Codexis, Inc. (CDXS): Business Model Canvas [Dec-2025 Updated]

You're trying to map out exactly how Codexis, Inc. is funding its aggressive pivot into next-gen therapeutics, especially with that new ECO Synthesis platform, so I've broken down their entire operation using the nine building blocks of the Business Model Canvas, grounded in their late 2025 reality. Honestly, seeing the structure makes it clear: they are balancing product sales-which saw a strong Q3 2025 gross margin of 64%-with massive R&D investment, like the $13.9 million spent in that quarter, all while securing major validation like the $37.8 million Supply Assurance Agreement with Merck. This isn't just about selling enzymes anymore; it's a strategic shift toward becoming a core manufacturing partner for RNA therapies, and you need to see the full picture of their resources, customers, and costs to truly gauge the near-term risk and upside. Dive in below to see the precise mechanics of this transition.

Codexis, Inc. (CDXS) - Canvas Business Model: Key Partnerships

You're looking at the core relationships Codexis, Inc. is building to pivot into a full-service manufacturing innovator, especially around its ECO Synthesis platform. These partnerships are the engine driving their expected revenue acceleration and cash runway extension through 2027.

The relationship with Merck & Co. is a cornerstone of the near-term financial outlook. Codexis signed a $37.8 million Supply Assurance Agreement in October 2025. Honestly, this non-dilutive cash infusion was a key factor in management's confidence to project 2025 revenue at or above the top end of guidance and extend the cash runway. To be fair, this isn't their first rodeo with Merck; they have a long-standing supply agreement for the sitagliptin enzyme, which was extended through December 31, 2026.

The agreement with Pfizer, while rooted in the supply of the enzyme CDX-616 for nirmatrelvir (PAXLOVID™) manufacturing, has evolved. The Q4 2024 results indicated that Pfizer applied the last portion of a retainer fee toward signing a new, longer-term agreement, setting up future revenue opportunities. Back in August 2022, Pfizer paid a $25.9 million fee, of which $23.3 million is creditable against future supply purchases under that existing Enzyme Supply Agreement.

Codexis is actively securing Contract Development and Manufacturing Organizations (CDMOs) to adopt and scale its proprietary ECO Synthesis® platform. A major step here was the October 2025 evaluation agreement with Nitto Denko Avecia, a CDMO specializing in oligonucleotide therapeutics, to explore using ECO Synthesis for therapeutic siRNA manufacturing. This follows earlier validation where 3 CDMOs, including Nitto Avecia, successfully replicated Codexis' ligation processes in their own facilities.

Securing internal GMP scale-up capability is critical for their transformation. Codexis announced in November 2025 that it signed a lease for a 34,000 square foot GMP manufacturing facility in Hayward, California. They expected to sign a dedicated GMP scale-up partner by the end of 2025 to support clinical and commercial siRNA production, complementing this new internal capacity. The company expects to begin facility modifications in early 2026.

The development of the ECO Synthesis platform, which replaces traditional solid-phase synthesis with an enzyme-catalyzed approach, relies on continuous innovation, which often involves external expertise. While specific 2025 financial figures for academic collaborations aren't public, the strategy involves leveraging their proprietary CodeEvolver® technology platform to discover and enhance novel, high-performance enzymes, a process that inherently involves deep scientific partnerships.

Here's a quick look at the key financial and operational anchors from these partnerships as of late 2025:

The strategic focus is clearly on leveraging these commercial relationships to support the ECO Synthesis transformation. Management signaled that restructuring efforts, combined with the Merck deal, are expected to extend the cash runway through 2027.

You can see the immediate impact of these external commitments through the following:

• Secured 11 revenue-generating contracts as of Q3 2025, with 40 more in the pipeline.
• Achieving pilot scale production of GLP-grade siRNA material using the ECO Synthesis Innovation Lab in 2025.
• The Merck revenue portion is expected to be recognized significantly in Q4 2025.
• The company expects to reduce its operational burn by approximately 25% following restructuring.

Codexis, Inc. (CDXS) - Canvas Business Model: Key Activities

You're looking at the core engine driving Codexis, Inc. right now, especially after the big strategic shift announced in November 2025. The Key Activities are centered on technology development and a pivot in commercial focus.

A primary activity is the engineering of high-performance enzymes using the proprietary CodeEvolver® platform. This platform is used to discover, develop, and enhance novel enzymes that solve real-world challenges in small molecule pharmaceuticals manufacturing and nucleic acid synthesis. This biocatalysis work helps engineer enzymes to run faster, at lower temperatures, with fewer by-products, and higher yields for drug R&D and commercial production.

The second major activity involves developing and commercializing the ECO Synthesis™ manufacturing platform. This platform is specifically aimed at enabling the scaled manufacture of RNAi therapeutics through an enzymatic route. Momentum here is clear: Codexis, Inc. secured its first revenue-generating contract for ECO Synthesis™ manufacturing services in March 2025. The company is transitioning from only offering initial enzyme parts to providing an integrated siRNA portfolio via this platform.

The third activity is the ongoing manufacturing and supplying of proprietary enzymes for Pharma Biocatalysis. This heritage business, which involves collaborating with pharma customers to insert an enzymatic stage or replace a chemical operation for clinical and commercial manufacturing, was the primary driver of Q2 2025 revenues. However, the strategy is shifting away from building this legacy enzyme business.

Investment in future capabilities is quantified by the recent spending on Research and development. For the third quarter of 2025, Codexis, Inc. spent $13.9 million on R&D, up from $11.5 million in the third quarter of 2024.

To align with the strategic shift, a significant operational activity was streamlining operations. This included a November 2025 workforce reduction of approximately 24% of its staff. This restructuring is expected to reduce the company's burn rate by approximately 25% and Codexis, Inc. expects to recognize an additional expense of approximately $3.5 million in the fourth quarter of 2025 related to this reduction.

Here's a quick look at the financial snapshot from the Q3 2025 results that underscore these operational activities:

The strategic focus on the ECO Synthesis platform is supported by recent commercial and financial milestones:

• Signed a Supply Assurance Agreement with Merck for $37.8 million.
• Organizational changes are expected to extend the cash runway through 2027.
• The company had well over 30 active engagements around ECO Synthesis as of August 2025.
• The first revenue-generating contract for ECO Synthesis was executed in March 2025.
• The company aims to achieve positive cash flow around the end of 2026.

Codexis, Inc. (CDXS) - Canvas Business Model: Key Resources

You're looking at the core assets Codexis, Inc. (CDXS) is relying on as it pivots its strategy, especially given the recent financial updates. Honestly, the resources here are heavily weighted toward intellectual property and the infrastructure to commercialize it.

The financial position, as of the end of the third quarter, gives a clear picture of the immediate liquidity available to fund operations before new cash infusions are fully realized.

The technology platforms represent the core intellectual property that underpins the value proposition. These are the engines for future revenue, especially in the oligonucleotide space.

• Proprietary CodeEvolver® technology platform: Used to discover, develop, and enhance novel, high-performance enzymes, driving faster reaction times.
• ECO Synthesis™ platform: A proprietary manufacturing technology designed for the scaled manufacture of RNAi therapeutics through an enzymatic route, which was featured in CBS News' Economy 4.0.
• Recent activity for ECO Synthesis™ included an evaluation agreement signed in October 2025 with Nitto Denko Avecia for therapeutic siRNA manufacturing.

The physical infrastructure commitment shows a clear intent to bring manufacturing in-house for key product lines. This is a tangible asset being secured for future scale.

The new facility lease is set for modifications to begin in early 2026. This multi-purpose facility is intended to expand internal capabilities for GMP manufacturing of siRNA and other oligonucleotides using the ECO Synthesis platform, and may also scale the manufacturing of high quality purified enzymes.

Regarding the talent, while specific headcount isn't public, the resource is defined by the output of the platforms and recent strategic actions. The company is relying on the expertise that developed the technology, even after recent organizational changes, including a new CEO in late 2025. The ability to secure a $37.8 million Supply Assurance Agreement with Merck in October 2025 demonstrates the perceived value of this specialized capability.

Finance: draft 13-week cash view by Friday.

Codexis, Inc. (CDXS) - Canvas Business Model: Value Propositions

Enabling greener, scalable RNA manufacturing via ECO Synthesis

• Codexis, Inc. is developing its proprietary ECO Synthesis® manufacturing platform to enable the scaled manufacture of RNAi therapeutics through an enzymatic route.
• The Company expected to sign a GMP scale-up partner by the end of 2025 to enable larger scale clinical and commercial siRNA production.
• In October 2025, Codexis, Inc. signed its second ECO Synthesis evaluation contract with a third party CDMO, Nitto Denko Avecia.
• As of August 2025, there were well over 30 opportunities at various stages of maturation for the ECO Synthesis platform.
• Six presentations featured the ECO Synthesis platform at the 2025 TIDES USA annual meeting in May 2025.

Delivering enzymes that outperform legacy methods in yield and quality

Codexis, Inc.'s unique enzymes can drive improvements such as higher yields, reduced energy usage and waste generation, and improved efficiency in manufacturing.

Improving efficiency and sustainability in small molecule pharma manufacturing

• Codexis, Inc. helps partners reduce waste, lower energy consumption, and minimize the use of hazardous chemicals.
• The shift in sales toward more profitable products contributed to the Q3 2025 Product Gross Margin of 64%.
• The Company's full fiscal year 2025 revenue guidance is in the range of $64 million to $68 million.

Providing precision-tuned enzyme solutions for molecular biology and diagnostics

• The CodeEvolver® platform enables tailored enzyme solutions with improved fidelity, enhanced selectivity, and increased activity.
• The Company is focused on expanding its pipeline of enzymes sold for clinical-stage drug candidates.

Enzymes currently used in manufacturing 16 commercially approved drugs

• As of December 31, 2024, Codexis, Inc. sold enzymes as biocatalysts to pharmaceutical manufacturers for 16 therapeutic drugs that were approved for commercial sales.
• These enzymes are sold at multi-kilograms to metric tons per annum scale for commercial requirements.
• The Company was also selling enzymes for 14 drug candidates in Phase 2 and Phase 3 clinical trials as of December 31, 2024.

The Merck Supply Assurance Agreement signed in October 2025 provides a $37.8 million non-dilutive cash infusion, expected by year-end 2025.

Organizational changes enacted in November 2025 included eliminating 46 positions (about 24% of the workforce) to reduce operating expenses by an expected 25%, extending the cash runway through 2027.

Codexis, Inc. (CDXS) - Canvas Business Model: Customer Relationships

You're looking at how Codexis, Inc. (CDXS) manages its key relationships as it pivots hard into oligonucleotide manufacturing. It's defintely a relationship-driven model, especially now.

Dedicated, long-term supply relationships with major pharma

The relationship with major pharmaceutical clients is being solidified through significant, non-dilutive cash infusions tied to future supply. For instance, in October 2025, Codexis signed a $37.8 million Supply Assurance Agreement with Merck. You should note that a substantial portion of this revenue is expected to be recognized in the fourth quarter of 2025, with the remainder in the first quarter of 2026. This type of agreement signals a deep, committed relationship beyond simple transactional sales.

High-touch, collaborative development services for custom enzymes

The move toward becoming a production solutions partner is centered on the ECO Synthesis platform. The level of engagement is high-touch, moving from initial evaluation to formal contracts. As of the second quarter of 2025, Codexis reported having well over 30 opportunities at various stages of maturation for this platform. By the third quarter of 2025, this had translated into 11 active revenue-generating contracts, with another 40 opportunities in the pipeline. One customer recently used their ligase technology to produce a 3-kilogram batch of siRNA, showing the progression from lab work to tangible production scale.

The nature of these relationships is best summarized by the current partnership metrics:

Strategic partnerships to co-develop and validate new platforms (e.g., ECO Synthesis)

Codexis, Inc. relies heavily on collaborations with Contract Development and Manufacturing Organizations (CDMOs) to validate and scale its technology. In October 2025, they signed an evaluation agreement with Nitto Denko Avecia, a CDMO specializing in oligonucleotide therapeutics, for the ECO Synthesis platform. This follows earlier validation where CDMO collaborators, including Bachem and ST Pharm, presented data on their successful use of Codexis' double-stranded RNA ligases to combine short RNA fragments.

Direct sales and technical support for product enzyme customers

The structure of customer support is undergoing a deliberate change. Management signaled the decision to reduce sales and marketing efforts in the small molecule biocatalysis segment. This means the direct sales focus is shifting away from legacy products toward servicing the newer, higher-margin ligase and ECO Synthesis engagements. The company expects to sign its first development contract for its ECO Synthesis manufacturing services in the first half of 2025, which requires a different level of technical support than simply supplying off-the-shelf enzymes.

Focus on evolving from a supplier to a production solutions partner

The entire relationship strategy is geared toward this evolution. The CEO stated the Merck agreement was a key piece for the transformation into a full-service manufacturing innovator in oligonucleotide manufacturing. The company is building its own GMP manufacturing capability, with plans to sign a GMP scale-up partner by the end of 2025 to support larger clinical and commercial production. This shift is reflected in the revenue mix, where product gross margin improved to 64% in Q3 2025, up from 61% in Q3 2024, largely due to a shift in sales toward more profitable products.

Codexis, Inc. (CDXS) - Canvas Business Model: Channels

Direct sales force targeting large global pharmaceutical companies

Codexis, Inc. delivered total revenues of $8.6 million for the third quarter of 2025, a decrease from $12.8 million in the third quarter of 2024. The trailing twelve months (TTM) revenue ending June 30, 2025, was approximately $57.2 million. Management reiterated the full fiscal year 2025 total revenue guidance in the range of $64 million to $68 million.

Direct supply of proprietary enzymes to manufacturing sites

The company is moving away from promoting its historical small molecule biocatalysis business due to pricing pressure on new prospective enzyme development contracts. The Pharma Biocatalysis business impacted Q2 2025 order volumes due to variability in customer manufacturing schedules and clinical trial progression. The ligase business saw the delivery of its first order to a large pharma customer in the first quarter of 2025.

Licensing agreements for the CodeEvolver® and ECO Synthesis platforms

A significant channel for non-dilutive cash infusion and platform commitment is the Supply Assurance Agreement signed with Merck in October 2025 for $37.8 million. Codexis expects to recognize a significant portion of this $37.8 million revenue in the fourth quarter of 2025, with the remainder recognized in the first quarter of 2026. The company also executed a licensing agreement in the second quarter of 2025.

Evaluation agreements with CDMOs for platform adoption

Codexis has well over 30 opportunities at various stages of maturation related to the ECO Synthesis platform. The company signed its second ECO Synthesis evaluation contract with a third party CDMO, Nitto Denko Avecia, in October 2025. In the second quarter of 2025, three leading CDMO collaborators featured the ECO Synthesis technology in their presentations at the TIDES USA annual meeting. The first revenue-generating contract for ECO Synthesis manufacturing services was secured in the first quarter of 2025.

Internal ECO Synthesis Innovation Lab for GLP-grade material production

The company is focused on achieving pilot scale production of GLP-grade siRNA material using the internal ECO Synthesis Innovation Lab during 2025. Codexis expects to sign a GMP scale-up partner by the end of 2025 to enable larger scale clinical and commercial siRNA production.

• R&D expenses for Q3 2025 were $13.9 million.
• SG&A expenses for Q3 2025 were $11.2 million.

Codexis, Inc. (CDXS) - Canvas Business Model: Customer Segments

You're looking at the customer base for Codexis, Inc. (CDXS) as they execute a major strategic pivot in late 2025. The focus has clearly shifted toward high-value, complex therapeutics manufacturing, especially oligonucleotides.

The customer segments are distinct, moving from broad enzyme supply to targeted, high-impact platform deployment. Here's the breakdown of who is driving the current and near-term revenue expectations, which management guided to be between $64 million to $68 million for the full fiscal year 2025.

Key Customer Segments

• Large global pharmaceutical companies (e.g., Merck, Pfizer)
• Contract Development and Manufacturing Organizations (CDMOs)
• Mid-tier pharmaceutical companies focused on small molecule therapeutics
• Companies in the molecular biology and diagnostic applications space
• Innovators developing RNAi therapeutics like siRNA

The financial activity shows where the immediate value is being captured. For instance, the third quarter of 2025 saw total revenues of $8.6 million, but the underlying strategic wins are more telling about the customer mix.

Customer Segment Deep Dive and Financial Linkages

The largest global pharmaceutical players are locking in future supply and technology access. This is a critical segment for validating the new platform.

The pivot toward oligonucleotide manufacturing is heavily reliant on innovators in the RNAi space and their manufacturing partners. Codexis, Inc. is actively building out its internal capacity to service this demand, which is a major capital commitment, but one they feel is supported by their current financial footing, extending their cash runway through 2027.

The pipeline of opportunities for the ECO Synthesis platform is substantial, showing strong market pull from these segments. Honestly, the Q3 revenue dip to $8.6 million is less concerning when you see the backlog building.

• Ongoing engagements around ECO Synthesis: well over 30 opportunities at various stages.
• Revenue-bearing contracts for the new platform: 11.
• Additional opportunities in the pipeline: approximately 40.
• Planned GMP scale-up partner signing: expected by the end of 2025.

The shift in product mix toward higher-margin offerings is evident in the gross margin figures. For Q3 2025, the product gross margin reached 64%, up from 61% in Q3 2024. This indicates that the customers driving the current revenue, particularly those utilizing the newer, more profitable enzyme solutions, are becoming a larger part of the business mix, even if overall revenue is lumpy due to customer manufacturing schedules.

Codexis, Inc. (CDXS) - Canvas Business Model: Cost Structure

You're looking at the expense side of the Codexis, Inc. equation for late 2025. It's a story of heavy investment in the future platform, even while making tough cuts to the current structure. The cost base reflects a company in transition, pivoting hard toward its next-generation technology.

The Research and Development (R&D) spend is definitely high, showing where the primary investment dollars are going. For the third quarter of 2025, R&D expenses hit $13.9 million, up from $11.5 million in the third quarter of 2024. The increase was primarily driven by higher headcount, higher lab supplies expense, and the internal reclassification of certain employees to the R&D function. This is the cost of powering the proprietary CodeEvolver® and ECO Synthesis™ platforms.

Personnel costs are a major component, even after significant adjustments. To be fair, Codexis enacted organizational changes in November 2025, eliminating 46 positions, which is approximately 24% of its workforce. They expect to recognize an additional expense of approximately $3.5 million in the fourth quarter of 2025 related to this. Still, the Q3 R&D increase suggests that the strategic R&D roles were retained or expanded, while other areas saw cuts.

The overhead, or Selling, General & Administrative (SG&A) expenses, shows some evidence of cost control following the restructuring. For Q3 2025, SG&A was $11.2 million, down from $13.6 million in Q3 2024. This decrease was primarily due to lower employee-related costs and legal expenses, plus reduced use of outside services. Honestly, managing this overhead while investing in R&D is a delicate balance right now.

The manufacturing side shows improving efficiency, which directly impacts the cost of goods sold. The Product gross margin for the third quarter of 2025 was 64%. This is an improvement over the 61% seen in Q3 2024, largely due to a strategic shift in sales toward more profitable products and away from less profitable, legacy products. You can see the trend in the margins:

Furthermore, you have to factor in the costs related to physical infrastructure supporting the pivot. Codexis announced the signing of a lease for a GMP Manufacturing Facility on November 10, 2025. While the specific operating and scaling costs aren't itemized in the immediate results, this move signals future capital and operating expenditures associated with scaling up their advanced manufacturing solutions for therapeutics.

Here is a snapshot comparing the major operating expense categories for Q3 2025 versus the prior year:

• Research and Development expenses (Q3 2025): $13.9 million
• Selling, General & Administrative expenses (Q3 2025): $11.2 million
• SG&A reduction year-over-year: $2.4 million ($13.6M in Q3 2024 vs $11.2M in Q3 2025)
• R&D increase year-over-year: $2.4 million ($11.5M in Q3 2024 vs $13.9M in Q3 2025)

Finance: draft 13-week cash view by Friday.

Codexis, Inc. (CDXS) - Canvas Business Model: Revenue Streams

You're looking at a business model for Codexis, Inc. (CDXS) where revenue streams are clearly segmented, showing a transition toward higher-margin, next-generation platforms, even as overall top-line figures fluctuate based on project timing. The company has reiterated its full-year expectations, which is a key anchor for your analysis.

The overall financial expectation for the year remains firm, despite quarterly variability:

• Total revenues guided to be between $64 million and $68 million for Fiscal Year (FY) 2025.

The revenue generated from the core enzyme business and new platform services is best understood by looking at the recent quarterly performance, which shows the impact of customer manufacturing schedules:

Specific revenue components contributing to the overall figure include the established enzyme sales, new service revenue, and upfront payments from partnerships. The shift in sales mix is also impacting profitability, as evidenced by the improving product gross margins:

• Product sales of high-performance enzymes for Pharma Biocatalysis: This segment saw increasing orders supporting late-phase and commercialized Active Pharmaceutical Ingredients (APIs) in Q2 2025.
• Development and service revenue from ECO Synthesis contracts: Codexis, Inc. secured its first revenue-generating contract for siRNA material manufacturing in March 2025, and later signed an evaluation agreement with Nitto Denko Avecia in October 2025.
• Licensing and milestone payments from platform technology agreements: Q1 2025 revenue included a $6.0 million recognition from an exclusive, global license agreement with Roche.
• Product gross margin for Q3 2025 was 64%, up from 45% in Q2 2024, reflecting a strategic shift toward more profitable products.

A significant, near-term, non-dilutive cash event is set to bolster liquidity and extend the operational runway:

• Non-dilutive cash infusion of $37.8 million from the Merck agreement: This Supply Assurance Agreement was signed in October 2025, with cash receipt anticipated by the end of 2025.