ASSEMBLY BIOSCIENCES, INC. 10-Q

Item 1. Financial Statements ASSEMBLY BIOSCIENCES, INC. CONDENSED CONSOLIDATED BALANCE SHEETS (In thousands except for share amounts and par value) September 30, December 31, 2020 2019 (Unaudited) ASSETS Current assets Cash and cash equivalents $ 58,311 $ 46,732 Marketable securities 179,630 227,311 Accounts receivable from collaboration 3,590 3,374 Prepaid expenses and other current assets 4,856 5,363 Total current assets 246,387 282,780 Property and equipment, net 1,904 1,830 Operating lease right-of-use (ROU) assets 10,397 11,975 Other assets 5,980 1,684 Indefinite-lived intangible asset 29,000 29,000 Goodwill 12,638 12,638 Total assets $ 306,306 $ 339,907 LIABILITIES AND STOCKHOLDERS' EQUITY Current liabilities Accounts payable $ 1,611 $ 1,731 Accrued clinical expenses 4,451 4,826 Other accrued expenses 7,404 8,286 Deferred revenue - short-term — 6,411 Operating lease liabilities - short-term 3,338 3,186 Total current liabilities 16,804 24,440 Deferred tax liabilities 2,531 2,531 Deferred revenue - long-term 8,987 30,637 Operating lease liabilities - long-term 7,435 9,082 Total liabilities 35,757 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 September 30, 2020 and December 31, 2019; 32,924,536 and 32,558,307 shares issued and outstanding as of September 30, 2020 and December 31, 2019, respectively 33 32 Additional paid-in capital 732,829 712,807 Accumulated other comprehensive loss ( 158 ) ( 201 ) Accumulated deficit ( 462,155 ) ( 439,421 ) Total stockholders' equity 270,549 273,217 Total liabilities and stockholders' equity $ 306,306 $ 339,907 See Accompanying Notes to Condensed Consolidated Financial Statements 1 ASSEMBLY BIOSCIENCES, INC. CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS (In thousands except for share and per share amounts) (Unaudited) Three Months Ended September 30, Nine Months Ended September 30, 2020 2019 2020 2019 Collaboration revenue $ 34,611 $ 4,231 $ 78,068 $ 11,197 Operating expenses: Research and development 26,941 21,736 73,314 63,141 General and administrative 11,689 8,488 29,888 22,085 Total operating expenses 38,630 30,224 103,202 85,226 Loss from operations ( 4,019 ) ( 25,993 ) ( 25,134 ) ( 74,029 ) Other income Interest and other income, net 670 983 2,400 3,446 Total other income 670 983 2,400 3,446 Loss before income taxes ( 3,349 ) ( 25,010 ) ( 22,734 ) ( 70,583 ) Income tax benefit — 15 — 33 Net loss $ ( 3,349 ) $ ( 24,995 ) $ ( 22,734 ) $ ( 70,550 ) Other comprehensive (loss) income Unrealized (loss) gain on marketable securities, net of tax ( 262 ) ( 18 ) 43 142 Comprehensive loss $ ( 3,611 ) $ ( 25,013 ) $ ( 22,691 ) $ ( 70,408 ) Net loss per share, basic and diluted $ ( 0.09 ) $ ( 0.96 ) $ ( 0.64 ) $ ( 2.74 ) Weighted average common shares outstanding, basic and diluted 35,506,042 25,912,568 35,321,393 25,765,414 See Accompanying Notes to Condensed Consolidated Financial Statements 2 ASSEMBLY BIOSCIENCES, INC. CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (In thousands) (Unaudited) Nine Months Ended September 30, 2020 2019 Cash flows from operating activities Net loss $ ( 22,734 ) $ ( 70,550 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 377 377 Stock-based compensation 18,106 14,049 Net accretion and amortization of investments in marketable debt securities ( 80 ) ( 1,503 ) Non-cash rent expense 3,463 3,344 Deferred income tax benefit — ( 33 ) Loss on disposal of fixed assets — 102 Other — 18 Changes in operating assets and liabilities: Accounts receivable from collaboration ( 216 ) ( 514 ) Prepaid expenses and other current assets 507 ( 3,763 ) Other assets ( 4,296 ) 1,677 Accounts payable ( 120 ) ( 984 ) Accrued clinical expenses ( 375 ) 670 Other accrued expenses ( 877 ) ( 1,000 ) Deferred revenue ( 28,061 ) ( 2,241 ) Operating lease liabilities ( 3,382 ) ( 3,188 ) Net cash used in operating activities ( 37,688 ) ( 63,539 ) Cash flows from investing activities Purchases of property and equipment ( 470 ) ( 1,539 ) Purchases of marketable securities ( 153,022 ) ( 149,327 ) Proceeds from maturities of marketable securities 165,252 166,911 Proceeds from sale of marketable securities 35,595 28,659 Net cash provided by investing activities 47,355 44,704 Cash flows from financing activities Proceeds from the exercise of stock options 1,445 1,716 Proceeds from the issuance of common stock under Employee Stock Purchase Plan (ESPP) 467 515 Net cash provided by financing activities 1,912 2,231 Net increase (decrease) in cash and cash equivalents 11,579 ( 16,604 ) Cash and cash equivalents at the beginning of the period 46,732 41,471 Cash and cash equivalents at the end of the period $ 58,311 $ 24,867 Supplemental non-cash investing and financing activities Operating lease liabilities arising from obtaining ROU assets $ 1,063 $ 15,261 See Accompanying Notes to Condensed Consolidated Financial Statements 3 ASSEMBLY BIOSCIENCES, INC. CONDENSED CONSOLIDATED STATEMENTS OF CHANGES IN STOCKHOLDERS’ EQUITY (In thousands except for share amounts) (Unaudited) For the Three Month Period Common Stock Additional Accumulated Other Total Shares Amount Paid-in Capital Comprehensive Income (Loss) Accumulated Deficit Stockholders' Equity Balance as of June 30, 2020 32,807,519 $ 33 $ 725,784 $ 104 $ ( 458,806 ) $ 267,115 Issuance of common stock upon exercise of stock options 81,066 — 843 — — 843 Issuance of shares of common stock for settlement of restricted stock units (RSUs) 35,951 — — — — — Unrealized loss on marketable debt securities — — — ( 262 ) — ( 262 ) Stock-based compensation — — 6,202 — — 6,202 Net loss — — — — ( 3,349 ) ( 3,349 ) Balance as of September 30, 2020 32,924,536 $ 33 $ 732,829 $ ( 158 ) $ ( 462,155 ) $ 270,549 Common Stock Additional Accumulated Other Total Shares Amount Paid-in Capital Comprehensive Loss Accumulated Deficit Stockholders' Equity Balance as of June 30, 2019 25,646,783 $ 26 $ 562,210 $ ( 187 ) $ ( 387,342 ) $ 174,707 Issuance of common stock upon exercise of stock options 192,606 — 1,385 — — 1,385 Issuance of shares of common stock for settlement of RSUs 33,334 — — — — — Unrealized loss on marketable debt securities, net of tax — — — ( 18 ) — ( 18 ) Stock-based compensation — — 5,410 — — 5,410 Net loss — — — — ( 24,995 ) ( 24,995 ) Balance as of September 30, 2019 25,872,723 $ 26 $ 569,005 $ ( 205 ) $ ( 412,337 ) $ 156,489 4 For the Nine Month Period Common Stock Additional Accumulated Other Total Shares Amount Paid-in Capital Comprehensive Income (Loss) Accumulated Deficit Stockholders' Equity Balance as of December 31, 2019 32,558,307 $ 32 $ 712,807 $ ( 201 ) $ ( 439,421 ) $ 273,217 Issuance of common stock upon exercise of stock options 172,779 1 1,444 — — 1,445 Issuance of common stock under ESPP 42,266 — 467 — — 467 Issuance of shares of common stock for settlement of RSUs 151,184 — — — — — Unrealized gain on marketable debt securities — — — 43 — 43 Stock-based compensation — — 18,111 — — 18,111 Net loss — — — — ( 22,734 ) ( 22,734 ) Balance as of September 30, 2020 32,924,536 $ 33 $ 732,829 $ ( 158 ) $ ( 462,155 ) $ 270,549 Common Stock Additional Accumulated Other Total Shares Amount Paid-in Capital Comprehensive Loss Accumulated Deficit Stockholders' Equity Balance as of December 31, 2018 25,495,425 $ 25 $ 552,762 $ ( 347 ) $ ( 341,787 ) $ 210,653 Issuance of common stock upon exercise of stock options 243,481 — 1,716 — — 1,716 Issuance of common stock under ESPP 36,804 — 515 — — 515 Issuance of shares of common stock for settlement of RSUs 97,013 1 ( 1 ) — — — Settlement of RSUs for cash — — ( 4 ) — — ( 4 ) Unrealized gain on marketable debt securities, net of tax — — — 142 — 142 Stock-based compensation — — 14,017 — — 14,017 Net loss — — — — ( 70,550 ) ( 70,550 ) Balance as of September 30, 2019 25,872,723 $ 26 $ 569,005 $ ( 205 ) $ ( 412,337 ) $ 156,489 See Accompanying Notes to Condensed Consolidated Financial Statements 5 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) 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 two innovative programs: a novel class of oral therapeutic candidates targeting chronic hepatitis B virus (HBV) infection and a novel class of oral live microbial biotherapeutic candidates, which are designed to treat disorders associated with the microbiome. The Company operates in one segment and is headquartered in South San Francisco, California, with operations in California, Connecticut and China. The Company’s HBV Cure program is pursuing multiple drug candidates that inhibit the HBV replication cycle and block the generation of covalently closed circular DNA (cccDNA), with the aim of increasing the current low cure rates for patients with chronic HBV infection. Assembly has discovered several novel core inhibitors, which are small molecules that directly target and allosterically modify the HBV core protein. The Company’s Microbiome program is centered on a fully integrated platform that includes a biological function-based strain isolation, identification, characterization and selection process, methods for strain purification and growth under conditions compliant with current Good Manufacturing Practice (cGMP) requirements. That platform is complemented by a licensed patented delivery system, GEMICEL®, which is designed to allow for targeted oral delivery of live biologic and conventional therapies to the lower gastrointestinal (GI) tract. Using the Company’s microbiome platform, the Company is exploring product candidates for multiple disease indications, including ulcerative colitis (UC), Crohn’s disease and irritable bowel syndrome (IBS) in connection with its Research, Development, Collaboration and License Agreement (the Allergan Agreement) with Allergan Pharmaceuticals International Limited (Allergan), which was acquired by AbbVie Inc. (AbbVie). In June 2020, AbbVie made a strategic portfolio decision to terminate the Allergan Agreement effective on October 10, 2020 (see Note 8). Assembly is also exploring the microbiome in connection with immune-mediated and metabolic disorders and oncology. 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, proceeds from the exercise of warrants and stock options, issuance of debt, an upfront payment related to the Allergan Agreement and an upfront payment related to the Company’s Collaboration Agreement (the BeiGene Agreement) with BeiGene, Ltd. (BeiGene). 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 12 months following the date that these unaudited condensed consolidated interim 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 6 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 global 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 sufficient 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 its current rate of spending through reductions in staff and delaying, scaling back, or stopping certain research and development programs, including more costly clinical trials. 6 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) Note 2 - Summary of Significant Accounting Policies and Recent Accounting Pronouncements Basis of Presentation The accompanying unaudited interim condensed consolidated financial statements include the accounts of the Company and its subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. The accompanying unaudited interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (U.S. GAAP) for interim financial information and pursuant to the instructions to Form 10-Q and Rule 10-01 of Regulation S-X of the U.S. Securities and Exchange Commission (SEC). In management’s opinion, the unaudited interim condensed consolidated financial statements have been prepared on the same basis as the annual audited consolidated financial statements and include normal recurring adjustments necessary for the fair presentation of the Company’s financial position and its results of operations and comprehensive loss and its cash flows for the periods presented. These statements do not include all disclosures required by U.S. GAAP and should be read in conjunction with the Company’s audited consolidated financial statements and accompanying notes for the fiscal year ended December 31, 2019, which are contained in the Company’s Annual Report on Form 10-K as filed with the SEC on March 4, 2020. The results for the three and nine months ended September 30, 2020 are not necessarily indicative of results to be expected for the entire year ending December 31, 2020 or future operating periods. Use of Estimates The preparation of the unaudited condensed consolidated financial statements in conformity with 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 unaudited condensed consolidated financial statements include revenue recognition, clinical trial accruals, recoverability and useful lives (indefinite or finite) of intangible assets, assessment of impairment of goodwill, provisions for income taxes, amounts receivable and recognized as revenue under the Company’s collaboration agreements, measurement of operating lease liabilities, and the fair value of stock options, stock appreciation rights, and restricted stock units (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 materially 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. Revenue Recognition and Accounts Receivable from Collaboration We analyze our 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, we consider whether the activities of the collaboration are considered to be distinct and deemed to be within the scope of the collaborative arrangement guidance and those that are more reflective of a vendor-customer relationship and, therefore, within the scope of the revenue with contracts with customers guidance. This assessment is performed throughout the life of the arrangement based on changes in the responsibilities of all parties in the arrangement. 7 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) For elements of collaboration arrangements that are not accounted for pursuant to the revenue from contracts with customers guidance, an appropriate recognition method is determined and applied consistently, generally by analogy to the revenue from contracts with customers guidance. 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 condensed 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 guidance, 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: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations, including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations; and (v) 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. 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. 8 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) 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. Income Taxes 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. The FFCR Act, CARES Act and A.B. 85 did not have a material impact on the Company’s condensed consolidated financial statements as of September 30, 2020; however, the Company continues to examine the impacts the FFCR Act, CARES Act and A.B. 85 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. 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 6). The pre-funded warrants are exercisable for shares of common stock at an exercise 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, are fully vested, and are exercisable after the original issuance date. 9 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) A reconciliation of the numerators and the denominators of the basic and diluted net loss per common share computations is as follows (in thousands, except per share amounts): Three Months Ended September 30, Nine Months Ended September 30, 2020 2019 2020 2019 Numerator: Net loss $ ( 3,349 ) $ ( 24,995 ) $ ( 22,734 ) $ ( 70,550 ) Denominator: Weighted average common shares and pre-funded warrants outstanding - basic and diluted 35,506,042 25,912,568 35,321,393 25,765,414 Net loss per share - basic and diluted $ ( 0.09 ) $ ( 0.96 ) $ ( 0.64 ) $ ( 2.74 ) Securities excluded from the computation of diluted loss per share because including them would have been antidilutive are as follows: September 30, 2020 2019 Warrants to purchase common stock - 15,296 Options to purchase common stock 6,660,918 5,462,773 Common stock subject to purchase under our ESPP 25,192 17,018 Unvested RSUs 851,589 668,515 Total 7,537,699 6,163,602 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 guidance 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 condensed 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 condensed 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 10 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) 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. T he adoption of this standard had no impact on the Company’s condensed consolidated financial statements and related disclosures. 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 guidance 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 guidance 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 condensed consolidated financial statements and related disclosures. Recent Accounting Pronouncements 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 guidance related to transition and clarification. In November 2019, the FASB issued 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 evaluating this new accounting standard but currently does not expect the adoption of this standard to have a material impact on its condensed 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 condensed consolidated financial statements and related disclosures. 11 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) Note 3 – Investments in Marketable Securities 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, accrued expenses, lease liability-short term and deferred revenue-short term. 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 that 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. Investments in marketable securities consisted of the following (in thousands): September 30, 2020 Amortized Cost Gross Unrealized Gain Gross Unrealized Loss Fair Value Cash equivalents Money market funds $ 56,444 $ — $ — $ 56,444 Total cash equivalents 56,444 — — 56,444 Short-term investments U.S. and foreign corporate debt securities 36,739 48 ( 1 ) 36,786 Asset-backed securities 13,394 16 ( 1 ) 13,409 U.S. treasury securities 48,018 69 — 48,087 U.S. and foreign commercial paper 81,348 — — 81,348 Total short-term investments 179,499 133 ( 2 ) 179,630 Total cash equivalents and investments $ 235,943 $ 133 $ ( 2 ) $ 236,074 December 31, 2019 Amortized Cost Gross Unrealized Gain (1) Gross Unrealized Loss (1) 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. 12 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) The contractual term to maturity of short-term marketable securities held by the Company as of September 30, 2020 is less than one year . There were no long-term marketable securities held by the Company as of September 30, 2020. Realized gains and losses for the three and nine months ended September 30, 2020 and 2019 were not significant. None of the Company’s investments have been in a continuous unrealized loss position for more than 12 months as of September 30, 2020. The following tables present the fair value of the Company’s financial assets measured at fair value on a recurring basis (in thousands): September 30, 2020 Level 1 Level 2 Level 3 Fair Value Cash equivalents Money market fund $ 56,444 $ — $ — $ 56,444 Total cash equivalents 56,444 — — 56,444 Short-term investments U.S. and foreign corporate debt securities — 36,786 — 36,786 Asset-backed securities — 13,409 — 13,409 U.S. treasury securities — 48,087 — 48,087 U.S. and foreign commercial paper — 81,348 — 81,348 Total short-term investments — 179,630 — 179,630 Total assets measured at fair value $ 56,444 $ 179,630 $ — $ 236,074 December 31, 2019 Level 1 Level 2 Level 3 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 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 were no transfers between Level 1, Level 2 or Level 3 during the periods presented. 13 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) Note 4 - Property and Equipment, Net Property and equipment consist of the following (in thousands): Useful life September 30, December 31, (Years) 2020 2019 Lab equipment 3 to 5 $ 292 $ 247 Office equipment 7 699 699 Leasehold improvement 1 to 5 2,490 2,084 Total property and equipment 3,481 3,030 Less: Accumulated depreciation and amortization ( 1,577 ) ( 1,200 ) Property and equipment, net $ 1,904 $ 1,830 Depreciation expense was $ 0.1 million and $ 0.4 million for the three and nine months ended September 30, 2020 and 2019, respectively and was recorded in both research and development expense and general and administrative expense in the unaudited condensed consolidated statements of operations and comprehensive loss. Substantially all of the Company’s property and equipment is located in the U.S. Note 5 – Accrued Expenses Accrued expenses consist of the following (in thousands): September 30, December 31, 2020 2019 Accrued expenses: Accrued compensation $ 6,172 $ 5,312 Accrued restructuring charges 697 2,094 Accrued professional fees and other 535 880 Total accrued expenses $ 7,404 $ 8,286 Accrued restructuring charges relate to the Company’s decision to relocate its headquarters to South San Francisco, California, which was approved by the Board of Directors in November 2019 and effective January 1, 2020. The Company accrued restructuring charges of $ 2.1 million in 2019 related to one-time 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 and is expected to be fully paid in 2020. Note 6 – Stockholders’ Equity The Company is authorized to issue 5,000,000 shares of preferred stock as of September 30, 2020 and December 31, 2019, respectively. As of September 30, 2020 and December 31, 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 September 30, 2020 and December 31, 2019, respectively. Sale of Common Stock and Pre-Funded Warrants In December 2017, the Company filed a shelf 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. 14 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) 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 additional 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 per warrant. 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 was 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. As of September 30, 2020, no shares have been sold under the 2020 Registration Statement. 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 The following warrants to purchase shares of the Company’s common stock were issued and outstanding: Issue date Expiration date Exercise Price per Share September 30, 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 There were no warrants exercised during the three and nine months ended September 30, 2020 or 2019. 15 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) Note 7 – Stock Plans and 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 number of 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 September 30, 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 September 30, 2020, the Company also had awards outstanding under the Assembly Biosciences, Inc. 2017 Inducement Award Plan (the 2017 Plan), the Assembly Biosciences, Inc. 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 and 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 A summary of the Company’s option activity and related information for the nine months ended September 30, 2020 is as follows: 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 1,486,780 16.79 Exercised ( 172,779 ) 9.78 Forfeited ( 266,436 ) 21.49 Outstanding as of September 30, 2020 6,660,918 $ 16.03 7.1 $ 26,951 Options vested and exercisable as of September 30, 2020 3,652,897 $ 14.34 5.6 $ 22,820 The weighted-average grant-date fair value of options granted was $ 11.01 and $ 10.79 during the nine months ended September 30, 2020 and 2019, respectively. The total intrinsic value of options exercised during the nine months ended September 30, 2020 and 2019 was $ 2.0 million and $ 1.6 million, respectively. 16 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) RSUs A summary of the Company’s RSUs and related information for the nine months ended September 30, 2020 is as follows: Number of RSUs Weighted Average Fair Value Per RSU at Grant Price Nonvested as of December 31, 2019 758,718 $ 25.47 Granted 531,164 16.31 Vested ( 228,925 ) 24.73 Forfeited ( 69,368 ) 23.68 Nonvested as of September 30, 2020 991,589 (1) $ 20.86 (1) Includes 140,000 RSUs that have vested but are subject to deferred settlement, which have a weighted average remaining contractual term of 2.4 years. The total fair value of RSUs vested and settled during the nine months ended September 30, 2020 and 2019 was $ 6.2 million and $ 3.6 million, respectively. The total intrinsic value of RSUs vested and settled during the nine months ended September 30, 2020 and 2019 was $ 3.9 million and $ 1.8 million, respectively. As of September 30, 2020, RSUs outstanding include 100,000 RSUs granted in September 2019 to the Company’s chief executive officer with performance-based conditions vesting 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 September 30, 2020. In July 2020, the performance condition for 45,000 RSUs granted in December 2017 to an executive officer was met. The Company recognized $ 0.7 million as a cumulative catch-up adjustment of stock-based compensation expense for this award for the nine months ended September 30, 2020. ESPP Employees purchased 42,266 and 36,804 shares of common stock under the 2018 ESPP during the nine months ended September 30, 2020 and 2019, respectively. Valuation Assumptions The fair value of the stock options granted or modified during the periods indicated was estimated using the Black-Scholes option pricing model, based on the following assumptions: Three Months Ended September 30, Nine Months Ended September 30, 2020 2019 2020 2019 Exercise price $20.14 - $23.30 $10.91 - $49.14 $14.45 - $23.30 $10.91 - $57.33 Expected volatility 68.9% - 81.6% 66.4% - 80.6% 66.4% - 82.2% 66.2% - 83.2% Risk-free rate 0.26% - 0.52% 1.36% - 1.89% 0.26% - 1.44% 1.36% - 2.65% Expected term (years) 5.5 - 7.0 5.5 - 9.6 5.5 - 7.5 5.0 - 9.6 Expected dividend yield 0 % 0 % 0 % 0 % The fair value of RSUs granted is determined based on the price of the Company’s common stock on the date of grant. The fair value of ESPP purchase rights were not material for any period presented. 17 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) Stock-Based Compensation Expense The following table summarizes the components of total stock-based compensation expense included in the condensed consolidated statements of operations and comprehensive loss (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2020 2019 2020 2019 Research and development $ 2,759 $ 2,464 $ 8,310 $ 8,309 General and administrative 3,289 2,940 9,796 5,740 (1) Total stock-based compensation expense $ 6,048 $ 5,404 $ 18,106 $ 14,049 (1) Includes the reversal of previously recognized stock-based compensation expense of $ 3.6 million related to forfeited awards resulting from the departure of one of the Company’s former officers during the period. As of September 30, 2020, there was $ 27.8 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. Note 8 - Collaboration Agreements Allergan Agreement In January 2017, the Company entered into the Allergan Agreement with Allergan to develop and commercialize select microbiome gastrointestinal disease therapies. The terms and conditions as well as the accounting analysis for the Allergan Agreement are described in Note 8 “Collaboration Agreement” to the consolidated financial statements in the Company’s Annual Report on Form 10-K. In June 2020, following its acquisition of Allergan, AbbVie, on behalf of Allergan, gave written notice of termination of the Allergan Agreement, which subsequently became effective 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 is obligated to continue to reimburse the Company for certain research and development costs through October 10, 2020. Upon effectiveness of the termination, such reimbursements will cease. 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 the period. For the three months ended September 30, 2020, the Company recognized $ 3.6 million in collaboration revenue associated with the Allergan Agreement, none of which had been included in deferred revenue at the beginning of the period. For the nine months ended September 30, 2020, the Company recognized $ 47.1 million in collaboration revenue associated with the Allergan Agreement, of which $ 37.0 million was included in deferred revenue as of the beginning of the period. For the three and nine months ended September 30, 2019, the Company recognized $ 4.2 million and $ 11.2 million in revenue, respectively, of which $ 1.2 million and $ 2.2 million, respectively, had been included in deferred revenue at the beginning of the period. Short-term and long-term deferred revenue contract liabilities related to the Allergan Agreement were $ 6.4 million and $ 30.6 million as of December 31, 2019. There were no deferred revenue contract liabilities as of September 30, 2020 due to the Company recognizing a cumulative catch-up adjustment of the remaining deferred revenue balance during the nine months ended September 30, 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 $ 3.6 million and $ 3.4 million were recorded as accounts receivable from collaboration on the condensed consolidated balance sheets as of September 30, 2020 and December 31, 2019, respectively. 18 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) BeiGene Agreement In July 2020, the Company and BeiGene entered into 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 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 knowhow 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. 19 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) 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 September 30, 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. During the three and nine months ended September 30, 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 unaudited condensed consolidated balance sheet as of September 30, 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 three and nine months ended September 30, 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 September 30, 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 condensed consolidated statements of operations, as the Company does no t consider performing research and development services for reimbursement to be a part of its ongoing major or central operations 20 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) Contract Liabilities The following table presents changes in the Company’s contract liabilities (in thousands): Balance at Beginning of Period Additions Deductions Balance at End of Period Nine Months Ended September 30, 2020 Contract liabilities: Deferred revenue $ 37,048 $ 40,000 $ ( 68,061 ) $ 8,987 Balance at Beginning of Period Additions Deductions Balance at End of Period Nine Months Ended September 30, 2019 Contract liabilities: Deferred revenue $ 40,660 $ — $ ( 2,241 ) $ 38,419 Note 9 - Milestones and Research 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 such fees for that year. A performance milestone totaling $ 0.1 million was determined to have occurred under this agreement and was paid during the three and nine months ended September 30, 2020. Additionally, the Company paid IURTC $ 0.7 million as a sublicensing fee during the three and nine months ended September 30, 2020. The milestone and license fees are included in research and development expenses in the condensed consolidated statements of operations and comprehensive loss. Amounts paid in the nine months ended September 30, 2019 were insignificant. 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. In addition, the Company must pay Therabiome lesser amounts for foreign regulatory milestones, which vary by country and region. The Company is also required to 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 such 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. No amounts were accrued for this agreement as of and for the nine months ended September 30, 2020. Two regulatory milestones totaling $ 0.3 million were determined to have occurred under this agreement and were paid during the nine months ended September 30, 2019. 21 ASSEMBLY BIOSCIENCES, INC. NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) Note 10 - Leases Operating Leases The Company leases office space for corporate, administrative and laboratory functions in South San Francisco, California under a sub-sublease that expires in December 2023. The Company also leases office space in Carmel, Indiana under a lease agreement that expires in August 2023, which the Company has subleased. The Company also leases office and laboratory space in Groton, Connecticut under a lease that expires in March 2021. The Company’s China subsidiary leases office space in Shanghai that expires in May 2021 and rents lab space in Shanghai under a lease agreement that expires in December 2020. 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. Certain equipment leases continue to expire in 2020, with the final lease expiring in 2023. 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. At September 30, 2020, the Company had operating lease liabilities of $ 10.8 million and ROU assets of $ 10.4 million, which were included in the condensed consolidated balance sheet. The following summarizes quantitative information about the Company’s operating leases (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2020 2019 2020 2019 Lease cost Operating lease cost $ 1,164 $ 1,136 $ 3,463 $ 3,344 Short-term lease cost 101 88 301 520 Variable lease cost 409 301 1,101 900 Total lease cost $ 1,674 $ 1,525 $ 4,865 $ 4,764 Nine Months Ended September 30, 2020 2019 Operating cash flows from operating leases $ 3,382 $ 3,188 ROU assets exchanged for new operating lease liabilities $ 1,063 $ 15,261 As of September 30, 2020 and December 31, 2019, the weighted-average remaining lease term for operating leases was 3.0 years and 2.7 years, respectively. As of September 30, 2020 and December 31, 2019, the weighted-average discount rate for operating leases was 9.3 % and 9.4 %, respectively. As of September 30, 2020, the maturities of the Company’s operating lease liabilities were as follows (in thousands): Three months ending December 31, 2020 $ 1,208 Year Ending December 31, 2021 4,182 Year Ending December 31, 2022 3,818 Year Ending December 31, 2023 3,436 Total 12,644 Less: present value discount ( 1,871 ) Operating lease liabilities $ 10,773 22