Maze Therapeutics, Inc.

Previous wording

The following discussion should be read in conjunction with the unaudited condensed financial statements and notes thereto included in Part I, Item 1 of this Quarterly Report on Form 10-Q; and the sections entitled “Business” and “Management’s Discussion and Analysis of Financial Condition and Results of Operations” contained in our Annual Report on Form 10-K for the year ended December 31, 2025 as filed with the SEC on March 25, 2026, or 2025 Form 10-K.

Current wording

The following discussion should be read in conjunction with the unaudited condensed financial statements and notes thereto included in Part I, Item 1 of this Quarterly Report on Form 10-Q; and the sections entitled “Business” and “Management’s Discussion and Analysis of Financial Condition and Results of Operations” contained in our Annual Report on Form 10-K for the year ended December 31, 2025 as filed with the SEC on March 25, 2026, or the 2025 Form 10-K.

Previous wording

Our most advanced program, MZE829, is an oral, small molecule, dual-mechanism inhibitor of apolipoprotein L1, or APOL1, for the treatment of patients with APOL1-mediated kidney disease, or AMKD, a genetically defined sub-set of chronic kidney disease, or CKD, for which there is no approved treatment today. We initiated a Phase 2 trial of MZE829 in November 2024 and dosed our first patient in February 2025. In March 2026, we announced positive topline clinical proof of concept data from our Phase 2 trial of MZE829 in patients with AMKD, in which we enrolled 15 patients. The results demonstrated that treatment with MZE829 led to a clinically meaningful mean reduction in proteinuria, as measured by urinary albumin-to-creatinine ratio. MZE829 was generally well tolerated, with no serious adverse events or severe treatment-related adverse events reported. We plan to continue enrollment in the Phase 2 trial and anticipate reporting additional data from this trial in late 2026 or early 2027. In addition, we plan to initiate a pivotal trial of MZE829 in the first half of 2027, subject to regulatory feedback.

Current wording

Our most advanced program, MZE829, is an oral, small molecule, dual-mechanism inhibitor of apolipoprotein L1, or APOL1, for the treatment of patients with APOL1-mediated kidney disease, or AMKD, a genetically defined sub-set of chronic kidney disease, or CKD, for which there is no approved treatment today. We initiated a Phase 2 trial of MZE829 in November 2024 and dosed our first patient in February 2025. In March 2026, we announced positive topline clinical proof of concept data from our Phase 2 trial of MZE829 in patients with AMKD, in which we enrolled 15 patients. The results demonstrated that treatment with MZE829 led to a clinically meaningful mean reduction in proteinuria, as measured by urinary albumin-to-creatinine ratio. MZE829 was generally well tolerated, with no serious adverse events or severe treatment-related adverse events reported. We have completed enrollment in the Phase 2 trial and anticipate reporting additional data from this trial in early 2027. In addition, we plan to initiate a pivotal trial of MZE829 in the first half of 2027, subject to regulatory feedback.

Previous wording

We have incurred significant losses and negative cash flows from operations and we expect to incur significant and increasing losses for the foreseeable future as a result of our continued research and development activities. During the three and six months ended June 30, 2026, we incurred a net loss of $44.7 million and $68.9 million, respectively. During the three and six months ended June 30, 2025, we incurred a net loss of $33.7 million and $66.5 million, respectively. As of June 30, 2026, we had an accumulated deficit of $558.5 million and do not expect positive cash flows from operations for the foreseeable future. Our net losses may fluctuate significantly from period to period, depending on the timing of and expenditures on our planned research and development activities, as well as upon revenue from our license agreements. We expect our research and development expenses to significantly increase in connection with the conduct of planned clinical trials for our lead programs, MZE829 and MZE782, further development of our Compass platform, planned preclinical studies, and potential Investigational New Drug Applications, or INDs, and clinical trials for future therapeutic candidates. We will also incur substantial additional expenses as we seek to expand our intellectual property portfolio, including through potential in-licensing opportunities, and hire additional personnel as we scale up our operations. In addition, we expect to incur additional costs associated with operating as a public company.

Current wording

We have incurred significant losses and negative cash flows from operations and we expect to incur significant and increasing losses for the foreseeable future as a result of our continued research and development activities. During the three and nine months ended September 30, 2026, we incurred a net loss of $48.0 million and $116.9 million, respectively. During the three and nine months ended September 30, 2025, we incurred a net loss of $30.1 million and $96.6 million, respectively. As of September 30, 2026, we had an accumulated deficit of $606.5 million and do not expect positive cash flows from operations for the foreseeable future. Our net losses may fluctuate significantly from period to period, depending on the timing of and expenditures on our planned research and development activities, as well as upon revenue from our license agreements. We expect our research and development expenses to significantly increase in connection with the conduct of planned clinical trials for our lead programs, MZE829 and MZE782, further development of our Compass platform, planned preclinical studies, and potential Investigational New Drug Applications, or INDs, and clinical trials for future therapeutic candidates. We will also incur substantial additional expenses as we seek to expand our intellectual property portfolio, including through potential in-licensing opportunities, and hire additional personnel as we scale up our operations. In addition, we expect to incur additional costs associated with operating as a public company.

Previous wording

As of June 30, 2026, we had cash, cash equivalents and marketable securities of $494.9 million. Since our inception, we have financed our operations primarily through issuances of our equity and convertible promissory notes, debt financing, and license agreements with biotechnology companies.

Current wording

As of September 30, 2026, we had cash, cash equivalents and marketable securities of $477.0 million. Since our inception, we have financed our operations primarily through issuances of our equity and convertible promissory notes, debt financing, and license agreements with biotechnology companies.

Previous wording

We recognized no license revenue for the three months ended June 30, 2026 and $20.0 million in license revenue for the six months ended June 30, 2026. We recognized no license revenue for the three and six months ended June 30, 2025. License revenue recognized in 2026 was related to achievement of a clinical development milestone upon dosing of the first patient in Shionogi's Phase 2 study of MZE001 in patients with Pompe disease under the License Agreement with Shionogi.

Current wording

We recognized no license revenue for the three months ended September 30, 2026 and $20.0 million in license revenue for the nine months ended September 30, 2026. We recognized no license revenue for the three and nine months ended September 30, 2025. License revenue recognized in 2026 was related to achievement of a clinical development milestone upon dosing of the first patient in Shionogi's Phase 2 study of MZE001 in patients with Pompe disease under the License Agreement with Shionogi.

Previous wording

Research and development expenses were $34.9 million and $28.1 million for the three months ended June 30, 2026 and 2025, respectively. The increase of $6.8 million between the comparative three month periods was primarily due to an increase of $4.3 million in personnel-related costs due to an increase in headcount and higher non-cash stock-based compensation expense, an increase of $3.2 million related to progression of our clinical development of the MZE829 program and an increase of $0.9 million related to our discovery research and other programs, partially offset by a $1.4 million decrease related to the MZE782 program primarily due to higher costs incurred in 2025 for the Phase 1 clinical trial in healthy adult volunteers that completed in 2025.

Current wording

Research and development expenses were $40.2 million and $25.2 million for the three months ended September 30, 2026 and 2025, respectively. The increase of $15.0 million between the comparative three month periods was primarily due to an increase of $6.9 million in personnel-related costs due to an increase in headcount and higher non-cash stock-based compensation expense, an increase of $3.5 million and $2.8 million related to progression of our clinical development of the MZE782 program and MZE829 program, respectively, $1.1 million related to our discovery research and other programs and $0.7 million for lab supplies and other costs.

Previous wording

Research and development expenses were $69.1 million and $55.7 million for the six months ended June 30, 2026 and 2025, respectively. The increase of $13.4 million between the comparative six month periods was primarily due to an increase of $7.9 million in personnel-related costs due to an increase in headcount and higher non-cash stock-based compensation expense, an increase of $5.7 million related to progression of our clinical development of the MZE829 program and an increase of $0.9 million related to our discovery research and other programs, partially offset by a $0.5 million decrease related to the MZE782 program primarily due to higher costs incurred in 2025 for the Phase 1 clinical trial in healthy adult volunteers that completed in 2025 and a $0.6 million decrease in lab supplies and other costs.

Current wording

Research and development expenses were $109.3 million and $80.9 million for the nine months ended September 30, 2026 and 2025, respectively. The increase of $28.4 million between the comparative nine month periods was primarily due to an increase of $14.9 million in personnel-related costs due to an increase in headcount and higher non-cash stock-based compensation expense, an increase of $8.5 million and $3.0 million related to progression of our clinical development of the MZE829 program and MZE782 program, respectively, and $1.9 million related to our discovery research.

Previous wording

General and administrative expenses were $13.1 million and $8.4 million for the three months ended June 30, 2026 and 2025, respectively. The increase of $4.7 million between the comparative three month periods was primarily due to an increase in personnel-related costs due to an increase in headcount and higher non-cash stock-based compensation expense.

Current wording

General and administrative expenses were $11.3 million and $7.8 million for the three months ended September 30, 2026 and 2025, respectively. The increase of $3.5 million between the comparative three month periods was primarily due to an increase in personnel-related costs, due to an increase in headcount and higher non-cash stock-based compensation expense, and higher professional fees.

Previous wording

Total other income, net was $3.3 million and $2.8 million for the three months ended June 30, 2026 and 2025, respectively. The increase of $0.5 million between the comparative three months periods primarily reflects an increase in interest income as a result of higher cash, cash equivalent, and marketable securities balances held during the three months ended June 30, 2026 resulting from the net proceeds received from the underwritten registered offering completed in April 2026 and proceeds from the initial term loan funded under the Hercules Loan Agreement in February 2026, partially offset by interest expense recognized on the Hercules Loan Agreement.

Current wording

Total other income, net was $3.5 million and $2.9 million for the three months ended September 30, 2026 and 2025, respectively. The net increase of $0.6 million between the comparative three month periods primarily reflects an increase in interest income as a result of higher cash, cash equivalents and marketable securities balances held during the three months ended September 30, 2026 resulting from the net proceeds received from the underwritten registered offering completed in April 2026 and proceeds from the initial term loan funded under the Hercules Loan Agreement in February 2026, partially offset by interest expense recognized on the Hercules Loan Agreement.

Previous wording

Total other income, net was $5.7 million and $5.4 million for the six months ended June 30, 2026 and 2025, respectively. The increase of $0.3 million between the comparative six months periods primarily reflects an increase in interest income as a result of higher cash, cash equivalent, and marketable securities balances held during the six months ended June 30, 2026 resulting from the net proceeds received from the underwritten registered offering completed in April 2026 and proceeds from the initial term loan funded under the Hercules Loan Agreement in February 2026, partially offset by interest expense recognized on the Hercules Loan Agreement.

Current wording

Total other income, net was $9.2 million and $8.3 million for the nine months ended September 30, 2026 and 2025, respectively. The net increase of $0.9 million between the comparative nine month periods primarily reflects an increase in interest income as a result of higher cash, cash equivalents and marketable securities balances held during the nine months ended September 30, 2026 resulting from the net proceeds received from the underwritten registered offering completed in April 2026 and proceeds from the initial term loan funded under the Hercules Loan Agreement in February 2026, partially offset by interest expense recognized on the Hercules Loan Agreement.

Previous wording

Since our inception, we have not generated any revenue from product sales and we do not expect to generate any revenue from commercial sales for the foreseeable future, if at all. We have incurred significant operating losses and negative cash flows from operations. We anticipate that we will continue to incur net losses for the foreseeable future. To date, we have financed our operations primarily through sales of our equity and convertible promissory notes, debt financing, as well as one-time, nonrefundable upfront payments we received pursuant to the license agreements we entered into with several biotechnology companies in 2024, including the exclusive license agreement with Shionogi. As of June 30, 2026, we had cash, cash equivalents and marketable securities of $494.9 million and an accumulated deficit of $558.5 million.

Current wording

Since our inception, we have not generated any revenue from product sales and we do not expect to generate any revenue from commercial sales for the foreseeable future, if at all. We have incurred significant operating losses and negative cash flows from operations. We anticipate that we will continue to incur net losses for the foreseeable future. To date, we have financed our operations primarily through sales of our equity and convertible promissory notes, debt financing, as well as one-time, nonrefundable upfront payments we received pursuant to the license agreements we entered into with several biotechnology companies in 2024, including the exclusive license agreement with Shionogi. As of September 30, 2026, we had cash, cash equivalents and marketable securities of $477.0 million and an accumulated deficit of $606.5 million.

Previous wording

In February 2026, we entered into an Open Market Sale Agreement with Jefferies LLC, serving as sales agent, with respect to an at-the-market offering program pursuant to which we may elect to issue and sell shares of our common stock having an aggregate offering price of up to $200.0 million, or the 2026 Sale Agreement, in such quantities and on such minimum price terms as we set from time to time through our sales agent. We have agreed to pay our sales agent an aggregate commission equal to up to 3.0% of the gross proceeds of the sales under the agreement. To date, no sales of common stock have occurred under the 2026 Sale Agreement.

Current wording

In February 2026, we entered into an Open Market Sale Agreement with Jefferies LLC, serving as sales agent, with respect to an at-the-market offering program pursuant to which we may elect to issue and sell shares of our common stock having an aggregate offering price of up to $200.0 million, or the 2026 Sale Agreement, in such quantities and on such minimum price terms as we set from time to time through our sales agent. We have agreed to pay our sales agent an aggregate commission equal to up to 3.0% of the gross proceeds of the sales under the agreement. During the three months ended September 30, 2026, we sold 548,723 shares of our common stock at a weighted average price of $27.42 per share for net proceeds of $14.4 million pursuant to the 2026 Sale Agreement, after deducting sales commission and offering costs. Subsequent to September 30, 2026, we sold 942,370 shares of our common stock at a weighted average price of $30.42 per share for net proceeds of $27.8 million pursuant to the 2026 Sale Agreement, after deducting sales commission and offering costs. We currently have approximately $156.3 million remaining capacity under the 2026 Sale Agreement.

Previous wording

Additionally, in February 2026, we entered into the Hercules Loan Agreement which provides for a senior secured term loan facility in an aggregate principal amount of up to $200.0 million. An initial term loan of $40.0 million was funded under the Hercules Loan Agreement and an aggregate of $160.0 million in additional term loans commitments will be available to us through February 2031, so long as we satisfy certain conditions precedent. The final tranche of $50.0 million is subject to approval by the lenders’ investment committee. The facility has a maturity date of February 1, 2031, and may be prepaid at any time, subject to prepayment premiums. This senior secured term facility will accrue interest at an annual rate determined by reference to the Prime Rate as reported in the Wall Street Journal, with interest rate floors that range from 7.95% to 9.25% depending on the tranche. The Hercules Term Loan Facility provides for payment of interest only until (a) 48 months after the Closing Date or (b) if certain performance and financing milestones are satisfied, 60 months after the Closing Date. Accrued interest on the Term Loans is payable on the first business day of each month. In connection with the Hercules Loan Agreement, we terminated an existing loan and security agreement with another bank that provided us with a line of credit of up to $50.0 million. We did not draw down any funds from this terminated debt facility. See Note 10, Loan and security agreements, of this Quarterly Report on Form 10-Q for further discussion of the Hercules Loan Agreement.

Current wording

Additionally, on February 4, 2026, or the Closing Date, we entered into the Hercules Loan Agreement which provides for a senior secured term loan facility in an aggregate principal amount of up to $200.0 million, or the Hercules Term Loan Facility. An initial term loan of $40.0 million was funded under the Hercules Loan Agreement and an aggregate of $160.0 million in additional term loan commitments will be available to us through February 2031, or the Term Loans, so long as we satisfy certain conditions precedent. The final tranche of $50.0 million is subject to approval by the lenders’ investment committee. The facility has a maturity date of February 1, 2031, and may be prepaid at any time, subject to prepayment premiums. This senior secured term facility will accrue interest at an annual rate determined by reference to the Prime Rate as reported in the Wall Street Journal, with interest rate floors that range from 7.95% to 9.25% depending on the tranche. The Hercules Term Loan Facility provides for payment of interest only until (a) 48 months after the Closing Date or (b) if certain performance and financing milestones are satisfied, 60 months after the Closing Date. Accrued interest on the Term Loans is payable on the first business day of each month. In connection with the Hercules Loan Agreement, we terminated an existing loan and security agreement with another bank that provided us with a line of credit of up to $50.0 million. We did not draw down any funds from this terminated debt facility. See Note 10, Loan and security agreements, of this Quarterly Report on Form 10-Q for further discussion of the Hercules Loan Agreement.

Previous wording

We have entered into consortium agreements with the University of Helsinki to access genomic information from patient samples and genetic and paired clinical data. As of June 30, 2026, we are obligated to pay $3.5 million under these agreements through the year ended December 31, 2027.

Current wording

We have entered into consortium agreements with the University of Helsinki to access genomic information from patient samples and genetic and paired clinical data. As of September 30, 2026, we are obligated to pay $3.2 million under these agreements through the year ending December 31, 2027.

Previous wording

Net cash used in operating activities was $54.2 million and $59.6 million for the six months ended June 30, 2026 and 2025, respectively. The net cash used in operating activities for the six months ended June 30, 2026 was primarily due to our net loss of $68.9 million combined with a net change in our operating assets and liabilities of $4.6 million, offset by $19.3 million in non-cash charges such as depreciation, stock-based compensation, lease expense and amortization of debt discount and debt issuance costs. The net cash used in operating activities for the six months ended June 30, 2025 was primarily due to our net loss of $66.5 million combined with a net change in our operating assets and liabilities of $2.5 million, offset by $9.4 million in non-cash charges such as depreciation, stock-based compensation and lease expense.

Current wording

Net cash used in operating activities was $87.0 million and $84.2 million for the nine months ended September 30, 2026 and 2025, respectively. The net cash used in operating activities for the nine months ended September 30, 2026 was primarily due to our net loss of $116.9 million, offset by $29.1 million in non-cash charges such as depreciation, stock-based compensation, lease expense and amortization of debt discount and debt issuance costs and a net change in our operating assets and liabilities of $0.8 million. The net cash used in operating activities for the nine months ended September 30, 2025 was primarily due to our net loss of $96.6 million combined with a net change in our operating assets and liabilities of $2.0 million, offset by $14.3 million in non-cash charges such as depreciation, stock-based compensation, lease expense and accretion of discounts on marketable securities.

Previous wording

Net cash used in investing activities was $122.2 million and $0.7 million for the six months ended June 30, 2026 and 2025. The net cash used in investing activities for the six months ended June 30, 2026 consisted of purchases of marketable securities of $186.0 million and purchases of property and equipment of $0.2 million, offset by maturities of marketable securities of $64.0 million. Net cash used in investing activities for the six months ended June 30, 2025 consisted of purchases of property and equipment of $0.7 million.

Current wording

Net cash used in investing activities was $153.6 million and $67.6 million for the nine months ended September 30, 2026 and 2025. The net cash used in investing activities for the nine months ended September 30, 2026 consisted of purchases of marketable securities of $254.2 million and purchases of property and equipment of $0.5 million, offset by maturities of marketable securities of $101.0 million. Net cash used in investing activities for the nine months ended September 30, 2025 consisted of purchases of marketable securities of $66.8 million and purchases of property and equipment of $0.8 million.

Previous wording

Net cash provided by financing activities for the six months ended June 30, 2026 was $189.8 million, which consisted of net proceeds of approximately $144.6 million from the issuance of common stock and 2026 Pre-Funded Warrants pursuant to the Underwritten Registered Offering, net proceeds of $38.5 million from the Hercules Loan Agreement, $5.8 million from the exercise of stock option awards and $1.0 million from the issuance of common stock under the 2025 Employee Stock Purchase Plan. For the six months ended June 30, 2025, net cash provided by financing activities was $128.0 million, which consisted of net proceeds of approximately $127.8 million from the issuance of common stock pursuant to our initial public offering, $0.6 million from the issuance of common stock under the 2025 Employee Stock Purchase Plan and $0.1 million from the exercise of stock option awards, offset by the payment of $0.5 million for the success fee under the loan and security agreement with Banc of California.

Current wording

Net cash provided by financing activities for the nine months ended September 30, 2026 was $205.6 million, which consisted of net proceeds of approximately $144.6 million from the issuance of common stock and 2026 Pre-Funded Warrants pursuant to the Underwritten Registered Offering, net proceeds of $38.5 million from the Hercules Loan Agreement, net proceeds of $14.6 million from the sale of common stock pursuant to the 2026 Sale Agreement, $6.9 million from the exercise of stock option awards and $1.0 million from the issuance of common stock under the 2025 Employee Stock Purchase Plan. For the nine months ended September 30, 2025, net cash provided by financing activities was $271.7 million, which consisted of net proceeds of approximately $127.8 million from the issuance of common stock pursuant to our initial public offering, $141.7 million of net proceeds from the issuance of common stock and Pre-Funded Warrants in the Private Placement, $2.1 million from the exercise of stock option awards and $0.6 million from the issuance of common stock under the 2025 Employee Stock Purchase Plan, partially offset by the payment of $0.5 million for the success fee under the loan and security agreement with Banc of California.

Previous wording

Our significant accounting policies are described in detail in the notes to our condensed financial statements included elsewhere in this Quarterly Report on Form 10-Q. We described the accounting policies that we believe involve a significant level of estimation and uncertainty, which could have a material impact on our financial condition or results of operations and are therefore deemed critical accounting policies, in our “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our Annual Report on Form 10-K for the year ended December 31, 2025, as filed with the SEC on March, 25, 2026. There have been no significant changes in our critical accounting policies and estimates during the six months ended June 30, 2026.

Current wording

Our significant accounting policies are described in detail in the notes to our condensed financial statements included elsewhere in this Quarterly Report on Form 10-Q. We described the accounting policies that we believe involve a significant level of estimation and uncertainty, which could have a material impact on our financial condition or results of operations and are therefore deemed critical accounting policies, in our “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our Annual Report on Form 10-K for the year ended December 31, 2025, as filed with the SEC on March 25, 2026. There have been no significant changes in our critical accounting policies and estimates during the nine months ended September 30, 2026.