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, 2025 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: 001-42490 MAZE THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) (State or other jurisdiction of incorpora ...

Exhibit 99.1 Maze Therapeutics Reports Second Quarter 2025 Financial Results and Recent Highlights MZE782 Phase 1 Trial in Healthy Volunteers to Provide Proof of Mechanism Data for Phenylketonuria (PKU) and Chronic Kidney Disease (CKD) Expected in Q3 2025 MZE829 Phase 2 HORIZON Trial Actively Enrolling Patients with APOL1-Mediated Kidney Disease; Initial Data Expected in Q1 2026 Strong Balance Sheet with $264.5 Million in Cash and Cash Equivalents, Expected to Provide Cash Runway into H2 2027 SOUTH SAN FRAN ...

Group 1 - Maze Therapeutics is a clinical-stage biopharmaceutical company focused on developing small molecule precision medicines for patients with renal, metabolic, and cardiovascular diseases [2] - The company will participate in two upcoming investor conferences in July, with live webcasts available on their website [1] - Maze Therapeutics utilizes its Compass platform to link genetic variants with biological pathways in disease, advancing a pipeline that includes two wholly owned programs, MZE829 and MZE782 [2] Group 2 - The H.C. Wainwright 4th Annual Kidney Virtual Conference is scheduled for July 14, 2025, at 2:30 p.m. ET [3] - The BTIG Virtual Biotech Conference will take place on July 30, 2025, at 9:20 a.m. ET [3]

Company Overview - Maze Therapeutics, Inc. is a clinical-stage biopharmaceutical company focused on developing small molecule precision medicines for patients with renal, metabolic, and cardiovascular diseases [3] - The company utilizes its Compass platform to gain insights into genetic variants associated with diseases and their biological pathways [3] Pipeline Development - Maze Therapeutics is advancing a pipeline that includes two wholly owned programs, MZE829 and MZE782, which represent novel precision medicine approaches [3] - The company aims to address conditions such as obesity and other related metabolic diseases through its innovative therapies [3] Upcoming Presentation - Jason Coloma, Ph.D., the CEO of Maze Therapeutics, will present a company overview at the Jefferies 2025 Global Healthcare Conference on June 5, 2025, at 2 p.m. ET [1] - A live webcast of the presentation will be available on the company's website and archived for 60 days [2]

[PART I FINANCIAL INFORMATION](index=6&type=section&id=PART%20I%20FINANCIAL%20INFORMATION) [Item 1. Financial Statements (Unaudited)](index=6&type=section&id=Item%201.%20Financial%20Statements%20(Unaudited)) The unaudited statements reflect a significantly improved cash position and stockholders' equity following the February 2025 IPO [Condensed Balance Sheets](index=6&type=section&id=Condensed%20Balance%20Sheets) The balance sheet reflects a substantial increase in assets and a shift from a stockholders' deficit to equity, driven by the IPO Condensed Balance Sheet Comparison (in thousands) | | March 31, 2025 | December 31, 2024 | | :--- | :--- | :--- | | **Assets** | | | | Cash and cash equivalents | $294,374 | $196,812 | | Total current assets | $299,707 | $201,671 | | Total assets | $332,840 | $240,542 | | **Liabilities and Stockholders' Equity (Deficit)** | | | | Total liabilities | $40,772 | $43,638 | | Redeemable convertible preferred stock | $— | $508,087 | | Total stockholders' equity (deficit) | $292,068 | $(311,183) | [Condensed Statements of Operations and Comprehensive Loss](index=7&type=section&id=Condensed%20Statements%20of%20Operations%20and%20Comprehensive%20Loss) The net loss remained stable year-over-year as increased operating expenses were offset by higher interest income Statement of Operations Summary (in thousands) | | Three Months Ended March 31, 2025 | Three Months Ended March 31, 2024 | | :--- | :--- | :--- | | Research and development | $27,580 | $21,877 | | General and administrative | $7,821 | $6,137 | | **Loss from operations** | **$(35,401)** | **$(28,014)** | | Interest and other income, net | $2,615 | $281 | | Change in fair value of convertible promissory notes | $— | $(4,761) | | **Net loss and comprehensive loss** | **$(32,786)** | **$(32,494)** | | Net loss per share, basic and diluted | $(1.15) | $(13.91) | [Condensed Statements of Cash Flows](index=9&type=section&id=Condensed%20Statements%20of%20Cash%20Flows) A significant cash inflow from the IPO offset increased cash used in operations, resulting in a net cash increase of $97.6 million Cash Flow Summary (in thousands) | | Three Months Ended March 31, 2025 | Three Months Ended March 31, 2024 | | :--- | :--- | :--- | | Net cash used in operating activities | $(29,516) | $(23,437) | | Net cash used in investing activities | $(299) | $(279) | | Net cash provided by financing activities | $127,378 | $24,581 | [Notes to Condensed Financial Statements](index=10&type=section&id=Notes%20to%20Condensed%20Financial%20Statements) Notes detail the $127.8M IPO, confirm one-year operational funding, and clarify 2024 revenue from license agreements - In February 2025, the company completed its IPO, selling 8,750,000 shares of common stock for net proceeds of approximately **$127.8 million**[30](index=30&type=chunk) - As of March 31, 2025, the company had **$294.4 million in cash and cash equivalents** and believes this is sufficient to fund operations for at least one year[33](index=33&type=chunk) - The company entered into significant license agreements in 2024 with Shionogi ($150.0M upfront), Trace ($15.0M upfront), and Neurocrine ($2.5M upfront), with revenue recognized in 2024[75](index=75&type=chunk)[78](index=78&type=chunk)[80](index=80&type=chunk) [Management's Discussion and Analysis of Financial Condition and Results of Operations](index=21&type=section&id=Item%202.%20Management's%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) Management analyzes rising R&D expenses for its clinical programs and the strengthened financial condition post-IPO [Results of Operations](index=24&type=section&id=Results%20of%20operations) Operating expenses increased by $7.4 million year-over-year, driven primarily by higher clinical trial and personnel costs Comparison of Operating Results (in thousands) | | Three Months Ended March 31, | Change | | :--- | :--- | :--- | | | **2025** | **2024** | | | Research and development | $27,580 | $21,877 | $5,703 | | General and administrative | $7,821 | $6,137 | $1,684 | | **Total operating expenses** | **$35,401** | **$28,014** | **$7,387** | | **Loss from operations** | **$(35,401)** | **$(28,014)** | **$(7,387)** | - The **$5.7 million increase in R&D expenses** was primarily driven by a $3.1 million rise in clinical trial expenses for the Phase 2 trial of MZE829 and the Phase 1 trial of MZE782[110](index=110&type=chunk) [Liquidity and Capital Resources](index=26&type=section&id=Liquidity%20and%20capital%20resources) The company's liquidity was significantly boosted by its February 2025 IPO, providing sufficient capital for at least the next year - As of March 31, 2025, the company had cash and cash equivalents of **$294.4 million** and an accumulated deficit of $391.2 million[116](index=116&type=chunk) - The company believes its existing cash and cash equivalents are **sufficient to fund operations for at least one year** from the date of the report[118](index=118&type=chunk) - Future funding requirements are substantial and depend on the progress of clinical trials for MZE829 and MZE782 and other pipeline candidates[120](index=120&type=chunk) [Quantitative and Qualitative Disclosures About Market Risk](index=30&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20About%20Market%20Risk) The company indicates it does not have material exposure to market risks requiring disclosure - The report states **"Not applicable"** for this item[138](index=138&type=chunk) [Controls and Procedures](index=30&type=section&id=Item%204.%20Controls%20and%20Procedures) Management concluded that disclosure controls and procedures were effective, with no material changes to internal controls - Based on an evaluation as of March 31, 2025, the Chief Executive Officer concluded that the company's **disclosure controls and procedures were effective**[140](index=140&type=chunk) - **No changes in internal control** over financial reporting occurred during the quarter that materially affected or are likely to materially affect internal controls[141](index=141&type=chunk) [PART II OTHER INFORMATION](index=31&type=section&id=PART%20II%20OTHER%20INFORMATION) [Legal Proceedings](index=31&type=section&id=Item%201.%20Legal%20Proceedings) The company is not currently party to any material legal proceedings - The company is not currently a party to any legal proceedings that management believes would have a **material adverse effect** on the business[144](index=144&type=chunk) [Risk Factors](index=31&type=section&id=Item%201A.%20Risk%20Factors) The company faces significant risks related to its history of losses, dependence on early-stage programs, and reliance on third parties - The company is a clinical-stage biopharmaceutical company with a limited operating history, a history of **significant operating losses**, and expects to incur continued losses[146](index=146&type=chunk)[147](index=147&type=chunk) - The business is **highly dependent on the success of its lead programs**, MZE829 and MZE782, which are in early stages of development[165](index=165&type=chunk) - The company **relies on third parties** for critical functions, including genetic data, manufacturing, and conducting clinical trials[204](index=204&type=chunk)[218](index=218&type=chunk)[226](index=226&type=chunk) - The company faces **significant competition** from major pharmaceutical and biotechnology companies with greater financial resources and expertise[291](index=291&type=chunk)[296](index=296&type=chunk) [Unregistered Sales of Equity Securities, Use of Proceeds, and Issuer Purchases of Equity Securities](index=82&type=section&id=Item%202.%20Unregistered%20Sales%20of%20Equity%20Securities%2C%20Use%20of%20Proceeds%2C%20and%20Issuer%20Purchases%20of%20Equity%20Securities) The company details its IPO proceeds and confirms no material change in their planned use - The company's IPO closed on February 3, 2025, resulting in **net proceeds of approximately $127.8 million** from the sale of 8,750,000 shares[418](index=418&type=chunk) - There has been **no material change** in the planned use of proceeds from the IPO as described in the final prospectus[419](index=419&type=chunk) [Defaults Upon Senior Securities](index=83&type=section&id=Item%203.%20Defaults%20Upon%20Senior%20Securities) The company reports no defaults upon its senior securities - The report states **"Not applicable"** for this item[420](index=420&type=chunk) [Mine Safety Disclosures](index=83&type=section&id=Item%204.%20Mine%20Safety%20Disclosures) This item is not applicable as the company is not engaged in mining operations - The report states **"Not applicable"** for this item[421](index=421&type=chunk) [Other Information](index=83&type=section&id=Item%205.%20Other%20Information) No directors or officers adopted, modified, or terminated a Rule 10b5-1 trading plan during the quarter - During the three months ended March 31, 2025, **no directors or officers adopted, modified, or terminated a Rule 10b5-1 trading arrangement**[422](index=422&type=chunk) [Exhibits](index=84&type=section&id=Item%206.%20Exhibits) This section lists the exhibits filed with the Form 10-Q, including required certifications and XBRL data [Signatures](index=85&type=section&id=SIGNATURES) The report is duly signed by the company's Chief Executive Officer on May 14, 2025

Financial Position - Maze Therapeutics reported a cash position of $294.4 million as of March 31, 2025, up from $196.8 million as of December 31, 2024, providing a cash runway into H2 2027[6]. - Total stockholders' equity improved to $292.1 million as of March 31, 2025, from a deficit of $311.2 million as of December 31, 2024[17]. Expenses - Research and Development (R&D) expenses increased to $27.6 million in Q1 2025 from $21.9 million in Q1 2024, primarily due to higher clinical trial expenses for MZE829 and MZE782[7]. - General and Administrative (G&A) expenses rose to $7.8 million in Q1 2025 compared to $6.1 million in Q1 2024, reflecting higher personnel-related expenses and professional services fees[8]. - Total operating expenses for Q1 2025 were $35.4 million, compared to $28.0 million in Q1 2024[15]. Net Loss - The net loss for Q1 2025 was $32.8 million, slightly higher than the net loss of $32.5 million in Q1 2024[8]. Clinical Trials - Maze is actively enrolling patients in the Phase 2 HORIZON trial of MZE829, with initial proof-of-concept data expected in Q1 2026[5]. - MZE782 is currently in a Phase 1 clinical trial, with initial data, including biomarker results, expected in Q3 2025[11]. - The company plans to initiate two separate Phase 2 clinical trials of MZE782 in CKD and PKU based on Phase 1 results[11]. Target Diseases - MZE829 targets APOL1 Kidney Disease, which affects over one million people in the U.S., while MZE782 targets approximately five million U.S. patients with CKD[3][4].

Core Insights - Maze Therapeutics is advancing two clinical programs, MZE829 and MZE782, which are expected to drive growth and innovation in the treatment of chronic kidney disease (CKD) and phenylketonuria (PKU) [2][10] Clinical Programs - MZE829 is an oral small molecule APOL1 inhibitor targeting APOL1 kidney disease (AKD), a subset of CKD affecting over one million people in the U.S. The Phase 2 HORIZON trial is actively enrolling patients and initial data is expected in Q1 2026 [3][7] - MZE782 is an oral small molecule targeting the solute transporter SLC6A19, with potential as a first-in-class treatment for approximately five million U.S. patients with CKD who do not adequately respond to existing therapies, and as a best-in-class therapy for PKU. Initial data from the Phase 1 trial is expected in Q3 2025 [4][8] Financial Performance - As of March 31, 2025, Maze Therapeutics reported cash and cash equivalents of $294.4 million, an increase from $196.8 million as of December 31, 2024. This cash position is expected to fund operations into the second half of 2027 [5][14] - Research and development expenses for Q1 2025 were $27.6 million, up from $21.9 million in Q1 2024, primarily due to increased clinical trial costs for MZE829 and MZE782 [6] - General and administrative expenses rose to $7.8 million in Q1 2025 from $6.1 million in Q1 2024, reflecting higher personnel-related costs [9] Company Overview - Maze Therapeutics is a clinical-stage biopharmaceutical company focused on developing small molecule precision medicines for renal, cardiovascular, and metabolic diseases. The company utilizes its Compass platform to link genetic variants with disease pathways [10]

Financial Performance - The company incurred a net loss of $100.4 million for the year ended December 31, 2023, and had an accumulated deficit of $358.4 million as of December 31, 2024[243]. - The company anticipates continued operating losses due to the high costs associated with clinical trials, preclinical studies, and regulatory approval processes[243]. - The company has incurred substantial losses and does not expect to become profitable in the near future, with limitations on the deductibility of federal net operating losses (NOLs) to 80% of current year taxable income starting from taxable years after December 31, 2020[429]. Cash and Funding - As of December 31, 2024, the company had cash and cash equivalents of $196.8 million, which, along with net proceeds of approximately $127.8 million from its initial public offering, is expected to fund operations for at least one year[252]. - The company may require additional capital to finance its operations and achieve its goals, with potential dilution to existing shareholders if capital is raised through equity offerings[250][255]. - The company’s future capital requirements will depend on various factors, including the costs of clinical trials, regulatory approvals, and potential partnerships[253]. Research and Development - The company expects significant increases in research and development expenses related to clinical trials for lead programs MZE829 and MZE782, as well as the expansion of its Compass platform[245]. - The company initiated a Phase 2 trial of MZE829 in November 2024 and expects to report proof of concept data in the first quarter of 2026[262]. - A Phase 1 clinical trial of MZE782 was initiated in September 2024[266]. Clinical Trials and Regulatory Challenges - The company faces high risks of failure in its early-stage programs, with potential therapeutic candidates needing to demonstrate safety and efficacy in extensive clinical trials before obtaining marketing approval[267]. - Delays in clinical trials can arise from regulatory approval issues, patient enrollment challenges, and external factors such as natural disasters or public health crises[268]. - The company must navigate various regulatory requirements and potential delays in obtaining necessary approvals for clinical trials[274]. Competition and Market Dynamics - The company faces significant competition in the biotechnology industry, with competitors potentially achieving regulatory approval before it does[382]. - There are currently no approved therapies for APOL1 kidney disease, but other companies are advancing therapeutic candidates in clinical trials targeting APOL1[385]. - The company may face challenges in obtaining adequate reimbursement for drugs, as coverage policies vary significantly among third-party payors in the U.S.[360]. Intellectual Property and Legal Risks - The company's success depends on obtaining and maintaining intellectual property rights, with challenges in protecting technologies and potential competition from similar products[432]. - The patenting process is costly and time-consuming, and the company may not be able to file all necessary patent applications in a timely manner[436]. - Changes in patent law could have a material adverse effect on the ability to obtain and enforce new patents[441]. Operational Risks - The company relies on third-party partners for the development and commercialization of therapeutic candidates, which limits control over resources and timelines[307]. - The company does not have manufacturing facilities and relies on third-party manufacturers, which increases risks related to supply adequacy and compliance with regulations[317]. - The company is dependent on the integrity of its information technology systems, and any failure could disrupt operations and lead to financial losses[414]. Compliance and Regulatory Environment - Compliance with healthcare laws and regulations may involve substantial costs, and violations could lead to significant penalties, including exclusion from government-funded healthcare programs[348]. - The company may need to implement costly compliance programs if it expands operations internationally, particularly under the Foreign Corrupt Practices Act[361]. - The company faces potential limitations on growth and increased development costs due to U.S. laws restricting the dissemination of classified information and certain products outside the United States[363]. Strategic Partnerships and Collaborations - The company has entered into strategic collaborations, including exclusive licenses for programs related to amyotrophic lateral sclerosis (ALS) and its first clinical stage therapeutic candidate, MZE001[305]. - Partnerships may not lead to efficient development or commercialization, and failure to recognize their benefits could adversely affect the company's financial condition and prospects[309]. - The company has formed joint ventures and spin-outs, such as with Alloy Therapeutics in 2020, to develop therapeutic targets outside its core expertise[310]. Data Privacy and Security - The company is at risk of reputational damage and financial loss due to potential breaches of data privacy obligations by third-party service providers[380]. - Any perceived failure to comply with privacy laws could lead to enforcement actions, significant fines, and loss of customer trust, adversely affecting the company's business[381]. - The company may face significant penalties under the EU GDPR, including fines of up to €20 million or 4% of annual global revenue for non-compliance[377]. Employee and Growth Challenges - The company’s ability to attract and retain qualified personnel is critical for its success in the competitive biotechnology and pharmaceutical industries[408]. - The company plans to expand its employee base to enhance managerial, operational, and financial resources as part of its growth strategy[411]. - There is a risk of misconduct by employees and partners, which could lead to regulatory sanctions and harm the company's reputation[412]. Economic and Market Conditions - Unfavorable global economic conditions could adversely affect the company's business, financial condition, and stock price, potentially leading to weakened demand for therapeutic candidates[431]. - The company anticipates continued pricing pressures globally due to state and federal healthcare reform measures that may impose downward pressure on product prices[355]. - Recent legislative changes may increase the difficulty and cost of obtaining marketing approval and could negatively affect pricing and third-party payment for therapeutic candidates[349].

Maze Therapeutics Reports Fourth Quarter and Full-Year 2024 Financial Results and Recent Highlights MZE829 Phase 2 HORIZON Trial Enrolling Patients with APOL1 Kidney Disease (AKD); Initial Data Expected in Q1 2026 MZE782 Phase 1 Healthy Volunteer Trial Ongoing; Initial Data Expected in H2 2025 Raised $140 Million in Gross Proceeds in Upsized IPO in February 2025, Providing Expected Cash Runway into H2 2027 SOUTH SAN FRANCISCO, CA, March 31, 2025 – Maze Therapeutics, Inc. (Nasdaq: MAZE), a clinical-stage bio ...