019-10, Financial Instruments—Credit Losses (Topic 326), Derivatives and Hedging (Topic 815), and Leases (Topic 842): Effective Dates (ASU 2019-10), which deferred the effective date of this standard for all entities except SEC filers that are not smaller reporting companies to fiscal years beginning after December 15, 2022, including interim periods within those fiscal years. Early adoption is permitted. The Company is currently evaluating the timing and impact of adopting this new accounting standard on its consolidated financial statements and related disclosures. In August 2020, the FASB issued ASU 2020-06, Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity (ASU 2020-06), which simplifies the accounting for certain financial instruments with characteristics of liabilities and equity, including convertible instruments and contracts on an entity’s own equity. Specifically, ASU 2020-06 simplifies accounting for convertible instruments by removing major separation models in ASC 470-20 that require separate accounting for embedded conversion features. The ASU also removes certain settlement conditions in ASC 815-40 that are required for equity contracts to qualify for the derivative scope exception, which will permit more equity contracts to qualify for the scope exception and simplifies the diluted EPS calculation in certain areas. The ASU is effective for interim and annual periods beginning after December 15, 2021, with early adoption permitted after December 15, 2020. Adoption of the ASU can either be on a modified retrospective or full retrospective basis. The Company is currently evaluating the impacts of ASU 2020-06 on its consolidated financial statements and related disclosures. In October 2020, the FASB issued ASU 2020-10, Codification Improvements – Disclosures. This ASU improves consistency by amending the codification to include all disclosure guidance in the appropriate disclosure sections and clarifies application of various provisions in the Codification by amending and adding new headings, cross referencing to other accounting standards, and refining or correcting termination. This ASU is effective for fiscal years beginning after December 15, 2020. The adoption of the ASU will not impact the Company’s consolidated financial statements or related disclosures. F-23 Note 3 - Investments in Marketable Securities Investments in marketable available-for-sale securities consisted of the following (in thousands): December 31, 2020 Amortized Cost Gross Unrealized Gain (1) Gross Unrealized Loss (1) Estimated Fair Value Cash equivalents Money market funds $ 47,553 $ — $ — $ 47,553 U.S. and foreign commercial paper 6,498 — — 6,498 Total cash equivalents 54,051 — — 54,051 Short-term investments U.S. and foreign corporate debt securities 16,939 3 ( 3 ) 16,939 Asset-backed securities 12,674 2 ( 1 ) 12,675 U.S. treasury securities 23,997 2 — 23,999 U.S. and foreign commercial paper 103,356 — — 103,356 Total short-term investments 156,966 7 ( 4 ) 156,969 Total cash equivalents and investments $ 211,017 $ 7 $ ( 4 ) $ 211,020 December 31, 2019 Amortized Cost Gross Unrealized Gain (1) Gross Unrealized Loss (1) Estimated Fair Value Cash equivalents Money market funds $ 33,095 $ — $ — $ 33,095 U.S. and foreign corporate debt securities 5,000 — ( 1 ) 4,999 U.S. and foreign commercial paper 4,484 — — 4,484 Total cash equivalents 42,579 — ( 1 ) 42,578 Short-term investments U.S. and foreign corporate debt securities 72,452 38 ( 4 ) 72,486 Asset-backed securities 34,008 17 — 34,025 U.S. treasury securities 44,692 24 ( 2 ) 44,714 U.S. and foreign commercial paper 76,086 — — 76,086 Total short-term investments 227,238 79 ( 6 ) 227,311 Total cash equivalents and investments $ 269,817 $ 79 $ ( 7 ) $ 269,889 (1) Gross unrealized gain (loss) is pre-tax. As of December 31, 2020, the contractual term to maturity of short-term marketable securities held by the Company is less than one year . There were no long-term marketable securities held by the Company as of December 31, 2020. Realized gains and losses for the years ended December 31, 2020, 2019 and 2018 were not significant. None of the Company’s investments have been in a continuous unrealized loss position for more than 12 months as of December 31, 2020. See Note 2 for further information regarding the fair value of our investments in marketable securities. F-24 Note 4 - Property and Equipment, Net Property and equipment consist of the following (in thousands): As of December 31, 2020 2019 Lab equipment $ 247 $ 247 Office equipment 699 699 Leasehold improvement 2,490 2,084 Total property and equipment 3,436 3,030 Less: Accumulated depreciation ( 1,836 ) ( 1,200 ) Property and equipment, net $ 1,600 $ 1,830 Depreciation expense for the years ended December 31, 2020, 2019 and 2018 was $ 0.7 million, $ 0.5 million, and $ 0.6 million, respectively, and was recorded in both research and development expense and general and administrative expense in the consolidated statements of operations and comprehensive loss. Primarily all of property and equipment is located in the U.S. Note 5 – Other Accrued Expenses Other accrued expenses consist of the following (in thousands): As of December 31, 2020 2019 Other accrued expenses: Accrued compensation $ 7,016 $ 5,312 Accrued restructuring charges 4,164 2,094 Accrued professional fees and other 807 880 Total other accrued expenses $ 11,987 $ 8,286 Note 6 – Restructurings 2019 Restructuring In November 2019, the Company’s Board of Directors approved the relocation of the Company corporate headquarters to South San Francisco, California which became effective January 1, 2020. The Company accrued restructuring charges of $ 2.1 million in 2019 related to one-time termination severance payments and other employee-related costs associated with the relocation plan. This represents the total amount expected to be incurred in connection with the relocation. 2020 Restructuring In December 2020, the Company and its Board of Directors determined that it was in the Company’s best interest to wind down its Microbiome program, enabling the Company to prioritize resources and focus on the advancement of its pipeline of novel core inhibitors for chronic HBV infection. The Company expects to complete the wind-down of the Microbiome program in early 2021. F-25 The following table summarizes the Company’s estimates of costs incurred and expected to be incurred (in thousands): Total Restructuring Cost Employee Severance and Related Benefits Asset Impairment and Other Costs Total estimated restructuring costs to be incurred $ 8,040 $ 6,461 $ 1,579 Restructuring costs incurred during the period: Total restructuring costs incurred for the year ended December 31, 2019 2,094 2,094 — Total restructuring costs incurred for the year ended December 31, 2020 5,684 4,105 1,579 Cumulative restructuring costs incurred through December 31, 2020 $ 7,778 $ 6,199 $ 1,579 The following table presents the activity in the accrued restructuring charges during the period, all of which are related to employee severance and related benefits (in thousands): Accrued balance as of January 1, 2019 $ — Costs incurred 2,094 Accrued balance as of December 31, 2019 $ 2,094 Costs incurred 3,843 Reductions for cash payments ( 1,773 ) Accrued balance as of December 31, 2020 $ 4,164 The Company also recognized $ 0.3 million of accelerated vesting for stock-based compensation for employees subject to the restructuring activities during 2020. The Company expects the accrued restructuring liability to be fully paid in 2021 . The following table presents where the restructuring charges were recognized (in thousands): Year Ended December 31, 2020 2019 Research and development $ 5,486 $ 433 General and administrative 198 1,661 Total $ 5,684 $ 2,094 Note 7 - Stockholders’ Equity The Company is authorized to issue 5,000,000 shares of preferred stock as of December 31, 2020 and 2019, respectively. As of December 31, 2020 and 2019, no shares of preferred stock were issued and outstanding. The Company is authorized to issue 100,000,000 shares of common stock as of December 31, 2020 and 2019, respectively. Sale of Common Stock and Pre-Funded Warrants In December 2017, the Company filed a registration statement on Form S-3 with the SEC, File No. 333-222366, that became effective January 10, 2018 (the 2018 Registration Statement). The 2018 Registration Statement gave the Company the ability to sell any combination of the securities described in the 2018 Registration Statement in one or more offerings up to an aggregate offering price of $ 250.0 million. In connection with the filing of the 2018 Registration Statement, the Company entered into a sales agreement that gave the Company the ability to sell shares of its common stock having an aggregate offering price of up to $ 75.0 million through “at the market offerings” (the 2017 ATM). The 2017 ATM was terminated effective September 6, 2020, and no shares were sold under the 2017 ATM prior to the termination. F-26 In July 2018, the Company sold to various investors an aggregate of 4,600,000 shares of common stock in a public offering at $ 36.00 per share, which included the exercise in full by the underwriters of their option to purchase 600,000 additional shares of common stock. The Company received aggregate net proceeds of $ 155.4 million from the offering and the option exercise, after deducting underwriting discounts and commissions and offering expenses payable by the Company. In December 2019, the Company sold to various investors an aggregate of 6,287,878 shares of common stock at a public offering price of $ 16.50 per share, which included the exercise in full by the underwriters of their option to purchase 1,136,363 shares of common stock, and pre-funded warrants to purchase 2,424,242 shares of common stock at a public offering price of $ 16.499 . The Company received aggregate net proceeds of $ 134.7 million from the offering and the option exercise, after deducting underwriting discounts and commissions and offering expenses payable by the Company. The pre-funded warrants became immediately exercisable upon issuance at an exercise price of $ 0.001 per share, but under their terms, the outstanding pre-funded warrants to purchase shares of the Company’s common stock generally may not be exercised if the holder’s ownership of the Company’s common stock would exceed 19.99 % following such exercise. The exercise price and number of shares of common stock issuable upon the exercise of the pre-funded warrants (Warrant Shares) are subject to adjustment in the event of any stock dividends and splits, reverse stock split, recapitalization, reorganization or similar transaction, as described in the pre-funded warrant agreements. Under certain circumstances, the pre-funded warrants may be exercisable on a “cashless” basis. Both the pre-funded warrants and the Warrant Shares are registered securities. The pre-funded warrants were classified as a component of permanent stockholders’ equity within additional paid-in-capital and were recorded at the issuance date using a relative fair value allocation method. The pre-funded warrants are equity classified because they are freestanding financial instruments that are legally detachable and separately exercisable from the equity instruments, are immediately exercisable, do not embody an obligation for the Company to repurchase its shares, permit the holders to receive a fixed number of common shares upon exercise, are indexed to the Company’s common stock and meet the equity classification criteria. In addition, such pre-funded warrants do not provide any guarantee of value or return. The Company valued the pre-funded warrants at issuance, concluding their sales price approximated their fair value, and allocated net proceeds from the sale proportionately to the common stock and pre-funded warrants of which $ 37.5 million allocated to the pre-funded warrants and recorded as a component of additional paid-in-capital. In August 2020, the Company filed a shelf registration statement on Form S-3 with the SEC, File No. 333-248469, that became effective on September 4, 2020 (the 2020 Registration Statement). The Company may from time to time sell any combination of the securities described in the 2020 Registration Statement in one or more offerings up to an aggregate offering price of $ 300.0 million. In connection with the filing of the 2020 Registration Statement, the Company entered into a sales agreement under which the Company may offer and sell shares of its common stock having an aggregate offering price of up to $ 100.0 million through “at-the-market” offerings (2020 ATM), which shares are included in the $ 300.0 million of securities registered pursuant to the 2020 Registration Statement. During the year ended December 31, 2020, the Company issued and sold 892,840 shares of common stock under the 2020 Registration Statement, for which the Company received net proceeds of $ 5.5 million, after deducting commissions, fees and expenses. The Company carried forward registration fees paid with respect to $ 21.4 million of securities that remained available under the 2018 Registration Statement. As such, as of the effectiveness of the 2020 Registration Statement, the 2018 Registration Statement was deemed terminated. Common Stock Warrants As of December 31, 2020, the following warrants to purchase shares of the Company’s common stock were issued and outstanding: Issue date Expiration date Exercise Price per Share December 31, 2020 December 31, 2019 September 10, 2010 September 10, 2020 $ 30.000 — 15,296 December 16, 2019 None $ 0.001 2,424,242 2,424,242 2,424,242 2,439,538 F-27 There were no warrants exercised during the years ended December 31, 2020, 2019 and 2018. During the year ended December 31, 2020, 15,296 warrants to purchase common stock expired unexercised. During the year ended December 31, 2018, 1,613 warrants to purchase common stock expired unexercised. Note 8 - Stock-Based Compensation Equity Incentive Plans In May 2018, the Company’s stockholders approved (1) the Assembly Biosciences, Inc. 2018 Stock Incentive Plan (the 2018 Plan) pursuant to which the Company reserved 1,900,000 shares of its common stock for issuance in connection with equity incentive awards and (2) the Assembly Biosciences, Inc. Employee Stock Purchase Plan (the 2018 ESPP) pursuant to which the Company reserved 400,000 shares of its common stock for issuance in connection with purchases by employees pursuant to this plan. In May 2019, the Company’s stockholders approved an amendment to the 2018 Plan that increased the aggregate shares of common stock reserved under the 2018 Plan to 3,000,000 . In June 2020, the Company’s stockholders approved an amendment to the 2018 Plan that increased the aggregate number of shares of common stock reserved under the 2018 Plan to 4,600,000 . As of December 31, 2020, the Company had awards outstanding under the following shareholder approved plans: 2010 Equity Incentive Plan (the 2010 Plan), which has been frozen; the Amended and Restated 2014 Stock Incentive Plan (the 2014 Plan); and the 2018 Plan. Shares of common stock underlying awards that are forfeited under the 2010 Plan on or after June 2, 2016 will become available for issuance under the 2014 Plan. As of December 31, 2020, the Company also had awards outstanding under the Assembly Biosciences, Inc. 2017 Inducement Award Plan (the 2017 Plan), the 2019 Inducement Award Plan (the 2019 Plan) and the Assembly Biosciences, Inc. 2020 Inducement Award Plan (the 2020 Plan). The Company issues new shares of common stock to settle options exercised or vested RSUs. The Company also issues new shares of common stock in connection with purchases of shares of common stock by eligible employees under the Company’s 2018 ESPP. Stock Plan Activity Stock Options The following table summarizes the stock option activity and related information for 2020: Number of Shares Weighted Average Exercise Price Per Share Weighted Average Remaining Contractual Term (Years) Total Intrinsic Value (in thousands) Outstanding as of December 31, 2019 5,613,353 $ 15.90 Granted 1,649,340 16.07 Exercised ( 175,579 ) 9.75 Forfeited ( 390,522 ) 22.81 Outstanding as of December 31, 2020 6,696,592 $ 15.70 6.9 $ 1,856 Exercisable as of December 31, 2020 3,926,732 $ 14.70 5.5 $ 1,813 The weighted-average grant-date fair value of options granted was $ 10.64 , $ 10.55 and $ 30.84 during the years ended December 31, 2020, 2019 and 2018, respectively. The total intrinsic value of options exercised in 2020, 2019 and 2018 was $ 2.0 million, $ 5.0 million and $ 31.1 million, respectively. F-28 RSUs The following table summarizes RSU activity and related information for 2020: Number of RSU's Weighted Average Fair Value Per RSU at Grant Price Nonvested as of December 31, 2019 758,718 $ 25.47 Granted 536,164 16.21 Vested ( 297,133 ) 23.65 Forfeited ( 110,881 ) 26.46 Nonvested as of December 31, 2020 886,868 (1) $ 20.36 (1) Includes 140,000 RSUs that have vested but are subject to deferred settlement, which have a weighted average remaining contractual term of 2.2 years. The total fair value of RSUs vested and settled during 2020, 2019 and 2018 was $ 7.8 million, $ 5.7 million, and $5.3 million, respectively. The total intrinsic value of RSUs vested and settled during 2020 and 2019 was $ 4.4 million and $ 2.9 million, respectively. The total intrinsic value of RSUs vested and settled during 2018 was nominal. As of December 31, 2020, RSUs outstanding include 100,000 RSUs granted in September 2019 to the Company’s chief executive officer with performance-based conditions. The 100,000 awards with an aggregate fair value of $ 1.2 million vest upon performance conditions not yet deemed probable and accordingly no stock-based compensation expense has been recognized as of December 31, 2020. In July 2020, the performance condition for 45,000 RSUs granted in December 2017 to a former executive officer was met associated with the execution of an HBV business development transaction. The Company recognized $ 0.7 million as a cumulative catch-up adjustment of stock-based compensation expense for this award for the year ended December 31, 2020. In the second quarter of 2019, 100,000 RSUs granted to a former officer were forfeited due to his departure. These RSUs had a grant date fair value of $ 2.4 million and were vesting over time but would have accelerated upon the achievement of certain performance-based conditions. The Company reversed the previously recognized expense of $ 0.5 million related to these forfeited awards upon the departure of the former officer in 2019. Employee Stock Purchase Plan The 2018 ESPP provides for the purchase by employees of up to an aggregate of 400,000 shares of the Company’s common stock at a discount to the market price. Subject to the annual statutory limits and the 2018 ESPP’s limit of 1,000 shares of common stock per offering, an eligible employee may participate through payroll deductions of up to 15 % of such employee’s compensation for each pay period Eligible employees can purchase the Company’s common stock at the end of a predetermined offering period at 85 % of the lower of the fair market value at the beginning or end of the offering period. Under the 2018 ESPP, the offering periods end on the last business day occurring on or before May 14 or November 14. The ESPP is compensatory and results in stock-based compensation expense. In November 2018, employees purchased 21,483 shares of common stock under the 2018 ESPP. In May and November 2019, employees purchased 36,804 and 22,566 shares of common stock, respectively, under the 2018 ESPP. In May and November 2020, employees purchased 42,266 and 44,546 shares of common stock, respectively, under the 2018 ESPP. As of December 31, 2020, 232,335 shares of common stock are available for future sale under the Company’s 2018 ESPP. Stock-based compensation expense recorded in connection with the 2018 ESPP was $ 0.5 million, $ 0.4 million and $ 0.2 million for the years December 31, 2020, 2019 and 2018, respectively. F-29 Valuation Assumptions The Company used the Black-Scholes option-pricing model for determining the estimated fair value and stock-based compensation related to stock options and ESPP purchase rights. A summary of the assumptions used to estimate the fair values of stock options grants for the years presented is as follows: Year Ended December 31, 2020 2019 2018 Exercise price $5.62 - $23.30 $9.31 - $23.04 $23.78 - $57.53 Expected volatility 66.4% - 92.3% 66.5% - 83.2% 75.6% - 86.1% Risk-free interest rate 0.26% - 1.44% 1.36% - 2.65% 2.56% - 3.04% Expected term (years) 5.5 - 7.5 5.5 - 7.5 5.5 - 7.0 Expected dividend yield 0 % 0 % 0 % The risk-free interest rate assumption was based on the rates for U.S. Treasury zero-coupon bonds with maturities similar to those of the expected term of the stock option being valued. The expected dividend yield was zero as the Company currently does not intend to pay dividends in the foreseeable future. The weighted average expected term of options was calculated using the simplified method as prescribed by accounting guidance for stock-based compensation due to the Company’s limited history of relevant stock option exercise activity. The expected volatility was calculated based on the Company’s historical stock prices, supplemented as necessary with historical volatility of the common stock of several peer companies with characteristics similar to those of the Company. The fair value of ESPP purchase rights were not material for any period presented. Stock-Based Compensation Expense The Company recognized stock-based compensation expense included in the consolidated statement of operations and comprehensive loss for the periods presented (in thousands): Year Ended December 31, 2020 2019 2018 Research and development $ 11,380 $ 11,376 $ 11,820 General and administrative 10,473 (1) 9,182 (2) 16,665 Total stock-based compensation expense $ 21,853 $ 20,558 $ 28,485 (1) Includes the reversal of previously recognized expense of $ 1.7 million related to forfeited awards resulting from the departure of one of our former executive officers during the year. (2) Includes the reversal of previously recognized expense of $ 3.6 million related to forfeited awards resulting from the departure of one of our former executive officers during the year. As of December 31, 2020 , there was $ 20.4 million of total unrecognized stock-based compensation related to outstanding equity awards which is expected to be recognized over a weighted average remaining amortization period of 1.8 years . F-30 Note 9 - Collaboration Agreements Allergan Agreement In January 2017, the Company and Allergan entered into the Allergan Agreement to develop and commercialize select microbiome gastrointestinal disease therapies. Pursuant to the Allergan Agreement, the Company granted Allergan an exclusive worldwide license to certain of its intellectual property, including its intellectual property arising under the Allergan Agreement, to develop and commercialize licensed compounds for ulcerative colitis (UC), Crohn’s disease, and two compounds for irritable bowel syndrome (IBS). Allergan and the Company also agreed to collaborate on research and development activities with respect to the licensed compounds in accordance with a mutually agreed upon research and development plan. Per the terms of the Allergan Agreement, Allergan could select backups and additional target indications to add to the licenses granted for additional consideration and also had the ability to enter into a contract manufacturing agreement with the Company for compound supply at cost plus an agreed upon margin. In addition, the Company participated on a Joint Development Committee (JDC) and Joint Patent Committee (JPC). Allergan had the right to terminate the Allergan Agreement at any time upon advance written notice. In June 2020, following its acquisition of Allergan, AbbVie Inc. (AbbVie), on behalf of Allergan, gave written notice of termination of the Allergan Agreement effective 120 days following the delivery of notice, on October 10, 2020. Upon termination, the licenses granted by the Company and its know-how reverted to the Company. Under the terms of the Allergan Agreement, AbbVie was obligated to continue to reimburse the Company for certain research and development costs through October 10, 2020. Upon effectiveness of the termination, such reimbursements ceased. Due to the delivery of the termination notice, the Company determined there were no further enforceable rights and obligations under the Allergan Agreement beyond June 2020 and the remaining $ 36.0 million of deferred revenue was recognized in 2020. Allergan paid the Company an upfront non-refundable payment of $ 50.0 million which was received in 2017. Additionally, the Company was eligible to receive variable consideration in the form of research and development cost reimbursements, up to $ 631.0 million related to seven development milestones and up to $ 2.14 billion related to 12 commercial development and sales milestones in connection with the successful development and commercialization of licensed compounds. In addition, the Company was eligible to receive tiered royalties at rates ranging from the mid-single digits to the mid-teens based on net sales. Allergan and the Company agreed to share research and development costs up to an aggregate of $ 75.0 million through proof-of-concept (POC) studies on a ⅔, ⅓ basis, respectively, and Allergan agreed to assume all post-POC development costs. In the event any pre-POC development costs would have exceeded $ 75.0 million in the aggregate, the Company may have elected either (a) to fund ⅓ of such costs in excess of $ 75.0 million or (b) to allow Allergan to deduct from future development milestone payments ⅓ of the development costs funded by Allergan in excess of $ 75.0 million plus a premium of 25 %. The Company had an option to co-promote the licensed programs in the U.S. and China, subject to certain conditions set forth in the Allergan Agreement. The Company concluded that Allegan was a customer, and the contract was not subject to accounting literature on collaborative arrangements. This is because the Company granted to Allergan licenses to its intellectual property and agreed to perform research and development services, all of which are outputs of the Company’s ongoing activities, in exchange for consideration. The Company identified the following material promises under the Allergan Agreement: (1) grant of a licenses to intellectual property for the four initial indications, inclusive of the related technology know-how (Licenses) and (2) the obligation to perform research development services through POC (Development Services). The Company’s participation on the JDC and JPC were considered to be immaterial in the context of the contract. The Company’s co-promotion option was not considered to be a performance obligation. Allergan’s selection of backups or additional target indications to add to the licenses granted for additional consideration and ability to enter into a contract manufacturing agreement with the Company for compound supply at cost plus an agreed upon margin were not considered to be performance obligations as the Company concluded the options were not offered at a discount that exceeds discounts available to other customers, and therefore were not material rights. The grant of additional licensing rights upon option exercises and contract manufacturing agreements were to be accounted for as separate contracts when or if they occurred. F-31 The Company concluded the Licenses each were considered to be functional as they had significant standalone functionality and were capable of being distinct. However, the Company determined that each of the Licenses individually were not distinct from the Development Services within the context of the agreement. This is because Allergan was dependent on the Company to execute the Development Services, which it was uniquely able to perform, in order for Allergan to benefit from the Licenses. As such, t he Company determined that it had four performance obligations under the Allergan Agreement associated with the grant of the four compound Licenses combined with the performance of the Development Services for each of the four compound indications. The Company determined that the four performance obligations would have be en performed over the duration of the contract, which began in February 2017 and ends upon receipt of the termination notice . The Company used a cost-based input method to measure proportional performance and to calculate the corresponding amount of revenue to recognize. The Company believe d this wa s the best measure of progress because other measures do not reflect how the Company transfers its performance obligation to Allegan. In applying the cost-based input method of revenue recognition, the Company measure d costs incurred relative to budgeted costs to fulfill the four performance obligations. These costs consist ed primarily of third-party contract costs and internal labor costs. Revenue will be recognized based on actual costs incurred as a percentage of total budgeted costs as the Company complete d its performance obligations. To allocate transaction price among the four performance obligations, the Company estimated their standalone selling price (SSP) using an income-based valuation approach for the estimated value a licensor of the compounds would receive considering the stage of the compounds’ development. A change in the assumptions used to determine its best estimate of selling price for the four performance obligations would not have had a significant effect on the allocation of consideration received to the four performance obligations. The transaction price at the inception of the agreement and upon adoption of the revenue from contracts with customers guidance was limited to the $ 50.0 million upfront payment. Of this amount, the Company allocated $ 12.5 million to each of the four performance obligations. Research and development cost reimbursement payments were included in the transaction price in the reporting period that the Company concludes that it was probable that recording revenue in the period would not have resulted in a significant reversal in amounts recognized. The variable consideration related to the remaining development and commercialization milestone payments was not included in the transaction price as these were fully constrained. As part of the Company’s evaluation of the development and commercialization milestones constraint, the Company determined the achievement of such milestones was contingent upon success in future clinical trials and regulatory approvals which was not within its control and uncertain at this stage. Any variable consideration related to sales-based milestones (including royalties) would have been recognized when the related sales occur as they were determined to relate predominantly to the license granted to Allergan. The Company re-evaluated the transaction price in each reporting period and as uncertain events were resolved or other changes in circumstances occurred. The Company did not incur any significant incremental costs of obtaining the Allergan contract. For the year ended December 31, 2020, 2019, and 2018 the Company recognized $ 48.1 million , $ 16.0 million and $ 14.8 million respectively, in collaboration revenue associated with the Allergan Agreement. Short-term and long-term deferred revenue contract liabilities related to the Allergan Agreement were $ 6.4 million and $ 30.6 million at December 31, 2019, respectively. There were no deferred revenue contract liabilities as of December 31, 2020 due to the Company recognizing a cumulative catch-up adjustment of the remaining deferred revenue balance during the year ended December 31, 2020 for the determined completion of the Company’s performance obligations under the Allergan Agreement upon receipt of the notice of termination from AbbVie. Contract asset balances of $ 1.0 million and $ 3.4 million were recorded as of December 31, 2020 and 2019, respectively. BeiGene Agreement In July 2020, the Company and BeiGene, Ltd. (BeiGene) entered into a Collaboration Agreement (the BeiGene Agreement) to develop and commercialize the Company’s novel core inhibitor product candidates VBR, ABI-H2158 and ABI-H3733 for chronic HBV infection (the Licensed Product Candidates) in the People’s Republic of China, Hong Kong, Taiwan and Macau (the Territory). Under the agreement, the Company and BeiGene are collaborating on certain global clinical studies and both the Company and BeiGene will independently conduct other clinical studies in their own respective territories. BeiGene agreed to pay all development and regulatory costs for the Licensed Product Candidates in the Territory up to an aggregate of $ 45.0 million. Development and regulatory costs for the Licensed Product Candidates for the Territory in excess of $ 45.0 million will be shared equally by the Company and BeiGene. If the Company conducts certain ancillary trials outside of the plan to develop these candidates in the Territory, BeiGene may elect to obtain access to F-32 the know-how and clinical data resulting for such ancillary trials and shall reimburse the Company proportionally for the Territory of the costs of such trials. Activities under the BeiGene Agreement will be governed by a joint steering committee (JSC) consisting of equal representatives from each party to the agreement. All decisions of the JSC are to be made by consensus with final decision-making authority granted to each party based on key areas of the collaboration for which they are responsible. During the term of the BeiGene Agreement, neither party will commercialize any competing products in the Territory. The Company will be responsible for manufacturing and supply of the candidates to be used in and outside of the Territory, although the parties may approve BeiGene to take on some or all of the commercial supply activities of the applicable Licensed Products in the Territory. The Company is not obligated to perform pre-phase 3 clinical trial development work outside the Territory on ABI-H2158 and ABI-H3733 but must provide BeiGene pre-Phase 3 clinical trial know-how and development results if and when such development efforts are completed. If, after ABI-H2158 and ABI-H3733 reach the end of Phase 2 clinical trials, the Company and BeiGene are unable to mutually agree on the terms of a Phase 3 global study, BeiGene may elect to terminate the BeiGene Agreement solely as it relates to that compound, as applicable. Such a termination would result in the Company regaining all rights to the applicable compound in the Territory. In addition, BeiGene may terminate the BeiGene Agreement for convenience at any time upon 90 days’ advance written notice to us. The BeiGene Agreement also contains customary provisions for termination by either party, including in the event of breach of the BeiGene Agreement, subject to cure. Pursuant to the terms of the BeiGene Agreement, the Company received an upfront cash payment of $ 40.0 million from BeiGene for the delivery of exclusive, royalty-bearing licenses to develop and commercialize the Licensed Product Candidates in the Territory, and the Company is eligible to receive up to approximately $ 500.0 million in cash milestone payments, comprised of up to $ 113.8 million for development and regulatory milestones and up to $ 385.0 million in net sales milestones. In addition, the Company is eligible to receive tiered royalties at percentages ranging from the mid-teens to the low thirties of net sales. The BeiGene Agreement is within the scope of the collaborative arrangements guidance as both parties are active participants and are exposed to significant risks and rewards dependent on the success of commercializing the Licensed Product Candidates in the Territory but that the unit of account related to the delivery of Licensed Product Candidates is within the scope of the contract with customers guidance. The remaining units of account related to participation on the JSC and subcommittees, clinical supply and other in Territory and global development activities (the Collaboration Activities) are within the scope of the collaborative arrangements guidance. Commercial supply will be evaluated as a separate contract when the agreement is executed and a purchase order is received from BeiGene. The Company identified the following material promises related to the contract with customers unit of account under the BeiGene Agreement : 1) the transfer of the VBR License, 2) the transfer of the ABI-H2158 License , and 3) the transfer of the ABI-H3733 License. The Company concluded each of these licenses to be functional as they have significant standalone functionality and grants BeiGene the right to use the Company’s intellectual property as it exists on the effective date of the license . The ABI-H2158 and ABI-H3733 Licenses have a continuing technology transfer obligation that is considered to be an attribute of these licenses. The agreed upon prices for the clinical and commercial supply of the Licensed Product Candidates to BeiGene do not represent material rights, and therefore are not performance obligations, and such pricing on an aggregate basis represents the standalone selling price an entity would typically pay for such a product in that region or market. There are also no minimum purchase commitments. The Company estimated the standalone selling price (SSP) of the Licenses using an income-based valuation approach for the estimated value a licensor of the compounds would receive considering the stage of the compound’s development. The Company believes a change in the assumptions used to determine its best estimate of SSP would not have a significant value on the allocation of consideration received. The transaction price at the inception of the agreement was limited to the $ 40.0 million upfront payment. The variable consideration related to the remaining development and commercialization milestone payments has not been included in the transaction price as these were fully constrained as of December 31, 2020. As part of the Company’s evaluation of the development and commercialization milestones constraint, the Company determined the achievement of such milestones are contingent upon success in future clinical trials and regulatory approvals which are not within its control and uncertain at this stage. Any variable consideration related to sales-based milestones (including royalties) will be recognized when the related sales occur as they were determined to relate predominantly to the Licensed Product Candidates granted to BeiGene. The Company will reevaluate the transaction price in each reporting period as uncertain events are resolved or other changes in circumstances occur. F-33 During the year ended December 31, 2020, the Company recognized $ 31.0 million as collaboration revenue for the amount allocated to the VBR License as substantial completion of the license technology transfer has occurred. The remaining transaction price allocated to the ABI-H2158 and ABI-H3733 Licenses of $ 9.0 million was recorded as a long-term deferred revenue contract liability on the consolidated balance sheet as of December 31, 2020. Revenue for these performance obligations will be recognized when the Company provides pre-Phase 3 clinical trial know-how and development results for these compounds to BeiGene or a termination of the BeiGene Agreement for the respective compound. Payments to, or reimbursements from, BeiGene related to the Collaboration Activities will be accounted for as an increase to or reduction of research and development expenses when incurred or realized, respectively. During the year ended December 31, 2020, the Company did no t recognize any increase or reduction of research and development expense under the BeiGene Agreement. The Company incurred $ 3.5 million in incremental costs of obtaining the BeiGene Agreement. These contract costs have been capitalized and are being recognized consistent with the pattern of recognition of revenue associated with the Licensed Product Candidates. As of December 31, 2020, $ 2.7 million has been amortized to general and administrative expenses and $ 0.8 million is included in other assets on the condensed consolidated balance sheet. Arbutus Agreement In August 2020, the Company and Arbutus Biopharma Corporation (Arbutus) entered into a Collaboration Agreement (Arbutus Agreement) to conduct a randomized, multi-center, open-label Phase 2 clinical trial to explore the safety, PK and antiviral activity of the triple combination of VBR, AB-729 and an NrtI compared to the double combinations of VBR with an NrtI and AB-729 with an NrtI. Assembly and Arbutus will share responsibility for the costs of the trial equally, excluding manufacturing supply which will be the burden of each company to supply their respective drugs VBR and AB-729. The Arbutus Agreement is within the scope of the collaborative arrangements guidance as both parties are active participants and are exposed to significant risks and rewards dependent on the success of the collaborative activity. Arbutus is not a customer as it does not obtain an output from the collaborative activities as they were not provided an exclusive license to VBR or the ability to manufacture VBR, and the Company does not consider performing such collaborative activities to be a part of its ongoing activities. The revenue from contracts with customers guidance was considered by analogy in determining the unit of account, and the recognition and measurement of such unit of account for collaborative activities under the Arbutus Agreement and concluded there is one activity, to run an open-label Phase 2 clinical trial , which is akin to performance obligation related to collaborative activities. Reimbursements and cost-sharing portions of this performance obligation will be reflected as a reduction of research and development expense when realized in the Company’s consolidated statements of operations, as the Company does not consider performing research and development services for reimbursement to be a part of its ongoing major or central operations. During the year ended December 31 , 2020, the Company recognized a reduction of research and development expense of $ 0.2 million under the Arbutus Agreement. Contract Liabilities The following tables present changes in the Company’s contract liabilities (in thousands): Balance at Beginning of Period Additions Deductions Balance at End of Period Year Ended December 31, 2020 Contract liabilities: Deferred revenue $ 37,048 $ 40,000 $ ( 68,061 ) $ 8,987 Year Ended December 31, 2019 Contract liabilities: Deferred revenue $ 40,660 $ — $ ( 3,612 ) $ 37,048 F-34 Year Ended December 31, 2020 2019 2018 Collaboration revenue recognized in the period from Amounts included in deferred revenue at the beginning of the period $ 37,048 $ 3,612 $ 5,125 Performance obligations satisfied in previous periods — — — Note 10 – Strategic License Agreements HBV Research Agreement with Indiana University Since September 2013, the Company has been party to an exclusive License Agreement dated September 3, 2013 with Indiana University Research and Technology Corporation (IURTC) from whom it has licensed aspects of the Company’s HBV program held by IURTC. The license agreement requires the Company to make milestone payments based upon the successful accomplishment of clinical and regulatory milestones. The aggregate amount of all performance milestone payments under the IURTC license agreement, should all milestones through development be met, is $ 0.8 million, with a portion related to the first performance milestone having been paid. The Company is obligated to pay IURTC royalty payments based on net sales of the licensed technology as well as a portion of any sublicensing revenue Assembly receives. The Company is also required to pay diligence maintenance fees each year to the extent that the royalty, sublicensing, and milestone payments to IURTC are less than the diligence maintenance fee for that year. A performance milestone totaling $ 0.1 million was determined to have occurred under this agreement and was paid during the year ended December 31, 2020. Additionally, the Company paid IURTC $ 0.7 million as a sublicensing fee during the year ended December 31, 2020. The Company made $ 0.1 million in milestone payments for the year ended December 31, 2018. No milestone payments were incurred or accrued for under this agreement as of and for the year ended December 31, 2019. The milestone and license fees are included in research and development expenses in the consolidated statements of operations and comprehensive loss. Microbiome Targeted Colonic Delivery Platform In November 2013, the Company entered into a License and Collaboration Agreement with Therabiome, LLC (Therabiome), for all intellectual property and know-how owned or controlled by Therabiome relating to the oral delivery of pharmaceutical drugs to specific sites in the intestine, using a pH sensitive controlled release capsule-in-capsule technology. The Company will be solely responsible for all research and development activities with respect to any product it develops under the license. The Company must pay Therabiome clinical and regulatory milestones for each product or therapy advanced from the platform for U.S. regulatory milestones. The Company also must pay Therabiome lesser amounts for foreign regulatory milestones, which vary by country and region. The Company also must pay Therabiome royalties on annual net sales of a product in the low to mid-single digit percentages plus, once annual net sales exceed certain thresholds, a one-time cash payment upon reaching the thresholds. Therabiome must pay the Company royalties on annual net sales of any product Therabiome is permitted to develop using the intellectual property in the low double to mid-double digit percentages, depending on the level of development or involvement the Company had in the product. Two regulatory milestones resulting in payments totaling $ 0.4 million were determined to have occurred under this agreement and were paid in the year ended December 31, 2019. No amounts were incurred or accrued for this agreement as of and for the years ended December 31, 2020 and 2018. In connection with the wind-down of the Microbiome program, the License and Collaboration Agreement with Therabiome was terminated in January 2021. F-35 Door Agreement In November 2020, the Company and Door Pharmaceuticals, LLC (Door) entered into an exclusive, two-year Collaboration Agreement and Sublicense Agreement (collectively, Door Agreement) focused on the development of a novel class of HBV inhibitors. Under the terms of the agreement, Door will build upon its previous efforts to lead and conduct new discovery research, which Assembly will fund. In return for an up-front payment of $ 1.8 million, success-based milestones up to $ 35.0 million, exercise and annual fees ranging from $ 0.1 million to $ 2.0 million and royalties in the low to mid-single digits, the Company will be granted an exclusive option to license compounds arising from the collaboration and will be responsible for the continued development and commercialization of optioned compounds. For the period ended December 31, 2020, the Company incurred $ 0.3 million of research and development funding in addition to the $ 1.8 million up-front payment. Under the consolidation accounting standard, the Company determined that Door is a VIE. The Company does not have the power to direct the activities that most significantly affect the economic performance of Door and as such the Company is not the primary beneficiary and consolidation is not required. As of December 31, 2020, the Company has not provided financial or other support to Door that was not contractually required. Note 11 - Income Taxes There was no current income tax provision for the years ended December 31, 2020, 2019 and 2018. The deferred income tax expense for the year ended December 31, 2020 was no t material. The Company recognized deferred income tax benefit of $ 0.8 million for the year ended December 31, 2019 and a deferred income tax expense of $ 1.1 million for the year ended December 31, 2018. The effective tax rate of our provision for income taxes differs from the federal statutory rate as follows: As of December 31, 2020 2019 2018 Statutory federal income tax rate 21.0 % 21.0 % 21.0 % State taxes, net of federal tax benefit 6.1 5.6 7.1 Stock based compensation 0.7 ( 3.8 ) 6.7 Research and development tax credits 2.2 5.6 2.4 State rate change — ( 1.4 ) 2.5 Uncertain tax positions 2.2 ( 2.1 ) ( 4.8 ) Return to provision adjustments 4.3 ( 2.5 ) 4.4 Other 0.1 ( 0.2 ) 0.8 Change in valuation allowance ( 36.6 ) ( 21.4 ) ( 41.3 ) Income taxes provision (benefit) 0.0 % 0.8 % ( 1.2 )% F-36 Significant components of the Company’s deferred taxes are as follows (in thousands): As of December 31, 2020 2019 Deferred tax assets: Federal and state-operating loss carryforwards $ 108,236 $ 81,584 Stock-based compensation 16,563 12,347 Intangible assets 1,463 1,774 Deferred revenue — 9,503 Operating lease liabilities 2,600 3,147 Research and development credits 8,872 7,499 Other 854 702 Total deferred tax assets 138,588 116,556 Valuation allowance ( 131,332 ) ( 108,577 ) Deferred tax asset, net of valuation allowance $ 7,256 $ 7,979 Deferred tax liabilities: In-process research and development $ ( 7,443 ) $ ( 7,439 ) Operating lease right-of-use assets ( 2,344 ) ( 3,071 ) Total deferred tax liabilities ( 9,787 ) ( 10,510 ) Net deferred tax liability $ ( 2,531 ) $ ( 2,531 ) The Company maintains a valuation allowance on deferred tax assets due to the uncertainty regarding the ability to utilize these deferred tax assets in the future. The increase in the valuation allowance for both the years ended December 31, 2020 and 2019 is primarily due to an increase in the Company’s federal and state-operating loss carryforwards. The in-process research and development deferred tax liability was recorded in connection with the merger with Assembly Pharmaceuticals, Inc. in 2014 and relates to the difference between the carrying amount of in-process research and development for financial statement purposes relative to the amount used for income tax purposes. As of December 31, 2020, the Company had potentially utilizable gross federal net operating loss carryforwards of $ 378.8 million with $ 264.1 million of net operating losses that carry forward indefinitely and $ 114.7 million of net operating losses which begin to expire in 2027 if not utilized. There are state net operating loss carryforwards of $ 446.8 million with $ 0.7 million carrying forward indefinitely and $ 446.1 million beginning to expire in 2031 . In addition, the Company has federal research and development credit carryforwards of $ 8.5 million which begin to expire in 2028 if not utilized and California research and development credit carryforwards of $ 3.6 million, which will carryforward indefinitely. Pursuant to Internal Revenue Code (IRC), Section 382 and 383, use of the Company’s U.S. federal and state net operating loss and research and development income tax credit carryforwards may be limited in the event of a cumulative change in ownership of more than 50.0% within a three-year period. The Company has performed an ownership change study through December 31, 2019 and has determined that a “change in ownership” as defined by IRC Section 382 and the rules and regulations promulgated thereunder, did occur in December 2010, January 2013 and October 2014. The Company has adjusted its net operating loss carryovers to appropriately reflect any attributes which will expire due to the limitation. The Company has not performed any additional analysis for IRC Sections 382 and 383 and there is a risk that additional changes in ownership could have occurred since December 31, 2018. If a change in ownership were to have occurred, additional net operating loss and tax credit carryforwards could be eliminated or restricted. If eliminated, the related asset would be removed from the deferred tax asset schedule with a corresponding reduction in the valuation allowance. F-37 The following table summarizes activity related to the Company’s gross unrecognized tax benefits (in thousands): As of December 31, 2020 2019 2018 Balances as of beginning of year $ 6,070 $ 4,613 $ — Increases related to prior year tax positions — 15 3,679 Decreases related to prior year tax positions ( 4,162 ) ( 934 ) — Increases related to current year tax positions 747 2,376 934 Balances as of end of year $ 2,655 $ 6,070 $ 4,613 The unrecognized tax benefits, if recognized, would not have an impact on the Company’s effective tax rate assuming the Company continues to maintain a full valuation allowance position. Based on prior year’s operations and experience, the Company does not expect a significant change to its unrecognized tax benefits over the next twelve months. The unrecognized tax benefits may increase or change during the next year for unexpected or unusual items for items that arise in the ordinary course of business. In subsequent periods, any interest and penalties related to uncertain tax positions will be recognized as a component of income tax expense. The Company files income tax returns in the U.S. federal, California and other state jurisdictions and is not currently under examination by federal, state, or local taxing authorities for any open tax years. Due to net operating loss carryforwards, all years effectively remain open for income tax examination by tax authorities in the U.S. and states in which the Company files tax returns. Note 12 - Leases Operating Leases The Company leases corporate office and laboratory space in South San Francisco, California under a sub-sublease that expires in December 2023. The sub-sublease contains scheduled rent increases over the lease term. Prior to moving into the South San Francisco office and laboratory space in February 2019, the Company leased office and laboratory space in San Francisco, California, under a sublease that expired in February 2019. The Company also leases office space for administrative functions in Carmel, Indiana under a lease agreement that expires in August 2023. In February 2021, the Company subleased substantially all of the office space under the Carmel, Indiana lease. The Company also leases office and laboratory space in Groton, Connecticut that supports the Microbiome program under a lease that expires in March 2021. Due to the wind-down of the Microbiome program, the lease will not be renewed. The Company’s China subsidiary leases office space and lab space in Shanghai. The lab space expired in December 2020 and the office space expires March 2021, neither of which are being renewed. Additionally, the Company’s China subsidiary leases office space in Beijing under a lease agreement that expires in December 2021. Certain lease contracts contain renewal clauses that the Company assesses on a case by case basis. The Company also leases certain laboratory equipment accounted for as operating leases expiring at various dates, with the final lease expiring in 2023. In February 2021, the Company purchased substantially all of the leased equipment used for the Microbiome program from its leasing agency and sold them to a third party. The loss on the sale is equal to the impairment loss the Company recognized on these assets for the year ended December 31, 2020 of $ 0.7 million. When the Company cannot determine the implicit rate in its leasing arrangements, the Company uses its incremental borrowing rate as the discount rate when measuring operating lease liabilities. The incremental borrowing rate represents an estimate of the interest rate the Company would incur at lease commencement to borrow an amount equal to the lease payments on a collateralized basis over the term of a lease within a particular currency environment. F-38 At December 31, 2020, the Company had operating lease liabilities of $ 10.1 million and right-of-use assets of $ 9.1 million. The following summarizes quantitative information about the Company’s operating leases (in thousands): Year Ended December 31, 2020 2019 Lease cost Operating lease cost $ 5,214 $ 4,454 Short-term lease cost 401 609 Variable lease cost 1,468 1,193 Total lease cost $ 7,083 $ 6,256 Year Ended December 31, 2020 2019 Operating cash flows from operating leases $ 4,513 $ 4,269 Right-of-use assets exchanged for new operating lease liabilities $ 1,302 $ 15,261 As of December 31, 2020, the weighted-average remaining lease term for operating leases was 2.7 years and the weighted-average discount rate for operating leases was 9.2 %. As of December 31, 2020, the maturities of the Company’s operating lease liabilities were as follows (in thousands): 2021 $ 4,369 2022 3,905 2023 3,502 Total 11,776 Less: present value discount ( 1,647 ) Operating lease liabilities $ 10,129 Operating lease costs were $ 7.1 million, $ 6.3 million and $ 4.2 million for the years ended December 31, 2020, 2019 and 2018, respectively. Note 13 - Employee Benefit Plan In January 2018, the Company established a defined contribution 401(k) plan (the Plan) for all employees who are at least 21 years of age. Employees are eligible to participate in the Plan upon commencement of employment. Under the terms of the Plan, employees may make voluntary contributions as a percentage of compensation. The Plan also permits the Company to make discretionary matching contributions. In 2020, 2019 and 2018, the Company made discretionary matching contributions of $ 0.9 million, $ 0.7 million and $ 0.7 million, respectively. F-39 Note 14 - Selected Quarterly Financial Data (Unaudited) The following table contains quarterly financial information for the four quarters of 2020 and 2019 which has been prepared in accordance with GAAP for interim financial information. The Company believes that the following information reflects all normal recurring adjustments necessary for a fair statement of the information for the periods presented. 2020 Quarter Ended March 31 June 30 September 30 December 31 (in thousands except for per share amounts) Collaboration revenue $ 4,081 $ 39,376 $ 34,611 $ 1,037 Operating expenses $ 31,775 $ 32,797 $ 38,630 $ 40,679 Interest and other income $ 1,039 $ 691 $ 670 $ 224 Net income (loss) $ ( 26,655 ) $ 7,270 $ ( 3,349 ) $ ( 39,418 ) Unrealized gain (loss) from marketable securities, net of tax $ 115 $ 190 $ ( 262 ) $ ( 112 ) Basic net income (loss) per common share $ ( 0.76 ) $ 0.21 $ ( 0.09 ) $ ( 1.11 ) Diluted net income (loss) per common share $ ( 0.76 ) $ 0.19 $ ( 0.09 ) $ ( 1.11 ) 2019 Quarter Ended March 31 June 30 September 30 December 31 (in thousands except for per share amounts) Collaboration revenue $ 3,885 $ 3,080 $ 4,231 $ 4,767 Operating expenses $ 32,221 $ 22,780 $ 30,224 $ 33,451 Interest and other income $ 1,276 $ 1,182 $ 983 $ 859 Net loss $ ( 27,052 ) $ ( 18,503 ) $ ( 24,995 ) $ ( 27,084 ) Unrealized gain (loss) from marketable securities, net of tax $ 108 $ 52 $ ( 18 ) $ 4 Basic and diluted net loss per common share $ ( 1.05 ) $ ( 0.72 ) $ ( 0.96 ) $ ( 0.99 ) Note 15 – Subsequent Events Subsequent to December 31, 2020, the Company sold 4,177,080 shares of common stock through its 2020 ATM resulting in net proceeds of $ 25.5 million. F-40