UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2025 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission File Number 001-37566 SYNLOGIC, INC. (Exact name of Registrant as specified in its Charter) Delaware (State or other jurisdiction of incorporat ...

[Company Information & Filing Details](index=1&type=section&id=Company%20Information%20%26%20Filing%20Details) [Filing Information](index=1&type=section&id=Filing%20Information) This report is SYNLOGIC, INC.'s 10-Q quarterly report for the period ended June 30, 2025, detailing its status as a non-accelerated filer and smaller reporting company - SYNLOGIC, INC. submitted its 10-Q quarterly report for the period ended June 30, 2025[2](index=2&type=chunk) Company Filing Status | Indicator | Status | | :--- | :--- | | Ticker Symbol | SYBX | | Listing Exchange | Nasdaq Capital Market | | Large Accelerated Filer | No | | Accelerated Filer | No | | Non-Accelerated Filer | Yes | | Smaller Reporting Company | Yes | | Emerging Growth Company | No | | Shell Company | No | - As of July 31, 2025, the company had **11,698,919** shares of common stock outstanding[5](index=5&type=chunk) [FORWARD-LOOKING STATEMENTS](index=2&type=section&id=FORWARD-LOOKING%20STATEMENTS) [Forward-Looking Statements Disclosure](index=2&type=section&id=Forward-Looking%20Statements%20Disclosure) This report contains forward-looking statements regarding strategic alternatives, R&D, clinical trials, and financing, with no obligation for future updates - This report contains forward-looking statements involving risks and uncertainties, covering strategic alternatives, R&D success, clinical trials, regulatory approvals, collaborations, commercialization, competitive technologies, and financing[8](index=8&type=chunk)[10](index=10&type=chunk) - The company is not obligated to update or revise these forward-looking statements, even if new information becomes available in the future[10](index=10&type=chunk) - Identifying words for forward-looking statements include “may,” “will,” “should,” “expect,” “intend,” “plan,” “anticipate,” “believe,” “estimate,” “predict,” “potential,” and “continue”[8](index=8&type=chunk) [PART I - FINANCIAL INFORMATION](index=3&type=section&id=PART%20I%20-%20FINANCIAL%20INFORMATION) [Item 1. Financial Statements](index=4&type=section&id=Item%201.%20Financial%20Statements) This section presents the company's unaudited consolidated financial statements for Q2 2025, reflecting its financial position and operating results after strategic restructuring [Unaudited Consolidated Balance Sheets](index=4&type=section&id=Unaudited%20Consolidated%20Balance%20Sheets) Consolidated Balance Sheet Key Data (thousand USD) | Indicator | June 30, 2025 | December 31, 2024 | Change (thousand USD) | Change (%) | | :--- | :--- | :--- | :--- | :--- | | Cash and cash equivalents | 17,027 | 18,860 | (1,833) | -9.72% | | Total current assets | 17,320 | 19,776 | (2,456) | -12.42% | | Total assets | 17,370 | 19,826 | (2,456) | -12.39% | | Total current liabilities | 4,777 | 7,075 | (2,298) | -32.48% | | Purchase warrant liabilities | 3,780 | 4,874 | (1,094) | -22.44% | | Total stockholders' equity | 12,593 | 12,751 | (158) | -1.24% | | Accumulated deficit | (441,863) | (441,651) | (212) | 0.05% | - As of June 30, 2025, total assets were **$17.37 million**, a **12.39% decrease** from **$19.83 million** on December 31, 2024[14](index=14&type=chunk) - Current liabilities significantly decreased by **32.48%**, primarily due to changes in the fair value of purchase warrant liabilities[14](index=14&type=chunk) [Unaudited Consolidated Statements of Operations and Comprehensive Income (Loss)](index=5&type=section&id=Unaudited%20Consolidated%20Statements%20of%20Operations%20and%20Comprehensive%20Income%20(Loss)) Consolidated Statements of Operations and Comprehensive Income (Loss) Key Data (thousand USD) - Q2 Comparison | Indicator | Q2 2025 | Q2 2024 | Change (thousand USD) | Change (%) | | :--- | :--- | :--- | :--- | :--- | | Revenue | — | — | — | — | | Research and development expenses | (14) | 2,197 | (2,211) | -100.64% | | General and administrative expenses | 800 | 1,179 | (379) | -32.15% | | Restructuring and other charges | (9) | (3,795) | 3,786 | -99.76% | | Total operating expenses | 777 | (419) | 1,196 | -285.44% | | Operating income (loss) | (777) | 419 | (1,196) | -285.44% | | Net income (loss) | (529) | 3,078 | (3,607) | -117.19% | | Net income (loss) per share - Basic and diluted | (0.04) | 0.25 | (0.29) | -116.00% | Consolidated Statements of Operations and Comprehensive Income (Loss) Key Data (thousand USD) - H1 Comparison | Indicator | H1 2025 | H1 2024 | Change (thousand USD) | Change (%) | | :--- | :--- | :--- | :--- | :--- | | Revenue | — | 8 | (8) | -100.00% | | Research and development expenses | 8 | 9,877 | (9,869) | -99.92% | | General and administrative expenses | 1,636 | 4,063 | (2,427) | -59.73% | | Restructuring and other charges | 31 | 24,494 | (24,463) | -99.87% | | Total operating expenses | 1,675 | 38,434 | (36,759) | -95.64% | | Operating income (loss) | (1,675) | (38,426) | 36,751 | -95.64% | | Net income (loss) | (212) | (22,528) | 22,316 | -99.06% | | Net income (loss) per share - Basic and diluted | (0.02) | (1.85) | 1.83 | -98.92% | - Net loss for Q2 2025 was **$0.529 million**, compared to a net income of **$3.078 million** in Q2 2024, primarily due to a significant decrease in R&D expenses and restructuring charges[17](index=17&type=chunk) - Net loss for H1 2025 was **$0.212 million**, a substantial reduction from **$22.528 million** in H1 2024, mainly driven by significant decreases in R&D and restructuring expenses[17](index=17&type=chunk) [Unaudited Consolidated Statements of Stockholders' Equity](index=6&type=section&id=Unaudited%20Consolidated%20Statements%20of%20Stockholders'%20Equity) Changes in Stockholders' Equity (thousand USD) | Indicator | June 30, 2025 | March 31, 2024 | Change (thousand USD) | | :--- | :--- | :--- | :--- | | Common stock | 12 | 12 | 0 | | Additional paid-in capital | 456,962 | 455,803 | 1,159 | | Accumulated deficit | (441,863) | (443,898) | 2,035 | | Treasury stock | (2,518) | (2,518) | 0 | | Total stockholders' equity | 12,593 | 9,399 | 3,194 | - Total stockholders' equity as of June 30, 2025, was **$12.593 million**, an increase from **$9.399 million** on March 31, 2024, primarily due to a reduction in accumulated deficit[20](index=20&type=chunk) - In Q2 2025, the company's net loss reduced stockholders' equity by **$0.529 million**, but equity-based compensation expenses increased by **$0.029 million**[20](index=20&type=chunk) [Unaudited Consolidated Statements of Cash Flows](index=7&type=section&id=Unaudited%20Consolidated%20Statements%20of%20Cash%20Flows) Consolidated Statements of Cash Flows Key Data (thousand USD) | Cash Flow Type | H1 2025 | H1 2024 | | :--- | :--- | :--- | | Net cash used in operating activities | (2,000) | (30,442) | | Net cash provided by investing activities | 167 | 25,237 | | Net cash provided by financing activities | — | 164 | | Net decrease in cash, cash equivalents, and restricted cash | (1,833) | (5,041) | | Cash, cash equivalents, and restricted cash at end of period | 17,077 | 20,016 | - Net cash used in operating activities significantly decreased to **$2.0 million** in H1 2025 from **$30.442 million** in H1 2024, primarily due to a narrower net loss and changes in operating assets and liabilities[23](index=23&type=chunk) - Net cash provided by investing activities decreased from **$25.237 million** in H1 2024 to **$0.167 million** in H1 2025, mainly due to the maturity and redemption of marketable securities in 2024[23](index=23&type=chunk) [Notes to Unaudited Consolidated Financial Statements](index=8&type=section&id=Notes%20to%20Unaudited%20Consolidated%20Financial%20Statements) [Note 1. Nature of Business](index=8&type=section&id=Note%201.%20Nature%20of%20Business) Synlogic, Inc. is a biopharmaceutical company focused on synthetic biologics, having terminated its main clinical trial and significantly reduced staff, with sufficient cash for the next 12 months - Synlogic, Inc. is a biopharmaceutical company developing synthetic biologics using synthetic biology[25](index=25&type=chunk) - In February 2024, the company terminated the Synpheny-3 trial and initiated a strategic alternatives review, resulting in significant layoffs and only one full-time employee remaining[26](index=26&type=chunk) - As of June 30, 2025, the company had **$17 million** in unrestricted cash and cash equivalents, expected to support operations for the next 12 months[27](index=27&type=chunk) [Note 2. Summary of Significant Accounting Policies](index=8&type=section&id=Note%202.%20Summary%20of%20Significant%20Accounting%20Policies) This note reiterates the company's significant accounting policies from its 2024 annual report, with no material changes for the six months ended June 30, 2025 - The company's significant accounting policies were disclosed in its 2024 annual report, with no material changes for the six months ended June 30, 2025[28](index=28&type=chunk) - Financial statements are prepared in accordance with U.S. GAAP and SEC regulations, applying consolidation principles to eliminate all intercompany accounts and transactions[29](index=29&type=chunk)[30](index=30&type=chunk) - Newly issued accounting pronouncements are not expected to have a material impact on the company's current or future financial statements[31](index=31&type=chunk) [Note 3. Fair Value of Financial Instruments](index=10&type=section&id=Note%203.%20Fair%20Value%20of%20Financial%20Instruments) This note details assets and liabilities measured at fair value, primarily money market funds and purchase warrant liabilities, valued using the Black-Scholes model - The company classifies purchase warrants as derivative liabilities, valued using the Black-Scholes option pricing model, with fair value changes recognized in the consolidated statements of operations and comprehensive income (loss)[34](index=34&type=chunk) Assets and Liabilities Measured at Fair Value (thousand USD) | Category | June 30, 2025 | December 31, 2024 | | :--- | :--- | :--- | | **Assets:** | | | | Money market funds (Level 1) | 17,027 | 18,860 | | **Liabilities:** | | | | Purchase warrant liabilities (Level 3) | 3,780 | 4,874 | Warrant Fair Value Determination Assumptions | Assumption | June 30, 2025 | December 31, 2024 | | :--- | :--- | :--- | | Expected term | 3.25 years | 3.75 years | | Weighted average risk-free interest rate | 3.7% | 4.3% | | Expected volatility | 90.8% | 90.0% | | Exercise price | $3.41 | $3.41 | | Stock price | $1.27 | $1.40 | [Note 4. Assets Held for Sale](index=12&type=section&id=Note%204.%20Assets%20Held%20for%20Sale) In February 2024, the company decided to sell its remaining laboratory equipment, generating $0.2 million in proceeds and an $0.08 million gain on disposal by June 30, 2025 - In February 2024, the company decided to sell its remaining laboratory equipment, classifying it as assets held for sale[37](index=37&type=chunk) - Within the six months ended June 30, 2025, equipment sales generated **$0.2 million** in proceeds and an **$0.08 million** gain on disposal[37](index=37&type=chunk) [Note 5. Prepaid Expenses and Other Current Assets](index=12&type=section&id=Note%205.%20Prepaid%20Expenses%20and%20Other%20Current%20Assets) Total prepaid expenses and other current assets significantly decreased to $0.293 million as of June 30, 2025, primarily due to reductions in prepaid insurance and R&D expenses Prepaid Expenses and Other Current Assets (thousand USD) | Item | June 30, 2025 | December 31, 2024 | | :--- | :--- | :--- | | Prepaid insurance | 136 | 517 | | Prepaid R&D | — | 128 | | Other prepaid expenses | 98 | 110 | | Other current assets | 59 | 75 | | **Total** | **293** | **830** | - Total prepaid expenses and other current assets decreased from **$0.83 million** on December 31, 2024, to **$0.293 million** on June 30, 2025, a **64.7% decrease**[38](index=38&type=chunk) [Note 6. Accrued Expenses](index=12&type=section&id=Note%206.%20Accrued%20Expenses) Total accrued expenses significantly decreased to $0.952 million as of June 30, 2025, mainly due to reductions in restructuring costs, payroll, and professional service fees Accrued Expenses (thousand USD) | Item | June 30, 2025 | December 31, 2024 | | :--- | :--- | :--- | | Payroll-related | 9 | 126 | | Professional services | 83 | 205 | | Restructuring costs | 841 | 1,656 | | Other | 19 | 50 | | **Total** | **952** | **2,037** | - Total accrued expenses decreased from **$2.037 million** on December 31, 2024, to **$0.952 million** on June 30, 2025, a **53.3% decrease**[39](index=39&type=chunk) - Restructuring costs, while the largest component of accrued expenses, decreased from **$1.656 million** to **$0.841 million**[39](index=39&type=chunk) [Note 7. Restructuring and Other Charges](index=12&type=section&id=Note%207.%20Restructuring%20and%20Other%20Charges) In February 2024, the company initiated strategic restructuring, terminating the Synpheny-3 trial and reducing staff to one employee, with $0.8 million in unpaid restructuring charges as of June 30, 2025 - In February 2024, the company decided to terminate the Synpheny-3 trial and undergo strategic restructuring, resulting in layoffs and only one full-time employee remaining[40](index=40&type=chunk)[41](index=41&type=chunk) Restructuring and Other Charges (thousand USD) | Item | Q2 2025 | Q2 2024 | H1 2025 | H1 2024 | | :--- | :--- | :--- | :--- | :--- | | Severance and related costs | 60 | 300 | 110 | 5,900 | | Accelerated equity-based compensation expense | — | 300 | — | 2,100 | | Gain on equipment sales | (70) | (1,000) | (80) | (1,100) | | Impairment of lease assets | — | — | — | 9,600 | | Impairment of fixed assets | — | — | — | 5,000 | | Gain on lease termination | — | — | — | (3,200) | | Impairment of prepaid R&D | — | — | — | 5,200 | - As of June 30, 2025, approximately **$0.8 million** in restructuring charges (primarily personnel costs and professional service fees) remained unpaid and were included in accrued restructuring costs[46](index=46&type=chunk) [Note 8. Stockholders' Equity](index=14&type=section&id=Note%208.%20Stockholders'%20Equity) This note details changes in stockholders' equity, including the expired rights plan and the October 2023 financing, where purchase warrants are classified as derivative liabilities - On February 20, 2024, the Board of Directors announced a rights plan, distributing one preferred stock purchase right per share of common stock, which expired on February 20, 2025, with no value[47](index=47&type=chunk)[48](index=48&type=chunk) - In October 2023, the company raised approximately **$19.6 million** through a public offering, issuing common stock, pre-funded warrants, and purchase warrants; purchase warrants are classified as derivative liabilities, with a fair value of **$3.8 million** as of June 30, 2025[49](index=49&type=chunk)[50](index=50&type=chunk)[51](index=51&type=chunk)[52](index=52&type=chunk)[53](index=53&type=chunk) Number of Common Shares Issuable in the Future as of June 30, 2025 | Item | Number of Shares | | :--- | :--- | | Common shares issuable upon exercise of pre-funded warrants | 552,309 | | Common shares issuable upon exercise of purchase warrants | 7,394,363 | | Common shares issuable upon exercise of Ginkgo pre-funded warrants | 169,874 | | Exercisable common stock options | 241,506 | | Employee stock purchase plan | — | | **Total** | **8,358,052** | [Note 9. Equity-based Compensation](index=16&type=section&id=Note%209.%20Equity-based%20Compensation) The company increased shares under its equity plans on January 1, 2025, and reported a significant decrease in equity-based compensation expenses in H1 2025 due to restructuring - On January 1, 2025, the company increased the number of shares issuable under its 2015 Equity Incentive Plan and 2015 Employee Stock Purchase Plan according to annual evergreen provisions[56](index=56&type=chunk) Equity-based Compensation Expense (thousand USD) | Expense Category | Q2 2025 | Q2 2024 | H1 2025 | H1 2024 | | :--- | :--- | :--- | :--- | :--- | | Research and development | — | 117 | — | 232 | | General and administrative | 29 | 58 | 54 | 364 | | Restructuring charges: accelerated recognition | — | 323 | — | 2,123 | | **Total** | **29** | **498** | **54** | **2,719** | - As of June 30, 2025, unrecognized equity-based compensation expense was **$0.04 million**, expected to be recognized over 1.25 years[58](index=58&type=chunk) [Note 10. Net Income (Loss) per Share](index=17&type=section&id=Note%2010.%20Net%20Income%20(Loss)%20per%20Share) This note details basic and diluted net income (loss) per share calculations, excluding anti-dilutive securities due to net losses in Q2 and H1 2025 Net Income (Loss) per Share Calculation (thousand USD, except share count) | Indicator | Q2 2025 | Q2 2024 | H1 2025 | H1 2024 | | :--- | :--- | :--- | :--- | :--- | | Net income (loss) | (529) | 3,078 | (212) | (22,528) | | Basic weighted-average common shares outstanding | 12,319,147 | 12,203,956 | 12,301,476 | 12,168,081 | | Diluted weighted-average common shares outstanding | 12,319,147 | 12,399,068 | 12,301,476 | 12,168,081 | | Basic and diluted net income (loss) per share | (0.04) | 0.25 | (0.02) | (1.85) | - Due to net losses in Q2 and H1 2025, potential common shares from purchase warrants, unvested restricted common stock, and outstanding options were excluded from diluted EPS calculations as they were anti-dilutive[62](index=62&type=chunk)[63](index=63&type=chunk) [Note 11. Commitments and Contingencies](index=18&type=section&id=Note%2011.%20Commitments%20and%20Contingencies) The company is not involved in any material legal proceedings, and there have been no significant changes to contractual obligations since its 2024 annual report - The company is not currently involved in any material legal proceedings[64](index=64&type=chunk) - As of June 30, 2025, there were no material changes to the contractual obligations and commitments disclosed in the company's 2024 annual report[65](index=65&type=chunk) [Note 12. Income Taxes](index=18&type=section&id=Note%2012.%20Income%20Taxes) The company recognized no income tax benefit in Q2 and H1 2025, fully reserving deferred tax assets, and is evaluating the impact of the OBBBA on future tax rates - The company recognized no income tax benefit in Q2 and H1 2025, having fully reserved its net deferred tax assets due to the unlikelihood of realizing federal and state deferred tax benefits[66](index=66&type=chunk) - The company is evaluating the impact of the Omnibus Beautiful Bill Act (OBBBA), enacted on July 4, 2025, on future effective tax rates[67](index=67&type=chunk) [Note 13. Segment Information](index=18&type=section&id=Note%2013.%20Segment%20Information) The company operates in one segment: synthetic biologics discovery and development, with the CODM focusing on consolidated financial performance and key expenses - The company operates in one operating segment: the discovery and development of synthetic biologics[68](index=68&type=chunk) - The Chief Operating Decision Maker (CODM) assesses performance and allocates resources based on consolidated financial information, primarily focusing on consolidated net income (loss)[69](index=69&type=chunk) Research and Development Expense Details (thousand USD) | Item | Q2 2025 | Q2 2024 | H1 2025 | H1 2024 | | :--- | :--- | :--- | :--- | :--- | | Clinical research and external costs | 10 | 1,208 | 15 | 4,914 | | Facilities and all other costs | — | 655 | — | 3,022 | | Compensation and benefits | (24) | 334 | (7) | 1,941 | | **Total R&D expenses** | **(14)** | **2,197** | **8** | **9,877** | General and Administrative Expense Details (thousand USD) | Item | Q2 2025 | Q2 2024 | H1 2025 | H1 2024 | | :--- | :--- | :--- | :--- | :--- | | Consulting and professional services | 598 | 585 | 1,226 | 2,050 | | Compensation and benefits | 149 | 264 | 294 | 1,261 | | Facilities and all other costs | 53 | 330 | 116 | 752 | | **Total G&A expenses** | **800** | **1,179** | **1,636** | **4,063** | Restructuring Expense Details (thousand USD) | Item | Q2 2025 | Q2 2024 | H1 2025 | H1 2024 | | :--- | :--- | :--- | :--- | :--- | | Facilities and all other costs | (68) | (4,534) | (80) | 15,502 | | Compensation and benefits | 61 | 595 | 109 | 8,024 | | Consulting and professional services | 19 | 397 | 19 | 666 | | Clinical research and external costs | (21) | (253) | (17) | 302 | | **Total restructuring expenses** | **(9)** | **(3,795)** | **31** | **24,494** | [Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations](index=20&type=section&id=Item%202.%20Management's%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) This section discusses the company's financial condition and operating results for Q2 2025, highlighting strategic shifts, reduced expenses, and a narrower net loss amid future uncertainties [Forward-Looking Information](index=20&type=section&id=Forward-Looking%20Information_MD%26A) - This discussion and analysis contains forward-looking statements and should be read in conjunction with the audited financial statements and risk factors sections in the company's 2024 annual report[74](index=74&type=chunk) [Overview](index=20&type=section&id=Overview_MD%26A) - The company is a biopharmaceutical company focused on rare metabolic diseases, with former lead product candidates SYNB1934 (phenylketonuria) and SYNB1353 (homocystinuria)[75](index=75&type=chunk) - In February 2024, the company decided to terminate the Synpheny-3 pivotal study for SYNB1934 due to an internal assessment indicating the trial was unlikely to meet its primary endpoint, not for safety or tolerability concerns[76](index=76&type=chunk) - The company's current strategic focus is actively pursuing strategic alternatives to enhance shareholder value, including but not limited to a merger or sale of the company[76](index=76&type=chunk) [Business Overview](index=22&type=section&id=Business%20Overview_MD%26A) - The company currently operates in one reportable business segment: the discovery and development of synthetic biologics, primarily funding operations through stock sales, warrants, and collaboration payments[80](index=80&type=chunk) - The company has not generated any revenue from product sales since inception and has consistently incurred operating losses, with an accumulated deficit of approximately **$441.9 million** as of June 30, 2025[81](index=81&type=chunk) - The company expects to continue incurring losses for the foreseeable future and plans to raise capital through equity or debt financing, collaborations, or licensing[81](index=81&type=chunk)[82](index=82&type=chunk) [Effects of Inflation](index=22&type=section&id=Effects%20of%20Inflation) - The company believes inflation did not materially impact its business or operating results during the reporting period, but future increases in inflationary costs and interest rates could have an adverse effect[83](index=83&type=chunk) [Financial Overview](index=23&type=section&id=Financial%20Overview_MD%26A) [Research and Development Expense](index=23&type=section&id=Research%20and%20Development%20Expense_MD%26A) R&D expenses include costs for product candidate discovery and development, with future expenses expected to remain low due to the Synpheny-3 trial termination and strategic evaluation - R&D expenses include external and internal costs for preclinical and clinical studies and product development[86](index=86&type=chunk)[92](index=92&type=chunk) - The company expects future R&D expenses to remain low due to the termination of the Synpheny-3 clinical trial and ongoing strategic alternative evaluation[88](index=88&type=chunk) [General and Administrative Expense](index=23&type=section&id=General%20and%20Administrative%20Expense_MD%26A) General and administrative expenses cover personnel, patent protection, facilities, IT, and professional services, with potential increases due to strategic alternative exploration - General and administrative expenses primarily include personnel compensation and benefits, patent protection, facilities, IT infrastructure, and professional service fees[90](index=90&type=chunk) - Future general and administrative expenses may increase due to the exploration of strategic alternatives, including potential legal, accounting, and consulting fees[90](index=90&type=chunk) [Restructuring and Other Charges](index=23&type=section&id=Restructuring%20and%20Other%20Charges_MD%26A) In February 2024, the company initiated strategic restructuring, terminating the Synpheny-3 trial and significantly reducing operations, incurring charges for severance, accelerated equity, and impairments - In February 2024, the company decided to terminate the Synpheny-3 trial and undergo strategic restructuring, resulting in a significant reduction in operations and layoffs to only one full-time employee[91](index=91&type=chunk) - Restructuring charges include severance, accelerated equity-based compensation, legal and contract termination costs, and impairment charges for leases, property and equipment, and prepaid R&D[91](index=91&type=chunk) [Other Income (Expense)](index=25&type=section&id=Other%20Income%20(Expense)_MD%26A) Other income (expense) primarily includes investment income, foreign currency gains/losses, and fair value remeasurement of purchase warrant liabilities - Other income (expense) primarily includes investment income, gains and losses on foreign currency invoices, and gains and losses from fair value remeasurement of purchase warrant liabilities[93](index=93&type=chunk) [Critical Accounting Policies and Estimates](index=25&type=section&id=Critical%20Accounting%20Policies%20and%20Estimates) - The company's critical accounting policies and estimates include warrants and research and development expenses, which require significant management judgment and assumptions[96](index=96&type=chunk) - Due to the company's restructuring and current focus on the strategic review process, revenue recognition is no longer a critical accounting policy[95](index=95&type=chunk) [Results of Operations](index=25&type=section&id=Results%20of%20Operations) [Three Months Ended June 30, 2025 Compared to Three Months Ended June 30, 2024](index=25&type=section&id=Three%20Months%20Ended%20June%2030,%202025%20Compared%20to%20Three%20Months%20Ended%20June%2030,%202024) In Q2 2025, the company reported a net loss of $0.529 million, a significant shift from Q2 2024 net income, driven by reduced R&D and other income Q2 2025 vs Q2 2024 Operating Results (thousand USD) | Indicator | Q2 2025 | Q2 2024 | Change (thousand USD) | | :--- | :--- | :--- | :--- | | Revenue | — | — | — | | Research and development expenses | (14) | 2,197 | (2,211) | | General and administrative expenses | 800 | 1,179 | (379) | | Restructuring and other charges | (9) | (3,795) | 3,786 | | Total operating expenses | 777 | (419) | 1,196 | | Operating loss | (777) | 419 | (1,196) | | Other income, net | 248 | 2,664 | (2,416) | | Net income (loss) | (529) | 3,078 | (3,607) | - R&D expenses decreased by **$2.211 million**, primarily due to the termination of the Labafenogene marselecobac (SYNB1934) clinical trial and layoffs[99](index=99&type=chunk)[103](index=103&type=chunk) - Other income decreased by **$2.416 million**, primarily related to changes in the fair value of purchase warrant liabilities[102](index=102&type=chunk) [Six Months Ended June 30, 2025 Compared to Six Months Ended June 30, 2024](index=28&type=section&id=Six%20Months%20Ended%20June%2030,%202025%20Compared%20to%20Six%20Months%20Ended%20June%2030,%202024) In H1 2025, the company reported a net loss of $0.212 million, a significant reduction from H1 2024, driven by substantial decreases in R&D and restructuring expenses H1 2025 vs H1 2024 Operating Results (thousand USD) | Indicator | H1 2025 | H1 2024 | Change (thousand USD) | | :--- | :--- | :--- | :--- | | Revenue | — | 8 | (8) | | Research and development expenses | 8 | 9,877 | (9,869) | | General and administrative expenses | 1,636 | 4,063 | (2,427) | | Restructuring and other charges | 31 | 24,494 | (24,463) | | Total operating expenses | 1,675 | 38,434 | (36,759) | | Operating loss | (1,675) | (38,426) | 36,751 | | Other income, net | 1,463 | 15,903 | (14,440) | | Net loss | (212) | (22,528) | 22,316 | - R&D expenses decreased by **$9.869 million**, primarily due to the termination of the Labafenogene marselecobac (SYNB1934) clinical trial and layoffs[106](index=106&type=chunk)[107](index=107&type=chunk)[113](index=113&type=chunk) - Other income decreased by **$14.4 million**, primarily related to changes in the fair value of purchase warrant liabilities[110](index=110&type=chunk) [Liquidity and Capital Resources](index=30&type=section&id=Liquidity%20and%20Capital%20Resources) The company, with an accumulated deficit of $441.9 million, has $17 million in cash, sufficient for 12 months, but future financing depends on strategic and development factors - The company has incurred continuous losses since inception, with an accumulated deficit of **$441.9 million** as of June 30, 2025, primarily funding operations through stock sales, warrants, and collaboration agreements[111](index=111&type=chunk) - As of June 30, 2025, the company had **$17 million** in cash and cash equivalents, expected to be sufficient to support operations for the next 12 months[111](index=111&type=chunk)[123](index=123&type=chunk) Cash Flow Summary (thousand USD) | Cash Flow Type | H1 2025 | H1 2024 | | :--- | :--- | :--- | | Net cash used in operating activities | (2,000) | (30,442) | | Net cash provided by investing activities | 167 | 25,237 | | Net cash provided by financing activities | — | 164 | | Net decrease in cash, cash equivalents, and restricted cash | (1,833) | (5,041) | - Net cash used in operating activities significantly decreased in H1 2025, primarily due to a narrower net loss and adjustments for non-cash items[116](index=116&type=chunk) - The company expects reduced expenses in the near term, but future financing needs will depend on strategic transactions, R&D progress, regulatory approvals, and commercialization activities[121](index=121&type=chunk)[127](index=127&type=chunk) [Related Party Transactions](index=33&type=section&id=Related%20Party%20Transactions) - For detailed information on related party transactions, refer to the "Certain Relationships and Related Party Transactions" section in the company's 2024 annual report amendment[124](index=124&type=chunk) [Recently Issued Accounting Pronouncements](index=33&type=section&id=Recently%20Issued%20Accounting%20Pronouncements_MD%26A) - For detailed information on recently issued accounting pronouncements and their impact on financial statements, refer to Note 2, "Summary of Significant Accounting Policies," in the unaudited consolidated financial statements of this quarterly report[125](index=125&type=chunk) [Item 3. Quantitative and Qualitative Disclosures about Market Risk](index=34&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20about%20Market%20Risk) As a smaller reporting company, the company is not required to provide quantitative and qualitative disclosures about market risk - As a smaller reporting company, the company is not required to provide quantitative and qualitative disclosures about market risk[128](index=128&type=chunk) [Item 4. Controls and Procedures](index=34&type=section&id=Item%204.%20Controls%20and%20Procedures) The company's disclosure controls and procedures were deemed ineffective as of June 30, 2025, due to a material weakness in internal control, for which a remediation plan is underway - The company's disclosure controls and procedures aim to ensure timely recording, processing, summarizing, and reporting of information, but have inherent limitations due to human error and circumvention[129](index=129&type=chunk)[130](index=130&type=chunk) - As of June 30, 2025, the company's disclosure controls and procedures were deemed ineffective due to a material weakness in internal control[131](index=131&type=chunk)[132](index=132&type=chunk) - The company has initiated a remediation plan, but this material weakness has not yet been fully corrected, and there were no significant changes in internal control during this quarter[132](index=132&type=chunk)[133](index=133&type=chunk) [PART II - OTHER INFORMATION](index=35&type=section&id=PART%20II%20-%20OTHER%20INFORMATION) [Item 1. Legal Proceedings](index=35&type=section&id=Item%201.%20Legal%20Proceedings) The company is not currently involved in any material legal proceedings - The company is not currently involved in any material legal proceedings[135](index=135&type=chunk) [Item 1A. Risk Factors](index=35&type=section&id=Item%201A.%20Risk%20Factors) No new material risk factors were reported in this quarterly report; refer to the "Risk Factors" section in the company's 2024 annual report - No new material risk factors were reported in this quarterly report; refer to the "Risk Factors" section in the company's 2024 annual report[136](index=136&type=chunk) [Item 2. Unregistered Sales of Equity Securities and Use of Proceeds](index=36&type=section&id=Item%202.%20Unregistered%20Sales%20of%20Equity%20Securities%20and%20Use%20of%20Proceeds) The company had no unregistered sales of equity securities or use of proceeds during this quarter - The company had no unregistered sales of equity securities or use of proceeds during this quarter[137](index=137&type=chunk) [Item 3. Defaults Upon Senior Securities](index=36&type=section&id=Item%203.%20Defaults%20Upon%20Senior%20Securities) The company had no defaults upon senior securities during this quarter - The company had no defaults upon senior securities during this quarter[138](index=138&type=chunk) [Item 4. Mine Safety Disclosures](index=36&type=section&id=Item%204.%20Mine%20Safety%20Disclosures) This item is not applicable to the company's business - This item is not applicable to the company's business[139](index=139&type=chunk) [Item 5. Other Information](index=36&type=section&id=Item%205.%20Other%20Information) During this quarter, no directors or executive officers adopted, modified, or terminated any Rule 10b5-1 trading plan - During this quarter, the company had no directors or executive officers who adopted, modified, or terminated any Rule 10b5-1 trading plan[140](index=140&type=chunk) [Item 6. Exhibits](index=37&type=section&id=Item%206.%20Exhibits) This section lists all exhibits filed with this quarterly report, including certifications from the CEO and CFO, and XBRL files - Exhibits include certifications from the Chief Executive Officer and Chief Financial Officer, XBRL instance documents, and taxonomy extension schemas[142](index=142&type=chunk) [Signatures](index=38&type=section&id=Signatures) This quarterly report was duly signed by SYNLOGIC, INC.'s CEO and CFO, Mary Beth Dooley, on August 7, 2025 - This report was signed by Mary Beth Dooley, Chief Executive Officer and Chief Financial Officer of SYNLOGIC, INC., on August 7, 2025[145](index=145&type=chunk)[146](index=146&type=chunk)

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2025 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission File Number 001-37566 SYNLOGIC, INC. (Exact name of Registrant as specified in its Charter) Delaware (State or other jurisdiction of PO Box 30 Winc ...

FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2024 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Commission File Number 001-37566 SYNLOGIC, INC. (Exact name of Registrant as specified in its Charter) (State or other jurisdiction of incorporation or organiza ...

WINCHESTER, Mass., Nov. 12, 2024 (GLOBE NEWSWIRE) -- Synlogic, Inc. (Nasdaq: SYBX), a biopharmaceutical company advancing novel therapeutics to transform the care of serious diseases, today reported financial results for the third quarter 2024 and provided a corporate update. As previously announced, the Company retained Lucid Capital Markets, LLC to act as its financial advisor to explore and evaluate strategic options for maximizing shareholder value. Potential strategic alternatives that may be explored ...

[PART I - FINANCIAL INFORMATION](index=3&type=section&id=PART%20I%20-%20FINANCIAL%20INFORMATION) [Item 1. Financial Statements](index=4&type=section&id=Item%201.%20Financial%20Statements) The unaudited Q1 2024 financial statements reflect a **$31.6 million net loss** and reduced assets, driven by significant restructuring and trial discontinuation [Notes to Unaudited Consolidated Financial Statements](index=8&type=section&id=Notes%20to%20Unaudited%20Consolidated%20Financial%20Statements) Notes detail Q1 2024 events, including trial discontinuation, 90% workforce reduction, **$28.3 million restructuring charges**, and sufficient liquidity post-restructuring - In February 2024, the company discontinued its pivotal Synpheny-3 trial and implemented a corporate restructuring, reducing its workforce by **90%**[26](index=26&type=chunk) - Despite a history of losses and an accumulated deficit of **$445.9 million**, management believes that following the restructuring, its cash and cash equivalents as of March 31, 2024, are sufficient to fund operations for at least the next **12 months**[27](index=27&type=chunk) - Total restructuring and other charges for Q1 2024 amounted to **$28.3 million**, which included **$5.6 million** for severance, **$1.8 million** in accelerated stock compensation, **$9.6 million** for right-of-use asset impairment, **$5.3 million** for property and equipment impairment, and a **$5.2 million** impairment for prepaid R&D with Ginkgo[48](index=48&type=chunk)[49](index=49&type=chunk)[50](index=50&type=chunk) - The company recorded a **$6.7 million** gain on the remeasurement of its purchase warrant liability during the three months ended March 31, 2024, as the fair value decreased from **$11.2 million** to **$4.4 million**[37](index=37&type=chunk)[55](index=55&type=chunk) - The collaboration with Ginkgo was effectively terminated due to the strategic shift, resulting in the write-off of the remaining **$5.2 million** in prepaid foundry services as a restructuring charge[65](index=65&type=chunk)[73](index=73&type=chunk) Consolidated Balance Sheet Highlights (Unaudited) | Account | March 31, 2024 (in thousands) | December 31, 2023 (in thousands) | | :--- | :--- | :--- | | **Assets** | | | | Cash and cash equivalents | $24,822 | $23,960 | | Short-term marketable securities | $7,489 | $23,786 | | Total current assets | $34,946 | $49,907 | | Total assets | $36,057 | $75,550 | | **Liabilities & Equity** | | | | Total current liabilities | $10,940 | $20,404 | | Total liabilities | $22,732 | $32,895 | | Total stockholders' equity | $13,325 | $42,655 | | Accumulated deficit | ($445,865) | ($414,301) | Consolidated Statement of Operations Highlights (Unaudited, Three Months Ended March 31) | Account | 2024 (in thousands) | 2023 (in thousands) | | :--- | :--- | :--- | | Revenue | $8 | $174 | | Research and development | $7,680 | $12,450 | | General and administrative | $2,884 | $3,967 | | Restructuring and other charges | $28,289 | $0 | | Loss from operations | ($38,845) | ($16,243) | | Net loss | ($31,564) | ($15,622) | | Net loss per share | ($2.60) | ($3.39) | Consolidated Statement of Cash Flows Highlights (Unaudited, Three Months Ended March 31) | Account | 2024 (in thousands) | 2023 (in thousands) | | :--- | :--- | :--- | | Net cash used in operating activities | ($15,436) | ($21,505) | | Net cash provided by investing activities | $16,282 | $30,270 | | Net cash provided by financing activities | $16 | $913 | [Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations (MD&A)](index=22&type=section&id=Item%202.%20Management%27s%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) MD&A details the strategic shift from drug development, including trial discontinuation and restructuring, resulting in a **$31.6 million net loss** but sufficient liquidity [Overview and Strategic Shift](index=22&type=section&id=Overview%20and%20Strategic%20Shift) Synlogic shifted strategy from drug development to exploring strategic alternatives after discontinuing its pivotal Synpheny-3 trial due to efficacy concerns - In February 2024, the company discontinued its pivotal Phase 3 study, Synpheny-3, for its lead product candidate for PKU, labafenogene marselecobac (SYNB1934)[76](index=76&type=chunk) - The decision was based on an internal review indicating the trial was unlikely to meet its primary endpoint, not on safety or tolerability concerns[76](index=76&type=chunk) - The current corporate strategy is focused on pursuing strategic alternatives to enhance stockholder value, including a potential merger or sale of the company[76](index=76&type=chunk) [Results of Operations](index=29&type=section&id=Results%20of%20Operations) Q1 2024 results show negligible revenue, reduced R&D and G&A expenses, **$28.3 million in restructuring charges**, and a **$31.6 million net loss** Comparison of Operating Results (Three Months Ended March 31) | Account | 2024 (in thousands) | 2023 (in thousands) | | :--- | :--- | :--- | | Revenue | $8 | $174 | | Research and development | $7,680 | $12,450 | | General and administrative | $2,884 | $3,967 | | Restructuring and other charges | $28,289 | $0 | | **Net loss** | **($31,564)** | **($15,622)** | - R&D expense decreased by **$4.8 million** YoY, primarily due to a **$2.9 million** reduction in internal costs from the workforce reduction and a **$1.9 million** net decrease in external costs following the discontinuation of clinical trials[101](index=101&type=chunk)[102](index=102&type=chunk) - Restructuring and other charges totaled **$28.3 million**, primarily from impairment charges on leases, equipment, and prepaid R&D, as well as severance payments and accelerated stock compensation[104](index=104&type=chunk) - Other income increased by **$6.7 million** YoY, primarily due to the change in fair value of the purchase warrants classified as liabilities[105](index=105&type=chunk) [Liquidity and Capital Resources](index=32&type=section&id=Liquidity%20and%20Capital%20Resources) As of March 31, 2024, Synlogic held **$32.3 million in liquidity** and expects sufficient cash to fund operations for at least 12 months post-restructuring - The company had **$32.3 million** in cash, cash equivalents, and short-term marketable securities as of March 31, 2024[106](index=106&type=chunk) - Management believes current cash and cash equivalents are sufficient to fund operations at current levels for at least the next **12 months** from the filing date[115](index=115&type=chunk) - Net cash used in operating activities was **$15.4 million** for Q1 2024, a decrease from **$21.5 million** in Q1 2023, and is expected to be lower in subsequent quarters of 2024 due to reduced operations[108](index=108&type=chunk)[109](index=109&type=chunk) [Item 3. Quantitative and Qualitative Disclosures about Market Risk](index=36&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20about%20Market%20Risk) As a smaller reporting company, Synlogic is not required to provide quantitative and qualitative disclosures about market risk - The company is a smaller reporting company as defined by Rule 12b-2 of the Exchange Act and is not required to provide the information required under this item[121](index=121&type=chunk) [Item 4. Controls and Procedures](index=36&type=section&id=Item%204.%20Controls%20and%20Procedures) Management concluded that disclosure controls and procedures were effective as of March 31, 2024, with no material changes to internal controls - Management concluded that the company's disclosure controls and procedures were effective as of the end of the period covered by the report[124](index=124&type=chunk) - There have not been any changes in internal controls over financial reporting during the fiscal quarter that have materially affected, or are reasonably likely to materially affect, these controls[125](index=125&type=chunk) [PART II - OTHER INFORMATION](index=37&type=section&id=PART%20II%20-%20OTHER%20INFORMATION) [Item 1. Legal Proceedings](index=37&type=section&id=Item%201.%20Legal%20Proceedings) The company is not currently involved in any material legal proceedings - Synlogic is not currently a party to any material legal proceedings[127](index=127&type=chunk) [Item 1A. Risk Factors](index=37&type=section&id=Item%201A.%20Risk%20Factors) This section details substantial risks, including uncertainty of strategic alternatives, potential liquidation, history of losses, and unproven synthetic biology platform - The company's business is almost entirely dependent on the success of its process to identify and evaluate strategic alternatives following the discontinuation of its lead candidate, SYNB1934, and this process may not be successful[132](index=132&type=chunk)[134](index=134&type=chunk) - If a strategic transaction is not successfully consummated, the board may pursue dissolution and liquidation, which could result in stockholders losing all or a significant portion of their investment[132](index=132&type=chunk)[135](index=135&type=chunk)[137](index=137&type=chunk) - The company has a history of losses, expects to continue incurring losses, and may never achieve profitability[132](index=132&type=chunk)[138](index=138&type=chunk) - The company's approach of using synthetic biology to create novel medicines is unproven and may never lead to marketable products[132](index=132&type=chunk)[161](index=161&type=chunk) [Item 2. Unregistered Sales of Equity Securities and Use of Proceeds](index=111&type=section&id=Item%202.%20Unregistered%20Sales%20of%20Equity%20Securities%20and%20Use%20of%20Proceeds) There were no unregistered sales of equity securities during the reporting period - None[362](index=362&type=chunk) [Item 3. Defaults Upon Senior Securities](index=111&type=section&id=Item%203.%20Defaults%20Upon%20Senior%20Securities) There were no defaults upon senior securities during the reporting period - None[363](index=363&type=chunk) [Item 4. Mine Safety Disclosures](index=111&type=section&id=Item%204.%20Mine%20Safety%20Disclosures) This item is not applicable to the company - Not applicable[364](index=364&type=chunk) [Item 5. Other Information](index=111&type=section&id=Item%205.%20Other%20Information) No directors or executive officers adopted, modified, or terminated Rule 10b5-1 trading plans during the quarter - During the quarter, none of the company's directors or executive officers adopted, modified, or terminated any Rule 10b5-1 trading plans[365](index=365&type=chunk) [Item 6. Exhibits](index=112&type=section&id=Item%206.%20Exhibits) This section provides an index of exhibits filed with the Form 10-Q, including officer certifications and interactive data files - The report includes an index of exhibits filed, such as officer certifications (31.1, 31.2, 32.1, 32.2) and a Statement of Work with Azzur Group (10.1)[368](index=368&type=chunk)

Exhibit 99.1 Synlogic Reports First Quarter 2024 Financial Results Cambridge, Mass. May 14, 2024 – Synlogic, Inc. (Nasdaq: SYBX), a biopharmaceutical company advancing novel therapeutics to transform the care of serious diseases, today reported financial results for the first quarter 2024 and provided a corporate update. In March 2024, the Company retained Lucid Capital Markets, LLC to act as its financial advisor to explore and evaluate strategic options for maximizing shareholder value. Potential strategi ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2023 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission File Number 001-37566 SYNLOGIC, INC. (Exact name of Registrant as specified in its Charter) 301 Binney St., Suite 402 Cambridge, MA 02142 (Address of ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2023 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission File Number 001-37566 SYNLOGIC, INC. (Exact name of Registrant as specified in its Charter) Delaware (State or other jurisdiction of incorporat ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2023 ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 FOR THE TRANSITION PERIOD FROM TO Commission File Number 001-37566 SYNLOGIC, INC. (Exact name of Registrant as specified in its Charter) Delaware (State or other jurisdiction of incorporation o ...