CODEXIS, INC.

Previous wording

We also use the CodeEvolver platform technology to develop enzymes for the synthesis of RNAi therapeutics through our ECO Synthesis manufacturing platform, where our enzymes are poised to deliver many of the same benefits we offer in pharma biocatalysis across purity, yield, and improved manufacturing efficiency. In November 2024, we presented data at the TIDES EU conference demonstrating the successful end-to-end enzymatic synthesis of an entire commercially approved small interfering ribonucleic acid (“siRNA”) therapeutic asset with the ECO Synthesis manufacturing platform. In addition to using full enzymatic sequential synthesis, adding one nucleotide at a time to synthesize the two strands from beginning to end, we demonstrated synthesis of the same siRNA asset using three other routes utilizing enzymatic ligation with our double-stranded RNA (“dsRNA”) ligase, which can stitch together fragments of chemically and/or enzymatically synthesized RNA to form the full siRNA drug structure. For the three other routes, our data highlighted that full-length oligos of equal quality and yields were obtained whether the fragments were made with enzymes or by traditional phosphoramidite chemistry. At the end of 2024, we completed the build out of our ECO Synthesis Innovation Lab, a facility that uses our ECO Synthesis manufacturing platform to synthesize gram-scale quantities of a customer’s desired siRNA construct suitable for pre-clinical testing. In May 2025, we presented data at the TIDES U.S. conference demonstrating our proprietary ECO Synthesis platform’s ability to support siRNA manufacturing by reducing purification costs, improving process performance, and demonstrating the potential to control stereochemistry. In addition, three presentations from contract development and manufacturing organizations (“CDMO”) validated the transferability of our ligation processes to their in-house facilities. In 2025, we expect to manufacture good laboratory practice (“GLP”)-grade siRNA for customers in our Innovation Lab under development services contracts model, and we anticipate entering a partnership with a large-scale CDMOto use our ECO Synthesis platform of enzymatic tools and processes to synthesize good manufacturing practices (“GMP”)-grade siRNA drug substance for our customers. We expect to expand our enzymatic tools and process offerings as we further enhance the ECO Synthesis platform to address the overall market needs for scalable and sustainable RNAi manufacturing.

Current wording

We also use the CodeEvolver platform technology to develop enzymes for the synthesis of RNAi therapeutics through our ECO Synthesis manufacturing platform, where our enzymes are poised to deliver many of the same benefits we offer in pharma biocatalysis across purity, yield, and improved manufacturing efficiency. In November 2024, we presented data at the TIDES EU conference demonstrating the successful end-to-end enzymatic synthesis of an entire commercially approved small interfering ribonucleic acid (“siRNA”) therapeutic asset with the ECO Synthesis manufacturing platform. In addition to using full enzymatic sequential synthesis, adding one nucleotide at a time to synthesize the two strands from beginning to end, we demonstrated synthesis of the same siRNA asset using three other routes utilizing enzymatic ligation with our double-stranded RNA (“dsRNA”) ligase, which can stitch together fragments of chemically and/or enzymatically synthesized RNA to form the full siRNA drug structure. For the three other routes, our data highlighted that full-length oligos of equal quality and yields were obtained whether the fragments were made with enzymes or by traditional phosphoramidite chemistry. At the end of 2024, we completed the build out of our ECO Synthesis Innovation Lab, a facility that uses our ECO Synthesis manufacturing platform to synthesize gram-scale quantities of a customer’s desired siRNA construct suitable for pre-clinical testing. In May 2025, we presented data at the TIDES U.S. conference demonstrating our proprietary ECO Synthesis platform’s ability to support siRNA manufacturing by reducing purification costs, improving process performance, and demonstrating the potential to control stereochemistry. In addition, three presentations from contract development and manufacturing organizations (“CDMO”) validated the transferability of our ligation processes to their in-house facilities. In 2025, we expect to manufacture good laboratory practice (“GLP”)-grade siRNA for customers in our Innovation Lab under development services contracts model, and in the near term we anticipate entering a partnership with a large-scale CDMO to use our ECO Synthesis platform of enzymatic tools and processes to synthesize good manufacturing practices (“GMP”)-grade siRNA drug substance for our customers. We expect to expand our enzymatic tools and process offerings as we further enhance the ECO Synthesis platform to address the overall market needs for scalable and sustainable RNAi manufacturing.

Previous wording

Total revenues increased by $7.3 million to $15.3 million in the three months ended June 30, 2025 compared to the same period in 2024. Total revenues decreased by $2.2 million to $22.9 million in the six months ended June 30, 2025 compared to the same period in 2024.

Current wording

Total revenues decreased by $4.2 million to $8.6 million in the three months ended September 30, 2025 compared to the same period in 2024. Total revenues decreased by $6.4 million to $31.5 million in the nine months ended September 30, 2025 compared to the same period in 2024.

Previous wording

Product revenue increased by $1.1 million to $7.4 million in the three months ended June 30, 2025 compared to the same period in 2024, and decreased by $2.4 million to $13.4 million in the six months ended June 30, 2025 compared to the same period in 2024, primarily due to variability in manufacturing schedules and timing in clinical trial progression of our customers, which impacted order volumes for our enzyme products.

Current wording

Product revenue decreased by $4.4 million to $6.8 million in the three months ended September 30, 2025 compared to the same period in 2024, and decreased by $6.7 million to $20.2 million in the nine months ended September 30, 2025 compared to the same period in 2024, primarily due to variability in manufacturing schedules and timing in clinical trial progression of our customers, which impacted order volumes for our enzyme products.

Previous wording

Research and development revenue increased by $6.2 million to $7.9 million in the three months ended June 30, 2025 compared to the same period in 2024 primarily due to$3.6 million higher revenue from legacy agreements and $2.5 million in revenue from a licensing agreement executed in the second quarter of 2025. Research and development revenue increased by $0.2 million to $9.4 million in the six months ended June 30, 2025 compared to the same period in 2024, primarily due to higher revenue being recognized in the second quarter of 2025 as compared to the same period in 2024, partially offset by $6.0 million in lower revenue from our licensing agreement with Roche Sequencing Solutions, Inc. in the first quarter of 2024 that did not reoccur in the current year.

Current wording

Research and development revenue increased by $0.1 million to $1.8 million in the three months ended September 30, 2025 compared to the same period in 2024 primarily due to higher revenue from existing collaboration agreements. Research and development revenue increased by $0.3 million to $11.2 million in the nine months ended September 30, 2025 compared to the same period in 2024, primarily due to higher license and milestone revenue being recognized in 2025 as compared to the same period in 2024, partially offset by $6.0 million in lower revenue from our licensing agreement with Roche Sequencing Solutions, Inc. in the first quarter of 2024 that did not reoccur in the current year.

Previous wording

(1) Cost of product revenue consists of both internal and third-party fixed and variable costs, including materials and supplies, labor, facilities and other overhead costs associated with our product revenue.

Current wording

(1) Cost of product revenue consists of both internal and third-party fixed and variable costs, including materials and supplies, labor, facilities and other over head costs associated with our product revenue.

Previous wording

Cost of product revenue decreased by $1.4 million and $3.5 million in the three and six months ended June 30, 2025, respectively, compared to the same periods in 2024. Product gross margins were 72% and 64% in the three and six months ended June 30, 2025, respectively, compared to 45% and 47% in the corresponding periods in 2024. The changes in cost of product revenue and product gross margins are primarily due to a shift in sales toward more profitable products, and declines in less profitable legacy products.

Current wording

Cost of product revenue decreased by $1.9 million and $5.3 million in the three and nine months ended September 30, 2025, respectively, compared to the same periods in 2024. Product gross margins were 64% in both the three and nine months ended September 30, 2025, compared to 61% and 53%, respectively, in the corresponding periods in 2024. The changes in cost of product revenue and product gross margins are primarily due to a shift in sales toward more profitable products, and declines in less profitable legacy products.

Previous wording

Research and development expenses increased by $2.4 million in the three months ended June 30, 2025 compared to the same period in 2024 prim arily due to a $1.4 million increase in employee-related costs, $1.1 million in higher allocable costs, and $0.2 million in higher lab supplies, partially offset by a $0.5 million decrease from lower use of outside services. The increase in research and development expenses of $4.1 million in the six months ended June 30, 2025, compared to the same period in 2024, was primarily due to a $2.3 million increase in employee-related costs, $2.1 million increase in allocable costs, and $0.3 million in higher lab supplies. These were partially offset by a$0.5 million decrease from lower use of outside services.

Current wording

Research and development expenses increased by $2.4 million in the three months ended September 30, 2025 compared to the same period in 2024 primarily due to a $0.7 million increase in employee-related costs, $1.3 million in higher lab supplies and $0.8 million in higher allocable costs, partially offset by a $0.4 million decrease from lower use of outside services. The increase in research and development expenses of $6.4 million in the nine months ended September 30, 2025, compared to the same period in 2024, was primarily due to a $2.8 million increase in employee-related costs, $2.9 million increase in allocable costs, and $1.9 million in higher lab supplies. These were partially offset by a $1.2 million decrease from lower use of outside services.

Previous wording

Selling, general and administrative expenses decreased by $3.4 million during the three months ended June 30, 2025, compared to the same period in 2024 primarily due to $2.2 million in lower stock-based compensation expenses, $0.9 million in lower legal costs, $0.3 million in lower consulting and outside services, and $0.3 million in lower allocable costs. These were partially offset by a $0.3 million increase inemployee-related costs. The decrease in selling, general and administrative expenses of $3.9 million during the six months ended June 30, 2025 as compared to the same period in 2024, was primarily due to $2.8 million in lower stock-based compensation expenses, $1.7 million in lower legal costs and $0.6 million in lower allocable costs. These were partially offset by a$0.8 million increase in employee-related costsand a $0.5 million increase in facilities associated costs.

Current wording

Selling, general and administrative expenses decreased by $2.4 million during the three months ended September 30, 2025, compared to the same period in 2024 primarily due to $1.1 million in lower consulting and outside services, $0.3 million decrease in employee-related costs, $0.6 million in lower legal costs, and $0.4 million in lower allocable costs. The decrease in selling, general and administrative expenses of $6.2 million during the nine months ended September 30, 2025 as compared to the same period in 2024, was primarily due to $2.9 million in lower stock-based compensation expenses, $2.3 million in lower legal costs,$1.2 millionin lower consulting and outside services, and $1.2 million in lower allocable costs. These were partially offset by a $0.6 million increase in employee-related costs and a $0.8 million increase in facilities associated costs.

Previous wording

Asset impairment and other charges for the three and six months ended June 30, 2024 was due to a $0.2 million write-down on assets held for sale.

Current wording

Asset impairment and other charges for the nine months ended September 30, 2024 was due to a $0.2 million write-down on assets held for sale during the second quarter of 2024.

Previous wording

Interest income decreased by $0.4 million and $0.5 million in the three and six months ended June 30, 2025, respectively, compared to the same periods in 2024, primarily due to lower average cash, cash equivalents and short-term investments balances.

Current wording

Interest income decreased by $0.2 million and $0.8 million in the three and nine months ended September 30, 2025, respectively, compared to the same periods in 2024, primarily due to lower average cash, cash equivalents and short-term investments balances.

Previous wording

The provision for income taxes for the three and six months ended June 30, 2025 and 2024, was primarily due to the accrual of interest and penalties on historic uncertain tax positions.

Current wording

The provision for income taxes for the three and nine months ended September 30, 2025 and 2024, was primarily due to the accrual of interest and penalties on historic uncertain tax positions.

Previous wording

Net loss for the three months ended June 30, 2025 was $13.3 million, or a net loss per basic and diluted share of $0.16. This compared to a net loss of $22.8 million, or a net loss per basic and diluted share of $0.32, for the three months ended June 30, 2024. The decrease in net loss was primarily related to higher revenues and lower costs and operating expenses.

Current wording

Net loss for the three months ended September 30, 2025 was $19.6 million, or a net loss per basic and diluted share of $0.22. This compared to a net loss of $20.6 million, or a net loss per basic and diluted share of $0.29, for the three months ended September 30, 2024. The decrease in net loss was primarily related to lower costs and operating expenses.

Previous wording

Net loss for the six months ended June 30, 2025 was $34.0 million, or a net loss per basic and diluted share of $0.40. This compared to a net loss of $34.3 million, or a net loss per basic and diluted share of $0.49, for the six months ended June 30, 2024. The decrease in net loss was primarily related to lower costs and operating expenses in 2025.

Current wording

Net loss for the nine months ended September 30, 2025 was $53.6 million, or a net loss per basic and diluted share of $0.62. This compared to a net loss of $54.9 million, or a net loss per basic and diluted share of $0.78, for the nine months ended September 30, 2024. The decrease in net loss was primarily related to lower costs and operating expenses in 2025.

Previous wording

On May 2, 2024, we entered into the Cantor Sales Agreement with Cantor, under which Cantor, at our discretion and at such times that we may determine from time to time, may sell up to a maximum of $75.0 million of shares of our common stock. Under the terms of the Cantor Sales Agreement, Cantor may sell the shares at market prices by any method that is deemed to be an “at the market offering” as defined in Rule 415 under the Securities Act. On May 2, 2024, we filed a registration statement on Form S-3 registering the offer and sale of these shares under the Securities Act which became effective on May 14, 2024. We will pay a commission of up to 3.0%of gross sales proceeds of any common stock sold under the Cantor Sales Agreement. In 2024, 10,440,000 shares of our common stock were issued and sold pursuant to the Cantor Sales Agreement, all during the third quarter of 2024, and we received net proceeds of $29.7 million after Cantor’s commissions and direct offering expenses. During the three and six months ended June 30, 2025, 7,244,966 shares of our common stock were issued and sold pursuant to the Cantor Sales Agreement and we received gross proceeds of $17.3 million, or $16.4 million in net proceeds after Cantor’s commissions and direct offering expenses of $0.8 million.

Current wording

On May 2, 2024, we entered into the Cantor Sales Agreement with Cantor, under which Cantor, at our discretion and at such times that we may determine from time to time, may sell up to a maximum of $75.0 million of shares of our common stock. Under the terms of the Cantor Sales Agreement, Cantor may sell the shares at market prices by any method that is deemed to be an “at the market offering” as defined in Rule 415 under the Securities Act. On May 2, 2024, we filed a registration statement on Form S-3 registering the offer and sale of these shares under the Securities Act which became effective on May 14, 2024. We will pay a commission of up to 3.0%of gross sales proceeds of any common stock sold under the Cantor Sales Agreement. In 2024, 10,440,000 shares of our common stock were issued and sold pursuant to the Cantor Sales Agreement, all during the third quarter of 2024, and we received net proceeds of $29.7 million after Cantor’s commissions and direct offering expenses. During the nine months ended September 30, 2025, 7,244,966 shares of our common stock were issued and sold pursuant to the Cantor Sales Agreement, all during the second quarter of 2025, and we received gross proceeds of $17.3 million, or $16.4 million in net proceeds after Cantor’s commissions and direct offering expenses of $0.8 million.

Previous wording

We believe that our existing cash and cash equivalents, combined with our future expectations for product revenues, research and development revenue, and expense management will provide adequate funds for ongoing operations, planned capital expenditures and working capital requirements for at least the next 12 months. We have based this estimate on assumptions that may prove to be wrong, and we could utilize our capital resources sooner than we expect.

Current wording

We believe that our existing cash and cash equivalents, combined with our future expectations for product revenues, research and development revenue, and expense management will provide adequate funds for planned ongoing operations, capital expenditures and working capital requirements for at least the next 12 months. We have based this estimate on assumptions that may prove to be wrong, and we could utilize our capital resources sooner than we expect.

Previous wording

The following is a summary of cash flows for the six months ended June 30, 2025 and 2024 (in thousands):

Current wording

The following is a summary of cash flows for the nine months ended September 30, 2025 and 2024 (in thousands):

Previous wording

The $11.8 million increase in net cash used in operating activities for the six months ended June 30, 2025 as compared to the same period in 2024, was primarily due to the net effect of decreases in cash received from revenue, increases in cash paid for operating expenses and changes in operating assets and liabilities.

Current wording

The $6.5 million increase in net cash used in operating activities for the nine months ended September 30, 2025 as compared to the same period in 2024, was primarily due to the net effect of decreases in cash received from revenue, increases in cash paid for operating expenses and unfavorable changes in working capital, including higher financial assets and lower accrued compensation.

Previous wording

The $67.1 million increase in net cash provided by investing activities for the six months ended June 30, 2025 as compared to the same period in 2024, was primarily due to proceeds from maturity of short-term investments in the first half of 2025 offset by cash utilized for purchase of short-term investments.

Current wording

The $71.9 million increase in net cash provided by investing activities for the nine months ended September 30, 2025 as compared to the same period in 2024, was primarily due to proceeds from maturity of short-term investments offset by cash utilized for purchase of short-term investments.

Previous wording

The $1.2 million decrease in net cash provided by financing activities for the six months ended June 30, 2025 as compared to the same period in 2024, was primarily due to the $29.5 million in proceeds from the first tranche of the Innovatus Loan in February 2024, partially offset by the proceeds from the funding of the second tranche of the Innovatus Loan in June 2025 and proceeds from issuance of common stock under the Cantor Sales Agreement during the second quarter of 2025.

Current wording

The $31.6 million decrease in net cash provided by financing activities for the nine months ended September 30, 2025 as compared to the same period in 2024, was primarily due to the $29.5 million in proceeds from the first tranche of the Innovatus Loan in February 2024, and higher proceeds from issuance of common stock under the Cantor Sales Agreement in 2024, partially offset by the proceeds from the funding of the second tranche of the Innovatus Loan in June 2025.

Previous wording

The preparation of financial statements in conformity with generally accepted accounting principles requires management to make judgments, estimates and assumptions in the preparation of our consolidated financial statements and accompanying notes. Actual results could differ from those estimates. There have been no material changes to our critical accounting policies or estimates during the three and six months ended June 30, 2025 from those discussed in our Annual Report.

Current wording

The preparation of financial statements in conformity with generally accepted accounting principles requires management to make judgments, estimates and assumptions in the preparation of our consolidated financial statements and accompanying notes. Actual results could differ from those estimates. There have been no material changes to our critical accounting policies or estimates during the three and nine months ended September 30, 2025 from those discussed in our Annual Report.