Nautilus Biotechnology, Inc. 10-Q

ITEM 1. FINANCIAL STATEMENTS iii Nautilus Biotechnology, Inc. Condensed Consolidated Balance Sheets As of September 30, 2023 and December 31, 2022 (Unaudited) (in thousands, except share and per share amounts) September 30, 2023 December 31, 2022 Assets Current assets: Cash and cash equivalents $ 74,104 $ 114,523 Short-term investments 109,185 69,948 Prepaid expenses and other current assets 3,499 2,738 Total current assets 186,788 187,209 Property and equipment, net 4,283 3,700 Operating lease right-of-use assets 33,669 28,866 Long-term investments 92,439 129,169 Other long-term assets 1,157 1,108 Total assets $ 318,336 $ 350,052 Liabilities and Stockholders’ Equity Current liabilities: Accounts payable $ 1,142 $ 1,272 Accrued expenses and other liabilities 4,285 3,528 Current portion of operating lease liability 3,467 1,991 Total current liabilities 8,894 6,791 Operating lease liability, net of current portion 32,169 28,337 Total liabilities 41,063 35,128 Commitments and contingencies (Note 8) Stockholders’ equity: Preferred stock, $ 0.0001 par value, 200,000,000 authorized as of September 30, 2023 and December 31, 2022; 0 shares issued and outstanding as of September 30, 2023 and December 31, 2022 — — Common stock, $ 0.0001 par value, 1,000,000,000 shares authorized as of September 30, 2023 and December 31, 2022; 124,940,774 and 124,865,485 shares issued and outstanding as of September 30, 2023 and December 31, 2022, respectively 12 12 Additional paid-in capital 464,509 455,330 Accumulated other comprehensive loss ( 2,033 ) ( 1,854 ) Accumulated deficit ( 185,215 ) ( 138,564 ) Total stockholders’ equity 277,273 314,924 Total liabilities and stockholders’ equity $ 318,336 $ 350,052 The accompanying notes are an integral part of these condensed consolidated financial statements. 1 Nautilus Biotechnology, Inc. Condensed Consolidated Statements of Operations Three and Nine Months Ended September 30, 2023 and 2022 (Unaudited) Three Months Ended September 30, Nine Months Ended September 30, (in thousands, except share and per share amounts) 2023 2022 2023 2022 Operating expenses Research and development $ 11,996 $ 9,571 $ 34,785 $ 28,085 General and administrative 7,079 6,249 21,366 19,229 Total operating expenses 19,075 15,820 56,151 47,314 Other income (expense): Interest income 3,197 1,889 9,517 2,929 Other expense — ( 132 ) ( 17 ) ( 130 ) Total other income $ 3,197 $ 1,757 $ 9,500 $ 2,799 Net loss $ ( 15,878 ) $ ( 14,063 ) $ ( 46,651 ) $ ( 44,515 ) Net loss per share attributable to common stockholders, basic and diluted $ ( 0.13 ) $ ( 0.11 ) $ ( 0.37 ) $ ( 0.36 ) Weighted-average shares used in computing net loss per share attributable to common stockholders, basic and diluted 124,933,837 124,651,318 124,896,975 124,522,164 The accompanying notes are an integral part of these condensed consolidated financial statements. 2 Nautilus Biotechnology, Inc. Condensed Consolidated Statements of Comprehensive Loss Three and Nine Months Ended September 30, 2023 and 2022 (Unaudited) Three Months Ended September 30, Nine Months Ended September 30, (in thousands) 2023 2022 2023 2022 Net loss $ ( 15,878 ) $ ( 14,063 ) $ ( 46,651 ) $ ( 44,515 ) Other comprehensive income (loss): Unrealized gain (loss) on securities available-for-sale 356 ( 1,113 ) ( 179 ) ( 1,697 ) Total other comprehensive income (loss) 356 ( 1,113 ) ( 179 ) ( 1,697 ) Comprehensive loss $ ( 15,522 ) $ ( 15,176 ) $ ( 46,830 ) $ ( 46,212 ) The accompanying notes are an integral part of these condensed consolidated financial statements. 3 Nautilus Biotechnology, Inc. Condensed Consolidated Statements of Stockholders’ Equity Three and Nine Months Ended September 30, 2023 and 2022 (Unaudited) Three Months Ended September 30, 2023 Additional Paid-in Capital Accumulated Other Comprehensive Loss Accumulated Deficit Total Stockholders’ Equity Common Stock (in thousands, except share amounts) Shares Amount Balances at June 30, 2023 124,930,899 $ 12 $ 461,387 $ ( 2,389 ) $ ( 169,337 ) $ 289,673 Issuance of common stock upon exercise of vested stock options 9,875 — 16 — — 16 Stock-based compensation expense — — 3,106 — — 3,106 Other comprehensive income — — — 356 — 356 Net loss — — — — ( 15,878 ) ( 15,878 ) Balances at September 30, 2023 124,940,774 $ 12 $ 464,509 $ ( 2,033 ) $ ( 185,215 ) $ 277,273 Three Months Ended September 30, 2022 Additional Paid-in Capital Accumulated Other Comprehensive Loss Accumulated Deficit Total Stockholders’ Equity Common Stock (in thousands, except share amounts) Shares Amount Balances at June 30, 2022 124,562,745 $ 12 $ 449,406 $ ( 768 ) $ ( 111,092 ) $ 337,558 Issuance of common stock upon exercise of vested stock options 160,780 — 86 — — 86 Stock-based compensation expense — — 2,870 — — 2,870 Other comprehensive loss — — — ( 1,113 ) — ( 1,113 ) Net loss — — — — ( 14,063 ) ( 14,063 ) Balances at September 30, 2022 124,723,525 $ 12 $ 452,362 $ ( 1,881 ) $ ( 125,155 ) $ 325,338 4 Nautilus Biotechnology, Inc. Condensed Consolidated Statements of Stockholders’ Equity Three and Nine Months Ended September 30, 2023 and 2022 (Unaudited) Nine Months Ended September 30, 2023 Additional Paid-in Capital Accumulated Other Comprehensive Loss Accumulated Deficit Total Stockholders’ Equity Common Stock (in thousands, except share amounts) Shares Amount Balances at December 31, 2022 124,865,485 $ 12 $ 455,330 $ ( 1,854 ) $ ( 138,564 ) $ 314,924 Issuance of common stock upon exercise of vested stock options 15,782 — 23 — — 23 Issuance of common stock under employee stock purchase plan 59,507 — 92 — — 92 Stock-based compensation expense — — 9,064 — — 9,064 Other comprehensive loss — — — ( 179 ) — ( 179 ) Net loss — — — — ( 46,651 ) ( 46,651 ) Balances at September 30, 2023 124,940,774 $ 12 $ 464,509 $ ( 2,033 ) $ ( 185,215 ) $ 277,273 Nine Months Ended September 30, 2022 Additional Paid-in Capital Accumulated Other Comprehensive Loss Accumulated Deficit Total Stockholders’ Equity Common Stock (in thousands, except share amounts) Shares Amount Balances at December 31, 2021 124,303,083 $ 12 $ 444,388 $ ( 184 ) $ ( 80,640 ) $ 363,576 Issuance of common stock upon exercise of vested stock options 372,089 — 274 — — 274 Issuance of common stock under employee stock purchase plan 48,353 — 153 — 153 Stock-based compensation expense — — 7,547 — — 7,547 Other comprehensive loss — — — ( 1,697 ) — ( 1,697 ) Net loss — — — — ( 44,515 ) ( 44,515 ) Balances at September 30, 2022 124,723,525 $ 12 $ 452,362 $ ( 1,881 ) $ ( 125,155 ) $ 325,338 The accompanying notes are an integral part of these condensed consolidated financial statements. 5 Nautilus Biotechnology, Inc. Condensed Consolidated Statements of Cash Flows Nine Months Ended September 30, 2023 and 2022 (Unaudited) Nine Months Ended September 30, (in thousands) 2023 2022 Cash flows from operating activities Net loss $ ( 46,651 ) $ ( 44,515 ) Adjustments to reconcile net loss to net cash used in operating activities Depreciation 1,294 871 Stock-based compensation 9,064 7,547 Amortization (accretion) of premium (discount) on securities, net ( 2,040 ) ( 340 ) Amortization of operating lease right-of-use assets 2,821 1,624 Changes in operating assets and liabilities: Prepaid expenses and other assets ( 878 ) 239 Accounts payable 22 ( 850 ) Accrued expenses and other liabilities 757 860 Operating lease liabilities ( 2,200 ) ( 865 ) Net cash used in operating activities ( 37,811 ) ( 35,429 ) Cash flows from investing activities Proceeds from maturities of securities 51,249 142,075 Purchases of securities ( 51,895 ) ( 101,665 ) Purchases of property and equipment ( 2,029 ) ( 2,095 ) Net cash (used in) provided by investing activities ( 2,675 ) 38,315 Cash flows from financing activities Proceeds from exercise of stock options 23 274 Proceeds from issuance of common stock under employee stock purchase plan 92 153 Net cash provided by financing activities 115 427 Net (decrease) increase in cash, cash equivalents and restricted cash ( 40,371 ) 3,313 Cash, cash equivalents and restricted cash at beginning of period 115,477 186,461 Cash, cash equivalents and restricted cash at end of period $ 75,106 $ 189,774 Supplementary cash flow information on non-cash activities Right-of-use asset obtained in exchange for operating lease liability $ 7,623 $ — Acquisitions of property and equipment included in accounts payable $ 22 $ 14 The accompanying notes are an integral part of these condensed consolidated financial statements 6 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements (Unaudited) 1. Description of Business and Basis of Presentation Nautilus Biotechnology, Inc. (the “Company”) is a biotechnology company incorporated in 2016 with corporate headquarters in Seattle, Washington and research and development headquarters in San Carlos, California. Since the Company’s incorporation in 2016, the Company has devoted substantially all of its resources to research and development activities, including with respect to its proteomics platform, business planning, establishing and maintaining its intellectual property portfolio, hiring personnel, raising capital and providing general and administrative support for these operations. On June 9, 2021, Nautilus Biotechnology, Inc. a Delaware corporation (f/k/a ARYA Sciences Acquisition Corp. III, a Cayman Islands exempted company and the Company’s predecessor company (“ARYA”)), consummated the previously announced business combination (the “Business Combination”) pursuant to the terms of that certain Business Combination Agreement, dated as of February 7, 2021 (the “BCA”), by and among ARYA, Mako Merger Sub, Inc., a Delaware corporation and wholly-owned subsidiary of ARYA (“Mako Merger Sub”), and Nautilus Subsidiary, Inc., a Delaware corporation (f/k/a Nautilus Biotechnology, Inc.) (“Legacy Nautilus”). As a result of the Business Combination, ARYA changed its name to “Nautilus Biotechnology, Inc.” and Mako Merger Sub merged with and into Legacy Nautilus with Legacy Nautilus surviving as the surviving company and becoming a wholly-owned subsidiary of ARYA (the “Merger” and, collectively with the other transactions described in the BCA, the “Reverse Recapitalization”). In addition, in conjunction with the completion of the Business Combination, certain investors (“PIPE Investors”) subscribed for the purchase of an aggregate of 20,000,000 shares of common stock of the Company (“New Nautilus Common Stock”) at a price of $ 10.00 per share for aggregate gross proceeds of $ 200.0 million (“PIPE Financing”). Basis of Presentation The condensed consolidated financial statements and accompanying notes are unaudited and have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) and regulations of the U.S. Securities and Exchange Commission (the “SEC”) for interim financial reporting. All intercompany transactions and balances have been eliminated upon consolidation. Certain information and footnote disclosures normally included in financial statements prepared in accordance with U.S. GAAP have been condensed or omitted pursuant to such rules and regulations. The condensed consolidated financial statements were prepared on the same basis as the audited financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments necessary for a fair statement of the Company’s financial position as of September 30, 2023, the results of its operations for the three and nine months ended September 30, 2023 and its cash flows for the nine months ended September 30, 2023 and 2022. The results of operations for the three and nine months ended September 30, 2023 are not necessarily indicative of the results that may be expected for the year ending December 31, 2023. These financial statements and accompanying notes should be read in conjunction with the consolidated financial statements and notes thereto in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2022 on file with the SEC. The Company’s reporting currency is the U.S. dollar. Going Concern The Company’s condensed consolidated financial statements have been prepared on the basis of continuity of operations, the realization of assets, and the satisfaction of liabilities in the ordinary course of business. Since inception, the Company has been engaged in developing its technology, raising capital, and recruiting personnel. The Company’s operating plan may change as a result of many factors currently unknown and there can be no assurance that the current operating plan will be achieved in the time frame anticipated by the Company, and it may need to seek additional funds sooner than planned. If adequate funds are not available to the Company on a timely basis, it may be required to delay, limit, reduce, or terminate certain commercial efforts, or pursue merger or acquisition strategies, all of which could adversely affect the holdings or the rights of the Company’s stockholders. The Company has incurred net operating losses and negative cash flows from operations in every year since 7 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) inception and expects this to continue for the foreseeable future. As of September 30, 2023, the Company had an accumulated deficit of $ 185.2 million. The Company has funded its operations primarily with proceeds from the issuance of redeemable convertible preferred stock and common stock. In June 2021, the Company received gross proceeds of approximately $ 345.5 million from PIPE Investors and the Business Combination offset by approximately $ 18.2 million of transaction costs and underwriters’ fees relating to the closing of the Business Combination. The Company had cash, cash equivalents, and short-term investments of $ 183.3 million as of September 30, 2023. As of the date on which these condensed consolidated financial statements were issued, the Company believes that its cash, cash equivalents, and short-term investments will be sufficient to fund its operations for the next twelve months following the issuance of the condensed consolidated financial statements. The Company’s actual results could vary as a result of, and its near and long-term future capital requirements will depend on many factors, including its growth rate and the timing and extent of spending to support its research and development efforts. The Company has based its estimates on assumptions that may prove to be wrong, and it could use its available capital resources sooner than it currently expects. The Company may be required to seek additional equity or debt financing. Future liquidity and cash requirements will depend on numerous factors. In the event that additional financing is required, the Company may not be able to raise it on acceptable terms or at all. If the Company is unable to raise additional capital when desired, or if it cannot expand its operations or otherwise capitalize on its business opportunities because it lacks sufficient capital, its business, operating results, and financial condition would be adversely affected. Impact of the COVID-19 Coronavirus The COVID-19 pandemic has already had an adverse effect on the global economy. Additionally, concerns over the economic impact of COVID-19 have caused extreme volatility in financial and other capital markets, which may adversely affect the Company’s ability to access capital markets in the future. The level and nature of the disruption caused by COVID-19 is unpredictable, may be cyclical and long-lasting, and may again in the future adversely affect the Company's operating results. 2. Significant Accounting Policies Use of Estimates The preparation of the condensed consolidated financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosures of contingent assets and liabilities as of the date of the condensed consolidated financial statements, and the reported amounts of expenses during the reporting period. Actual results could differ from those estimates. Significant estimates include determining the estimated lives of property and equipment, stock-based compensation, research and development accruals, and the valuation allowance for deferred tax assets. These estimates and assumptions are based on management’s best estimates and judgment. Management evaluates its estimates and assumptions on an ongoing basis using historical experience and other factors, including the current economic environment, which management believes to be reasonable under the circumstances. The Company adjusts such estimates and assumptions when facts and circumstances dictate. Changes in those estimates resulting from continuing changes in the economic environment will be reflected in the financial statements in future periods. As future events and their effects cannot be determined with precision, actual results could materially differ from those estimates and assumptions. Concentrations of Credit Risk and Other Risks and Uncertainties Credit risk represents the accounting loss that would be recognized as of the reporting date if counterparties failed to perform as contracted. Financial instruments, which potentially subject the Company to concentration of credit risk, consist of cash balances maintained in excess of federal depository insurance limits and investments in marketable debt securities that are not federally insured. The Company has not experienced any losses in such accounts and believes it is not exposed to significant credit risk on cash or investments. The Company relies, and expects to continue to rely, on a number of vendors to provide services, supplies and materials related to its research and development programs. The 8 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) Company relies on single source suppliers for certain components and materials used in the Nautilus platform. The loss of any of these single source suppliers would require the Company to expend significant time and effort to locate and qualify an alternative source of supply for these components. The Company also relies, and expects to continue to rely, on third-party manufacturers and, in many cases, single third-party manufacturers for the production of certain reagents and antibodies. These programs could be adversely affected by a significant interruption in these services or the availability of materials. The Company is subject to risks similar to those of pre-clinical stage companies in the biopharmaceutical industry, including dependence on key individuals, the need to develop commercially viable products, competition from other companies, many of whom are larger and better capitalized, the impact of the COVID-19 pandemic and the need to obtain adequate additional financing to fund the development of its products. There can be no assurance that the Company’s research and development will be successfully completed, that adequate protection for the Company’s intellectual property will be maintained, that any products developed will obtain required regulatory approval or that any approved products will be commercially viable. Even if the Company’s development efforts are successful, it is uncertain when, if ever, the Company will generate significant revenue from the sale of its products. Segment Reporting Operating segments are defined as components of an entity where discrete financial information is evaluated regularly by the chief operating decision m aker (“CODM”) in deciding how to allocate resources and in assessing performance. The Company’s Chief Executive Officer is its CODM. The Company’s CODM re views financial information presented on a consolidated basis for the purposes of making operating decisions, allocating resources and evaluating financial performance. As such, the Company has determined that it operates in one operating and one reportable segment. The Company’s long-lived assets are entirely based in the United States. Cash and Cash Equivalents The Company considers all highly-liquid investments with an original maturity of three months or less as of the date of acquisition to be cash equivalents. Investments The Company considers investments with an original maturity greater than three months and remaining maturities less than one year to be short-term investments. The Company classifies those investments that are not required for use in current operations and that mature in more than 12 months as long-term investments. The Company classifies its marketable debt securities as available for sale and reports them at fair value, with unrealized gains and losses recorded in accumulated other comprehensive income (loss). For investments sold prior to maturity, the cost of investments sold is based on the specific identification method. Realized gains and losses on the sale of investments are recorded in other income (expense), net in the condensed consolidated statement of operations. If the estimated fair value of a marketable debt security is below its amortized cost basis, the Company evaluates whether it is more likely than not that the Company will be required to sell the security before its anticipated recovery in market value and whether credit losses exist for the related securities. Credit-related losses are recognized as an allowance for credit losses on the balance sheet with a corresponding adjustment to earnings. Unrealized gains and losses that are unrelated to credit deterioration are reported in accumulated other comprehensive income (loss). No credit-related losses or allowance for credit losses were necessary during the periods presented. 9 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) Fair Value of Financial Instruments Fair value is defined as the price that would be received for sale of an asset or paid for transfer of a liability, in an orderly transaction between market participants at the measurement date. U.S. GAAP establishes a three-tier fair value hierarchy, which prioritizes the inputs used in measuring fair value. The hierarchy gives the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1 measurements) and the lowest priority to unobservable inputs (Level 3 measurements). These tiers include: Level 1, defined as observable inputs such as quoted prices for identical instruments in active markets; Level 2, defined as inputs other than quoted prices in active markets that are either directly or indirectly observable such as quoted prices for similar instruments in active markets or quoted prices for identical or similar instruments in markets that are not active; and Level 3, defined as unobservable inputs in which little or no market data exists, therefore requiring an entity to develop its own assumptions, such as valuations derived from valuation techniques in which one or more significant inputs or significant value drivers are unobservable. In some circumstances, the inputs used to measure fair value might be categorized within different levels of the fair value hierarchy. In those instances, the fair value measurement is categorized in its entirety in the fair value hierarchy based on the lowest level input that is significant to the fair value measurement. The carrying amounts of cash and cash equivalents, prepaid expenses and other current assets, accounts payable and accrued expenses and other liabilities approximate their respective fair values due to their short-term nature. Leases The Company determines if an arrangement includes a lease at inception by assessing whether there is an identified asset and whether the contract conveys the right to control the use of the identified asset for a period of time in exchange for consideration. Operating leases with a term of more than one year are included in operating lease right-of-use (“ROU”) assets and operating lease liabilities on the Company's condensed consolidated balance sheets. ROU assets represent the Company's right to use an underlying asset for the lease term and lease liabilities represent the obligation to make lease payments. Operating lease ROU assets and liabilities are recognized on the lease commencement date based on the present value of the future minimum lease payments over the lease term. The Company uses the incremental borrowing rate commensurate with the lease term based on the information available at the lease commencement date in determining the present value of the lease payments as the Company's leases generally do not provide an implicit rate. ROU assets initially equal the lease liability, adjusted for any prepaid lease payments and initial direct costs incurred, less any lease incentives received. Certain of the Company's leases include renewal options which allow the Company to, at its election, renew or extend the lease for a fixed or indefinite period of time. These renewal periods are included in the lease terms when the Company is reasonably certain the options will be exercised. Lease expense is recognized on a straight-line basis over the lease term when leases are operating leases. If it is considered a finance lease, expense is recognized over the lease term within interest expense and amortization in the Company’s condensed consolidated statements of operations. The Company also has lease arrangements with lease and non-lease components. The Company elected the practical expedient not to separate non-lease components from lease components for the Company's facility leases and to account for the lease and non-lease components as a single lease component. The Company also elected to apply the short-term lease measurement and recognition exemption in which ROU assets and lease liabilities are not recognized for leases with terms of 12 months or less. 10 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) Comprehensive Loss Comprehensive loss consists of net loss and other gains or losses affecting stockholders’ equity that, under U.S. GAAP are excluded from net loss. For the three and nine months ended September 30, 2023 and 2022, net unrealized gains and losses on marketable debt securities were included as a component of comprehensive income (loss). Accounting Pronouncements The Company is provided the option to adopt new or revised accounting guidance as an “emerging growth company” under the Jumpstart Our Business Startups Act of 2012 (the “JOBS Act”) either (1) within the same periods as those otherwise applicable to public business entities, or (2) within the same time periods as non-public business entities, including early adoption when permissible. With the exception of standards the Company elected to early adopt, when permissible, the Company has elected to adopt new or revised accounting guidance within the same time period as non-public business entities, as indicated below. Recently Adopted Accounting Standards In June 2016, the FASB issued ASU No. 2016-13, “Financial Instruments- Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments,” which amends existing guidance on the impairment of financial assets and adds an impairment model that is based on expected losses rather than incurred losses and requires an entity to recognize as an allowance its estimate of expected credit losses for its financial assets. An entity will apply this guidance through a cumulative-effect adjustment to retained earnings upon adoption (a modified-retrospective approach) while a prospective transition approach is required for debt securities for which an other-than-temporary impairment had been recognized before the effective date. This ASU is effective for the Company for its fiscal year ending December 31, 2023. Early adoption is permitted. The Company adopted this ASU on January 1, 2023 and the adoption did not have a material impact on its consolidated financial statements. 3. Fair Value Measurements The following table details the assets carried at fair value and measured on a recurring basis within the three levels of fair value as of September 30, 2023 and December 31, 2022: (in thousands) Gross Unrealized Reported as: September 30, 2023 Amortized Cost Gains Losses Fair Value Cash equivalents Short-term investments Long-term investments Level 1 Mutual funds $ 1,370 $ — $ — $ 1,370 $ 1,370 $ — $ — U.S. treasury securities 62,200 — ( 654 ) 61,546 — 37,683 23,863 Total Level 1 63,570 — ( 654 ) 62,916 1,370 37,683 23,863 Level 2 Commercial paper 81,490 — ( 33 ) 81,457 72,527 8,930 — Corporate debt securities 6,931 — ( 64 ) 6,867 — 1,963 4,904 Agency securities 125,563 — ( 1,282 ) 124,281 — 60,609 63,672 Total Level 2 213,984 — ( 1,379 ) 212,605 72,527 71,502 68,576 Total Level 1 and Level 2 $ 277,554 $ — $ ( 2,033 ) $ 275,521 $ 73,897 $ 109,185 $ 92,439 11 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) (in thousands) Gross Unrealized Reported as: December 31, 2022 Amortized Cost Gains Losses Fair Value Cash equivalents Short-term investments Long-term investments Level 1 Mutual funds $ 1,121 $ — $ — $ 1,121 $ 1,121 $ — $ — U.S. treasury securities 52,686 4 ( 774 ) 51,916 — 2,873 49,043 Total Level 1 53,807 4 ( 774 ) 53,037 1,121 2,873 49,043 Level 2 Commercial paper 156,419 3 ( 266 ) 156,156 113,402 42,754 — Corporate debt securities 14,154 — ( 71 ) 14,083 — 7,224 6,859 Agency securities 91,114 33 ( 783 ) 90,364 — 17,097 73,267 Total Level 2 261,687 36 ( 1,120 ) 260,603 113,402 67,075 80,126 Total Level 1 and Level 2 $ 315,494 $ 40 $ ( 1,894 ) $ 313,640 $ 114,523 $ 69,948 $ 129,169 Contractual maturities of short-term investments as of September 30, 2023 and December 31, 2022 are due in one year or less. Contractual maturities of long-term investments as of September 30, 2023 and December 31, 2022 are due after 1 year through 2 years. The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of September 30, 2023 and December 31, 2022 are as follows: (in thousands) Securities in Unrealized Loss Position Less than 12 months Securities in Unrealized Loss Position Greater than 12 months Total September 30, 2023 Gross Unrealized Losses Fair Market Value Gross Unrealized Losses Fair Market Value Gross Unrealized Losses Fair Market Value U.S. treasury securities $ 256 $ 28,690 $ 398 $ 32,856 $ 654 $ 61,546 Commercial paper 33 81,457 — — 33 81,457 Corporate debt securities 64 6,867 — — 64 6,867 Agency securities 870 90,443 412 33,838 1,282 124,281 Total $ 1,223 $ 207,457 $ 810 $ 66,694 $ 2,033 $ 274,151 (in thousands) Securities in Unrealized Loss Position Less than 12 months Securities in Unrealized Loss Position Greater than 12 months Total December 31, 2022 Gross Unrealized Losses Fair Market Value Gross Unrealized Losses Fair Market Value Gross Unrealized Losses Fair Market Value U.S. treasury securities $ 774 $ 49,114 $ — $ — $ 774 $ 49,114 Commercial paper 266 151,354 — — 266 151,354 Corporate debt securities 14 6,859 57 7,224 71 14,083 Agency securities 670 50,531 113 8,887 783 59,418 Total $ 1,724 $ 257,858 $ 170 $ 16,111 $ 1,894 $ 273,969 We review our investment portfolio based on the underlying risk profile of the securities and have a no loss expectation for these investments. We also regularly review the securities in an unrealized loss position and evaluate the current expected credit loss by considering factors such as historical experience, market data, issuer-specific factors, and current economic conditions. We recognized no credit losses on our investments during the three and nine months ended September 30, 2023 and 2022, and had no allowance for credit losses as of September 30, 2023. 12 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) 4. Composition of Certain Condensed Consolidated Financial Statement Line Items Property and Equipment, Net Property and equipment consisted of the following: (in thousands) September 30, 2023 December 31, 2022 Laboratory equipment $ 6,124 $ 4,892 Leasehold improvements 118 13 Computer hardware 222 166 Furniture, fixtures and office equipment 324 25 Prototype equipment 732 332 Construction in progress 942 1,235 8,462 6,663 Less: Accumulated depreciation ( 4,179 ) ( 2,963 ) Total $ 4,283 $ 3,700 The Company recorded depreciation expense of $ 0.5 million and $ 1.3 million for the three and nine months ended September 30, 2023 and $ 0.3 million and $ 0.9 million for the three and nine months ended September 30, 2022, respectively, which was primarily allocated to research and development expense. Accrued Expenses and Other Liabilities Accrued expenses and other liabilities consisted of the following: (in thousands) September 30, 2023 December 31, 2022 Employee compensation $ 2,999 $ 1,669 Accrued research and development 796 970 Accrued professional and consulting fees 241 451 Other 249 438 Total $ 4,285 $ 3,528 Cash, Cash Equivalents and Restricted Cash Cash, cash equivalents and restricted cash consisted of the following: (in thousands) September 30, 2023 December 31, 2022 Cash and cash equivalents $ 74,104 $ 114,523 Restricted cash included in other long-term assets (Note 8) 1,002 954 Total $ 75,106 $ 115,477 Other long-term assets consisted of $ 1.0 million of restricted cash and $ 0.2 million of deposits as of September 30, 2023, and $ 0.9 million of restricted cash and $ 0.2 million of deposits as of December 31, 2022. 13 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) 5. Common Stock There were 124,940,774 shares issued and outstanding as of September 30, 2023. Common Stock Reserved for Future Issuance Shares of common stock reserved for future issuance on an as-if converted basis, were as follows: September 30, 2023 December 31, 2022 Shares available for grant under 2021 Equity Incentive Plan 20,374,783 17,298,043 Stock options issued and outstanding 14,636,195 11,485,443 Shares available for grant under 2021 Employee Stock Purchase Plan 3,577,882 2,388,735 Total shares of common stock reserved 38,588,860 31,172,221 6. Income Taxes The Company accounts for income taxes under the asset and liability method. Under this method, deferred tax assets and liabilities are determined based on the difference between the financial statement and tax bases of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to affect taxable income. Valuation allowances are established when necessary to reduce deferred tax assets to the amounts expected to be realized. For the three and nine months ended September 30, 2023 and 2022, no income tax expense or benefit was recognized, primarily due to a full valuation allowance recorded against its deferred tax assets. 7. Equity Incentive Plans and Stock-based Compensation On June 8, 2021, the stockholders of the Company approved the 2021 Equity Incentive Plan (“2021 Plan”) and the 2021 Employee Stock Purchase Plan ( “2021 ESPP”). As of September 30, 2023, 20,374,783 and 3,577,882 shares were available for grant under the 2021 Plan and 2021 ESPP, respectively. 2021 Employee Stock Purchase Plan Under the 2021 ESPP, the Company can grant stock options to employees to purchase shares of Common Stock at a purchase price which is equal to 85 % of the fair market value of common stock on the enrollment date or on the exercise date, whichever is lower. Participants are permitted to purchase shares of the Company’s Common Stock at 85 % of the lower of the fair market value of the Company’s Common Stock on the first trading day of an offering period or on the last trading date in each purchase period. Participants may end their participation at any time during an offering and will be paid their accrued contributions that have not yet been used to purchase shares. Participation ends automatically upon termination of employment with the Company. The number of shares of common stock available for issuance under the 2021 ESPP will be increased on the first day of each fiscal year beginning on January 1, 2022, in an amount equal to the least of (i) 3,734,500 shares of common stock, (ii) a number of s hares of common stock equal to one percent ( 1 %) of the total number of shares of all classes of common stock of the Company on the last day of the immediately preceding fiscal year, or (iii) such number of shares determined by the Administrator no later than the last day of the immediately preceding fiscal year. On January 1, 2023, the number of shares available under the 2021 ESPP increased by 1,248,654 shares pursuant to this feature. The first offering period was from October 1, 2021 through June 1, 2022. For subsequent offering periods, the Company offers a six month purchase period. As of September 30, 2023, 158,702 shares of common stock were purchased under the 2021 ESPP. 14 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) 2021 Equity Incentive Plan Under the 2021 Plan, the Company can grant incentive stock options, nonstatutory stock options, stock appreciation rig hts, restricted stock, restricted stock units and performance awards to employees, directors and consultants. Options generally expire ten years after the date of grant. The number of shares available for issuance under the 2021 Plan will be increased on the first day of each fiscal year, beginning on January 1, 2022, in an amount equal to the least of (i) 18,672,200 shares, (ii) a number of shares equal to five percent ( 5 %) of the total number of shares of all classes of common stock of the Company outstanding on the last day of the immediately preceding fiscal year, or (iii) such number of shares determined by the Administrator no later than the last day of the immediately preceding fiscal year . On January 1, 2023, the number of shares available under the 2021 Plan increased by 6,243,274 shares pursuant to this feature. 2017 Equity Incentive Plan At the time of adoption of the 2021 Plan and the 2021 ESPP, no further awards will be granted under the 2017 Equity Incentive Plan (“2017 Plan”) and 7,106,767 shares of common stock were initially reserved for outstanding awards issued under the 2017 Plan. In determining the compensation cost of the option awards, the fair value for each option award has been estimated using the Black Scholes model . The significant assumptions used in these calculations are summarized as follows: Three Months Ended September 30, Nine Months Ended September 30, 2023 2022 2023 2022 Expected term (in years) 6.0 - 6.1 6.0 - 6.1 5.3 - 6.4 5.3 - 6.1 Expected volatility 103.4 % - 103.7 % 109.3 % - 110.2 % 102.7 % - 107.5 % 105.2 % - 110.2 % Expected dividend rate 0.0 % 0.0 % 0.0 % 0.0 % Risk free interest rate 3.99 % - 4.44 % 2.81 % - 3.69 % 3.50 % - 4.44 % 1.73 % - 3.69 % Expected term: The expected term of stock options represents the weighted-average period the stock options are expected to remain outstanding. The Company does not have sufficient historical exercise and post-vesting termination activity to provide accurate data for estimating the expected term of options and has opted to use the “simplified method,” whereby the expected term equals the arithmetic average of the vesting term and the original contractual term of the option. Expected volatility: Historically, the Company has been a private company and lacked company‑specific historical and implied volatility information for its common stock. Therefore, the expected volatility of the Company’s common stock was determined by using an average of historical volatilities of selected industry peers deemed to be comparable to the Company’s business corresponding to the expected term of the awards and the Company expects to continue to do so until such time as the Company has adequate historical data regarding the volatility of its traded common stock price. Expected dividend yield: The expected dividend rate is zero as the Company has no history or expectation of declaring dividends on its common stock. Risk-free interest rate: The risk-free interest rate is based on the U.S. Treasury yield curve in effect at the time of grant for zero-coupon U.S. Treasury notes with maturities corresponding to the expected term of the awards. 15 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) The following table summarizes option award activity during the nine months ended September 30, 2023: Number of Stock Option Awards Weighted Average Exercise Price Weighted Average Remaining Contractual Life (Years) Aggregate Intrinsic Value (in thousands) Outstanding as of December 31, 2022 11,485,443 $ 4.12 Granted 3,627,375 $ 2.37 Exercised ( 15,782 ) $ 1.42 Forfeited ( 460,841 ) $ 5.99 Outstanding as of September 30, 2023 14,636,195 $ 3.63 8.1 $ 13,111 Options vested and expected to vest as of September 30, 2023 14,636,195 $ 3.63 Vested and exercisable at September 30, 2023 6,870,884 $ 3.88 7.3 $ 7,626 As of September 30, 2023, there was $ 21.7 million of total unrecognized compensation expense expected to be recognized over a weighted average-period of 2.2 years. Aggregate intrinsic value represents the difference between the fair market value of the common stock and the exercise price of outstanding, in-the-money options. Stock-based Compensation Expense The following sets forth the total stock-based compensation expense included in the Company’s condensed consolidated statement of operations: Three Months Ended September 30, Nine Months Ended September 30, (in thousands) 2023 2022 2023 2022 Research and development $ 1,090 $ 1,012 $ 3,113 $ 2,854 General and administrative 2,016 1,858 5,951 4,693 Total stock-based compensation expense $ 3,106 $ 2,870 $ 9,064 $ 7,547 8. Commitments and Contingencies Purchase Commitments Open purchase commitments are for the purchase of goods and services related to, but not limited to, research and development, facilities, and professional services under non-cancellable contracts. They were not recorded as liabilities on the condensed consolidated balance sheet as of September 30, 2023 as the Company had not yet received the related goods or services. As of September 30, 2023, the Company had open purchase commitments for goods and services of $ 1.4 million, of which $ 1.2 million are expected to be received through the next 12 months. Legal Proceedings From time to time, the Company may become involved in litigation relating to claims arising from the ordinary course of business. Management believes that there are currently no claims or actions pending against the Company where the ultimate disposition could have a material adverse effect on the Company’s results of operations, financial condition or cash flows. Leases The Company is obligated under certain non-cancellable operating leases for office space and laboratory space. This space includes operating leases in Seattle, Washington, San Carlos, California, and San Diego, California. 16 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) Seattle Lease In July 2021, the Company entered into a 7 -year non-cancellable operating lease, which commenced in August 2021, for an additional office space in Seattle, Washington. Total non-cancellable payments under this lease aggregate $ 4.5 million through June 2028. San Carlos Leases In December 2020, the Company entered into a new lease in San Carlos, California for ten years which commenced in October 2021 and expiring in October 2031 with total minimum lease payments of $ 40.7 million. In December 2021, the Company entered into another lease in San Carlos, California for nine years commencing in March 2023. The Company can terminate this lease after five years from the commencement date without bearing any significant termination penalties and therefore the Company concluded that the lease term is five years with total minimum lease payments of $ 7.2 million. The Company utilized $ 2.0 million from the landlord with an interest rate of 7 % to finance its tenant improvements. The principal and interest payments are included in the payments used to measure the lease liability. San Diego Lease In November 2022, the Company entered into a lease in San Diego, California for 39 months commencing in December 2022. Total non-cancellable payments under this lease aggregate $ 2.1 million through March 2026. The components of lease costs, which were included in operating expenses in condensed consolidated statements of operations, were as follows: Three Months Ended September 30, Nine Months Ended September 30, (in thousands) 2023 2022 2023 2022 Fixed operating lease costs $ 1,810 $ 1,182 $ 4,900 $ 3,547 Variable operating lease costs 630 431 1,803 1,249 Short-term lease costs — 6 2 17 Total lease costs $ 2,440 $ 1,619 $ 6,705 $ 4,813 For the nine months ended September 30, 2023 and 2022, cash paid for amounts included in the measurement of operating lease liabilities included in cash flows used in operating activities was $ 4.5 million and $ 2.8 million, respectively. As of September 30, 2023, the weighted-average remaining lease term and weighted-average discount rate for operating leases was 6.9 years and 9.1 % respectively. 17 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) The following table summarizes the Company's future principal contractual obligations for operating lease commitments as of September 30, 2023: Lease Obligations (in thousands) Three months ending December 31, 2023 $ 1,207 2024 6,992 2025 7,186 2026 6,878 2027 6,893 2028 and thereafter 19,028 Total future minimum lease payments 48,184 Less: Imputed interest ( 12,548 ) Total operating lease liabilities $ 35,636 Guarantees and Indemnifications In the ordinary course of business, the Company enters into agreements that may include indemnification provisions. Pursuant to such agreements, the Company may indemnify, hold harmless and defend an indemnified party for losses suffered or incurred by the indemnified party. Some of the provisions will limit losses to those arising from third-party actions. In some cases, the indemnifications will continue after the termination of the agreement. The maximum potential amount of future payments the Company could be required to make under these provisions is not determinable. The Company has never incurred material costs to defend lawsuits or settle claims related to these indemnification provisions. The Company has also agreed to indemnify its directors and executive officers for costs associated with any fees, expenses, judgments, fines and settlement amounts incurred by them in any action or proceeding to which any of them are, or are threatened to be, made a party by reason of their service as a director or officer. The Company maintains director and officer insurance coverage that would generally enable it to recover a portion of any future amounts paid. The Company may be subject to indemnification obligation by law with respect to the actions of its employees under certain circumstances and in certain jurisdictions. Letters of Credit In conjunction with the San Carlos lease agreement entered in December 2020, the Company issued a cash-collateralized letter of credit in lieu of security deposit of $ 0.6 million. In conjunction with the San Carlos lease agreement entered in December 2021, the Company issued a cash-collateralized letter of credit in lieu of security deposit of $ 0.2 million. In conjunction with the San Diego lease agreement entered in November 2022, the Company issued a cash-collateralized letter of credit in lieu of a security deposit of $ 0.1 million. 18 Nautilus Biotechnology, Inc. Notes to Condensed Consolidated Financial Statements—(Continued) (Unaudited) 9. Basic and Diluted Net Loss per Share The following tables set forth the computation of the Company’s basic and diluted net loss per share attributable to common stockholders for the three and nine months ended September 30, 2023 and 2022: Three Months Ended September 30, Nine Months Ended September 30, (in thousands, except share and per share amounts) 2023 2022 2023 2022 Numerator: Net loss attributable to common stockholders $ ( 15,878 ) $ ( 14,063 ) $ ( 46,651 ) $ ( 44,515 ) Denominator: Weighted average shares used in computing net loss per share attributable to common stockholders, basic and diluted 124,933,837 124,651,318 124,896,975 124,522,164 Net loss per share attributable to common stockholders, basic and diluted: $ ( 0.13 ) $ ( 0.11 ) $ ( 0.37 ) $ ( 0.36 ) The potential shares of common stock that were excluded from the computation of diluted net loss per share attributable to common stockholders for the periods presented because including them would have had an antidilutive effect were as follows: Three and Nine Months Ended September 30, 2023 2022 Options to purchase common stock 14,636,195 11,515,123 Employee stock purchase plan 74,407 54,733 Total potentially dilutive common share equivalents 14,710,602 11,569,856 19