Core Insights - Maze Therapeutics announced positive Phase 1 clinical results for MZE782, indicating its potential as a best-in-class therapy for phenylketonuria (PKU) and a first-in-class therapy for chronic kidney disease (CKD) [1][2] Study Design - The Phase 1 trial was a randomized, double-blind, placebo-controlled study involving 112 healthy adult volunteers, assessing single ascending doses (SAD) and multiple ascending doses (MAD) of MZE782 [3][4] - SAD doses ranged from 30 to 960 mg, while MAD doses ranged from 120 to 240 mg twice daily and 120 to 720 mg once daily [3] Safety and Tolerability Profile - MZE782 was well tolerated across all doses, with no serious adverse events reported [5][6] - Mild treatment-related adverse events included headache (4%) and diarrhea (2%) in the SAD cohort, with no adverse events in the MAD cohort [6] Pharmacokinetics - MZE782 demonstrated a favorable plasma pharmacokinetic profile, with consistent absorption and a half-life of 11 hours [7] - Steady-state was achieved by Day 3, supporting a once- or twice-daily dosing regimen for Phase 2 trials [7] Pharmacodynamics - MZE782 produced dose-dependent increases in urinary excretion of phenylalanine (Phe) and glutamine (Gln), confirming target engagement [8][9] - A 42-fold increase in urinary Phe excretion was observed in the 240 mg twice-daily dose cohort after seven days [9] Estimated Glomerular Filtration Rate (eGFR) - MZE782 showed a dose-dependent initial eGFR dip similar to SGLT2 inhibitors, suggesting a potential beneficial effect on kidney physiology [9] - The combined 240 mg BID cohorts demonstrated a change of -11.5 mL/min/1.73m² after seven days, compared to -2.5 mL/min/1.73m² in the placebo cohort [9] Next Steps - The company plans to initiate two Phase 2 proof-of-concept trials for MZE782 in 2026, focusing on plasma Phe reduction in PKU and proteinuria reduction in CKD [10] Company Overview - Maze Therapeutics is a clinical-stage biopharmaceutical company focused on developing small molecule precision medicines for kidney and metabolic diseases, utilizing its Compass platform [15]

Core Insights - Maze Therapeutics has appointed Misbah Tahir as Chief Financial Officer, effective immediately, during a critical phase for the company [1][2] - The company is preparing for significant milestones, including data releases for MZE782 and MZE829 in 2025 and 2026 [2] - Mr. Tahir brings over 20 years of experience in the biopharmaceutical industry, having previously served as CFO at IGM Biosciences and held senior finance roles at other notable companies [2][3] Company Overview - Maze Therapeutics is a clinical-stage biopharmaceutical company focused on developing small molecule precision medicines for kidney and metabolic diseases [4] - The company utilizes its Compass platform to pursue genetically validated targets, integrating variant discovery and functionalization [4] - Maze's pipeline includes MZE829, an oral APOL1 inhibitor in Phase 2 development, and MZE782, an oral SLC6A19 inhibitor in Phase 1, targeting chronic kidney disease and phenylketonuria [4] Financial Position - Maze Therapeutics has a strong balance sheet with an expected cash runway extending into the second half of 2027 [3] - The company aims to create significant value for patients and shareholders through its differentiated precision genetics platform and disciplined development approach [3]

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 ...

Core Insights - Maze Therapeutics is advancing two clinical-stage programs, MZE782 and MZE829, targeting chronic kidney disease (CKD) and phenylketonuria (PKU) [2][4] - The company reported a strong cash position of $264.5 million, expected to fund operations into the second half of 2027 [5][16] - Significant milestones are anticipated, including initial data from the Phase 1 trial of MZE782 in Q3 2025 and proof-of-concept data from the Phase 2 HORIZON trial of MZE829 in Q1 2026 [1][7][8] Company Overview - Maze Therapeutics is a clinical-stage biopharmaceutical company focused on developing small molecule precision medicines for kidney and metabolic diseases [13] - The company utilizes its Compass platform to pursue genetically validated targets, aiming for first- or best-in-class therapies [13] Clinical Programs - MZE829 is an oral APOL1 inhibitor for APOL1-mediated kidney disease, which affects over one million people in the U.S. [3] - MZE782 targets the solute transporter SLC6A19 and has potential as a first-in-class treatment for approximately five million U.S. patients with CKD who do not adequately respond to existing therapies [4] Financial Performance - For Q2 2025, Maze reported no license revenue, contrasting with $165 million in license revenue for the same period in 2024, primarily due to an upfront payment from Shionogi [6][12] - Research and development expenses increased to $28.1 million for Q2 2025, up from $19.5 million in Q2 2024, reflecting higher clinical trial and manufacturing costs [10] - General and administrative expenses also rose to $8.4 million in Q2 2025, compared to $5.9 million in Q2 2024 [11] Balance Sheet Highlights - As of June 30, 2025, total assets were $303.5 million, with total liabilities at $41.3 million, indicating a strong financial position [16] - The company’s total stockholders' equity improved to $262.2 million from a deficit of $311.2 million as of December 31, 2024 [16]

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]