CODEXIS, INC. 10-Q

Item 1. Financial Statements Codexis, Inc. Condensed Consolidated Balance Sheets (Unaudited) (In Thousands, Except Per Share Amounts) March 31, 2023 December 31, 2022 Assets Current assets: Cash and cash equivalents $ 102,831 $ 113,984 Restricted cash, current 525 521 Financial assets: Accounts receivable 9,934 31,904 Contract assets 2,449 2,116 Unbilled receivables 7,797 7,016 Total financial assets 20,180 41,036 Less: allowances ( 163 ) ( 163 ) Total financial assets, net 20,017 40,873 Inventories 1,996 2,029 Prepaid expenses and other current assets 4,585 5,487 Total current assets 129,954 162,894 Restricted cash 1,526 1,521 Investment in non-marketable equity securities ($ 0 and $ 13,921 with a related party) 21,310 20,510 Right-of-use assets - Operating leases, net 38,013 39,263 Property and equipment, net 23,609 22,614 Goodwill 3,241 3,241 Other non-current assets 415 350 Total assets $ 218,068 $ 250,393 Liabilities and Stockholders' Equity Current liabilities: Accounts payable $ 4,494 $ 3,246 Accrued compensation 6,611 11,453 Other accrued liabilities 8,340 15,279 Current portion of lease obligations - Operating leases 5,492 5,360 Deferred revenue 13,374 13,728 Total current liabilities 38,311 49,066 Deferred revenue, net of current portion 15,508 16,881 Long-term lease obligations - Operating leases 36,845 38,278 Other long-term liabilities 1,388 1,371 Total liabilities 92,052 105,596 Commitments and Contingencies (Note 10) Stockholders' equity: Preferred stock, $ 0.0001 par value per share; 5,000 shares authorized, none issued and outstanding — — Common stock, $ 0.0001 par value per share; 100,000 shares authorized; 66,696 shares and 65,811 shares issued and outstanding as of March 31, 2023 and December 31, 2022, respectively 6 6 Additional paid-in capital 569,917 566,081 Accumulated deficit ( 443,907 ) ( 421,290 ) Total stockholders' equity 126,016 144,797 Total liabilities and stockholders' equity $ 218,068 $ 250,393 See accompanying notes to the unaudited condensed consolidated financial statements. 3 Codexis, Inc. Condensed Consolidated Statements of Operations (Unaudited) (In Thousands, Except Per Share Amounts) Three Months Ended March 31, 2023 2022 Revenues: Product revenue $ 8,364 $ 30,690 Research and development revenue ($ 0 and $ 245 from a related party) 4,618 4,650 Total revenues 12,982 35,340 Costs and operating expenses: Cost of product revenue 4,521 8,521 Research and development 16,655 19,500 Selling, general and administrative 15,399 15,705 Restructuring charges 72 — Total costs and operating expenses 36,647 43,726 Loss from operations ( 23,665 ) ( 8,386 ) Interest income 1,089 42 Other expense, net ( 25 ) ( 3 ) Loss before income taxes ( 22,601 ) ( 8,347 ) Provision for income taxes 16 9 Net loss $ ( 22,617 ) $ ( 8,356 ) Net loss per share, basic and diluted $ ( 0.34 ) $ ( 0.13 ) Weighted average common stock shares used in computing net loss per share, basic and diluted 65,931 65,096 See accompanying notes to the unaudited condensed consolidated financial statements. 4 Codexis, Inc. Condensed Consolidated Statements of Stockholders' Equity (Unaudited) (In Thousands) Common Stock Additional Paid-in Capital Accumulated Deficit Total Stockholders' Equity Three Months Ended March 31, 2023 Shares Amount Balance as of January 1, 2023 65,811 $ 6 $ 566,081 $ ( 421,290 ) $ 144,797 Exercise of stock options 143 — 281 — 281 Release of stock awards 479 — — — — Employee stock-based compensation — — 2,809 — 2,809 Issuance of common stock, net of issuance costs of $ 390 328 — 1,150 — 1,150 Taxes paid related to net share settlement of equity awards ( 65 ) — ( 404 ) — ( 404 ) Net loss — — — ( 22,617 ) ( 22,617 ) Balance as of March 31, 2023 66,696 $ 6 $ 569,917 $ ( 443,907 ) $ 126,016 Common Stock Additional Paid-in Capital Accumulated Deficit Total Stockholders' Equity Three Months Ended March 31, 2022 Shares Amount Balance as of January 1, 2022 65,109 $ 6 $ 552,083 $ ( 387,698 ) $ 164,391 Exercise of stock options 78 — 181 — 181 Release of stock awards 190 — — — — Employee stock-based compensation — — 3,777 — 3,777 Non-employee stock-based compensation — — 61 — 61 Taxes paid related to net share settlement of equity awards ( 73 ) — ( 1,419 ) — ( 1,419 ) Net loss — — — ( 8,356 ) ( 8,356 ) Balance as of March 31, 2022 65,304 $ 6 $ 554,683 $ ( 396,054 ) $ 158,635 See accompanying notes to the unaudited condensed consolidated financial statements. 5 Codexis, Inc. Condensed Consolidated Statements of Cash Flows (Unaudited) (In Thousands) Three Months Ended March 31, 2023 2022 Operating activities: Net loss $ ( 22,617 ) $ ( 8,356 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation 1,466 1,215 Amortization expense - right-of-use assets - operating and finance leases 1,249 1,200 Stock-based compensation 2,809 3,838 Equity securities earned from research and development activities ($ 0 and ($ 245 ) from a related party) ( 50 ) ( 245 ) Other non-cash items ( 5 ) ( 7 ) Changes in operating assets and liabilities: Financial assets 20,856 ( 6,463 ) Inventories 33 ( 400 ) Prepaid expenses and other assets 586 1,397 Accounts payable 694 ( 1,029 ) Accrued compensation and other accrued liabilities ( 11,091 ) ( 121 ) Other long-term liabilities ( 1,415 ) ( 1,192 ) Deferred revenue ( 1,727 ) ( 1,023 ) Net cash used in operating activities ( 9,212 ) ( 11,186 ) Investing activities: Purchase of property and equipment ( 2,539 ) ( 5,089 ) Proceeds from sale of property and equipment 5 7 Investment in non-marketable securities ( 750 ) ( 5,000 ) Net cash used in investing activities ( 3,284 ) ( 10,082 ) Financing activities: Proceeds from exercises of stock options 281 181 Proceeds from issuance of common stock in connection with public offering 1,540 — Costs incurred in connection with issuance of common stock at public offering ( 65 ) ( 42 ) Taxes paid related to net share settlement of equity awards ( 404 ) ( 1,419 ) Net cash provided by (used in) financing activities 1,352 ( 1,280 ) Net decrease in cash, cash equivalents and restricted cash ( 11,144 ) ( 22,548 ) Cash, cash equivalents and restricted cash at the beginning of the period 116,026 118,895 Cash, cash equivalents and restricted cash at the end of the period $ 104,882 $ 96,347 Supplemental disclosure of cash flow information: Interest paid $ 7 $ 5 Income taxes paid $ 193 $ — Supplemental non-cash investing and financing activities: Capital expenditures incurred but not yet paid $ 819 $ 789 6 The following table provides a reconciliation of cash, cash equivalents and restricted cash reported within the unaudited condensed consolidated balance sheets as of March 31, 2023 and 2022 to the total of the same such amounts shown above in the unaudited condensed consolidated statements of cash flows: March 31, 2023 2022 Cash and cash equivalents $ 102,831 $ 94,260 Restricted cash, current and non-current 2,051 2,087 Total cash, cash equivalents and restricted cash $ 104,882 $ 96,347 See accompanying notes to the unaudited condensed consolidated financial statements. 7 Codexis Inc. Notes to Condensed Consolidated Financial Statements (Unaudited) Note 1. Description of Business In these notes to the unaudited condensed consolidated financial statements, the “Company,” “we,” “us,” and “our” refers to Codexis, Inc. and its subsidiaries on a consolidated basis. We are a leading enzyme engineering company leveraging our CodeEvolver ® technology platform to discover, develop, enhance, and commercialize novel, high performance enzymes and other classes of proteins. We report our financial results based o n two r eportable segments: Performance Enzymes and Novel Biotherapeutics. Our Novel Biotherapeutics business includes a diverse pipeline of product candidates in clinical and preclinical development. Our Performance Enzymes business consists primarily of two focus areas: i) biocatalysts for the sustainable manufacturing of pharmaceuticals and ii) enzymes for life science applications, including genomic sequencing and nucleic acid synthesis. The segment information aligns with how the chief operating decision maker (CODM), who is our Chief Executive Officer (CEO), reviews and manages the business. Note 2. Basis of Presentation and Summary of Significant Accounting Policies Basis of Presentation and Principles of Consolidation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally accepted accounting principles in the United States of America ("GAAP") and the applicable rules and regulations of the Securities and Exchange Commission ("SEC") for interim financial information but does not include all the information and notes required by GAAP for complete financial statements. These interim unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto contained in our Annual Report on Form 10-K for the year ended December 31, 2022. The condensed consolidated balance sheet at December 31, 2022 has been derived from the audited consolidated financial statements at that date, but does not include all disclosures, including notes, required by GAAP for complete financial statements. The significant accounting policies used in preparation of the unaudited condensed consolidated financial statements for the three months ended March 31, 2023 and 2022, are consistent with those discussed in Note 2 to the audited consolidated financial statements in the Company’s 2022 Annual Report on Form 10-K and are updated below as necessary. There have been no significant changes in our significant accounting policies or critical accounting estimates since December 31, 2022. The unaudited condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all adjustments of a normal recurring nature considered necessary to present fairly our financial position as of March 31, 2023, results of our operations for the three months ended March 31, 2023 and 2022, changes in stockholders' equity for the three months ended March 31, 2023 and 2022, and cash flows for the three months ended March 31, 2023 and 2022. The interim results are not necessarily indicative of the results for any future interim period or for the entire year. The unaudited condensed consolidated financial statements include the accounts of Codexis, Inc. and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. Use of Estimates The preparation of our unaudited condensed consolidated financial statements in conformity with GAAP requires us to make estimates, judgments and assumptions that may affect the reported amounts of assets, liabilities, equity, revenues and expenses and related disclosure of contingent assets and liabilities. We regularly assess these estimates which primarily affect revenue recognition, inventories, valuation of equity investments, goodwill arising out of business acquisitions, accrued liabilities, stock awards, and the valuation allowances associated with deferred tax assets. Actual results could differ from those estimates and such differences may be material to the consolidated financial statements. The full extent to which the COVID-19 pandemic will directly or indirectly impact our business, results of operations and financial condition, including sales, expenses, reserves and allowances, manufacturing, research and development costs and employee-related amounts, will depend on future developments that are highly uncertain, and may not be accurately predicted, including as a result of new information that may emerge concerning COVID-19 and the actions taken to contain or treat COVID-19, as well as the economic impact on local, regional, national and international customers, markets and economies. 8 Accounting Pronouncements Recently adopted accounting pronouncements or recently issued accounting pronouncements not yet adopted There were no recent accounting pronouncements or changes in accounting pronouncements during the three months ended March 31, 2023, that are of significance or potential significance to us. Note 3. Revenue Recognition Disaggregation of Revenue The following table provides information about disaggregated revenue from contracts with customers into the nature of the products and services, and geographic regions, and includes a reconciliation of the disaggregated revenue with reportable segments. The geographic regions that are tracked are the Americas (United States, Canada, and Latin America), EMEA (Europe, Middle East, and Africa), and APAC (Australia, New Zealand, Southeast Asia, and China). Segment information is as follows (in thousands): Three Months Ended March 31, 2023 Three Months Ended March 31, 2022 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Major products and service: Product revenue $ 8,364 $ — $ 8,364 $ 30,690 $ — $ 30,690 Research and development revenue 1,122 3,496 4,618 2,409 2,241 4,650 Total revenues $ 9,486 $ 3,496 $ 12,982 $ 33,099 $ 2,241 $ 35,340 Primary geographical markets: Americas $ 918 $ 1,666 $ 2,584 $ 2,553 $ 1,179 $ 3,732 EMEA 1,259 1,830 3,089 3,065 1,062 4,127 APAC 7,309 — 7,309 27,481 — 27,481 Total revenues $ 9,486 $ 3,496 $ 12,982 $ 33,099 $ 2,241 $ 35,340 Contract Balances The following table presents balances of contract assets, unbilled receivables, contract costs, and contract liabilities (in thousands): March 31, 2023 December 31, 2022 Contract assets $ 2,449 $ 2,116 Unbilled receivables $ 7,797 $ 7,016 Contract costs $ 2 $ 19 Contract liabilities: deferred revenue $ 28,882 $ 30,609 We ha d no a sset impairment charges related to financial assets in the three months ended March 31, 2023 and 2022. The increase in contract assets was primarily due to increases in product revenue from contracts subject to over time revenue recognition. The increase in unbilled receivables was primarily due to the timing of billings. The decrease in deferred revenue was primarily due to timing of recognition of revenue. 9 We recognized t he following revenues ( in thousands): Three Months Ended March 31, Revenue recognized in the period for: 2023 2022 Amounts included in contract liabilities at the beginning of the period: Performance obligations satisfied $ 1,602 $ 1,094 Changes in the period: Changes in the estimated transaction price allocated to performance obligations satisfied in prior periods ( 216 ) 215 Performance obligations satisfied from new activities in the period - contract revenue 11,596 34,031 Total revenues $ 12,982 $ 35,340 Performance Obligations The following table includes estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied or partially unsatisfied at the end of the reporting periods. The estimated revenue does not include contracts with original durations of one year or less, amounts of variable consideration attributable to royalties, or contract renewals that are unexercised as of March 31, 2023. Th e balances in the table below are partially based on judgments involved in estimating future orders from customers subject to the exercise of material rights pursuant to respective contracts as of March 31, 2023 (in thousands): Remainder of 2023 2024 2025 2026 and Thereafter Total Product revenue $ 5,891 $ 12,050 $ 100 $ 3,339 $ 21,380 Research and development revenue 7,480 22 — — 7,502 Total revenues $ 13,371 $ 12,072 $ 100 $ 3,339 $ 28,882 Note 4. N et Loss per S hare Basic net loss per share is computed by dividing the net loss by the weighted-average number of shares of common stock outstanding, less restricted stock awards ("RSAs") subject to forfeiture. Diluted net loss per share is computed by dividing net loss by the weighted-average number of shares of common stock shares outstanding, less RSAs subject to forfeiture, plus all additional common shares that would have been outstanding, assuming dilutive potential common stock shares had been issued for other dilutive securities. For all periods presented, diluted and basic net loss per share, are identical since potential common stock shares are excluded from the calculation, as their effect was anti-dilutive. Anti-Dilutive Securities In periods of net loss, the weighted average number of shares outstanding, prior to the application of the treasury stock method, excludes potentially dilutive securities from the computation of diluted net loss per common share because including such shares would have an anti-dilutive effect. The following shares were not considered in the computation of diluted net loss per share because their effect was anti-dilutive (in thousands): Three Months Ended March 31, 2023 2022 Shares issuable under the Equity Incentive Plan 9,397 5,899 Note 5. Investments in Non-Marketable Securities Non-Marketable Equity Securities In March 2023, we purchased an additional 985,545 shares of Molecular Assemblies, Inc. (“MAI”) Series B preferred stock for $ 0.8 million. As of March 31, 2023, we hold an aggregate of 19,277,914 shares of MAI's Series A and B preferred stock that we have earned or purchased from MAI. See Note 11 “Related Party Transactions” for additional information on our investment in MAI. 10 In March 2022, we entered into a Stock Purchase Agreement with seqWell, Inc. (“seqWell”), a privately held biotechnology company, pursuant to which we purchased 1,000,000 shares of seqWell's Series C preferred stock for $ 5.0 million. In March 2023, we entered into a Master Collaboration Agreement and Research Agreement with seqWell (the “seqWell Agreement”), pursuant to which we are providing research and experimental screening and protein engineering activities in exchange for compensation in the form of additional shares of seqWell's common stock. We received 47,933 shares of seqWell's common stock from research and development services with seqWell and we recognized $ 50 thousand in research and development revenue from these services with seqWell during the three months ended March 31, 2023. We own 207,070 shares of Series B-2 preferred stock of Arzeda Corp. (“Arzeda”), an early-stage computational protein design company. Our non-marketable equity securities are investments in privately held companies without readily determinable market value and primarily relate to our investments in MAI, seqWell and Arzeda. These investments are accounted for under the measurement alternative and are measured at cost minus impairment, if any, plus or minus changes resulting from observable price changes for identical or similar securities of the same issuer. Non-marketable equity securities are measured at fair value on a non-recurring basis and classified within Level 2 in the fair value hierarchy because we estimate the fair value of these investments using the observable transaction price paid by third party investors for the same or similar security of the same issuers. We adjust the carrying value of non-marketable equity securities which have been remeasured during the period and recognize resulting gains or losses as a component of other expense, net in the unaudited condensed consolidated statements of operations. There was no remeasurement event for our investments in MAI, seqWell, Arzeda, and other non-marketable equity securities that occurred during the three months ended March 31, 2023 and 2022. We recognized no realized gains or losses during the three months ended March 31, 2023 and 2022. The following table presents the carrying value of our non-marketable equity securities (in thousands): March 31, 2023 December 31, 2022 MAI $ 14,671 $ 13,921 seqWell 5,050 5,000 Arzeda 1,289 1,289 Other investments in non-marketable equity securities 300 300 Total non-marketable equity securities $ 21,310 $ 20,510 Note 6. Fair Value Measurements The following tables present the financial instruments that were measured at fair value on a recurring basis within the fair value hierarchy (in thousands): March 31, 2023 Level 1 Level 2 Level 3 Total Money market funds $ 100,165 $ — $ — $ 100,165 December 31, 2022 Level 1 Level 2 Level 3 Total Money market funds $ 77,309 $ — $ — $ 77,309 During the three months ended March 31, 2023 and 2022, we did no t recognize any significant credit losses no r other-than-temporary impairment losses on non-marketable securities. 11 Note 7. Balance Sheets Details Cash Equivalents Cash equivalents consisted of the following (in thousands): March 31, 2023 December 31, 2022 Adjusted Cost Estimated Fair Value Adjusted Cost Estimated Fair Value Money market funds (1) $ 100,165 $ 100,165 $ 77,309 $ 77,309 (1) Money market funds are classified in cash and cash equivalents on our unaudited condensed consolidated balance sheets. Average contractual maturities (in days) is not applicable. As of March 31, 2023, the total cash and cash equivalents balance of $ 102.8 million consisted of money market funds of $ 100.2 million and cash of $ 2.6 million held with major financial institutions. As of December 31, 2022, the total cash and cash equivalents balance of $ 114.0 million consisted of money market funds of $ 77.3 million and cash of $ 36.7 million held with major financial institutions. Inventories Inventories consisted of the following (in thousands): March 31, 2023 December 31, 2022 Raw materials $ 108 $ 108 Work in process 36 91 Finished goods 1,852 1,830 Total Inventories $ 1,996 $ 2,029 Inventories are recorded net of reserves o f $ 1.2 million a s of March 31, 2023 and December 31, 2022. Property and Equipment, net Property and equipment, net consisted of the following (in thousands): March 31, 2023 December 31, 2022 Laboratory equipment $ 40,489 $ 39,679 Leasehold improvements 16,694 16,633 Computer equipment and software 3,039 3,039 Office equipment and furniture 1,360 1,345 Construction in progress 3,189 1,739 Property and equipment 64,771 62,435 Less: accumulated depreciation and amortization ( 41,162 ) ( 39,821 ) Property and equipment, net $ 23,609 $ 22,614 Depreciation expense included in both research and development expenses and selling, general and administrative expenses in the unaudited condensed consolidated statements of operations was as follows (in thousands): Three Months Ended March 31, 2023 2022 Depreciation expense $ 1,466 $ 1,215 Goodwill Goodwill had a carrying value of $ 3.2 million as of March 31, 2023 and December 31, 2022. 12 Other Accrued Liabilities Other accrued liabilities consisted of the following (in thousands): March 31, 2023 December 31, 2022 Accrued professional and outside service fees $ 4,256 $ 3,495 Accrued purchases 2,896 10,852 Other 1,188 932 Total other accrued liabilities $ 8,340 $ 15,279 Note 8. Stock-based Compensation Equity Incentive Plans In January 2023, our board of directors (the “Board”) approved the 2022 Employment Inducement Award Plan (the “2022 Inducement Plan”) which provides for the grant of non-qualified stock options, restricted stock awards (“RSAs”), restricted stock units (“RSUs”), performance awards, other stock awards and dividend equivalents to eligible employees with respect to an aggregate of up to 2,000,000 shares of our common stock. In 2019, the Board and stockholders approved the 2019 Incentive Award Plan (the “2019 Plan”). The 2019 Plan superseded and replaced in its entirety our 2010 Equity Incentive Plan (the “2010 Plan”) which was effective in March 2010, and no further awards will be granted under the 2010 Plan; however, the terms and conditions of the 2010 Plan will continue to govern any outstanding awards thereunder. The 2019 Plan provides for the grant of stock options, including incentive stock options and non-qualified stock options, stock appreciation rights, RSA, RSUs, performance-contingent restricted stock units (“PSUs”), performance based options (“PBOs”), other stock or cash based awards and dividend equivalents to eligible employees and consultants of the Company or any parent or subsidiary, as well as members of the Board. The number of shares of our common stock available for issuance under the 2019 Plan is equal to the sum of (i) 7,897,144 shares, and (ii) any shares subject to awards granted under the 2010 Plan that were outstanding as of April 22, 2019 and thereafter terminate, expire, lapse or are forfeited; provided that no more than 14,000,000 shares may be issued upon the exercise of incentive stock options (“ISOs”). In June 2019, 8.1 million shares authorized for issuance under the 2019 Plan were registered under the Securities Act of 1933, as amended (the “Securities Act”). The 2010 Plan provided for the grant of incentive stock options, non-statutory stock options, RSUs, RSAs, PSUs, PBOs, stock appreciation rights, and stock purchase rights to our employees, non-employee directors and consultants. Stock Options The option exercise price for incentive stock options must be at least 100 % of the fair value of our common stock on the date of grant and the option exercise price for non-statutory stock options is at least 85 % of the fair value of our common stock on the date of grant, as determined by the Board. If, at the time of a grant, the optionee directly or by attribution owns stock possessing more than 10 % of the total combined voting power of all of our outstanding capital stock, the exercise price for these options must be at least 110 % of the fair value of the underlying common stock. Stock options granted to employees generally have a maximum term of ten years and vest over four years from the date of grant, of which 25 % vest at the end of one year , and 75 % vest monthly over the remaining three years . We may grant options with different vesting terms from time to time. Unless an employee's termination of service is due to disability or death, upon termination of service, any unexercised vested options will be forfeited at the end of three months or the expiration of the option, whichever is earlier. Restricted Stock Units ("RSUs") We also grant employees RSUs, which generally vest over either a three-year period with 33 % of the shares subject to the RSUs vesting on each yearly anniversary of the vesting commencement date or over a four-year period with 25 % of the shares subject to the RSU vesting on each yearly anniversary of the vesting commencement date, in each case contingent upon such employee’s continued service on such vesting date. RSUs are generally subject to forfeiture if employment terminates prior to the release of vesting restrictions. We may grant RSUs with different vesting terms from time to time. 13 Performance-contingent Restricted Stock Units ("PSUs") and Performance Based Options ("PBOs") The compensation committee of the Board approved, solely in respect of non-executive employees, delegated to our CEO the authority to approve grants of PSUs. The compensation committee of the Board also approved grants of PBOs and PSUs to our executives. The PSUs and PBOs vest based upon both the successful achievement of certain corporate operating milestones in specified timelines and continued employment through the applicable vesting date. When the performance goals are deemed to be probable of achievement for these types of awards, recognition of stock-based compensation expense commences. Once the number of shares eligible to vest is determined, those shares vest in two equal installments with 50 % vesting upon achievement, as determined by the compensation committee of the Board, and the remaining 50 % vesting on the first anniversary of achievement, in each case, subject to the recipient’s continued service through the applicable vesting date. If the performance goals are achieved at the threshold level, the number of shares eligible to vest in respect of the PSUs and PBOs would be equal to half the number of PSUs granted and one-quarter the number of shares underlying the PBOs granted. If the performance goals are achieved at the target level, the number of shares eligible to vest in respect of the PSUs and PBOs would be equal to the number of PSUs granted and half of the shares underlying the PBOs granted. If the performance goals are achieved at the superior level, the number of shares eligible to vest in respect of the PSUs would be equal to two times the number of PSUs granted and equal to the number of PBOs granted. The number of shares issuable upon achievement of the performance goals at the levels between the threshold and target levels for the PSUs and PBOs or between the target level and superior levels for the PSUs would be determined using linear interpolation. Achievement below the threshold level would result in no shares being eligible to vest in respect of the PSUs and PBOs. No PSUs and PBOs were granted during the first quarter of 2023. In 2022, we awarded PSUs ("2022 PSUs") and PBOs ("2022 PBOs"), each of which commence vesting based upon the achievement of various weighted performance go als, including finance and corporate strategy, performance enzymes and biotherapeutics deliverables, research plans, and organizational development. In the first quarter of 2023, the compensation committee of the Board determined that the 2022 PSUs and 2022 PBOs performance goals had been achieved at 85 % and 42.5 % of the target level, respectively, and recognized stock-based compensation expenses accordingly. Accordingly, 50 % of the shares underlying the 2022 PSUs and PBOs vested in the first quarter of 2023 and 50 % of the shares underlying the 2022 PSUs and PBOs will vest in the first quarter of 2024, in each case , subject to the recipient’s continued service on each vesting date. In 2021, we awarded PSUs ("2021 PSUs") and PBOs ("2021 PBOs"), each of which commence vesting based upon the determination by the compensation committee of the Board of the achievement of various weighted performance goals, including total revenues, product revenue, performance enzymes pipeline advancements, biotherapeutics pipeline advancements, organization and infrastructure upgrades, and significant events that can be publicly announced. In the first quarter of 2022, we determined that the 2021 PSUs and 2021 PBOs performance goals had been achieved at 146 % and 73 % of the target level, respectively, and recognized stock-based compensation expenses accordingly. Accordingly, 50 % of the shares underlying the 2021 PSUs and PBOs vested in the first quarter of 2022 and 50 % of the shares underlying the 2021 PSUs and PBOs vested in the first quarter of 2023, in each case , subject to the recipient’s continued service on each vesting date. Stock-Based Compensation Expense Stock-based compensation expense is included in the unaudited condensed consolidated statements of operations as follows (in thousands): Three Months Ended March 31, 2023 2022 Cost of product revenue $ 129 $ 100 Research and development 722 1,039 Selling, general and administrative 1,958 2,699 Total $ 2,809 $ 3,838 14 The following table presents total stock-based compensation expense by security type included in the unaudited condensed consolidated statements of operations (in thousands): Three Months Ended March 31, 2023 2022 Stock options $ 922 $ 806 RSUs and RSAs 1,126 1,162 PSUs 837 872 PBOs ( 76 ) 998 Total $ 2,809 $ 3,838 As of March 31, 2023, unr ecognized stock-based compensation expense, net of expected forfeitures, was $ 11.9 million related to unvested stock options, $ 8.6 million related to unvested RSUs and RSAs, $ 1.1 million related to unvested PSUs, and $ 0.2 million related to unvested PBOs based on current estimates of the level of achievement. Stock-based compensation expense for these awards will be recognized through 2027. Note 9. Capital Stock Exercise of Options For the three months ended March 31, 2023 and March 31, 2022, we issued 142,856 and 77,600 shares, respectively, upon option exercises at a weighted-average exercise price of $ 1.97 and $ 2.33 per share, respectively, with net cash proceeds of $ 0.3 million and $ 0.2 million, respectively. Equity Distribution Agreement In May 2021, we filed a Registration Statement on Form S-3 with the SEC, that automatically became effective upon its filing, under which we may sell common stock, preferred stock, debt securities, warrants, purchase contracts, and units from time to time in one or more offerings. On February 27, 2023, we filed a post-effective amendment to that Registration on Form S-3. Pursuant to that post-effective amendment, we registered an aggregate $ 200.0 million of securities. In May 2021, we entered into an Equity Distribution Agreement ("EDA") with Piper Sandler & Co ("PSC"), under which PSC, as our exclusive agent, at our discretion and at such times that we may determine from time to time, may sell over a three-year period from the execution of the EDA up to a maximum of $ 50.0 million of shares of our common stock. Under the terms of the EDA, PSC may sell the shares at market prices by any method that is deemed to be an "at the market offering" as defined in Rule 415 under the Securities Act of 1933, as amended. We are not required to sell any shares at any time during the term of the EDA. The EDA will terminate upon the earlier of: (i) the issuance and sale of all shares through PSC on the terms and conditions of the EDA, or (ii) the termination of the EDA in accordance with its terms. Either party may terminate the EDA at any time upon written notification to the other party in accordance with the EDA, and upon such notification, the offering will terminate. Under no circumstances shall any shares be sold pursuant to the EDA after the date which is three years after the registration statement is first declared effective by the SEC. We agreed to pay PSC a commission of 3 % of the gross sales price of any shares sold pursuant to the EDA. With the exception of certain expenses, we will pay PSC up to 8 % of the gross sales price of the shares sold pursuant to the EDA for a combined amount of commission and reimbursement of PSC's expenses and fees. During the three months ended March 31, 2023, 327,480 shares of our common stock were issued pursuant to the EDA. We received gross proceeds of $ 1.5 million, or $ 1.2 million in net proceeds after PSC's commissions and direct offering expenses of $ 0.4 million. As of March 31, 2023, $ 48.5 million worth of shares remained available for sale under the EDA. During the three months ended March 31, 2022, no shares of our common stock were issued pursuant to the EDA. 15 Note 10. Commitments and Contingencies Operating Leases Our headquarters are located in Redwood City, California, where we occupy approximately 77,300 square feet of office and laboratory space in multiple buildings within the same business park of Metropolitan Life Insurance Company ("MetLife"). Our lease agreement with MetLife ("RWC Lease") includes approximately 28,200 square feet of space located at 200 and 220 Penobscot Drive, Redwood City, California (the “200/220 Penobscot Space”) and approximately 37,900 square feet of space located at 400 Penobscot Drive, Redwood City, California (the “400 Penobscot Space”) (the 200/220 Penobscot Space and the 400 Penobscot Space are collectively referred to as the “Penobscot Space”), and approximately 11,200 square feet of space located at 501 Chesapeake Drive, Redwood City, California (the “501 Chesapeake Space”). We entered into the initial lease with MetLife for our facilities in Redwood City in 2004 and the RWC Lease has been amended multiple times since then to adjust the leased space and terms of the Lease. In February 2019, we entered into an Eighth Amendment to the Lease (the “Eighth Amendment”) with MetLife with respect to the Penobscot Space and the 501 Chesapeake Space to extend the term of the Lease for additional periods. Pursuant to the Eighth Amendment, the term of the lease of the Penobscot Space has been extended through May 2027. The lease term for the 501 Chesapeake Space has been extended to May 2029. We have one (1) option to extend the term of the lease for the Penobscot Space for five ( 5 ) years, and one (1) separate option to extend the term of the lease for the 501 Chesapeake Space for five ( 5 ) years. Pursuant to the terms of the RWC Lease, we exercised our right to deliver a letter of credit in lieu of a security deposit. The letter of credit is collateralized by deposit balances held by the bank in the amount of $ 1.1 million a s of March 31, 2023 and December 31, 2022, and are recorded as non-current restricted cash on the unaudited condensed consolidated balance sheets. In January 2021, we entered into a lease agreement with ARE-San Francisco No. 63, LLC ("ARE") to lease a portion of a facility consisted of approximately 36,593 rentable square feet in San Carlos, California to serve as additional office and research and development laboratory space (the "San Carlos Space"). The lease has a 10 -year term from the lease commencement date of November 30, 2021 with one option to extend the term for an additional period of 5 years. We have provided ARE with a $ 0.5 million security deposit in the form of a letter of credit and is recorded as non-current restricted cash on the consolidated balance sheets. We are required to restore certain areas of the Redwood City and San Carlos facilities that we are renting to their original form. We are expensing the asset retirement obligation over the terms of the respective leases. We review the estimated obligation each reporting period and make adjustments if our estimates change. We recorded asset retirement obligations of $ 0.5 million as of March 31, 2023 and December 31, 2022, which are included in other liabilities on the unaudited condensed consolidated balance sheets. Accretion expense related to our asset retirement obligations was nominal in the three months ended March 31, 2023 and 2022. Lease and other information Lease costs, amounts included in measurement of lease obligations and other information related to non-cancellable operating leases and finance leases were as follows (in thousands): Three Months Ended March 31, 2023 2022 Finance lease costs $ — $ 18 Operating lease cost 1,830 1,831 Short-term lease costs (1) — 30 Total lease cost (2) $ 1,830 $ 1,879 (1) Short-term lease costs on leases with terms of over one month and less than one year. (2) The Company had no variable lease costs. Other information: Operating Leases Weighted-average remaining lease term (in years) 7.0 years Weighted-average discount rate 5.4 % 16 Three Months Ended March 31, Cash paid (in thousands) : 2023 2022 Operating cash flows from operating leases $ 1,882 $ 1,022 As of March 31, 2023, our maturity analysis of annual undiscounted cash flows of the non-cancellable operating leases are as follows (in thousands): Years Ending December 31, Operating Leases 2023 (remaining 9 months) $ 5,686 2024 7,783 2025 8,004 2026 8,232 2027 5,835 Thereafter 14,871 Total minimum lease payments 50,411 Less: imputed interest 8,074 Lease obligations $ 42,337 Reconciliation of operating lease liabilities as shown within the unaudited condensed consolidated balance sheets: Current portion of lease obligations - Operating leases $ 5,492 Long-term lease obligations - Operating leases 36,845 Total operating lease liabilities $ 42,337 Other Commitments We enter into supply and service arrangements in the normal course of business. Supply arrangements are primarily for fixed-price manufacture and supply. Service agreements are primarily for the development of manufacturing processes and certain studies. Commitments under service agreements are subject to cancellation at our discretion which may require payment of certain cancellation fees. The timing of completion of service arrangements is subject to variability in estimates of the time required to complete the work. The following table provides quantitative data regarding our other commitments. Future minimum payments reflect amounts that we expect to pay including potential obligations under services agreements subject to risk of cancellation by us (in thousands): Payments Due by Period Total 2023 (Remaining 9 Months) 2024 and Thereafter Development and manufacturing services agreements $ 3,734 $ 2,543 $ 1,191 Facility maintenance agreement 2,491 2,491 — Total other commitments $ 6,225 $ 5,034 $ 1,191 Credit Facility In June 30, 2017, we entered into a credit facility (the “Credit Facility”) with Western Alliance Bank consisting of term loans (“Term Debt”) up to $ 10.0 million, and advances (“Advances”) under a revolving line of credit ("Revolving Line of Credit") up to $ 5.0 million with an accounts receivable borrowing base of 80 % of eligible accounts receivable. The right to take draws on the Term Debt expired on December 31, 2022. We terminated the loan agreement with Western Alliance Bank in March 2023. 17 Legal Proceedings We may be involved in legal actions in the ordinary course of business, including inquiries and proceedings concerning business practices and intellectual property infringement, employee relations and other claims. We will recognize a loss contingency in the condensed consolidated financial statements when it is probable a liability has been incurred and the amount of the loss can be reasonably estimated. We will disclose any loss contingencies that do not meet both conditions if there is a reasonable possibility that a material loss may have been incurred. Gain contingencies are not recorded until they are realized. Indemnifications We are required to recognize a liability for the fair value of any obligations we assume upon the issuance of a guarantee. We have certain agreements with licensors, licensees and collaborators that contain indemnification provisions. In such provisions, we typically agree to indemnify the licensor, licensee and collaborator against certain types of third-party claims. The maximum amount of the indemnifications is not limited. We accrue for known indemnification issues when a loss is probable and can be reasonably estimated. There were no accruals for expenses related to indemnification issues for any periods presented. Note 11. Related Party Transactions Molecular Assemblies, Inc. In June 2020, we entered into a Stock Purchase Agreement with MAI pursuant to which we purchased 1,587,050 shares of MAI's Series A preferred stock for $ 1.0 million. Mr. Nicols, our former President and CEO until August 2022, also joined MAI’s board of directors in June 2020. Concurrently with our initial equity investment, we entered into a Master Collaboration and Research Agreement with MAI (the “MAI Agreement”), pursuant to which performed services utilizing our CodeEvolver ® protein engineering platform technology to improve DNA polymerase enzymes in exchange for compensation in the form of additional shares of MAI's Series A and B preferred stock which are valued based on the observed transaction price of similar securities that MAI issued to third parties. We completed the R&D service with MAI pursuant to the MAI Agreement during the first quarter of 2022. In addition to our initial equity investment and the shares we have received under the MAI Agreement, in April 2021, we purchased an additional 1,000,000 shares of MAI's Series A preferred stock for $ 0.6 million and in September 2021, we purchased 9,198,423 shares of MAI's Series B preferred stock for $ 7.0 million. Revenues recognized from transactions with MAI in the three months ended March 31, 2023, and subsequent to the related party period which ended in August 2022, are included in the condensed consolidated statement of operations. We recognize d $ 0.2 million in research and development revenue from transactions with MAI in the three months ended March 31, 2022 and during the related party period . Note 12. Segment, Geographical and Other Revenue Information Segment Information We manage our business as two business segments: Performance Enzymes and Novel Biotherapeutics. Our business segments are primarily based on our organizational structure and our operating results as used by our CODM in assessing performance and allocating resources for the Company. We report corporate-related expenses such as legal, accounting, information technology, and other costs that are not otherwise included in our reportable business segments as "corporate costs." All items not included in income (loss) from operations are excluded from the business segments. We manage our assets on a total company basis, not by business segment, as the majority of our operating assets are shared or commingled. Our CODM does not review asset information by business segment in assessing performance or allocating resources, and accordingly, we do not report asset information by business segment. All of our long-lived assets are located in the United States. 18 Factors considered in determining the two reportable segments of the Company include the nature of business activities, the management structure directly accountable to our CODM for operating and administrative activities, availability of discrete financial information and information presented to the Board of Directors. Our CODM regularly reviews our segments and the approach provided by management for performance evaluation and resource allocation. Operating expenses that directly support the segment activity are allocated based on segment headcount, revenue contribution or activity of the business units within the segments, based on the corporate activity type provided to the segment. The expense allocation excludes certain corporate costs that are separately managed from the segments. This provides the CODM with more meaningful segment profitability reporting to support operating decisions and allocate resources. The following table provides financial information by our reportable business segments along with a reconciliation to consolidated loss before income taxes (in thousands): Three Months Ended March 31, 2023 Three Months Ended March 31, 2022 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Revenues: Product revenue $ 8,364 $ — $ 8,364 $ 30,690 $ — $ 30,690 Research and development revenue 1,122 3,496 4,618 2,409 2,241 4,650 Total revenues 9,486 3,496 12,982 33,099 2,241 35,340 Costs and operating expenses: Cost of product revenue 4,521 — 4,521 8,521 — 8,521 Research and development (1) 8,099 7,312 15,411 6,122 12,346 18,468 Selling, general and administrative (1) 2,798 951 3,749 3,541 720 4,261 Restructuring charges — 72 72 — — — Total segment costs and operating expenses 15,418 8,335 23,753 18,184 13,066 31,250 Income (loss) from operations $ ( 5,932 ) $ ( 4,839 ) ( 10,771 ) $ 14,915 $ ( 10,825 ) 4,090 Corporate costs (2) ( 10,364 ) ( 11,205 ) Unallocated depreciation and amortization ( 1,466 ) ( 1,232 ) Loss before income taxes $ ( 22,601 ) $ ( 8,347 ) (1) Research and development expenses and selling, general and administrative expenses exclude depreciation and amortization of finance leases. (2) Corporate costs include unallocated selling, general and administrative expenses, interest income, and other expense, net. The following table provides stock-based compensation expense included in income (loss) from operations (in thousands): Three Months Ended March 31, 2023 2022 Performance Enzymes Novel Biotherapeutics Corporate cost Total Performance Enzymes Novel Biotherapeutics Corporate cost Total Stock-based compensation $ 1,035 $ 413 $ 1,361 $ 2,809 $ 1,690 $ 410 $ 1,738 $ 3,838 Significant Customers Customers that each accounted for 10% or more of our total revenues were as follows: Percentage of Total Revenues for the Three Months Ended March 31, 2023 2022 Customer A * 61 % Customer B 23 % * Customer C 14 % * Customer D 13 % * Customer E 10 % * * Percentage was less than 10% 19 Customers that each accounted for 10% or more of accounts receivable balances as of the periods presented as follows: Percentage of Accounts Receivables as of March 31, 2023 December 31, 2022 Customer A * 53 % Customer B 21 % * Customer C 11 % 10 % Customer F 14 % * Customer G 12 % * * Percentage was less than 10% Geographical Information Geographic revenues are identified by the location of the customer and consist of the following (in thousands): Three Months Ended March 31, 2023 2022 Revenues: Americas $ 2,584 $ 3,732 EMEA 3,089 4,127 APAC 7,309 27,481 Total revenues $ 12,982 $ 35,340 Identifiable long-lived assets by location was as follows (in thousands): March 31, 2023 December 31, 2022 United States $ 61,622 $ 61,877 Identifiable goodwill by reporting unit was as follows (in thousands): As of March 31, 2023 and December 31, 2022 Performance Enzymes Novel Biotherapeutics Total Goodwill $ 2,463 $ 778 $ 3,241 Note 13. Allowance for Credit Losses The following table summarizes the financial assets allowance for credit losses (in thousands): Three Months Ended March 31, 2023 2022 Balance at beginning of period $ 163 $ 416 Provision for credit losses — — Write-offs — — Adjustment to the existing allowance — — Balance at end of period $ 163 $ 416 20 The following tables summarize accounts receivable by aging category (in thousands): March 31, 2023 Current 31-60 Days 61-90 Days 91 Days and over Total over 31 Days Total balance Accounts receivable $ 7,385 $ 508 $ 321 $ 1,720 $ 2,549 $ 9,934 December 31, 2022 Current 31-60 Days 61-90 Days 91 Days and over Total over 31 Days Total balance Accounts receivable $ 28,896 $ 1,747 $ 469 $ 792 $ 3,008 $ 31,904 Note 14. Restructuring Charges In November 2022, we announced a plan for a workforce reduction of approximat ely 18 % of our total employee to realign and optimize our workforce requirements in alignment with our refined corporate strategy. The plan was substantially completed in December 2022 and severance costs were paid through the first quarter of 2023. During the three months ended March 31, 2023, we recorded an additional restructuring charge of $ 0.1 million related to severance, bonus and other termination benefits in connection with the workforce reduction, which is expected to be paid in the second quarter of 2023. We do not expect to record any significant future charges related to the restructuring plan initiated in 2022. 21