Protagonist Therapeutics, Inc 10-Q

ITEM 1. FINANCIAL STATEMENTS PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Balance Sheets (Unaudited) (In thousands, except share and per share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2020 2019 Assets ​ ​ ​ ​ ​ ​ Current assets: ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 83,625 ​ $ 33,006 Marketable securities ​ ​ 110,349 ​ ​ 100,011 Restricted cash - current ​ ​ 10 ​ ​ 10 Receivable from collaboration partner and contract asset - related party ​ ​ 2,789 ​ ​ 6,755 Research and development tax incentive receivable ​ ​ 535 ​ ​ — Prepaid expenses and other current assets ​ ​ 6,843 ​ ​ 5,529 Total current assets ​ ​ 204,151 ​ ​ 145,311 Marketable securities - noncurrent ​ ​ 6,025 ​ ​ — Property and equipment, net ​ ​ 1,459 ​ ​ 1,681 Restricted cash - noncurrent ​ ​ 450 ​ ​ 450 Operating lease right-of-use asset ​ ​ 5,235 ​ ​ 6,042 Deferred tax asset ​ ​ — ​ ​ 1,433 Total assets ​ $ 217,320 ​ $ 154,917 Liabilities and Stockholders’ Equity ​ ​ ​ ​ ​ ​ Current liabilities: ​ ​ ​ ​ ​ Accounts payable ​ $ 2,797 ​ $ 2,790 Payable to collaboration partner - related party ​ ​ 2,077 ​ ​ 1,262 Accrued expenses and other payables ​ ​ 15,518 ​ ​ 12,360 Deferred revenue - related party - current ​ ​ 16,765 ​ ​ 17,738 Operating lease liability - current ​ ​ 1,406 ​ ​ 1,256 Total current liabilities ​ ​ 38,563 ​ ​ 35,406 Long-term debt, net ​ ​ — ​ ​ 9,794 Deferred revenue - related party - noncurrent ​ ​ 4,112 ​ ​ 23,792 Operating lease liability - noncurrent ​ ​ 4,885 ​ ​ 5,961 Other liability - noncurrent ​ ​ 170 ​ ​ — Total liabilities ​ ​ 47,730 ​ ​ 74,953 Commitments and contingencies (Note 10) ​ ​ ​ ​ ​ ​ Stockholders’ equity: ​ ​ ​ ​ ​ ​ Preferred stock, $ 0.00001 par value, 10,000,000 shares authorized; no shares issued and outstanding ​ ​ — ​ ​ — Common stock, $ 0.00001 par value, 90,000,000 shares authorized; 37,314,873 and 27,206,447 shares issued and outstanding as of September 30, 2020 and December 31, 2019, respectively ​ ​ — ​ ​ — Additional paid-in capital ​ ​ 434,603 ​ ​ 297,846 Accumulated other comprehensive loss ​ ​ ( 88 ) ​ ​ ( 221 ) Accumulated deficit ​ ​ ( 264,925 ) ​ ​ ( 217,661 ) Total stockholders’ equity ​ ​ 169,590 ​ ​ 79,964 Total liabilities and stockholders’ equity ​ $ 217,320 ​ $ 154,917 ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ 1 Table of Contents PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Statements of Operations (Unaudited) (In thousands, except share and per share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ 2020 2019 2020 2019 License and collaboration revenue - related party ​ $ 13,114 ​ $ 4,141 ​ $ 22,978 ​ $ ( 2,488 ) Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development ​ ​ 15,995 ​ ​ 17,293 ​ ​ 55,020 ​ ​ 49,092 General and administrative ​ 4,891 ​ 4,015 ​ 13,644 ​ 11,642 Total operating expenses ​ 20,886 ​ 21,308 ​ 68,664 ​ 60,734 Loss from operations ​ ( 7,772 ) ​ ( 17,167 ) ​ ( 45,686 ) ​ ( 63,222 ) Interest income ​ 87 ​ 762 ​ 820 ​ ​ 2,134 Interest expense ​ ​ ( 19 ) ​ ​ — ​ ​ ( 471 ) ​ ​ — Loss on early repayment of debt ​ ​ — ​ ​ — ​ ​ ( 585 ) ​ ​ — Other expense, net ​ ​ ( 59 ) ​ ​ ( 106 ) ​ ​ ( 37 ) ​ ​ ( 145 ) Loss before income tax benefit (expense) ​ ​ ( 7,763 ) ​ ​ ( 16,511 ) ​ ​ ( 45,959 ) ​ ​ ( 61,233 ) Income tax benefit (expense) ​ ​ — ​ ​ 102 ​ ​ ( 1,305 ) ​ ​ 1,547 Net loss ​ $ ( 7,763 ) ​ $ ( 16,409 ) ​ $ ( 47,264 ) ​ $ ( 59,686 ) Net loss per share, basic and diluted ​ $ ( 0.21 ) ​ $ ( 0.61 ) ​ $ ( 1.45 ) ​ $ ( 2.36 ) Weighted-average shares used to compute net loss per share, basic and diluted ​ 37,386,881 26,956,957 ​ 32,647,524 25,315,512 ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ 2 Table of Contents PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Statements of Comprehensive Loss (Unaudited) (In thousands) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ 2020 2019 2020 2019 Net loss ​ $ ( 7,763 ) ​ $ ( 16,409 ) ​ $ ( 47,264 ) ​ $ ( 59,686 ) Other comprehensive loss: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Gain on translation of foreign operations ​ 129 ​ 10 ​ 143 ​ 6 (Loss) gain on marketable securities ​ ( 9 ) ​ 3 ​ ( 10 ) ​ 73 Comprehensive loss ​ $ ( 7,643 ) ​ $ ( 16,396 ) ​ $ ( 47,131 ) ​ $ ( 59,607 ) ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ 3 Table of Contents PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Statements of Stockholders’ Equity (Unaudited) (In thousands, except share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ Other ​ ​ ​ Total ​ ​ Common ​ Paid-In ​ Comprehensive ​ Accumulated ​ Stockholders' ​ ​ Stock ​ Capital ​ Gain (Loss) ​ Deficit ​ Equity Three months ended September 30, 2020 Shares Amount ​ ​ ​ ​ ​ ​ ​ Balance at June 30, 2020 36,802,139 $ — ​ $ 424,855 $ ( 208 ) ​ $ ( 257,162 ) $ 167,485 Issuance of common stock pursuant to public offering, net of issuance costs ​ — ​ ​ — ​ ​ ( 3 ) ​ ​ — ​ ​ — ​ ​ ( 3 ) Issuance of common stock pursuant to at-the-market offering, net of issuance costs ​ 333,047 ​ ​ — ​ ​ 6,368 ​ ​ — ​ ​ — ​ ​ 6,368 Issuance of common stock under equity incentive and employee stock purchase plans 179,687 — ​ 1,495 — ​ — 1,495 Stock-based compensation expense — — ​ 1,888 — ​ — 1,888 Other comprehensive gain (loss) — — ​ — 120 ​ — 120 Net loss — — ​ — — ​ ( 7,763 ) ( 7,763 ) Balance at September 30, 2020 37,314,873 $ — ​ $ 434,603 $ ( 88 ) ​ $ ( 264,925 ) $ 169,590 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ Other ​ ​ ​ Total ​ ​ Common ​ Paid-In ​ Comprehensive ​ Accumulated ​ Stockholders' ​ ​ Stock ​ Capital ​ Gain (Loss) ​ Deficit ​ Equity Three months ended September 30, 2019 Shares Amount ​ ​ ​ ​ ​ ​ ​ Balance at June 30, 2019 ​ 24,967,603 ​ $ — ​ $ 268,234 ​ $ ( 167 ) ​ $ ( 183,751 ) ​ $ 84,316 Issuance of common stock pursuant to at-the-market offering, net of issuance costs ​ 1,924,957 ​ ​ — ​ ​ 23,949 ​ ​ — ​ ​ — ​ ​ 23,949 Issuance of common stock under equity incentive and employee stock purchase plans ​ 313,887 — ​ 1,288 — ​ — 1,288 Stock-based compensation expense — — ​ 2,201 — ​ — 2,201 Other comprehensive gain (loss) — — ​ — 13 ​ — 13 Net loss — — ​ — — ​ ( 16,409 ) ( 16,409 ) Balance at September 30, 2019 27,206,447 $ — ​ $ 295,672 $ ( 154 ) ​ $ ( 200,160 ) $ 95,358 ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ 4 Table of Contents PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Statements of Stockholders’ Equity (continued) (Unaudited) (In thousands, except share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ Other ​ ​ ​ Total ​ ​ Common ​ Paid-In ​ Comprehensive ​ Accumulated ​ Stockholders' ​ ​ Stock ​ Capital ​ Gain (Loss) ​ Deficit ​ Equity Nine months ended September 30, 2020 Shares Amount ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2019 27,217,649 $ — ​ $ 297,846 $ ( 221 ) ​ $ ( 217,661 ) $ 79,964 Issuance of common stock pursuant to public offering, net of issuance costs ​ 8,050,000 ​ ​ — ​ ​ 105,328 ​ ​ — ​ ​ — ​ ​ 105,328 Issuance of common stock pursuant to at-the-market offering, net of issuance costs ​ 1,565,840 ​ ​ — ​ ​ 23,011 ​ ​ — ​ ​ — ​ ​ 23,011 Issuance of common stock under equity incentive and employee stock purchase plans 481,384 — ​ 2,486 — ​ — 2,486 Stock-based compensation expense — — ​ 5,932 — ​ — 5,932 Other comprehensive gain (loss) — — ​ — 133 ​ — 133 Net loss — — ​ — — ​ ( 47,264 ) ​ ( 47,264 ) Balance at September 30, 2020 37,314,873 $ — ​ $ 434,603 $ ( 88 ) ​ $ ( 264,925 ) $ 169,590 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ Other ​ ​ ​ Total ​ ​ Common ​ Paid-In ​ Comprehensive ​ Accumulated ​ Stockholders' ​ ​ Stock ​ Capital ​ Gain (Loss) ​ Deficit ​ Equity Nine months ended September 30, 2019 Shares Amount ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2018 ​ 23,187,219 ​ $ — ​ $ 253,222 ​ $ ( 233 ) ​ $ ( 140,474 ) ​ $ 112,515 Issuance of common stock pursuant to at-the-market offering, net of issuance costs ​ 2,846,641 ​ ​ — ​ ​ 34,492 ​ ​ — ​ ​ — ​ ​ 34,492 Issuance of common stock pursuant to exercise of Exchange Warrants ​ 599,997 ​ ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ — Issuance of common stock under equity incentive and employee stock purchase plans ​ 572,590 — ​ 1,765 — ​ — 1,765 Stock-based compensation expense — — ​ 6,193 — ​ — 6,193 Other comprehensive gain (loss) — — ​ — 79 ​ — 79 Net loss — — ​ — — ​ ( 59,686 ) ( 59,686 ) Balance at September 30, 2019 27,206,447 $ — ​ $ 295,672 $ ( 154 ) ​ $ ( 200,160 ) $ 95,358 ​ The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ ​ 5 Table of Contents PROTAGONIST THERAPEUTICS, INC. Condensed Consolidated Statements of Cash Flows (Unaudited) (In thousands) ​ ​ ​ ​ ​ ​ ​ ​ ​ Nine Months Ended September 30, ​ 2020 2019 CASH FLOWS FROM OPERATING ACTIVITIES ​ ​ ​ Net loss ​ $ ( 47,264 ) ​ $ ( 59,686 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ Stock-based compensation ​ ​ 5,932 ​ ​ 6,193 Change in deferred tax asset ​ ​ 1,404 ​ ​ ( 1,548 ) Operating lease right-of-use asset amortization ​ ​ 1,331 ​ ​ 1,347 Loss on early repayment of debt ​ ​ 585 ​ ​ — Depreciation and amortization ​ ​ 601 ​ ​ 501 Amortization of debt issuance costs and accretion of debt discount ​ ​ 22 ​ ​ — Accretion of discount on marketable securities, net of premium amortization ​ ​ ( 155 ) ​ ​ ( 397 ) Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Research and development tax incentive receivable ​ ​ ( 517 ) ​ ​ 1,237 Receivable from collaboration partner - related party ​ ​ 3,966 ​ ​ 2,642 Prepaid expenses and other assets ​ ​ ( 1,566 ) ​ ​ ( 1,586 ) Accounts payable ​ ​ 32 ​ ​ ( 4,165 ) Payable to collaboration partner - related party ​ ​ 815 ​ ​ ( 41 ) Accrued expenses and other payables ​ ​ 3,130 ​ ​ ( 781 ) Deferred revenue - related party ​ ​ ( 20,653 ) ​ ​ ( 1,409 ) Operating lease liability ​ ​ ( 1,450 ) ​ ​ 30,455 Other liability ​ ​ 170 ​ ​ — Net cash used in operating activities ​ ​ ( 53,617 ) ​ ​ ( 27,238 ) CASH FLOWS FROM INVESTING ACTIVITIES ​ ​ ​ ​ ​ ​ Proceeds from maturities of marketable securities ​ ​ 131,383 ​ ​ 77,400 Purchase of marketable securities ​ ​ ( 147,600 ) ​ ​ ( 117,807 ) Purchases of property and equipment ​ ​ ( 346 ) ​ ​ ( 749 ) Net cash used in investing activities ​ ​ ( 16,563 ) ​ ​ ( 41,156 ) CASH FLOWS FROM FINANCING ACTIVITIES ​ ​ ​ ​ ​ ​ Proceeds from public offering of common stock, net of issuance costs ​ ​ 105,478 ​ ​ — Proceeds from at-the-market offering, net of issuance costs ​ ​ 23,219 ​ ​ 34,492 Proceeds from issuance of common stock upon exercise of stock options and purchases under employee stock purchase plan ​ ​ 2,486 ​ ​ 1,765 Issuance costs related to long-term debt ​ ​ ( 14 ) ​ ​ — Early repayment of long-term debt ​ ​ ( 10,524 ) ​ ​ — Net cash provided by financing activities ​ ​ 120,645 ​ ​ 36,257 Effect of exchange rate changes on cash, cash equivalents and restricted cash ​ ​ 154 ​ ​ 99 Net increase (decrease) in cash, cash equivalents and restricted cash ​ ​ 50,619 ​ ​ ( 32,038 ) Cash, cash equivalents and restricted cash, beginning of period ​ 33,466 ​ 82,693 Cash, cash equivalents and restricted cash, end of period ​ $ 84,085 ​ $ 50,655 SUPPLEMENTAL DISCLOSURE OF NON-CASH FINANCING AND INVESTING INFORMATION: ​ ​ ​ ​ ​ ​ Issuance costs related to at-the-market offering of common stock included in prepaid expenses and other assets at the end of the previous year ​ $ 191 ​ $ — Issuance costs related to public offering of common stock included in prepaid expenses and other assets at the end of the previous year ​ $ 125 ​ $ — Purchases of property and equipment in accounts payable and accrued liabilities ​ $ 27 ​ $ 157 Issuance costs related to public offering of common stock included in accrued liabilities and other payables ​ $ 25 ​ $ — Issuance costs related to at-the-market offering of common stock included in accrued liabilities and other payables ​ $ 17 ​ $ — The accompanying notes are an integral part of these unaudited condensed consolidated financial statements. ​ ​ 6 Table of Contents PROTAGONIST THERAPEUTICS, INC. Notes to Unaudited Condensed Consolidated Financial Statements Note 1. Organization and Description of Business Protagonist Therapeutics, Inc. (the “Company”) was incorporated in the state of Delaware on August 22, 2006 and is headquartered in Newark, California. The Company is a clinical-stage biopharmaceutical company that utilizes a proprietary technology platform to discover and develop novel peptide-based drugs to transform existing treatment paradigms for patients with significant unmet medical needs. Protagonist Pty Limited (“Protagonist Australia”) is a wholly-owned subsidiary of the Company and is located in Brisbane, Queensland, Australia. Protagonist Australia was incorporated in Australia in September 2001. The Company manages its operations as a single operating segment. Liquidity The Company has incurred net losses from operations since inception and has an accumulated deficit of $ 264.9 million as of September 30, 2020. The Company’s ultimate success depends on the outcome of its research and development and collaboration activities. The Company expects to incur additional losses in the future and anticipates the need to raise additional capital to continue to execute its long-range business plan. Since the Company’s initial public offering in August 2016, it has financed its operations primarily through offerings of common stock, payments received under license and collaboration agreements and proceeds received from long-term debt. Risks and Uncertainties The Company is subject to risks and uncertainties as a result of the COVID-19 pandemic. The extent of the impact of the COVID-19 pandemic on the Company's activities is highly uncertain and difficult to predict, as the response to the pandemic is ongoing and information continues to evolve. Capital markets and economies worldwide have been negatively impacted by the COVID-19 pandemic, which has contributed to the current global economic recession. Such economic disruption could have a material adverse effect on the Company’s business. Policymakers around the globe have responded with fiscal policy actions to support the healthcare industry and economy as a whole. The magnitude and overall effectiveness of these actions remains uncertain. The severity of the impact of the COVID-19 pandemic on the Company's activities will depend on a number of factors, including, but not limited to, the duration and severity of the pandemic, including the severity of any additional periods of increases or spikes in the number of cases in the areas the Company and its suppliers operate and areas where the Company’s clinical trial sites are located. Accordingly, the extent and severity of the impact on the Company's existing and planned clinical trials and collaboration activities and operations, all of which are uncertain and cannot be predicted. The Company has experienced delays in its existing and planned clinical trials due to the worldwide impacts of the pandemic. The Company's future results of operations and liquidity could be adversely impacted by further delays in existing and planned clinical trials and collaboration activities, continued difficulty in recruiting patients for these clinical trials, supply chain disruptions, the ongoing effect of the impact on its operating activities and employees, and the ongoing impact of any initiatives or programs that the Company may undertake to address financial and operational challenges. As of the date of issuance of these condensed consolidated financial statements, the extent to which the COVID-19 pandemic may materially impact the Company's future financial condition, liquidity or results of operations is uncertain. Note 2. Summary of Significant Accounting Policies Basis of Presentation 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 applicable rules and regulations of the SEC regarding interim financial reporting. As permitted under those rules, certain footnotes or other financial information that are normally required by GAAP have been condensed or omitted, and accordingly the condensed consolidated balance sheet as of December 31, 2019 has been derived from the Company’s audited 7 Table of Contents consolidated financial statements at that date but does not include all of the information required by GAAP for complete consolidated financial statements. These unaudited interim condensed consolidated financial statements have been prepared on the same basis as the Company’s annual consolidated financial statements and, in the opinion of management, reflect all adjustments (consisting of normal recurring adjustments) that are necessary for a fair presentation of the Company’s consolidated financial statements. The results of operations for the three and nine months ended September 30, 2020 are not necessarily indicative of the results to be expected for the year ending September 30, 2020 or for any other interim period or for any other future year. The accompanying condensed consolidated financial statements and related financial information should be read in conjunction with the audited consolidated financial statements and the related notes thereto for the year ended December 31, 2019 included in the Company’s Annual Report on Form 10-K, filed with the SEC on March 10, 2020. Principles of Consolidation The accompanying unaudited interim condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiary. All intercompany transactions and balances have been eliminated upon consolidation. Use of Estimates The preparation of the condensed consolidated financial statements in conformity with GAAP requires management to make estimates, assumptions and judgments that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. On an ongoing basis, management evaluates its estimates, including those related to revenue recognition, accruals for research and development activities, stock-based compensation, income taxes, marketable securities and leases. Estimates related to revenue recognition include actual costs incurred versus total estimated costs of the Company’s deliverables to determine percentage of completion in addition to the application and estimates of potential revenue constraints in the determination of the transaction price under its license and collaboration agreements. Management bases these estimates on historical and anticipated results, trends, and various other assumptions that the Company believes are reasonable under the circumstances, including assumptions as to forecasted amounts and future events. Due to the COVID-19 pandemic, there has been uncertainty and disruption in the global economy and financial markets. The Company has taken into consideration any known COVID-19 impacts in its accounting estimates to date and is not aware of any additional specific events or circumstances that would require any additional updates to its estimates or judgments or a revision of the carrying value of its assets or liabilities as of the date of issuance of this Quarterly Report on Form 10-Q. These estimates may change as new events occur and additional information is obtained. Actual results could differ materially from these estimates under different assumptions or conditions. Concentrations of Credit Risk Financial instruments that potentially subject the Company to a concentration of credit risk consist of cash, cash equivalents and marketable securities. Substantially all of the Company’s cash is held by two financial institutions that management believes are of high credit quality. Such deposits may, at times, exceed federally insured limits. The primary focus of the Company’s investment strategy is to preserve capital and to meet liquidity requirements. The Company’s cash equivalents and marketable securities are managed by external managers within the guidelines of the Company’s investment policy. The Company’s investment policy addresses the level of credit exposure by limiting concentration in any one corporate issuer and establishing a minimum allowable credit rating. To manage its credit risk exposure, the Company maintains its portfolio of cash equivalents and marketable securities in fixed income securities denominated and payable in U.S. dollars. Permissible investments of fixed income securities include obligations of the U.S. government and its agencies, money market instruments including commercial paper and negotiable certificates of deposit, and highly rated corporate debt obligations and money market funds. As of the date of issuance of these 8 Table of Contents condensed consolidated financial statements, the COVID-19 pandemic has not had a material impact on the Company’s credit exposure, and the extent to which the COVID-19 pandemic may materially impact the Company's future level of credit exposure is uncertain. Cash Equivalents Cash equivalents that are readily convertible to cash are stated at cost, which approximates fair value. The Company considers all highly liquid investments purchased with an original maturity of three months or less to be cash equivalents. Restricted Cash Restricted cash consists of cash balances primarily held as security in connection with a letter of credit related to the Company’s facility lease entered into in March 2017 and the Company’s corporate credit card. Cash as Reported in Condensed Consolidated Statements of Cash Flows Cash as reported in the condensed consolidated statements of cash flows includes the aggregate amounts of cash and cash equivalents and the restricted cash as presented on the condensed consolidated balance sheets. Cash as reported in the condensed consolidated statements of cash flows consists of (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ 2020 2019 Cash and cash equivalents ​ $ 83,625 ​ $ 50,195 Restricted cash - current ​ 10 ​ 10 Restricted cash - noncurrent ​ 450 ​ 450 Cash balance in consolidated statements of cash flows ​ $ 84,085 ​ $ 50,655 ​ Marketable Securities All marketable securities have been classified as “available-for-sale” and are carried at estimated fair value as determined based upon quoted market prices or pricing models for similar securities. Management determines the appropriate classification of its marketable securities at the time of purchase and reevaluates such designation as of each balance sheet date. Short-term marketable securities have maturities greater than three months but no longer than 365 days as of the balance sheet date. Long-term marketable securities have maturities of 365 days or longer as of the balance sheet date. Unrealized gains and losses are excluded from earnings and are reported as a component of comprehensive loss. Realized gains and losses and declines in fair value judged to be other than temporary, if any, on available-for-sale securities are included in interest income. The cost of securities sold is based on the specific-identification method. Interest on marketable securities is included in interest income. Revenue Recognition ​ The Company follows Accounting Standards Codification Topic 606, Revenue from Contracts with Customers (“ASC 606”). Under ASC 606, the Company recognizes revenue when its customer obtains control of promised goods or services, in an amount that reflects the consideration which the Company expects to receive in exchange for those goods or services. To determine revenue recognition for arrangements that the Company determines are within the scope of ASC 606, the Company performs the following five steps: (i) identify the contract(s) with a customer; (ii) identify the performance obligations in the contract; (iii) determine the transaction price; (iv) allocate the transaction price to the performance obligations in the contract; and (v) recognize revenue when (or as) the Company satisfies a performance obligation. The Company applies the five-step model to contracts when it is probable that the Company will collect the consideration it is entitled to in exchange for the goods or services it transfers to the customer. At contract inception, the Company assesses the goods or services promised within each contract, determines those that are performance obligations, and assesses whether each promised good or service is distinct. The Company then recognizes 9 Table of Contents as revenue the amount of the transaction price that is allocated to the respective performance obligations when (or as) the performance obligations are satisfied. The Company constrains its estimate of the transaction price up to the amount (the “variable consideration constraint”) that a significant reversal of recognized revenue is not probable. Licenses of intellectual property: If a license to the Company’s intellectual property is determined to be distinct from the other performance obligations identified in an arrangement, the Company recognizes revenue from non-refundable, upfront fees allocated to the license when the license is transferred to the customer and the customer is able to use and benefit from the license. For licenses that are bundled with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring proportional performance for purposes of recognizing revenue from non-refundable, upfront fees. The Company evaluates the measure of proportional performance each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. Milestone payments: At the inception of each arrangement or amendment that includes development, regulatory or commercial milestone payments, the Company evaluates whether the milestones are considered probable of being reached and estimates the amount to be included in the transaction price. ASC 606 suggests two alternatives to use when estimating the amount of variable consideration: the expected value method and the most likely amount method. Under the expected value method, an entity considers the sum of probability-weighted amounts in a range of possible consideration amounts. Under the most likely amount method, an entity considers the single most likely amount in a range of possible consideration amounts. Whichever method is used, it should be consistently applied throughout the life of the contract; however, it is not necessary for the Company to use the same approach for all contracts. The Company expects to use the most likely amount method for development and regulatory milestone payments. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the control of the Company or the licensee, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. If there is more than one performance obligation, the transaction price is then allocated to each performance obligation on a relative stand-alone selling price basis. The Company recognizes revenue as or when the performance obligations under the contract are satisfied. At the end of each subsequent reporting period, the Company re-evaluates the probability or achievement of each such milestone and any related constraint, and if necessary, adjusts its estimates of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenues and earnings in the period of adjustment. Royalties: For arrangements that include sales-based royalties, including milestone payments based on the level of sales, and the license is deemed to be the predominant item to which the royalties relate, the Company recognizes revenue at the later of (i) when the related sales occur, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied (or partially satisfied). Upfront payments and fees are recorded as deferred revenue upon receipt or when due and may require deferral of revenue recognition to a future period until the Company performs its obligations under these arrangements. Amounts payable to the Company are recorded as accounts receivable when the Company’s right to consideration is unconditional. Amounts payable to the Company and not yet billed to the collaboration partner are recorded as contract assets. The Company does not assess whether a contract has a significant financing component if the expectation at contract inception is such that the period between payment by the customer and the transfer of the promised goods or services to the customer will be one year or less. Contractual cost sharing payments made to a customer or collaboration partner are accounted for as a reduction to the transaction price if such payments are not related to distinct goods or services received from the customer or collaboration partner. Contracts may be amended to account for changes in contract specifications and requirements. Contract modifications exist when the amendment either creates new, or changes existing, enforceable rights and obligations. When contract modifications create new performance obligations and the increase in consideration approximates the standalone selling price for goods and services related to such new performance obligations as adjusted for specific 10 Table of Contents facts and circumstances of the contract, the modification is considered to be a separate contract. If a contract modification is not accounted for as a separate contract, the Company accounts for the promised goods or services not yet transferred at the date of the contract modification (the remaining promised goods or services) prospectively, as if it were a termination of the existing contract and the creation of a new contract, if the remaining goods or services are distinct from the goods or services transferred on or before the date of the contract modification. The Company accounts for a contract modification as if it were a part of the existing contract if the remaining goods or services are not distinct and, therefore, form part of a single performance obligation that is partially satisfied at the date of the contract modification. In such case the effect that the contract modification has on the transaction price, and on the entity’s measure of progress toward complete satisfaction of the performance obligation, is recognized as an adjustment to revenue (either as an increase in or a reduction of revenue) at the date of the contract modification (the adjustment to revenue is made on a cumulative catch-up basis). The period between when the Company transfers control of promised goods or services and when the Company receives payment is expected to be one year or less, and that expectation is consistent with the Company’s historical experience. Upfront payment contract liabilities resulting from the Company’s license and collaboration agreements do not represent a financing component as the payment is not financing the transfer of goods and services, and the technology underlying the licenses granted reflects research and development expenses already incurred by the Company. As such, the Company does not adjust its revenues for the effects of a significant financing component . Research and Development Costs Research and development costs are expensed as incurred, unless there is an alternate future use in other research and development projects or otherwise. Research and development costs include salaries and benefits, stock-based compensation expense, laboratory supplies and facility-related overhead, outside contracted services including clinical trial costs, manufacturing and process development costs for both clinical and pre-clinical materials, research costs, development milestone payments under license and collaboration agreements, and other consulting services. The Company accrues for estimated costs of research and development activities conducted by third-party service providers, which include the conduct of pre-clinical studies and clinical trials, and contract manufacturing activities. The Company records the estimated costs of research and development activities based upon the estimated services provided but not yet invoiced and includes these costs in accrued expenses and other payables in the condensed consolidated balance sheets and within research and development expense in the condensed consolidated statements of operations. The Company accrues for these costs based on factors such as estimates of the work completed and in accordance with agreements established with its third-party service providers. As actual costs become known, the Company adjusts its accrued liabilities. The Company has not experienced any material differences between accrued liabilities and actual costs incurred. However, the status and timing of actual services performed, number of patients enrolled, the rate of patient enrollment and number of locations of sites activated may vary from the Company’s estimates, resulting in adjustments to expense in future periods. Changes in these estimates that result in material changes to the Company’s accruals could materially affect the Company’s results of operations. The Company has received orphan drug designation from the U.S. Food and Drug Administration (“FDA”) for its clinical asset PTG-300 for the treatment of polycythemia vera and beta-thalassemia and may qualify for a related 25% U.S. Federal income tax credit on qualifying clinical study expenditures. Research and Development Tax Incentive The Company is eligible under the AusIndustry research and development tax incentive program to obtain either a refundable cash tax incentive or a taxable credit in the form of a non-cash tax incentive from the Australian Taxation Office (“ATO”). The refundable cash tax incentive is available to the Company on the basis of specific criteria with which the Company must comply. Specifically, the Company must have annual turnover of less than AUD 20.0 million and cannot be controlled by income tax exempt entities. The refundable cash tax incentive is recognized as a reduction to research and development expense when the right to receive has been attained and funds are considered to be collectible. The tax incentive is denominated in Australian dollars and, therefore, the related receivable is remeasured into U.S. dollars as of each reporting date. The Company may alternatively be eligible for a taxable credit 11 Table of Contents in the form of a non-cash tax incentive in years when the annual turnover exceeds the limit. The Company evaluates its eligibility under tax incentive programs as of each balance sheet date and makes accrual and related adjustments based on the most current and relevant data available. Net Loss per Share ​ Basic net loss per share is calculated by dividing the Company’s net loss by the weighted average number of shares of common stock and Exchange Warrants outstanding during the period, without consideration of potentially dilutive securities. In accordance with Accounting Standards Codification Topic 260, Earnings Per Share , the Exchange Warrants are included in the computation of basic net loss per share because the exercise price is negligible, and they are fully vested and exercisable after the original issuance date. Diluted net loss per share is the same as basic net loss per share for all periods presented since the effect of potentially dilutive securities is anti-dilutive given the net loss of the Company in each period. See Note 11. Stockholder’s Equity for additional information regarding the Exchange Warrants. Recently Adopted Accounting Pronouncements In August 2018, the FASB issued ASU No. 2018-13, Fair Value Measurement (Topic 820) – Disclosure Framework – Changes to the Disclosure Requirements for Fair Value Measurement , which modifies the disclosure requirements on fair value measurements and is intended to improve the effectiveness of disclosures, including the consideration of costs and benefits. The Company adopted this guidance as of January 1, 2020. The adoption of this guidance did not have a material impact on the Company’s consolidated financial statements or disclosures. In November 2018, the FASB issued ASU No. 2018-18, Collaborative Arrangements (Topic 808): Clarifying the Interaction Between Topic 808 and Topic 606 , which is intended to clarify the circumstances under which certain transactions in collaborative arrangements should be accounted for under the revenue recognition standard. Certain transactions between collaboration arrangement participants should be accounted for as revenue under ASC Topic 606 when the collaborative arrangement participant is a customer in the context of a unit of account. This guidance is effective for fiscal years and interim periods within those years beginning after December 15, 2019. The Company adopted this guidance as of January 1, 2020. The adoption of this guidance did not have a material impact on the Company’s consolidated financial statements and disclosures. Recently Issued Accounting Pronouncements Not Yet Adopted as of September 30, 2020 In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326) , which is intended to provide financial statement users with more useful information about expected credit losses on financial assets held by a reporting entity at each reporting date. The new standard replaces the existing incurred loss impairment methodology with a methodology that requires consideration of a broader range of reasonable and supportable forward-looking information to estimate all expected credit losses. This guidance was originally effective for fiscal years and interim periods within those years beginning after December 15, 2019, with early adoption permitted for fiscal years and interim periods within those years beginning after December 15, 2018. In November 2019, the FASB issued ASU No. 2019-10, Financial Instruments – Credit Losses (Topic 326), Derivatives and Hedging (Topic 815), and Leases (Topic 842): Effective Dates , which amended the mandatory effective date of ASU No. 2016-13 for smaller reporting companies to fiscal years and interim periods beginning after December 15, 2022. The Company is currently evaluating the impact of this new guidance on its consolidated financial statements and disclosures. In December 2019, the FASB issued ASU No. 2019-12, Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes, which removes certain exceptions and amends certain requirements in the existing income tax guidance to ease accounting requirements. This guidance is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2020 and must be applied on a retrospective basis. The Company does not expect the adoption of this guidance to have a material impact on its consolidated financial statements and disclosures. 12 Table of Contents Note 3. License and Collaboration Agreement Agreement Terms On May 26, 2017, the Company and Janssen Biotech, Inc., (“Janssen”), one of the Janssen Pharmaceutical Companies of Johnson & Johnson, entered into an exclusive license and collaboration agreement (the “Janssen License and Collaboration Agreement”) for the development, manufacture and potential commercialization of PTG-200 worldwide for the treatment of Crohn’s disease (“CD”) and ulcerative colitis (“UC”). Janssen is a related party to the Company as Johnson & Johnson Innovation - JJDC, Inc., a significant stockholder of the Company, and Janssen are both subsidiaries of Johnson & Johnson. PTG-200 is the Company’s orally delivered gut-restricted Interleukin 23 receptor (“IL-23R”) antagonist drug candidate currently in development. The Janssen License and Collaboration Agreement became effective on July 13, 2017. Upon the effectiveness of the agreement, the Company received a non-refundable, upfront cash payment of $ 50.0 million from Janssen. Under the Janssen License and Collaboration Agreement, the Company granted to Janssen an exclusive worldwide license to develop, manufacture and commercialize PTG-200 and related IL-23R antagonist compounds for all indications, including CD and UC. The Company was responsible, at its own expense, for the conduct of the Phase 1 clinical trial for PTG-200, and Janssen is responsible for the conduct of the Phase 2 clinical trial for PTG-200 in CD, including filing the U.S. Investigational New Drug application (“IND”). Development costs for the Phase 2 clinical trial are shared between the parties on an 80 / 20 basis, with Janssen assuming the larger share. Janssen submitted an IND for PTG-200 in CD during the second quarter of 2019, which took effect in July 2019. Janssen and the Company initiated a Phase 2 clinical study for PTG-200 in CD in the fourth quarter of 2019. The Company entered into an amendment (the “First Amendment”) to the Janssen License and Collaboration Agreement effective May 7, 2019. The First Amendment builds upon the Company’s ongoing development collaboration with Janssen for PTG-200 and, upon the effectiveness of the First Amendment, the Company became eligible to receive a $ 25.0 million payment from Janssen, which was received during the second quarter of 2019. The First Amendment expanded the scope of the Janssen License and Collaboration Agreement by supporting research efforts towards identifying and developing second-generation IL-23R antagonists (“second-generation compounds”). As part of the services added in the First Amendment, Janssen will pay certain costs and milestones related to advancing pre-clinical candidates from the second-generation research program through Phase 1 studies, including funding of a certain number of full-time equivalent employees (“FTEs”) at the Company for a set period of time. The Company will pay 100 % of the costs for the Phase 1 studies for the first second-generation compound, and 50 % of the costs of the Phase 1 studies for the second and third second-generation compounds; thereafter Janssen will pay 100 % of any further Phase 1 development costs. Development costs for the Phase 2 clinical trials for second-generation compounds are shared between the parties on an 80 / 20 basis, with Janssen assuming the larger share. The Company’s Phase 1 and Phase 2 development costs are also limited by overall spending caps. In December 2019, the Company became eligible to receive a $ 5.0 million payment trigged by the successful nomination of a second-generation development compound, which was received during the first quarter of 2020. The Company will be eligible to receive a $ 7.5 million milestone payment at the completion of a Phase 1 study for the first second-generation compound. Prior to the effectiveness of the First Amendment, the Company had been eligible to receive a $ 25.0 million milestone payment upon Janssen’s filing of the IND. This amount had been considered constrained until a time at which the Company would have become eligible to receive the $ 25.0 million payment from Janssen. Payments to the Company for research and development services are generally billed and collected as services are performed or assets are delivered, including research activities and Phase 1 and Phase 2 development activities. Janssen bills the Company for its 20 % share of the Phase 2 development costs as expenses are incurred by Janssen. Milestone payments are received after the related milestones are achieved. 13 Table of Contents Pursuant to the First Amendment, the Company will be eligible to receive clinical development, regulatory and sales milestones, if and as achieved, and/or payments relating to Janssen’s elections to maintain or expand its license rights. The next anticipated such payment is a $ 50.0 million payment based on Phase 2a clinical trial results, as follows: ● Janssen can elect to advance PTG-200 into Phase 2b following receipt of the top line results of the CD Phase 2a clinical trial for PTG-200 by paying a $ 50.0 million maintenance fee (the “Amended First Opt-in Election”); or ● Janssen would make a $ 50.0 million milestone payment following dosing of the third patient in the first Phase 2b clinical trial for CD for a second-generation product. Janssen can also then elect to receive exclusive, worldwide commercial rights for both PTG-200 and second-generation products following the Phase 2b completion date for PTG-200 or a second-generation product by paying a $ 50.0 million payment (the “Amended Second Opt-in Election”). The Company will also be eligible for certain additional milestone payments including a potential payment of either $ 100.0 million upon a Phase 3 CD clinical trial meeting a primary clinical endpoint with respect to PTG-200 or $ 115.0 million upon a Phase 3 CD clinical trial meeting a primary clinical endpoint with respect to a second-generation compound. Pursuant to the First Amendment, the Company will be eligible to receive tiered royalties on net product sales at percentages ranging from mid-single digits to ten percent. Under the terms of the First Amendment, the Company is eligible to receive up to $ 1.0 billion in research, development, regulatory and sales milestones. The Janssen License and Collaboration Agreement remains in effect until the royalty obligations cease following patent and regulatory expiry, unless terminated earlier. Upon a termination of the Janssen License and Collaboration Agreement, all rights revert back to the Company, and in certain circumstances, if such termination occurs during ongoing clinical trials, Janssen would, if requested, provide certain financial and operational support to the Company for the completion of such trials. Revenue Recognition The Company concluded that the amended Janssen License and Collaboration Agreement continued to contain a single performance obligation for the development license; second-generation compound research services; Phase 1 development services for PTG-200 and potential second-generation compounds; the Company’s services associated with Phase 2 development for PTG-200 until Phase 2a; the Company’s services associated with Phase 2 development for a second-generation product until the dosing of the third patient in Phase 2b; and all other such services that the Company may perform at the request of Janssen to support the development of PTG-200, second-generation research services, or the development of a second-generation compound. The Company concluded that the Amended First Opt-in Election and the Amended Second Opt-in Election options are not considered to be material rights. The Company determined that the license was not distinct from the added research and development services within the context of the agreement because the added research and development services significantly increase the utility of the intellectual property. The Company also determined that the remaining research and development services are not distinct from the partially delivered combined promise comprised under the agreement prior to the First Amendment of the development license and PTG-200 services, including compound supply and other services. Therefore, the First Amendment is treated as if it were part of the original Janssen License and Collaboration Agreement. The First Amendment was accounted for as if it were an extension of services under the initial Janssen License and Collaboration Agreement by applying a cumulative catch-up adjustment to revenue. As of the effective date of the First Amendment, the Company calculated the adjusted cumulative revenue under the amended Janssen License and Collaboration Agreement by updating the transaction price for the incremental consideration to be received, net of the incremental development cost reimbursement to be paid to Janssen, and an updated percentage complete, which resulted in a cumulative adjustment recorded during the year ended December 31, 2019 that reduced revenue by $ 9.4 million. 14 Table of Contents The contract duration is defined as the period in which parties to the contract have present enforceable rights and obligations. For revenue recognition purposes, the Company determined that the duration of the Janssen License and Collaboration Agreement, as amended, began on the effective date of July 13, 2017 and ends upon the later of end of Phase 2a for PTG-200 or upon dosing of the third patient in Phase 2b for a second-generation compound. The Company uses the most likely amount method to estimate variable consideration included in the transaction price. Variable consideration after the First Amendment consists of future milestone payments and cost sharing payments from Janssen for agreed upon services offset by development costs reimbursement payable to Janssen. Cost sharing payments from Janssen relate to the agreed upon services for development activities that the Company performs within the duration of the contract are included in the transaction price at the Company’s share of the estimated budgeted costs for these activities, including primarily internal full-time equivalent effort and third party contract costs. Cost sharing payments to Janssen relate to agreed-upon services for Phase 2 activities that Janssen performs within the duration of the contract are not a distinct service that Janssen transfers to the Company. Therefore, the consideration payable to Janssen is accounted for as a reduction in the transaction price. The Company concluded that the transaction price of the initial performance obligation under the Janssen License and Collaboration Agreement was $ 99.4 million as of September 30, 2020, a decrease of $ 14.5 million from the transaction price of $ 113.9 million as of June 30, 2020, following an update to the estimate for remaining services to be performed under the performance obligation. In order to determine the transaction price, the Company evaluated all payments to be received during the duration of the contract, net of Phase 2 development costs reimbursement expected to be payable to Janssen. The Company determined that the transaction price of the initial performance obligation as of September 30, 2020 includes the $ 50.0 million upfront payment, the $ 25.0 million payment received upon the effectiveness of the First Amendment, the $ 5.0 million payment triggered by the successful nomination of a second-generation compound, $ 18.4 million of reimbursement from Janssen for services performed for PTG-200 Phase 2 and for second-generation compound research costs and other services, and estimated variable consideration consisting of a $ 7.5 million milestone payment subject to the completion of a Phase 1 study for a second-generation compound, offset by $ 6.5 million of net cost reimbursement to Janssen for services performed. The Company evaluated whether the variable component of the transaction price should be constrained to ensure that a significant reversal of revenue recognized on a cumulative basis as of September 30, 2020 is not probable. The Company concluded that the variable consideration constraint does not further decrease the estimated transaction price as of September 30, 2020. The additional potential development, regulatory and sales milestone payments after the completion of Phase 2b activities that the Company would be eligible to receive are currently outside the contract term as defined for revenue recognition purposes and as such have been excluded from the transaction price. Janssen has also opted in for certain additional services to be performed by the Company that are outside the initial performance obligation, revenue is recognized as these services are delivered. The Company re-evaluates the transaction price, including variable consideration, at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur. The Company and Janssen make quarterly cost sharing payments to one another in amounts necessary to ensure that each party bears its contractual share of the overall shared costs incurred. The Company utilizes a cost-based input method to measure proportional performance and to calculate the corresponding amount of revenue to recognize. In applying the cost-based input methods of revenue recognition, the Company uses actual costs incurred relative to expected costs to fulfill the combined performance obligation. These costs consist primarily of internal FTE effort and third-party contract costs. Revenue will be recognized based on actual costs incurred as a percentage of total estimated costs as the Company completes its performance obligations. A cost-based input method of revenue recognition requires management to make estimates of costs to complete the Company’s performance obligations. The Company believes this is the best measure of progress because other measures do not reflect how the Company transfers its performance obligation to Janssen. In making such estimates, significant judgment is required to evaluate assumptions related to cost estimates. The cumulative effect of revisions to estimated costs to complete the Company’s performance obligations will be recorded in the period in which changes are identified and amounts can be reasonably estimated. A significant change in these assumptions and estimates could have a material impact on the timing and amount of revenue recognized in future periods. 15 Table of Contents For the three and nine months ended September 30, 2020, the Company recognized license and collaboration revenue of $ 12.6 million and $ 22.0 million, respectively, which was primarily related to an update in the amounts forecast for future services remaining to be performed under the Janssen License and Collaboration Agreement and recognized based on proportional performance. In addition, the Company recorded $ 0.5 million and $ 1.0 million in revenue for the three and nine months ended September 30, 2020 related to additional services provided by the Company under the Janssen Collaboration Agreement. For the three months ended September 30, 2019, the Company recorded $ 4.1 million of license and collaboration revenue following the contract modification for the First Amendment. For the nine months ended September 30, 2019, the Company recorded a $ 9.4 million cumulative catchup adjustment reducing license and collaboration revenue, partially offset $ 5.3 million of license and collaboration revenue following the contract modification for the First Amendment and $ 1.6 million of license and collaboration revenue recognized during the first quarter of 2019 under the original Janssen license and collaboration agreement. No revenue for additional services was recognized for the three and six months ended June 30, 2019. The following tables present changes in the Company’s contract assets and liabilities during the periods presented (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at ​ ​ ​ ​ ​ Balance at ​ ​ Beginning of ​ ​ ​ ​ ​ End of Nine Months Ended September 30, 2020 Period ​ Additions Deductions Period Contract assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Receivable from collaboration partner - related party ​ $ 5,955 ​ $ 5,284 ​ $ ( 8,450 ) ​ $ 2,789 Contract asset - related party ​ $ 800 ​ $ 342 ​ $ ( 1,142 ) ​ $ — Contract liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Deferred revenue - related party ​ $ 41,530 ​ $ 3,500 ​ $ ( 24,153 ) ​ $ 20,877 Payable to collaboration partner - related party ​ $ 1,262 ​ $ 2,114 ​ $ ( 1,299 ) ​ $ 2,077 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at ​ ​ ​ ​ ​ ​ ​ Balance at ​ ​ Beginning of ​ ​ ​ ​ ​ End of Nine Months Ended September 30, 2019 Period ​ Additions Deductions Period Contract assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Receivable from collaboration partner - related party ​ $ 2,042 ​ $ 30,882 ​ $ ( 31,905 ) ​ $ 1,019 Contract asset - related party ​ $ 2,545 ​ $ 926 ​ $ ( 2,545 ) ​ $ 926 Contract liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Deferred revenue - related party ​ $ 8,223 ​ $ 36,441 ​ $ ( 5,986 ) ​ $ 38,678 Payable to collaboration partner - related party ​ $ 1,061 ​ $ 1,226 ​ $ ( 1,267 ) ​ $ 1,020 ​ During the three and nine months ended September 30, 2020, the Company recognized revenue of $ 8.5 million and $ 11.8 million, respectively, from amounts included in the deferred revenue contract liability balance at the beginning of each period. During the three and nine months ended September 30, 2019, the Company recognized revenue of $ 2.9 million and $ 4.5 million, respectively, from amounts included in the deferred revenue contract liability balance at the beginning of each period. None of the costs to obtain or fulfill the contract were capitalized. Note 4. Fair Value Measurements Financial assets and liabilities are recorded at fair value. The accounting guidance for fair value provides a framework for measuring fair value, clarifies the definition of fair value and expands disclosures regarding fair value measurements. Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability (an exit price) in an orderly transaction between market participants at the reporting date. The accounting guidance 16 Table of Contents establishes a three-tiered hierarchy, which prioritizes the inputs used in the valuation methodologies in measuring fair value as follows: Level 1 —Inputs are unadjusted quoted prices in active markets for identical assets or liabilities at the measurement date. Level 2— Inputs (other than quoted market prices included in Level 1) are either directly or indirectly observable for the asset or liability through correlation with market data at the measurement date and for the duration of the instrument’s anticipated life. Level 3 —Inputs reflect management’s best estimate of what market participants would use in pricing the asset or liability at the measurement date. Consideration is given to the risk inherent in the valuation technique and the risk inherent in the inputs to the model. In determining fair value, the Company utilizes quoted market prices, broker or dealer quotations, or valuation techniques that maximize the use of observable inputs and minimize the use of unobservable inputs to the extent possible and considers counterparty credit risk in its assessment of fair value. The following table presents the fair value of the Company’s financial assets determined using the inputs defined above (in thousands). ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 45,337 ​ $ — ​ $ — $ 45,337 Commercial paper ​ — ​ 41,683 ​ — 41,683 Corporate debt securities ​ — ​ 21,434 ​ — 21,434 U.S. Treasury and agency securities ​ — ​ 87,205 — 87,205 Total financial assets ​ $ 45,337 ​ $ 150,322 $ — $ 195,659 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 12,964 ​ $ — ​ $ — $ 12,964 Commercial paper ​ — ​ 44,282 ​ — 44,282 Corporate debt securities ​ — ​ 33,662 — 33,662 U.S. Treasury and agency securities ​ — ​ 40,810 — 40,810 Total financial assets ​ $ 12,964 ​ $ 118,754 $ — $ 131,718 ​ The Company’s commercial paper, corporate debt securities and U.S. Treasury and agency securities, including U.S. Treasury bills, are classified as Level 2 as they were valued based upon quoted market prices for similar instruments in active markets, quoted prices for identical or similar instruments in markets that are not active and model-based valuation techniques for which all significant inputs are observable in the market or can be corroborated by observable market data for substantially the full term of the assets. ​ 17 Table of Contents Note 5. Cash Equivalents and Marketable Securities ​ Cash equivalents and marketable securities consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, 2020 ​ ​ Amortized ​ Gross Unrealized ​ ​ Cost Gains Losses Fair Value Money market funds ​ $ 45,337 ​ $ — $ — ​ $ 45,337 Commercial paper ​ 41,683 ​ — — ​ 41,683 Corporate debt securities ​ 21,435 ​ 3 ​ ( 4 ) ​ 21,434 U.S. Treasury and agency securities ​ 87,195 ​ 10 — ​ 87,205 Total cash equivalents and marketable securities ​ $ 195,650 ​ $ 13 $ ( 4 ) ​ $ 195,659 Classified as: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ $ 79,285 Marketable securities - current ​ ​ ​ ​ ​ ​ ​ 110,349 Marketable securities - noncurrent ​ ​ ​ ​ ​ ​ ​ 6,025 Total cash equivalents and marketable securities ​ ​ ​ ​ ​ ​ ​ $ 195,659 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2019 ​ ​ Amortized ​ Gross Unrealized ​ ​ Cost Gains Losses Fair Value Money market funds ​ $ 12,964 ​ $ — $ — ​ $ 12,964 Commercial paper ​ 44,284 ​ 2 ( 4 ) ​ 44,282 Corporate debt securities ​ 33,653 ​ 11 ( 2 ) ​ 33,662 U.S. Treasury and agency securities ​ 40,798 ​ 14 ( 2 ) ​ 40,810 Total cash equivalents and marketable securities ​ $ 131,699 ​ $ 27 $ ( 8 ) ​ $ 131,718 Classified as: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ $ 31,707 Marketable securities - current ​ ​ ​ ​ ​ ​ ​ 100,011 Total cash equivalents and marketable securities ​ ​ ​ ​ ​ ​ ​ $ 131,718 ​ Marketable securities – current of $ 110.3 million and $ 100.0 million held at September 30, 2020 and December 31, 2019, respectively, had contractual maturities of less than one year. Marketable securities – noncurrent of $ 6.0 million held at September 30, 2020 had contractual maturities of at least one year but less than two years. There were no material realized gains or realized losses on marketable securities for the periods presented. The Company has not experienced any material credit losses on its investments. The Company does not intend to sell its securities that are in an unrealized loss position, and it is unlikely that the Company will be required to sell its securities before recovery of their amortized cost basis, which may be maturity. Factors considered in determining whether a loss is temporary include the length of time and extent to which the fair value has been less than the amortized cost basis and whether the Company intends to sell the security or whether it is more likely than not that the Company would be required to sell the security before recovery of the amortized cost basis. ​ ​ 18 Table of Contents Note 6. Accrued Expenses and Other Payables Accrued expenses and other payables consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2020 ​ 2019 Accrued clinical and research related expenses ​ $ 10,160 ​ $ 7,232 Accrued employee related expenses ​ 4,371 ​ 4,637 Accrued professional service fees ​ ​ 857 ​ ​ 301 Accrued interest payable ​ ​ 2 ​ ​ 68 Other ​ 128 ​ 122 Total accrued expenses and other payables ​ $ 15,518 ​ $ 12,360 ​ Note 7. Research Collaboration and License Agreement In October 2013, the Company’s former collaboration partner decided to abandon a collaboration program with the Company and, pursuant to the terms of the agreement between the Company and the former collaboration partner, the Company elected to assume responsibility for the development and commercialization of the product. Upon the former collaboration partner’s abandonment, it assigned to the Company certain intellectual property that relates to the products arising from the collaboration. The Company has the right, but not the obligation, to further develop and commercialize the product and, if the Company successfully develops and commercializes PTG-300 without a partner, the former collaboration partner could be eligible to receive up to an additional aggregate of $ 128.0 million for the achievement of certain development, regulatory and sales milestone events pursuant to the terms of the agreement between the Company and the former collaboration partner. Milestone payments to collaboration partners are recorded as research and development expenses in the period that the expense is incurred. No research and development expense was recorded under the agreement between the Company and the former collaboration partner for the three and nine months ended September 30, 2020 and 2019. See Note 10. Commitments and Contingencies – Legal Proceedings for additional information on arbitration proceedings related to this research collaboration and license agreement. Note 8. Government Programs Research and Development Tax Incentive During the three and nine months ended September 30, 2020, the Company recognized AUD 0.4 million ($ 0.3 million) and AUD 0.8 million ($ 0.5 million), respectively, as a reduction of research and development expenses in connection with the research and development cash tax incentive from the ATO. During the nine months ended September 30, 2019, the Company recognized AUD 1.8 million ($ 1.2 million) of research and development expense in connection with the research and development tax incentive from the ATO because the Company determined that it had exceeded the annual turnover limit to claim such amounts following the receipt of certain payments under the Janssen License and Collaboration Agreement. No such amounts were recorded during the three months ended September 30, 2019. As of September 30, 2020, the research and development cash tax incentive receivable was AUD 0.8 million ($ 0.5 million). There was no research and development cash tax incentive receivable as of December 31, 2019. Small Business Innovation Research (“SBIR”) Grants The Company has received SBIR grants from the National Institutes of Health (“NIH”) in support of research aimed at its product candidates. The Company recognizes a reduction to research and development expenses when expenses related to the grants have been incurred and the grant funds become contractually due from NIH. The Company recorded $ 0.3 million as a reduction of research and development expenses for the nine months ended September 30, 2020. No such amounts were recorded during the three months ended September 30, 2020. The Company recorded $ 0.6 million and $ 1.1 million as a reduction of research and development expenses for the three and nine months ended September 30, 2019, respectively. The Company recorded a receivable for $ 0.3 million as of 19 Table of Contents December 31, 2019 to reflect the eligible costs incurred under the grants that are contractually due to the Company. The Company recorded no such receivable as of September 30, 2020. This receivable is included in prepaid expenses and other current assets on the condensed consolidated balance sheets. Note 9. Debt On October 30, 2019, the Company entered into a Credit and Security Agreement, dated as of October 30, 2019 (the “Closing Date”) by and among the Company, MidCap Financial Trust, as a lender, Silicon Valley Bank, as a lender, the other lenders party thereto from time to time and MidCap Financial Trust, as administrative agent and collateral agent (“Agent”) (the “Term Loan Credit Agreement”), which provides for a $ 50.0 million term loan facility. The Term Loan Credit Agreement provides for (i) on the Closing Date, $ 10.0 million aggregate principal amount of term loans, (ii) at the Company’s option, until December 31, 2020, an additional $ 20.0 million term loan facility subject to the satisfaction of certain conditions, including clinical milestone achievement, and (iii) at the Company’s option, until September 30, 2021, an additional $ 20.0 million term loan facility subject to the satisfaction of certain conditions, including clinical milestone achievement, (collectively, the “Term Loans”). The Company intends to use any proceeds from drawdowns on the Term Loans for general corporate purposes The Term Loans are subject to an origination fee of 0.25 % for each funded tranche under the Term Loan Credit Agreement and bear interest at an annual rate based on prime rate plus 2.91 %, subject to a prime rate floor of 4.94 %. The Company will make interest-only payments on the Term Loans outstanding during the initial 24 months , followed by 24 months of principal and interest payments. At the Company’s option, the Company may prepay the outstanding principal balance of the Term Loans in whole or in part, subject to a prepayment premium of 3.0 % of any amount prepaid if the prepayment occurs through and including the first anniversary of the Closing Date, 2.0 % of the amount prepaid if the prepayment occurs after the first anniversary of the closing date through and including the second anniversary of the closing date, and 1.0 % of any amount prepaid after the second anniversary of the closing date and prior to October 1, 2023. An additional fee of 2.85 % of the amount of Term Loans advanced by the Lenders will be due upon prepayment or repayment of the Term Loans. The Term Loan Credit Agreement requires the Company to maintain cash and cash equivalents of at least 35 % of the outstanding Term Loans at all times and is secured by a perfected security interest in all of the Company's assets except for intellectual property and certain other customary excluded property pursuant to the terms of the Term Loan Credit Agreement. The Term Loan Credit Agreement contains other covenants that limit the Company’s ability and the ability of its subsidiaries to perform certain actions, including obligations to not pay dividends and to maintain unrestricted cash balance above certain threshold, non-occurrence of material adverse change, non-occurrence of change of control and other customary affirmative and negative covenants. The violation of any provision of covenants will result in default for the Company. The Term Loan Credit Agreement includes a clause which allows lenders to accelerate repayment upon the occurrence of certain events of default. In June 2020, the Company prepaid the outstanding $ 10.0 million balance on the term loan as well as $ 0.6 million for related prepayment and exit fees. Accordingly, the company accelerated amortization of $ 0.1 million related to capitalized and unamortized debt issuance costs, which is included as part of the $ 0.6 million loss on early repayment of debt. As of September 30, 2020, the Company was in compliance with the debt covenants, no event of default occurred and the probability of occurrence of event of default was considered remote. The Company’s long-term debt balance was as follows for the periods presented (dollars in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Annual ​ September 30, ​ ​ December 31, ​ ​ Interest Rate ​ 2020 ​ ​ 2019 Term loan (matures October 1, 2023) ​ ​ 7.85 % ​ $ — ​ ​ $ 10,000 Debt issuance costs, net of amortization ​ ​ ​ ​ — ​ ​ ( 222 ) Accrued final payment fee ​ ​ ​ ​ ​ — ​ ​ ​ 16 Long-term debt, net ​ ​ ​ ​ $ — ​ ​ $ 9,794 ​ 20 Table of Contents Note 10. Commitments and Contingencies Legal Proceedings The Company is a party to the legal action described below. The Company recognizes accruals for such actions to the extent that it concludes that a loss is both probable and reasonably estimable. The Company accrues for the best estimate of a loss within a range; however, if no estimate in the range is better than any other, it accrues the minimum amount in the range. If the Company determines that a loss is reasonably possible and the loss or range of loss can be estimated, it discloses the possible loss. On January 23, 2020, the Company initiated arbitration proceedings with the International Court of Arbitration of the International Chamber of Commerce against Zealand Pharma A/S (“Zealand”) related to a collaboration agreement the Company and Zealand entered into in 2012 and terminated in 2014. The agreement provides for certain post-termination payment obligations to Zealand with respect to compounds related to the collaboration that the Company elects to further develop and meet specified conditions. In the Company’s arbitration claim, it is seeking a declaration that the Company has no past, present or future milestone or royalty payment obligations under the agreement with respect to PTG-300 because PTG-300 is not a compound relating to the collaboration for which post-termination payments to Zealand apply. The Company is also seeking repayment of $ 1.0 million in milestone payments it has made, as well as its costs, fees, and expenses of the proceeding. Zealand disputes the Company’s claims and has filed counterclaims for payment of an additional future milestone, as well as payment of their arbitration costs, fees and expenses . The arbitration is pending. If Zealand prevails in the arbitration, the Company could be required to make contractual payments to Zealand described in its prior periodic reports filed with the SEC. Those payments could include milestone payments for the achievement of certain development, regulatory and sales milestone events, and a low single digit royalty on worldwide net sales of PTG-300. Although the Company cannot predict with certainty the ultimate outcome of these arbitration proceedings, it has concluded that the probability of any related loss is remote and therefore no related accruals were recognized as of September 30, 2020. Note 11. Stockholders’ Equity In September 2017, the Company filed a registration statement on Form S-3 with the Securities and Exchange Commission (File No. 333-220314) that was declared effective as of October 5, 2017 and permits the offering, issuance, and sale by the Company of up to a maximum aggregate offering price of $ 200.0 million of its common stock, preferred stock and certain debt securities (the “2017 Form S-3”). Up to a maximum of $ 50.0 million of the maximum aggregate offering price of $ 200.0 million may be issued and sold pursuant to an ATM financing facility under a sales agreement (the “2017 Sales Agreement”). The 2017 Sales Agreement was terminated in 2019. The Company sold 1,924,957 and 2,846,641 shares of its common stock pursuant to the 2017 Sales Agreement during the three and nine months ended September 30, 2019, respectively, for net proceeds of $ 23.9 and $ 34.5 million, respectively, after deducting issuance costs. As of September 30, 2020, $ 72.0 million of common stock remained available for sale under the 2017 Form S-3, which subsequently expired in October 2020. In August 2018, the Company entered into a Securities Purchase Agreement with certain accredited investors (each, an “Investor” and, collectively, the “Investors”), pursuant to which the Company sold an aggregate of 2,750,000 shares of its common stock at a price of $ 8.00 per share, for aggregate net proceeds of $ 21.7 million, after deducting offering expenses payable by the Company. In a concurrent private placement, the Company issued the Investors warrants to purchase an aggregate of 2,750,000 shares of its common stock (each, a “Warrant” and, collectively, the “Warrants”). Each Warrant is exercisable from August 8, 2018 through August 8, 2023. Warrants to purchase 1,375,000 shares of the Company’s common stock have an exercise price of $ 10.00 per share and Warrants to purchase 1,375,000 shares of the Company’s common stock have an exercise price of $ 15.00 per share. The exercise price and number of shares of common stock issuable upon the exercise of the Warrants (the “Warrant Shares”) are subject to adjustment in the event of any stock dividends and splits, reverse stock split, recapitalization, reorganization or similar transaction, as described in the Warrants. Under certain circumstances, the Warrants may be exercisable on a “cashless” basis. In connection with the issuance and sale of the common stock and Warrants, the Company granted the Investors certain registration rights with respect to the Warrants and the Warrant Shares. The common stock and warrants are classified as equity in accordance with Accounting Standards Codification Topic 480 , Distinguishing Liabilities from 21 Table of Contents Equity (“ASC 480”) , and the net proceeds from the transaction were recorded as a credit to additional paid-in capital. As of September 30, 2020, none of the Warrants have been exercised. In December 2018, the Company entered into an exchange agreement (the “Exchange Agreement”) with an Investor and its affiliates (the “Exchanging Stockholders”), pursuant to which the Company exchanged an aggregate of 1,000,000 shares of the Company’s common stock, par value $ 0.00001 per share, owned by the Exchanging Stockholders for pre-funded warrants (the “Exchange Warrants”) to purchase an aggregate of 1,000,000 shares of common stock (subject to adjustment in the event of any stock dividends and splits, reverse stock split, recapitalization, reorganization or similar transaction, as described in the Exchange Warrants), with an exercise price of $ 0.00001 per share. The Exchange Warrants will expire ten years from the date of issuance. The Exchange Warrants are exercisable at any time prior to expiration except that the Exchange Warrants cannot be exercised by the Exchanging Stockholders if, after giving effect thereto, the Exchanging Stockholders would beneficially own more than 9.99 % of the Company’s common stock, subject to certain exceptions. In accordance with Accounting Standards Codification Topic 505, Equity , the Company recorded the retirement of the common stock exchanged as a reduction of common stock shares outstanding and a corresponding debit to additional paid-in-capital at the fair value of the Exchange Warrants on the issuance date. The Exchange Warrants are classified as equity in accordance with ASC 480 , and fair value of the Exchange Warrants was recorded as a credit to additional paid-in capital and is not subject to remeasurement. The Company determined that the fair value of the Exchange Warrants is substantially similar to the fair value of the retired shares on the issuance date due to the negligible exercise price for the Exchange Warrants. During the second quarter of 2019, Exchange Warrants to purchase 600,000 shares were net exercised, resulting in the issuance of 599,997 shares of common stock. As of September 30, 2020, 400,000 of the Exchange Warrants remain unexercised In October 2019, the Company filed a registration statement on Form S-3 (File No. 333-234414) that was declared effective as of November 22, 2019 and permits the offering, issuance, and sale by the Company of up to a maximum aggregate offering price of $ 250.0 million of its common stock, preferred stock, debt securities and warrants (the “2019 Form S-3”). Up to a maximum of $ 75.0 million of the maximum aggregate offering price of $ 250.0 million may be issued and sold pursuant to an ATM financing facility under a sales agreement entered into by the Company on November 27, 2019 (the “2019 Sales Agreement”). In May 2020, the Company completed an underwritten public offering of 7,000,000 shares of common stock at a public offering price of $ 14.00 per share, and issued an additional 1,050,000 shares of its common stock at a price of $ 14.00 per share following the underwriters’ exercise of their option to purchase additional shares. Net proceeds, after deducting underwriting commissions and offering costs paid by the Company, were $ 105.3 million. The Company sold 333,047 and 1,565,840 shares of its common stock pursuant to the 2019 Sales Agreement during the three and nine months ended September 30, 2020, respectively, for net proceeds of $ 6.4 million and $ 23.0 million, respectively, after deducting issuance costs. As of September 30, 2020, a total of $ 113.5 million of common stock remained available for sale under the 2019 Form S-3, $ 51.2 million of which remained available for sale under the ATM financing facility. Note 12. Equity Plans Equity Incentive Plan In July 2016, the Company’s board of directors and stockholders approved the Company’s 2016 Equity Incentive Plan (the “2016 Plan”) to replace the 2007 Stock Option Plan. The 2016 Plan is administered by the board of directors or a committee appointed by the board of directors, which determines the types of awards to be granted, including the number of shares subject to the awards, the exercise price and the vesting schedule. Awards granted under the 2016 Plan expire no later than ten years from the date of grant. As of September 30, 2020, 552,511 shares were available for issuance under the 2016 Plan. Inducement Plan In May 2018, the Company’s board of directors approved the 2018 Inducement Plan, a non-stockholder approved stock plan, under which it reserved and authorized up to 750,000 shares of the Company’s common stock in order to award options and restricted stock unit awards to persons that were not previously employees or directors of the Company, or following a bona fide period of non-employment, as an inducement material to such persons entering 22 Table of Contents into employment with the Company, within the meaning of Rule 5635(c)(4) of the NASDAQ Listing Rules. The 2018 Inducement Plan is administered by the board of directors or the Compensation Committee of the board, which determines the types of awards to be granted, including the number of shares subject to the awards, the exercise price and the vesting schedule. Awards granted under the 2018 Inducement Plan expire no later than ten years from the date of grant. On February 18, 2020, the Compensation Committee of the board approved the amendment and restatement of the 2018 Inducement Plan (the “Amended and Restated Inducement Plan”) to provide for the reservation of an additional 500,000 shares of the Company’s common stock for issuance under the Amended and Restated Inducement Plan. As of September 30, 2020, 630,000 shares were available for issuance under the Amended and Restated Inducement Plan. Stock Options Stock option activity under the Company’s equity incentive and inducement plans is set forth below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ Weighted- ​ ​ ​ ​ ​ ​ Average ​ Average ​ ​ ​ ​ ​ ​ Exercise ​ Remaining ​ Aggregate ​ ​ Options ​ Price Per ​ Contractual ​ Intrinsic ​ Outstanding Share Life (years) Value (1) ​ ​ ​ ​ ​ ​ ​ ​ ​ (in millions) Balances at December 31, 2019 3,681,521 $ 11.64 7.78 ​ ​ Options granted 1,370,600 ​ ​ 10.32 ​ Options exercised ( 257,714 ) ​ ​ 7.34 ​ ​ ​ Options forfeited ​ ( 197,588 ) ​ ​ 11.88 ​ ​ ​ ​ ​ Balances at September 30, 2020 4,596,819 $ 11.47 7.81 ​ $ 38.8 Options exercisable – September 30, 2020 ​ 2,464,699 $ 12.15 6.82 ​ $ 19.6 Options vested and expected to vest – September 30, 2020 ​ 4,596,819 ​ $ 11.47 7.81 ​ $ 38.8 (1) The aggregate intrinsic values were calculated as the difference between the exercise price of the options and the closing price of the Company’s common stock on September 30, 2020. The calculation excludes options with an exercise price higher than the closing price of the Company’s common stock on September 30, 2020. During the nine months ended September 30, 2020, the estimated weighted-average grant-date fair value of common stock underlying options granted to employees was $ 6.82 per share. Stock Options Valuation Assumptions The fair value of employee stock option awards was estimated at the date of grant using a Black-Scholes option-pricing model with the following assumptions: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, ​ Nine Months Ended September 30, ​ ​ 2020 ​ 2019 ​ 2020 ​ 2019 Expected term (in years) 5.27 - 6.08 5.00 - 6.08 ​ 5.27 - 6.08 5.00 - 6.08 Expected volatility 84.5 % - 85.1 % ​ 61.0 % - 63.4 % ​ 72.1 % - 85.1 % ​ 61.0 % - 63.4 % Risk-free interest rate 0.23 % - 0.40 % ​ 1.42 % - 1.90 % ​ 0.23 % - 1.44 % ​ 1.42 % - 2.58 % Dividend yield — — ​ — — ​ In determining the fair value of the options granted, the Company uses the Black-Scholes option-pricing model and assumptions discussed below. Each of these inputs is subjective, and expected volatility generally requires significant judgment to determine. Expected Term —The Company’s expected term represents the period that the Company’s options granted are expected to be outstanding and is determined using the simplified method (based on the mid-point between the vesting date and the end of the contractual term). The Company has limited historical information to develop reasonable 23 Table of Contents expectations about future exercise patterns and post-vesting employment termination behavior for its stock option grants. Expected Volatility — Prior to January 1, 2020, the Company’s expected volatility was estimated based on the average volatility for comparable publicly traded biopharmaceutical companies over a period equal to the expected term of the stock option grants. Beginning January 1, 2020, the Company’s expected volatility was estimated based upon a mix of 75 % of the average volatility for comparable publicly traded biopharmaceutical companies over a period equal to the expected term of the stock option grants and 25 % of the volatility of the Company’s stock price since its initial public offering in August 2016. Risk-Free Interest Rate —The risk-free interest rate is based on the U.S. Treasury zero coupon issues in effect at the time of grant for periods corresponding with the expected term of option. Expected Dividend —The Company has never paid dividends on its common stock and has no plans to pay dividends on its common stock. Therefore, the Company used an expected dividend yield of zero. Restricted Stock Units Restricted stock unit activity under the Company’s equity incentive plans is set forth below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted ​ ​ ​ ​ Average ​ ​ Number of ​ Grant Date ​ Shares Fair Value Unvested at December 31, 2019 ​ 278,482 ​ $ 10.08 Granted 142,000 ​ 7.80 Vested ( 131,147 ) ​ 9.52 Forfeited ​ ( 26,727 ) ​ ​ 8.97 Unvested at September 30, 2020 ​ 262,608 ​ $ 9.24 ​ Employee Stock Purchase Plan ​ The 2016 Employee Stock Purchase Plan (“2016 ESPP”) allows eligible employees to purchase shares of the Company’s common stock at a discount through payroll deductions of up to 15 % of their eligible compensation. At the end of each offering period, eligible employees are able to purchase shares at 85 % of the lower of the fair market value of the Company’s common stock at the beginning of the offering period or at the end of each applicable purchase period. During the three and nine months ended September 30, 2020, a total of 35,781 and 92,523 shares of common stock were issued under the 2016 ESPP, respectively, and 757,647 shares remain available for issuance. Stock-Based Compensation ​ Total stock-based compensation expense was as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ 2020 2019 2020 2019 Research and development ​ $ 1,006 ​ $ 1,137 ​ $ 3,098 ​ $ 3,237 General and administrative ​ 882 ​ 1,064 ​ 2,834 ​ 2,956 Total stock-based compensation expense ​ $ 1,888 ​ $ 2,201 ​ $ 5,932 ​ $ 6,193 ​ As of September 30, 2020, total unrecognized stock-based compensation expense was approximately $ 14.7 million, which the Company expects to recognize over a weighted-average period of approximately 2.8 years. 24 Table of Contents Note 13. Income Taxes The Company recorded income tax expense of $ 1.3 million for the nine months ended September 30, 2020, representing an effective income tax rate of 2.8 %. No income tax expense was recorded for the three months ended September 30, 2020. The Company recorded income tax benefit of $ 0.1 million and $ 1.5 million for the three and nine months ending September 30, 2019, respectively, representing an effective income tax rate of ( 0.6 )% and ( 2.5 )%, respectively. Income tax for all periods presented was primarily related to foreign income tax. During the second quarter of 2020, the Company’s Australia subsidiary sold beneficial rights to discovery intellectual property to its U.S. entity, and the U.S. entity reimbursed the Australia subsidiary for certain direct development costs. Upon completion of the sale, the Company analyzed tax planning strategies and future income and concluded that a valuation allowance is necessary for its Australia subsidiary. Income tax expense for the nine months ended September 30, 2020 reflects this sale of intellectual property rights, cost reimbursements and related adjustments to the deferred tax asset, establishing a valuation allowance and certain uncertain tax position liabilities. Income tax benefit for the nine months ended September 30, 2019 included a discrete tax benefit of approximately $ 1.1 million for the 2017 Australia refundable research and development tax offset. The Company’s effective income tax rate for all periods presented differs from the Company’s federal statutory rate of 21 %, primarily because its U.S. loss cannot be benefited due to the full valuation allowance position and reduced by foreign taxes. On March 27, 2020, the Coronavirus Aid, Relief and Economic Security Act (“CARES Act”) was enacted and signed into law in response to the COVID-19 pandemic. GAAP requires recognition of the tax effects of new legislation during the reporting period that includes the enactment date. The CARES Act includes changes to the tax provisions that benefits business entities and makes certain technical corrections to the 2017 Tax Cuts and Jobs Act. The tax relief measures for businesses include a five-year net operating loss carryback, suspension of the annual deduction limitation of 80 % of taxable income from net operating losses generated in a tax year beginning after December 31, 2017, changes in the deductibility of interest, acceleration of alternative minimum tax credit refunds, payroll tax relief, technical corrections on net operating loss carryforwards for fiscal year taxpayers and allows accelerated deduction qualified improvement property. The CARES Act also provides other non-tax benefits to assist those impacted by the pandemic. The Company evaluated the impact of the CARES Act and determined that there is no material impact to the income tax provision for the three and nine months ended September 30, 2020. On June 29, 2020, California Assembly Bill 85 was signed into law. The legislation suspends the California net operating loss deductions for 2020, 2021, and 2022 for certain taxpayers and imposes a limitation of certain California tax credits for 2020, 2021, and 2022. The legislation disallows the use of California net operating loss deductions if the taxpayer recognizes business income and its adjusted gross income is greater than $ 1,000,000 . The carryover periods for net operating loss deductions disallowed by this provision will be extended. Additionally, any business credit will only offset a maximum of $ 5,000,000 of California tax. Given the Company’s expected loss position in the current year, the new legislation will not impact the current year provision. The Company will continue to monitor possible California net operating loss and credit limitations in future periods. 25 Table of Contents Note 14. Net Loss per Share As the Company had net losses for the three and nine months ended September 30, 2020 and 2019, respectively, all potential common shares were determined to be anti-dilutive. The following table sets forth the computation of basic and diluted net loss per share (in thousands, except share and per share data): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ Nine Months Ended ​ ​ September 30, ​ September 30, ​ 2020 2019 2020 2019 Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 7,763 ) ​ $ ( 16,409 ) ​ $ ( 47,264 ) ​ $ ( 59,686 ) Denominator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-average shares used to compute net loss per common share, basic and diluted ​ 37,386,881 ​ 26,956,957 ​ 32,647,524 25,315,512 Net loss per shares, basic and diluted ​ $ ( 0.21 ) ​ ​ ( 0.61 ) ​ $ ( 1.45 ) ​ $ ( 2.36 ) ​ The following outstanding shares of potentially dilutive securities have been excluded from diluted net loss per share computations for the periods presented because their inclusion would be anti-dilutive: ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ 2020 2019 Options to purchase common stock ​ 4,596,819 3,709,631 Common stock warrants ​ 2,750,000 ​ 2,750,000 Restricted stock units ​ 262,608 ​ 284,445 ESPP shares ​ 28,618 ​ 41,263 Total 7,638,045 6,785,339 ​ Note 15. Restructuring On May 7, 2020, the Company approved a limited reduction in force plan affecting approximately 12 % of the Company’s employee base and informed the affected employees. The reduction-in-force plan was completed by the end of the second quarter of 2020. Total cash expenditures for the reduction in force plan were $ 0.3 million, substantially all of which were related to employee severance and benefits costs. Note 16. Subsequent Event The Company sold 917,879 shares of its common stock under its ATM financing facility pursuant to the 2019 Sales Agreement during the period from October 1, 2020 through the date of issuance of this Quarterly Report on Form 10-Q. Net proceeds were $ 18.9 million, after deducting issuance costs. As of the date of issuance of this Quarterly Report on Form 10-Q, a total of $ 94.2 million of common stock remained available for sale under the 2019 Form S-3, $ 31.9 million of which remained available for sale under the ATM financing facility. ​ 26 Table of Contents