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Item 1. Business

2026-03-11 compared with 2025-02-27 · 128 added, 147 removed, 162 unchanged (63% of the section changed)

COMPANY OVERVIEW

We are a leading provider of enzymatic solutions for efficient and scalable therapeutics manufacturing, and we leverage o ur proprietary CodeEvolver ® directed evolution technology platform to discover, develop, enhance, and commercialize novel, high-performance enzymes and other classes of proteins.

Enzymes are naturally occurring biological molecules critical to almost all biochemical reactions that sustain life.

They can be precisely engineered and optimized for specific functions, and to have particular characteristics, such as an ability to survive environments in which natural enzymes cannot, or to perform (bio)chemical transformations different than those for which they naturally evolved.

We focus on leveraging our technology and capacity to enhance the properties and performance of enzymes to drive pivotal improvements in manufacturing of complex therapeutics across two key focus areas:

our foundational, revenue-generating pharma biocatalysis business and our Enzyme-Catalyzed Oligonucleotide Synthesis™ (“ECO Synthesis™”) manufacturing platform, which is comprised of enzymatic tools, and processes, designed to enable large-scale manufacture of RNA interference (“RNAi”) therapeutics.

In July 2023, we announced that we discontinued investment in certain development programs, primarily in our novel biotherapeutics business segment.

As part of this strategic prioritization, during 2024 we completed the divestiture and monetization of certain biotherapeutics assets as well as certain non-core life science assets, including in genomics and next generation sequencing applications.

In our revenue-generating pharma biocatalysis business (formerly our pharmaceuticals manufacturing business), we utilize our CodeEvolver technology platform to develop optimized enzymes that are used by some of the world’s largest pharmaceutical companies to improve the efficiency and productivity of their manufacturing processes for small molecule therapeutics.

Our unique enzymes drive improvements such as higher yields, increased purity, reduced energy usage and waste generation, all of which lead to improved efficiency and reduced costs in small-molecule manufacturing.

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.

We are a leading provider of technology solutions to improve therapeutics manufacturing.

We focus on impacting the manufacturing process by using o ur proprietary CodeEvolver ® directed evolution technology platform to discover, develop, enhance, and commercialize novel, high-performance enzymes and other classes of proteins.

Enzymes are naturally occurring biological molecules critical to almost all biochemical reactions.

They can be precisely engineered and optimized for specific functions, and to have particular characteristics, such as an ability to survive environments in which natural enzymes cannot, or to perform (bio)chemical transformations that are different than those for which they naturally evolved.

We employ our technology and expertise to enhance the properties and performance of enzymes to drive pivotal improvements in manufacturing of complex therapeutics across two key areas:

our ECO synthesis manufacturing platform and our small molecule pharma biocatalysis business.

ECO Synthesis manufacturing platform

Our ECO Synthesis ® manufacturing platform is comprised of enzymatic tools and processes that are designed to enable large-scale manufacture of RNA interference (“RNAi”) therapeutics.

We use the CodeEvolver platform technology to develop enzymes for the synthesis of RNAi therapeutics in production processes that deliver improvements, including purity, yield, and manufacturing efficiency.

In November 2024, we presented data at the TIDES Europe 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 phosphoramididte 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 addition, it allows us to provide process development, analytical method development and other manufacturing process optimization which is required before the siRNA enters clinical-stage manufacturing and testing.

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 contract development and manufacturing organization (“CDMO”) to use our ECO platform of enzymatic tools and processes to synthesize good manufacturing practices ( “ GMP ” ) -grade siRNA drug substance for our customers.

For the three other routes, our data highlighted that full-length oligonucleotides of equal quality and yields were obtained whether the fragments were made with enzymes or by traditional solid phase oligonucleotide synthesis (“SPOS”) (current standard production route for oligonucleotide manufacturing).

At the end of 2024, we completed the build out of our ECO Synthesis Innovation Lab, a facility where our ECO Synthesis manufacturing platform is deployed to synthesize gram-scale quantities of a customer’s desired siRNA construct suitable for pre-clinical testing.

In addition, the infrastructure allows us to provide process development, analytical method development and other manufacturing process optimization which is required to enable the siRNA to proceed to clinical-stage manufacturing and testing.

In 2025, we successfully manufactured non- good manufacturing practice (“GMP”)-grade siRNA drug substance for customers in our Innovation Lab under development services contracts.

We also entered into partnerships with three large-scale contract development and manufacturing organizations (“CDMOs”) to evaluate our ECO platform of enzymatic tools and processes to ultimately synthesize GMP -grade siRNA drug substance for our customers.

In each of these agreements, we are currently in the feasibility testing stage and expect to advance at least one of these partnerships, including initiating a technology transfer to that organization, in 2026.

We believe these relationships to be a vital extension of our strategy to be a technology solutions provider for our customers.

Through these arrangements, our customers will have access to proven, large-scale commercial manufacturers who are familiar with our process, and who can then offer a seamless manufacturing scale-up of our customers’ products.

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.

Small molecule pharma biocatalysis

In our small molecule pharma biocatalysis business, we utilize our CodeEvolver technology platform to develop optimized enzymes that are used by some of the world’s largest pharmaceutical companies to improve the efficiency and productivity of their manufacturing processes for small molecule therapeutics.

History and Core Technology

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The CodeEvolver technology platform has the power to transform the performance of an enzyme, tailoring it for a specific application and/or process.

Using powerful machine learning tools and sophisticated molecular, cellular, and bioanalytical workflows, we design and screen libraries of thousands of variants every few weeks.

Content-rich libraries screened under real-world conditions can yield dense and valuable datasets, which when data-mined effectively enables us to optimize multiple parameters in parallel.

The resulting evolved variants often have a combination of enhanced properties, such as increased activity, specificity, and stability under desired conditions, or improved manufacturability in the production host.

Using powerful machine learning tools and sophisticated molecular, cellular, and bioanalytical workflows, we can design and screen libraries of thousands of variants.

Content-rich libraries screened under real-world conditions can yield dense and valuable datasets, which, when data-mined, allow us to optimize multiple parameters in parallel.

The resulting evolved variants often have a combination of enhanced properties, such as increased activity, specificity, and stability under desired conditions, and improved manufacturability in the production host.

These enhanced properties provide differentiated technical performance in the target application and can provide our customers increased value in the commercial deployment of their products.

Key Strategic Focus Areas

We provide enzyme-based solutions to our clients that address complex therapeutic manufacturing challenges in the areas of pharma biocatalysis and RNAi manufacturing.

Both areas overlap in the technical enzyme engineering expertise required and also include similar potential customers.

Many of our longstanding pharma biocatalysis customers are currently investing in both pharma biocatalysis for the development of small-molecule therapeutics and in the development of RNAi therapeutics, providing us a unique advantage in terms of our commercial reach.

Further, our pharma biocatalysis business establishes credibility for the ECO Synthesis manufacturing platform by demonstrating our proven history of engineering technically complex enzymes for large pharmaceutical companies and effectively scaling up to multiple metric tons of manufactured product using our existing platforms.

Pharma Biocatalysis

We believe the pharmaceutical industry represents a significant market opportunity for our enzymes as pharmaceutical companies constantly developing new small molecule drugs and are under significant competitive pressure both to improve manufacturing efficiencies and to increase the speed to market for their products.

To address these pressures, pharmaceutical companies are driven to identify reliable, cost-effective, and sustainable manufacturing processes to produce both their new drug candidates and their existing products, while not impacting drug safety and efficacy.

Manufacturing economies of scale are increasingly important to our pharmaceutical customers as they get closer to their commercial drug launch.

Over the lifecycle of the drug, market pressures further intensify as pharmaceutical companies lose their patent exclusivities and begin to experience competition from generic manufacturers of their products.

Many of our customers are large global pharmaceutical companies who partner with us to develop engineered enzymes for use as biocatalysts, meeting precisely defined criteria.

Their goals are to improve the efficiency, productivity and sustainability of their manufacturing processes.

As of December 31, 2024, we sell enzymes as biocatalysts to pharmaceutical manufacturers for 16 therapeutic drugs that are currently approved for commercial sales.

We currently sell these enzymes, that have already been engineered and installed in a customer’s commercial manufacturing process at multi-kilograms to metric tons per annum scale.

For example, we sell enzymes to Merck, Sharp & Dohme ( “Merck”) for their manufacture of sitagliptin, the active ingredient in JANUVIA, to Urovant Sciences GmbH ( “ Urovant ” ) and KYORIN Pharmaceutical Co., Ltd.

( “ Kyorin ” ) for the manufacture of vibegron, the active ingredient in Urovant’s GEMTESA and Kyorin’s BEOVA products for the treatment of overactive bladder, as well as supporting other products and customers for which public disclosures have not been made.

In addition to these larger volumes of enzymes that are sold for our customers’ ongoing commercial requirements, we also sell smaller quantities of engineered enzymes for use in a customer’s clinical-stage manufacturing.

As of December 31, 2024, Codexis is selling enzymes to pharmaceutical manufacturers f or 14 dr ug candidates currently in Phase 2 and Phase 3 clinical trials, or to customers working to convert to an enzymatic manufacturing process for drugs that have been commercially approved.

We are focused on expanding this pipeline to ensure our ability to grow this business over time.

Finally, we also sell even smaller quantities of enzymes (typically grams to multi-kilogram scale) to customers for manufacturing and testing in their discovery and pre-clinical phase.

In addition to the sale of enzymes, we also offer contracted research and development partnerships to our customers.

These research and development activities are typically governed by collaboration agreements, which often contain research and development fees and intellectual property provisions, under which we screen and/or engineer enzymes for customers in connection with their process development efforts.

In these collaborations, we typically receive consideration in the form of one or more of the following:

upfront payments, milestone payments, payments for screening and engineering, followed by fees for manufacturing scale-up and supply of enzymes, licensing fees and/or royalties as the customer’s product commercializes.

We also have licensed our CodeEvolver technology platform to pharmaceutical companies to help them develop custom-designed enzymes that are highly optimized for efficient manufacturing processes.

To date, we have entered into platform technology licensing agreements with each of GlaxoSmithKline Intellectual Property Development Limited, a subsidiary of GlaxoSmithKline plc (“GSK”), Merck & Co., Inc.

(“Merck & Co”) and Novartis Pharma AG (“Novartis”).

ECO Synthesis Manufacturing Platform

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A key strategic priority for Codexis is the advancement and commercialization of our ECO Synthesis manufacturing platform, which is designed to enable the commercial scale manufacture of RNAi therapeutics.

As of December 31, 2024, there are six approved siRNA therapeutics on the market in the United States, primarily targeting rare orphan disease indications.

However, there are more than 450 RNAi therapeutic assets in development, including over one hundred that are in Phase 2 and Phase 3 clinical trials, with more th an 40 of these targeting large disease indications such as Alzheimer’s, hyperlipidemia and hypertension.

As of December 31, 2025 , there were eight approved siRNA therapeutics on the market in the United States, primarily targeting rare disease indications.

However, there are hundreds of RNAi therapeutic assets in development, including 41 assets in Phase 2 and Phase 3 clinical trials.

As we move through 2026, the RNAi pipeline is pivoting from rare conditions to high-prevalence diseases like Alzheimer’s, hyperlipidemia and hypertension.

We expect worldwide demand for RNAi therapeutics to grow significantly as RNAi therapeutic assets progress through clinical development and are commercially approved.

The current industry standard for manufacturing RNAi therapeutics is a well-established, chemical-based method commonly called solid-phase oligonucleotide synthesis (“SPOS”) utilizing phosphoramidite chemistry.

The current industry standard for manufacturing RNAi therapeutics is a well-established, chemical-based method SPOS utilizing phosphoramidite chemistry.

This approach has existed for more than forty years and works effectively for small-scale manufacturing required during the discovery stage of clinical development.

However, SPOS and phosphoramidite chemistry face multiple limitations in the context of commercial-scale manufacture of RNAi therapeutics.

This approach requires significant infrastructure and capital investment to meet the anticipated future growth in demand for RNAi therapeutics.

SPOS and phosphoramidite chemistry are also currently limited to single-digit kilogram synthesis batch sizes, which presents challenges around quality control and scalability.

This approach will require significant infrastructure and capital investment to meet the anticipated future growth in demand for RNAi therapeutics.

SPOS and phosphoramidite chemistry are also currently limited to single-digit kilogram synthesis batch sizes, and present challenges around quality control and scalability.

Further, chemical synthesis requires large volumes of acetonitrile, a highly-flammable, organic solvent with high waste disposal costs, to facilitate the reaction environment necessary to produce RNAi therapeutics.

As additional RNAi therapeutic candidates are approved for large disease indications, we believe using traditional SPOS and phosphoramidite chemical synthesis for commercial scale production will become prohibitively expensive, time-intensive, and challenging for many drug developers seeking to produce enough drug substance to address patient indications that require dosing more than 1 million patients annually.

As additional RNAi therapeutic candidates are approved for disease indications with higher prevalence, we believe using traditional SPOS and phosphoramidite chemical synthesis for commercial scale production will become prohibitively expensive, time-intensive, and challenging for many drug developers seeking to produce enough drug substance to address these larger patient populations.

We believe that the ECO Synthesis manufacturing platform presents several advantages to potentially address the limitations of SPOS and phosphoramidite chemistry.

First, the platform is being developed to integrate within existing manufacturing facilities and utilizes equipment currently available in the industry, potentially eliminating much of the infrastructure investment required for commercial scale manufacturing of RNAi therapeutics with phosphoramidite chemistry.

The ECO Synthesis manufacturing platform is also being designed to manufacture tens to hundreds of kilograms of high-purity RNA per synthesis batch, with a closed-loop system intended to increase volumetric reagent efficiency which enables large batch synthesis.

Finally, our process is aqueous based, potentially mitigating the need for high volumes of acetonitrile, significantly decreasing chemical waste streams, and reducing heavy disposal and purification costs.

At the TIDES Europe meeting in November 2024, we presented data in a joint poster presentation with Bachem, one of the world’s leading CDMOs in oligonucleotide manufacturing, the data provided compelling external validation of the superior performance of our engineered dsRNA ligases over the wild type enzymes in use today across both volumetric productivity and substrate versatility.

We also announced we completed a proof-of-concept technical collaboration with a major siRNA drug innovator, where we synthesized their desired oligonucleotide fragments using our enzymatic process.

Our platform can be integrated within existing manufacturing facilities and utilizes equipment currently available in the industry, potentially eliminating much of the infrastructure investment required for SPOS and phosphoramidite chemistry.

ECO Synthesis is not constrained by the same process limitations as SPOS, and, by design, has the potential to manufacture tens to a hundred kilograms of high-purity RNA per run, with a closed-loop system intended to increase volumetric reagent efficiency which enables large batch synthesis.

Finally, our process is aqueous based, mitigating the need for high volumes of acetonitrile, significantly decreasing chemical waste streams, and reducing heavy disposal and purification costs.

ECO Synthesis Innovation Lab

We completed the build-out of our ECO Synthesis Innovation Lab at the end of 2024.

This facility allows us to optimize the development and scaling of a specific manufacturing process of a customer’s specific siRNA asset before completing the technology transfer to a CDMO partner for bulk GMP-grade production of drug substance to supply the customer’s clinical trials and eventual commercialization.

It is also designed to enable the manufacture of GLP-grade RNAi therapeutic material in sufficient quantities to support customers’ preclinical development.

This facility allows us to optimize the development and scaling of a manufacturing process of a customer’s specific siRNA asset before completing the technology transfer to a CDMO partner for GMP-grade production of drug substance to supply the customer’s clinical trials and eventual commercialization.

It is also designed to enable the manufacture of non-GMP-grade RNAi therapeutic material in sufficient quantities to support customers’ preclinical development.

The ECO Synthesis manufacturing platform is a set of enzymatic tools and processes that are used together to manufacture siRNA.

With this platform, we work with our customers to optimize the manufacturing of the customer’s asset.

This platform allows us to use enzymatically synthesized RNAi sequences, to conjugate tissue targeting moieties such as GalNAc, onto an RNA strand, which is a common modification included on RNAi therapeutics to assist with targeted tissue delivery and to ligate (connect) RNAi sequences together.

This platform produces enzymatically synthesized RNAi sequences, and the conjugation of tissue targeting moieties such as GalNAc, onto an RNA strand (which is a common modification included on RNAi therapeutics to assist with targeted tissue delivery) and to ligate (connect) RNAi sequences together.

All of these capabilities are used to create a full-length and completed RNAi therapeutic asset.

Our goal is to be a value-added service provided to pharmaceutical innovators.

Our goal is to be a value-added technology solutions provider to pharmaceutical innovators.

Many of our potential clients seek expertise in areas that they cannot develop on their own, but seek to partner with companies who provide expertise in manufacturing.

Through our ECO Synthesis platform, we offer a true partnership approach to drug manufacturing.

Through our ECO Synthesis platform, we offer a partnership approach to drug manufacturing.

The services we provide include:

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We believe their familiarity with our ability to engineer and scale complex enzymes is a significant commercial advantage for our ECO Synthesis manufacturing platform.

However, there are also key differences that make this platform a compelling opportunity as compared to our existing pharma biocatalysis business.

Pharma biocatalysis generally requires one-to-one custom enzyme engineering projects, which involve significant time and resource investment from Codexis.

Our top five selling pharma biocatalysis enzymes in 2024, excluding sales of CDX-616 to Pfizer Inc.

(“Pfizer”) related to PAXLOVID, generated on average between $2.0 million to $9.0 million annually per enzyme between 2021 and 2024.

By contrast, the ECO Synthesis manufacturing platform could be applicable to many pharmaceutical and CDMO customers and has the potential to manufacture multiple different RNAi therapeutic assets with the same of enzymes and processes.

However, there are also key differences of this platform compared to our existing pharma biocatalysis business.

Pharma biocatalysis generally requires custom enzyme engineering projects specific to a single therapeutic asset, which involves significant time and resource investment from Codexis.

Further, the potential scalability of our solution is differentiated from phosphoramidite chemistry, which is limited in batch size and requires high volumes of toxic solvent.

We believe that the ECO Synthesis manufacturing platform could enable CDMOs and drug developers to scale production of RNA therapeutics with significantly less capital expenditure for infrastructure capacity and as a result, could potentially command significantly better economic terms than the current annual revenues for pharma biocatalysis enzymes.

Our business model for the ECO Synthesis manufacturing platform is centered around selling contract development and manufacturing services delivered through the ECO Synthesis Innovation Lab.

We believe that the ECO Synthesis manufacturing platform could enable CDMOs and drug developers to scale production of RNA therapeutics with significantly less capital expenditure for production infrastructure and as a result, could potentially command significantly better economic terms than the current revenues for pharma biocatalysis enzymes.

Our business model for the ECO Synthesis manufacturing platform involves several points of interaction with our customers:

• ECO Synthesis Innovation Lab.

We provide contract development and manufacturing services at smaller scale non-GMP conditions in our ECO Synthesis Innovation Lab.

These activities are typically governed by development agreements which include fees for process development, process optimization, analytical method development and qualification, CMC documentation and small-scale manufacturing of siRNA drug substance.

• ISO 9001 certified manufacturing facility .

We provide purified enzymes and immobilized purified enzymes from our non-GMP manufacturing facility.

These products are core components of the ECO Synthesis manufacturing platform and they are released according to a full specification from our quality control labs.

All of these operations occur within our Quality Management System which is certified as ISO 9001.

• Future services from our GMP manufacturing facility .

In November 2025, we signed a lease for a GMP manufacturing facility in Hayward, California.

We are currently working on designs to retrofit this facility to manufacture RNAi therapeutics for our customers in quantities sufficient for Phase 1 and potentially Phase 2 clinical trials.

We believe this facility to be of high strategic importance to our ECO Synthesis business, capturing more of the economics of the drug supply chain, and also offering a GMP tech transfer to very large scale operations once customers make the decision to advance their drug candidates to larger scale clinical trials or commercial launch.

We anticipate beginning construction in the fall of 2026, with the facility in full production capability by the end of 2027 .

Pharma Biocatalysis

Pharmaceutical companies are driven to identify reliable, cost-effective, and sustainable manufacturing process improvements to produce both their new drug candidates and their existing products, while not impacting drug safety and efficacy.

Many of our customers are large pharmaceutical companies who partner with us to develop engineered enzymes for use as biocatalysts, meeting precisely defined criteria.

Their goals are to improve the efficiency, productivity and sustainability of their manufacturing processes.

As of December 31, 2025, we sold enzymes as biocatalysts to pharmaceutical manufacturers for 18 therapeutic drugs that are currently approved for commercial sales.

We currently sell these enzymes, that have already been engineered and installed in a customer’s commercial manufacturing process at multi-kilograms to metric tons per annum scale.

As of December 31, 2025, Codexis is selling enzymes to pharmaceutical manufacturers for 15 drug candidates currently in Phase 2 and Phase 3 clinical trials, or to customers working to convert to an enzymatic manufacturing process for drugs that have been commercially approved.

In addition to the sale of enzymes, we also offer contracted research and development partnerships to our customers.

In these collaborations, we typically receive consideration in the form of one or more of the following:

In November 2025, we announced we were reducing our emphasis on seeking new projects in our small-molecule biocatalysis business, primarily due to reduced pricing opportunity of the broader enzyme market.

We continue to provide these services to existing and prospective customers who have challenging products that require unique solutions, where we can engineer more value-added and differentiated enzymes.

We also have licensed our CodeEvolver technology platform to pharmaceutical companies to help them develop custom-designed enzymes that are highly optimized for efficient manufacturing processes.

(“Merck & Co”) and Novartis Pharma AG (“Novartis”).

Other Differentiated Enzymes

In addition to RNAi manufacturing and pharma biocatalysis applications, we have also applied our CodeEvolver technology platform to develop customized enzymes for customers using across other molecular biology applications, such as template dependent mRNA manufacturing, next generation sequencing, diagnostic testing and DNA oligonucleotide synthesis.

In June 2020, we entered into a co-marketing and enzyme supply collaboration agreement with Alphazyme LLC (“Alphazyme”) for the production and co-marketing of enzymes for life science applications.

This collaboration enabled the commercialization of Codex HiFi DNA Polymerase, Codex HiFi Hot Start DNA Polymerase, Codex HiFi Hot Start 2X NGS Mix, Codex HiCap RNA Polymerase, Codex HiFi UL DNA Polymerase, and Codex HiTemp Reverse Transcriptase.

In September 2024, we entered into a new non-exclusive commercial and manufacturing license agreement with Alphazyme (terminating the prior agreement), including licenses for the Codex HiFi DNA Polymerase, Codex HiTemp Reverse Transcriptase, Codex HiRev Isothermal Polymerase and other enzymes that were in development directed towards genomics and diagnostics applications prior to our strategic shift announced in July 2023.

Under the terms of the agreement, we are eligible to receive sales-based royalties.

In June 2020, we entered into a Master Collaboration and Research Agreement with Molecular Assemblies, Inc.

(“MAI ” ) (the “MAI Agreement”), and between June 2020 and April 2022, we leveraged our CodeEvolver technology platform to improve the DNA polymerase enzymes that are critical for enzymatic DNA synthesis.

At the time we entered into the MAI Agreement, we purchased $1.0 million in MAI’s Series A financing.

In August 2022, we and MAI announced that we had entered into a Commercial License and Enzyme Supply Agreement with MAI (the “MAI Supply Agreement”) under which Codexis shall manufacture and supply to MAI an enzyme engineered under the MAI Agreement for use in a specific field.

Between 2020 and 2024, in connection with the execution of the MAI Agreement and via separate purchases, we acquired shares of MAI’s Series A and B preferred stock.

On January 28, 2025, Maravai LifeSciences, Inc.

(“Maravai”), a global provider of life science reagents and services to researchers and biotech innovators, announced its acquisition of intellectual property and relevant assets from MAI.

In January 2025, MAI assigned the MAI Supply Agreement to Maravai in connection with the sale of its related assets to Maravai.

In addition to RNAi manufacturing and pharma biocatalysis applications, we have also applied our CodeEvolver technology platform to develop customized enzymes for customers across other molecular biology applications, such as template dependent mRNA manufacturing, next generation sequencing, diagnostic testing and DNA oligonucleotide synthesis.

In December 2024, we entered into a license agreement whereby Pfizer obtained a license to make a specific Codexis enzyme for use in the manufacture of Pfizer’s products.

As part of the agreement, Pfizer utilized remaining credit from a supply agreement between the parties toward the upfront fee.

Under the terms of the license agreement, Codexis is eligible to receive development and sales-based milestone payments based upon the future use of the enzyme in drug substance manufacturing.

In September 2024, we entered into a new non-exclusive commercial and manufacturing license agreement with Alphazyme LLC (“Alphazyme”).

In connection with this new agreement, we terminated all prior agreements with Alphazyme, including licenses for the Codex HiFi DNA Polymerase, Codex HiTemp Reverse Transcriptase, Codex HiRev Isothermal Polymerase and other enzymes that were in development directed towards genomics and diagnostics applications prior to our strategic shift announced in July 2023.

Under the terms of the new agreement, we are eligible to receive sales-based royalties.

In December 2023, we entered into an exclusive licensing agreement with Aldevron LLC (“Aldevron”), a global leader in the custom development and manufacture of plasmid DNA, RNA and proteins for the biotech industry, whereby Aldevron licensed our Codex HiCap RNA Polymerase.

Under the terms of the deal, Aldevron received global manufacturing and commercialization rights to the Codex HiCap RNA Polymerase in exchange for payments for near-term technical milestones, along with commercial milestones and sales-based royalties for research use only material as well as GMP material.

In March 2022, we entered into a Stock Purchase Agreement with seqWell, Inc.

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In line with our strategy relating to non-core Life Sciences assets, in January 2025 we sold assets that were developed under the seqWell Agreement to seqWell in exchange for the right to receive a cash payment upon future events and a warrant to purchase seqWell’s common stock exercisable upon future events, and terminated the seqWell Agreement.

In December, 2024, we entered into a license agreement whereby Pfizer obtained a license to make a specific Codexis enzyme for use in the manufacture of Pfizer’s products.

As part of the agreement, Pfizer utilized remaining credit from a supply agreement between the parties toward the upfront fee.

Under the terms of the license agreement, Codexis is eligible to receive development and sales-based milestone payments based upon the future use of the enzyme in drug substance manufacturing.

Licensing Our CodeEvolver Directed Evolution Technology Platform

In May 2019, we entered into a Platform Technology Transfer and License Agreement (the “Novartis CodeEvolver Agreement”) with Novartis.

The Novartis CodeEvolver Agreement allows Novartis to use our proprietary CodeEvolver platform technology in the field of human healthcare.

Under the terms of the Novartis CodeEvolver Agreement, we granted Novartis a worldwide license to use certain patents, patent applications and know-how from our CodeEvolver technology platform to research, develop and manufacture novel enzymes for use by or on behalf of Novartis as biocatalysts in the chemical synthesis of small molecule and bioconjugate APIs.

The license is exclusive for the research, development and manufacture of novel enzymes for use by Novartis as biocatalysts in the chemical synthesis of API owned or controlled by Novartis (“Novartis Exclusive Field”) and non-exclusive for the research, development and manufacture of novel enzymes for use by Novartis in the chemical synthesis of API not owned or controlled by Novartis or any third party (“Novartis Non-Exclusive Field”).

In July 2021, we announced the completion of the technology transfer period during which we transferred our proprietary CodeEvolver technology platform to Novartis (the “Technology Transfer Period”).

Pursuant to the Novartis CodeEvolver Agreement , we received an upfront payment of $5.0 million shortly after the effective date.

We completed the second technology milestone transfer under the agreement and received a milestone payment of $4.0 million in 2020.

We have also received an aggregate of $5.0 million for the completion of the third technology transfer milestone in 2021.

In consideration for the continued disclosure and license of improvements to the technology and materials during a multi-year period that began on the conclusion of the Technology Transfer Period (the “Improvements Term”), Novartis will pay us annual payments over four years which amount to an additional $8.0 million in aggregate.

We also have the potential to receive quantity-dependent, usage payments for each API that is manufactured by Novartis using one or more enzymes that have been developed or are in development using the CodeEvolver technology platform during the period beginning on the conclusion of the Technology Transfer Period and ending on the expiration date of the last to expire licensed patent.

These product-related usage payments, if any, will be paid by Novartis to Codexis for each quarter that Novartis manufactures API using a CodeEvolver-developed enzyme.

The licenses to Novartis are granted under patents, patent applications and know-how that Codexis owns or controls as of the effective date of the Novartis CodeEvolver Agreement and that cover the CodeEvolver technology platform.

Any improvements to the CodeEvolver technology platform during the Technology Transfer Period will also be included in the license grants from Codexis to Novartis.

In June 2020, we entered into a Master Collaboration and Research Agreement with Molecular Assemblies, Inc.

(“MAI ” ) (the “MAI Agreement”), under which we provided enzyme evolution services and sold enzymes to MAI in the field of DNA synthesis.

Between 2020 and 2024, in connection with the execution of the MAI Agreement and via separate purchases, we acquired shares of MAI’s Series A and B preferred stock.

On January 28, 2025, Maravai LifeSciences, Inc.

(“Maravai”), a global provider of life science reagents and services to researchers and biotech innovators, announced its acquisition of intellectual property and relevant assets from MAI.

In January 2025, MAI assigned the MAI Supply Agreement to Maravai in connection with the sale of its related assets to Maravai.

Biotherapeutics Divestitures

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Under the terms of the Acquisition Agreement, Nestlé is solely responsible for the continued development and commercialization of CDX-7108, including all associated costs, with Codexis retaining an economic interest in the program through an upfront payment, future potential milestone payments and net-sales based royalties.

In addition, we used our CodeEvolver technology platform to engineer a series of transgenes that code for enzymes that may be used as gene therapies to treat rare lysosomal storage disorders, such as Fabry Disease and Pompe Disease, as well as a blood factor disorder, with Takeda Pharmaceutical Co.

In April 2023, Takeda discontinued its efforts in adeno-associated virus (“AAV”) gene therapy, including these development programs.

In July 2024, we entered into an asset purchase agreement with Crosswalk Therapeutics (“Crosswalk”) for our investigational Fabry and Pompe disease compounds, both of which were previously part of our collaboration agreement with Takeda.

Under the terms of the agreement with Crosswalk, we are eligible to receive future development and commercial milestone payments in addition to a low-to-mid single-digit percentage net sales-based royalty.

Additionally, in April 2024 we entered into an asset acquisition agreement with another private biotherapeutics company under which we divested assets related to our investigational homocystinuria and maple syrup urine disease programs, and in June 2024, we entered into an asset sale agreement under which we divested assets related to our programs for the GLB1, GBM1, and SGSH genes, and our investigational AAV capsid technology.

Additionally, in April 2024 we entered into an asset acquisition agreement with another private biotherapeutics company under which we divested assets related to our investigational homocystinuria and maple syrup urine disease programs, and in June 2024, we entered into an asset sale agreement under which we divested assets related to our programs for the GLB1, GM1, and SGSH genes, and our investigational AAV capsid technology.

Under these agreements, Codexis is eligible to receive milestone and earnout payments.

Our strategy is to grow our revenues, profits, and stockholder value by selling customized enzymes and providing services from our ECO Synthesis platform.

We intend to monetize our technology in the following ways:

• Growing our foundational revenue-generating pharma biocatalysis business.

We intend to pursue opportunities in the pharmaceutical market to use our enzymes to improve the manufacturing efficiencies for the production of small-molecule drugs.

We intend to increase the number of pharmaceutical customers and products that utilize and benefit from our novel, enabling engineered enzymes.

• Developing and commercializing our ECO Synthesis manufacturing platform for use in RNAi manufacturing .

We intend to enable customers to manufacture RNAi therapeutics at commercial scale.

This also includes a hybrid ligation approach using our dsRNA ligase, a completely enzymatic route, and the development of enzymes and processes to enable the manufacture of building blocks, starter materials, and targeting moieties.

We intend to increase the number of customers utilizing our ECO Synthesis manufacturing platform by providing development and manufacturing services through our ECO Synthesis Innovation Lab.

• Monetizing non-core assets and leveraging channel partners with strong commercial reach to drive penetration of other developed, non-core enzymes.

Consistent with our strategy to focus on programs that we believe have the strongest probability of creating significant value in the near-term and beyond, we have monetized non-core assets and are leveraging channel partners with stronger commercial reach to drive penetration of other developed, non-core enzymes.

Examples of this strategy include monetizing CDX-7108 through the purchase agreement with Nestl é and the exclusive licensing agreement with Aldevron for our Codex HiCap RNA Polymerase, both of which were announced in December 2023, as well as the exclusive licensing agreement with Roche in February 2024 for the newly engineered DNA ligase, the non-exclusive license with Alphazyme in September 2024 for a portfolio of our life sciences enzymes, and the purchase agreement for transposase with seqWell executed in January 2025.

• Advancement of our CodeEvolver platform to maintain leadership in enzyme engineering .

We leverage our proprietary CodeEvolver directed evolution technology platform to discover, develop, enhance, and commercialize novel, high-performance enzymes for the manufacturing of complex therapeutics.

We intend to maintain technology leadership in enzyme engineering through continued investments in data science, computational biology, and laboratory operational efficiency to maintain our primary source of competitive advantage.

INTELLECTUAL PROPERTY

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Likewise, in the generic pharmaceutical area, protection of our proprietary technology, products and services directed to our enzymes and methods of producing pharmaceutical products, through patent or trade secret laws or other legal protections is important for us and our customers to maintain a lower cost production advantage over competitors.

As of December 31, 2024, we owned or controlled approximate ly 1,760 active issued patents and pending patent applications in the United States and in various foreign jurisdictions, many of which are directed to our enabling technologies and specific methods and products that support our business in the pharmaceutical and oligonucleotide synthesis markets.

This portfolio also includes patents and pending patent applications in the biotherapeutics, mo lecular diagnostics, and other markets.

As of December 31, 2025, we owned or controlled approximate ly 1,600 active issued patents and pending patent applications in the United States and in various foreign jurisdictions, many of which are directed to our enabling technologies and specific methods and products that support our business in the pharmaceutical, biotherapeutics, and oligonucleotide synthesis markets, including related to our ECO Synthesis platform.

As of December 31, 2025, our patents and pending patent applications, if issued, have terms that expire between 2026 and approximately 2046.

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These include, but are not limited to:

Codexis, Codex, CodeEvolver, MOSAIC, SAGE, MicroCYP, MCYP, ProSAR, Unlock the Power of Proteins, the Codexis Protein Engineering Experts logo, Strategist, Continuity, Ameli, Forager, Analogene, Harvester, Atoms, Riptide, APS and a Codexis design mark (i.e., the stylized Codexis logo), as well as pending registration applications for ECO Synthesis and ecoRNA .

Codexis, Codex, CodeEvolver, ECO Synthesis, MOSAIC, SAGE, MicroCYP, MCYP, ProSAR, Unlock the Power of Proteins, the Codexis Protein Engineering Experts logo, Strategist, Continuity, Ameli, Forager, Analogene, Harvester, Atoms, Riptide, APS and a Codexis design mark (i.e., the stylized Codexis logo), as well as a pending registration application for ecoRNA .

We face differing forms of competition in pharmaceutical biocatalysis and RNAi therapeutics manufacturing, as set forth below.

ECO Synthesis Manufacturing Platform for RNAi Therapeutics

We market our ECO Synthesis manufacturing platform and contract development services through our ECO Synthesis Innovation Lab to drug sponsors developing RNAi therapeutics.

SPOS using phosphoramidite chemistry is the current and long-established industry standard for the manufacture of RNAi therapeutics, examples including antisense oligonucleotides, siRNA, RNA aptamers, and guide RNA.

CDMOs in this space, such as Agilent Technologies, have made significant capital investment to expand their RNA manufacturing capabilities using phosphoramidite chemistry.

In addition, CDMOs and large pharmaceutical companies are seeking to make incremental improvements to phosphoramidite chemistry, including the development of ligation-based approaches, liquid-phase synthesis, and solvent recycling technologies.

However, many drug developers and CDMOs are already exploring the use of enzymatic technology, including our dsRNA ligase, in their manufacturing processes due to the potential benefits around increased yield, purity, and efficiency.

Additionally, there are opportunities for us to collaborate with CDMO partners to enable the manufacture of siRNA material at a greater scale than is currently possible within Codexis facilities.

In 2026, we anticipate signing and announcing additional partnerships with CDMOs to provide enzymatically synthesized GMP-grade siRNA material to drug developer customers in the near term.

There are also multiple early-stage competitors who are pursuing fully enzymatic approaches to the manufacture of RNA, including EnPlusOne Biosciences, a private startup company, and a UK-based consortium led by the Centre for Process Innovation ( “ CPI ”) and consisting of multiple academic and research organizations, including The University of Manchester and large pharmaceutical companies, including AstraZeneca plc and Novartis.

Pharma Biocatalysis

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There is also competition in the enzyme customization and optimization area from several smaller companies, such as BRAIN AG, evoxx technologies GmbH, c-LEcta GmbH, Enzymicals AG, and Enzymaster.

The market for the manufacture and supply of APIs and intermediates is large, with many established companies.

These companies include many of our large innovator and generic pharmaceutical customers, such as Merck, GSK, Novartis, Pfizer, Bristol-Myers Squibb Company (“Bristol-Myers”), Kyorin, Urovant, and Teva Pharmaceutical Industries Limited (“Teva”) , which have significant internal research and development efforts directed at developing processes to manufacture APIs and intermediates for use in their drug product manufacturing.

There is also a large network of CDMOs servicing the innovator companies with supply of APIs and/or intermediates.

These C(D)MOs include Cambrex Corporation, Asymchem, WuXi STA and Almac Group Ltd, among many others.

The processes used by these companies (both C(D)MOs and innovators) include classical organic chemistry reactions, chemo-catalytic reactions, biocatalytic reactions or combinations thereof.

Our biocatalyst-based manufacturing processes must compete effectively on cost and efficiency with these internally developed routes.

We believe that our principal advantage is our ability to rapidly deliver customized enzymes for existing and new intermediates and APIs in the pharma biocatalysis market.

This capability has allowed us to create a breadth of enzymes with improved performance characteristics including, for example, better activity, stability, and activity on a range of substrates, compared to traditional chemistry-based manufacturing processes and naturally occurring (and thus not optimized) biocatalysts.

We believe that our CodeEvolver technology platform can provide substantially superior results, in shorter time frames, than companies offering competing enzyme development services.

ECO Synthesis Manufacturing Platform for RNAi Therapeutics

We market our ECO Synthesis manufacturing platform and contract development services through our ECO Synthesis Innovation Lab to drug sponsors developing RNAi therapeutics.

CDMOs in this space, such as Agilent Technologies, have made significant capital investment to expand their RNA manufacturing capabilities using phosphoramidite chemistry.

Additionally, there are opportunities for us to collaborate with CDMO partners to enable the manufacture of siRNA material at a greater scale than is currently possible within Codexis facilities.

In 2025, we anticipate signing and announcing a CDMO scale-up partnership to provide a path to enzymatically synthesized GMP-grade siRNA material to drug developer customers in the near term.

Core Technology

We are a leader in the field of enzyme engineering to create novel enzymes, and our work across pharma biocatalysis and the ECO Synthesis manufacturing platform relies on our core technology.

We are aware that other companies, organizations and persons have developed technologies that appear to have some similarities to our patented proprietary technologies.

We are aware that other companies, organizations and persons have developed technologies that appear to have some similarities to our patented proprietary CodeEvolver technologies.

For example, we are aware that other companies, includin g Ginkgo Bioworks, BRAIN, and Enzymicals AG, have alternative methods for obtaining and generating genetic diversity or use mutagenesis techniques to produce genetic diversity.

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We rely on certain key customers for a significant portion of our total revenues and our accounts receivable balances.

For the year ended December 31, 2024, four customers accounted for approximately 18%, 13%, 10%, and 10% of our total revenues.

As of December 31, 2024, four customers accounted for approximately 18%, 16%, 12%, and 10% of our accounts receivable balances.

For more information, see Note 15, “Segment, Geographical and Other Revenue Information” in the Notes to the Consolidated Financial Statements set forth in Item 8 of this Annual Report on Form 10-K.

For the year ended December 31, 2025, one customer accounted for approximately 51% of our total revenues.

As of December 31, 2025, three customers accounted for approximately 40%, 14% and 13% of our accounts receivable balances.

For more information, see Note 15, “Segment, Geographical and Other Revenue I nformation” in the Notes to the Consolidated Financial Statements set forth in Item 8 of this Annual Report on Form 10-K.

Our corporate headquarters are located in Redwood City, California and provide general administrative support to our business and are the center of our research, development and business operations.

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We also supply initial commercial quantities of biocatalysts for use by our collaborators to produce pharmaceutical intermediates and manufacture biocatalysts that we sell.

For the ECO Synthesis manufacturing platform, our ECO Synthesis Innovation Lab is located within our corporate headquarters and is designed to supply GLP-grade material in sufficient quantities to support customers’ preclinical development.

For the ECO Synthesis manufacturing platform, our ECO Synthesis Innovation Lab is located within our corporate headquarters and is designed to supply non-GMP-grade material in sufficient quantities to support customers’ preclinical development.

We expect to partner with one or more CDMOs for bulk GMP-grade siRNA production to supply customers’ clinical trials and beyond in the near term.

In September 2023, we announced that we had entered into an agreement for the assignment and assumption of lease for our San Carlos, California facility.

In the first quarter of 2021, we entered into an arrangement to lease this facility to serve as an additional office and research and development laboratory space which we occupied beginning December 20 21.

I n November 2025, we signed a lease for a GMP manufacturing facility in Hayward, California.

We are currently working on designs to retrofit this facility to manufacture RNAi therapeutics for our customers in quantities sufficient for Phase 1 and potentially Phase 2 clinical trials

As part of the restructuring of our business announced in July 2023, we consolidated operations to our Redwood City headquarters and discontinued investment in biotherapeutics.

In September 2023, we announced that we had entered into an agreement for the assignment and assumption of the lease for our San Carlos, California facility.

For additional information on the San Carlos facility, s ee Note 13, “Commitments and Contingencies” in the Notes to the Consolidated Financial Statements set forth in Item 8 of this Annual Report on Form 10-K.

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• FDA review and approval of the NDA or BLA prior to any commercial marketing, sale or distribution of the product.

Any products manufactured or distributed pursuant to FDA approvals are subject to pervasive and continuing regulation by the FDA, including, among other things, requirements relating to record-keeping, reporting of adverse experiences, periodic reporting, product sampling and distribution, and advertising and promotion of the product.

Drug and biologic manufacturers and other entities involved in the manufacture and distribution of approved drugs are required to register their establishments with the FDA and certain state agencies and are subject to periodic unannounced inspections by the FDA and certain state agencies for compliance with cGMPs and other laws and regulations.

Changes to the manufacturing process are strictly regulated, and, depending on the significance of the change, may require prior FDA approval before being implemented.

Accordingly, manufacturers must continue to expend time, money and effort in the area of production and quality control to maintain compliance with cGMPs and other aspects of regulatory compliance.

The FDA may withdraw or limit approval if compliance with regulatory requirements and standards is not maintained or if problems occur after the product reaches the market.

Later discovery of previously unknown problems with a product, including adverse events of unanticipated severity or frequency, or with manufacturing processes, or failure to comply with regulatory requirements, may result in restrictions on the marketing or manufacturing of the product, complete withdrawal of the product from the market or product recalls;

fines, warning letters, or untitled letters;

clinical holds on ongoing or planned clinical studies;

refusal of the FDA to approve pending applications or supplements to approved applications, or suspension or revocation of approvals;

product seizure or detention, or refusal to permit the import or export of products;

consent decrees, corporate integrity agreements, debarment or exclusion from federal healthcare programs;

mandated modification of promotional materials and labeling and the issuance of corrective information;

the issuance of safety alerts, Dear Healthcare Provider letters, press releases and other communications containing warnings or other safety information about the product;

or injunctions or the imposition of civil or criminal penalties.

Environmental, Health and Safety Regulations

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Our contracts with outside suppliers and vendors require compliance with applicable laws and regulations.

Data Privacy and Security Laws

Numerous state, federal and foreign laws, regulations and standards govern the collection, use, access to, confidentiality and security of health-related and other personal information, and could apply now or in the future to our operations or the operations of our partners.

In the United States, numerous federal and state laws and regulations, including data breach notification laws, health information privacy and security laws and consumer protection laws and regulations govern the collection, use, disclosure, and protection of health-related and other personal information.

In addition, certain foreign laws govern the privacy and security of personal data, including health-related data.

Privacy and security laws, regulations, and other obligations are constantly evolving, may conflict with each other to complicate compliance efforts, and can result in investigations, proceedings, or actions that lead to significant civil and/or criminal penalties and restrictions on data processing.

HUMAN CAPITAL RESOURCES

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Diversity, equity and inclusion

We are renewing our commitment to increase diversity and foster an inclusive work environment that supports our global workforce and the communities we serve.

We are proud of our commitment to diversity and foster an inclusive work environment that supports our global workforce and the communities we serve.

We recruit the best people for the job regardless of gender, ethnicity or other protected traits and it is our policy to not only comply with all laws applicable to discrimination in the workplace, but to promote a safe and equitable environment for all employees.

Our diversity, equity and inclusion principles are also reflected in our employee training and policies.

Our diversity, equity and inclusion policies are reviewed regularly and guided by our executive leadership team.

Our executive leadership team reviews these policies regularly.

Health and safety

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Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-K

Item 1. Business