Codexis, Inc. (NASDAQ:CDXS) Q3 2025 Earnings Call Transcript

Codexis, Inc. (NASDAQ:CDXS) Q3 2025 Earnings Call Transcript November 7, 2025

Operator: Greetings, and welcome to the Codexis Third Quarter 2025 Earnings Conference Call. [Operator Instructions] Please note that this conference is being recorded. I will now turn the conference over to your host, Georgia Erbez, Chief Financial Officer. Thank you. You may begin.

Georgia Erbez: Thank you, operator. With me today are Dr. Stephen Dilly, CEO and Chairman; Dr. Alison Moore, Chief Technical Officer; and Britton Jimenez, Senior Vice President, Sales and Marketing, who will be available for Q&A to follow. During this call, we will be making a number of forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, including our guidance for 2025 revenue, anticipated milestones, including product launches, pilot scale manufacturing and paths to scale up technical milestones and public announcements related thereto as well as our strategies and prospects for revenue growth, path to profitability and successful execution of current and future programs and partnerships.

To the extent that statements contained in this call are not descriptions of historical facts regarding Codexis, they are forward-looking statements reflecting our beliefs and expectations as of the statement date, November 6, 2025. You should not place undue reliance on these forward-looking statements because they involve known and unknown risks, uncertainties and other factors that are, in some cases, beyond Codexis’ control and that could materially affect actual results. Additional information about factors that could materially affect actual results can be found in Codexis’ filings with the Securities and Exchange Commission. Codexis expressly disclaims any intent or obligation to update these forward-looking statements, except as required by law.

And now I’ll turn the call over to Stephen.

Stephen Dilly: Thank you, Georgia, and thanks, everyone, for joining. We’ve had a very exciting and important few months that have set us up extremely well for the changes we’re announcing today. First, we were very pleased to sign the supply assurance agreement with Merck. We’ve been working on this for months, and it was a key reason why we had the confidence in our revenue projections for the year. More importantly, it was one of the final pieces of the jigsaw we needed to fall into place for us to be ready to commit to the transformation of Codexis into a full-service manufacturing innovator in the field of oligonucleotide manufacturing. We also expect to sign the lease for our new facility in the next week or 2, which will give us the capability to manufacture GMP-grade siRNA in kilogram quantities using our ECO Synthesis technologies.

We are really excited by the commercial trajectory of the ECO platform. This time last year, we were closing in on our first revenue-bearing contract. Today, we have 11 with 40 more in the pipeline. Finally, the technical team has continued to make spectacular progress on perfecting and scaling the ECO platform, and we will be presenting new data at TIDES EU next week. So in summary, we have the financial resources, the real estate, the expertise and the demand lined up to move Codexis into the next phase of our transition. On a personal note, this completes the task I came here to do as CEO. Over the past 3 years, in an effort expertly led by Kevin Norrett, we’ve conducted a thorough assessment of the most attractive markets that can be accessed using our CodeEvolver technology.

About 2 years ago, we got very excited about the enzymatic synthesis of siRNA, an endeavor that led to the ECO Synthesis platform you see today. Now that we are confident in the market and the potential of the platform, the time is right to optimize and streamline the organization to maximize our ability to succeed. Evolving from an enzyme supplier to an innovative manufacturing solutions provider allows us to streamline our existing organization. This will significantly reduce our cost base while improving our responsiveness and nimbleness and allowing us to build further for the future. We’ve looked to optimize every level of the organization. With that in mind, I’m extremely excited that Alison Moore, our Chief Technical Officer, will succeed me as CEO.

I intend to remain with Codexis as Executive Chair. There’s a saying that successful CDMOs are run by leaders with deep technical expertise. Alison is a great leader and has deep experience and expertise in perfecting and scaling novel manufacturing platforms. Similarly, Kevin has handed over the commercial reins to Britton Jimenez, a domain expert in commercial leadership of CDMOs. Britton is here on the call to answer your commercial questions. With that, I’m going to hand over to Alison.

Alison Moore: Thank you, Stephen. I’ve been part of Codexis for the last 5 years, first as Board member and then as member of executive leadership. I’ve had the pleasure of seeing Codexis evolve into an innovation leader in oligonucleotide manufacturing. Our technology has the potential to truly enable the delivery of a breadth of siRNA therapeutic opportunities to all patient populations. And I’m excited to have the opportunity to lead the company in executing on this important goal. I spent 20 years at Amgen in different operations roles, including process development, manufacturing and supply chain management. I’m very familiar with the complexities and challenges of deploying new technologies to the manufacturing space. In addition, I also have experienced the challenges of developing and scaling genomic medicines from my time at Allogene, where I spent 5 years leading their efforts to industrialize and scale CAR-T cells.

Across modalities and in various therapeutic areas, I have been fortunate enough to have been part of bringing several advanced medicines, some of which are billion-dollar drugs to hundreds of thousands or even millions of patients. We know we’re in the right area with the right technology that has the potential to expand the use of siRNA, a really important emerging class of drugs. We have streamlined our organization to focus on what we excel at, ECO Synthesis, both manufacturing and providing production technologies to our customers. It’s exciting to see Codexis evolve from an enzyme supplier to a production solutions partner. For example, recently, one of our customers has used our ligase to produce a 3-kilogram batch of siRNA. Our organization is now aligned to deliver services and products to all our customers.

I want to emphasize that our heritage small molecule biocatalysis business remains a crucial part of Codexis. We have a long history of delivering enzymes on time and in full to our customers, and we intend to continue this performance. As important as execution will be in the next few years, continuing to fill our pipeline is equally as important. Our sales force has been reconfigured under Britton’s leadership to expand our customer base further into the oligonucleotide therapeutics market. We have the resources, both operationally and financially to execute on this plan. With that, I’ll turn the call over to Georgia, who can describe our current financial performance and give you a glimpse of what to expect going forward. Georgia?

Georgia Erbez: Thanks, Alison. Good afternoon, everyone. We announced many important events at the company today, but they are all connected to give Codexis the best chance to succeed. We’ve been working on the Merck agreement for months. And while the timing was uncertain, we were confident it would happen this year. The agreement gives us a vital infusion of nondilutive cash that allows us to execute on our business plans that also include building out the GMP facility. We will recognize a significant portion of the revenue from the Merck contract in the fourth quarter with the rest recognized in the first quarter of 2026. While finalizing the division between the 2 quarters is still in process, we can confirm that we will make or slightly exceed the top end of our guidance range for 2025.

Part of repositioning Codexis envisions altering our priorities. We are moving away from promoting our historical small molecule biocatalysis business. The market dynamics in this business segment have changed over the last 3 years. We see pricing pressure on new prospective enzyme development contracts. A dollar spent in winning new business and developing the enzyme does not produce the same return as it did 5 years ago. We have made the decision to reduce our sales and marketing efforts in this segment and refocus our efforts on new business in the ligase and ECO Synthesis business lines. However, we have a long and successful history of supplying our customers, and this remains of vital importance to Codexis going forward. We may experience a drop in service revenue next year from our historical business, but this will be replaced by development services in the ligase and ECO areas.

We still expect our historical business to grow for the next 5 to 10 years. Because of the work we’ve done in the past, there are 14 drugs using our enzymes in Phase III clinical trials, many of which will have data readouts in the next 12 months. With a modest success rate, we expect to fuel growth in our existing pipeline of products that will require little to no additional investment from us, which should allow us to maintain favorable margins. Revenue is half the equation. And during the last few months, we’ve examined our spend across all areas of the company. We made the hard decision to reduce our headcount across every group, including reducing the size of our research and commercial groups to reflect the shift in strategy away from building the heritage enzyme business.

We are still working through our financials for 2026, and we’ll give more specific guidance after the first of the year, but we expect this restructuring will reduce our burn by approximately 25%. Together with the cash received from Merck agreement, we are able to extend our runway through 2027. We have a number of projects similar to the Merck agreement in our line of sight, and we’ll keep you informed as those discussions mature, and we understand the nature of those transactions and their size and timing. Starting on Slide 6, I will provide a brief overview of our financial results here on the call and invite you to review our 10-Q filed today for a more detailed discussion. Total revenues were $8.6 million for the third quarter of 2025 compared to $12.8 million in the third quarter of 2024.

The decrease was primarily due to variability in customers’ manufacturing schedules and clinical trial progression. Product gross margin was 64% for the third quarter of 2025 compared to 61% in the third quarter of 2024. The increase in gross margin was largely due to a shift in sales towards more profitable products and declines in less profitable legacy products. Research and development expenses for the third quarter of 2025 were $13.9 million compared to $11.5 million in the third quarter of 2024. The increase was primarily driven by higher headcount, higher lab supply expense and internal reclassification of certain employees to the research and development function. Selling, general and administrative expenses for the third quarter of 2025 were $11.2 million compared to $13.6 million in the third quarter of 2024.

The decrease was primarily due to lower employee-related costs and legal expenses and reduced use of outside services. The net loss for the third quarter of 2025 was $19.6 million or $0.22 per share compared to a net loss of $20.6 million or $0.29 per share for the third quarter of 2024. We ended the third quarter in a strong cash position with $58.7 million in cash, cash equivalents and investments. As a reminder, this number does not include any funds from the Merck agreement. As I mentioned earlier, together with the new infusion of cash, which we expect to receive in the fourth quarter, our cash will be sufficient to fund our planned operations through the end of 2027. With that, we’d be happy to take your questions. Operator?

Q&A Session

Operator: [Operator Instructions] And our first question comes from Kristen Kluska with Cantor Fitzgerald.

Kristen Kluska: I just want to wish everybody on the management team all the best during this transition. Those of you that are stepping down or leaving, you were a very instrumental part of this transition. So congratulations on that. First question for me is just if you could speak about this transition and if it’s going to impact some of the plans you laid out on the last call, namely the partnership strategy you might like to take for potential partners starting with as many early programs as possible to create more shots on goal as well as plans to have a GMP scale-up partner signed?

Stephen Dilly: So thanks, Kristen, and I’m still here. It doesn’t change our plan one jot. And we’re really very, very encouraged with what we’ve done. You’ve seen Nitto coming across the line with the start of a scaling partnership there. We’ve talked before about others who are still in the hopper. We are continuing to land those early phase contracts. And I mentioned that we’ve moved from 1 to 11. Many of those are sort of what we consider having big fish in waiting where we are starting small, proving that the technology can support the molecule and then growing with the product. And the other thing I’d like you to note from the prepared remarks is — the comment that our ligase has now been used in a production run of a 3-kilo batch. So we think things are developing in a very, very promising way.

Kristen Kluska: And as we think about some of these early partners, including this ligase example you ran, I guess, how much are you able to talk or utilize some of these initial findings to think about future partner conversations? Obviously, I can respect there’s confidentiality agreements between these companies, but a lot of these early partners are going to be instrumental in some of the discoveries and seeing what this engine can do that can potentially influence more discussions in the future.

Alison Moore: This is Alison. I’ll take a shot at that one. I think that, yes, our platform is proving itself as we speak with larger numbers of customers. Those customers seem to be so far, very pleased with the product that we’re making with every customer, since customers come to us with unique requests and unique sequences, we are understanding better and better how our platform performs at baseline and how it can flex and be adaptable to what our customers need. So we’re really, really happy with the trajectory right now, very excited to progress in 2026, hopefully, into larger co-development development type relationships.

Stephen Dilly: And one of the things that we’re doing is maintaining our optionality in terms of what we can provide to the customer out of our own facilities. So there are essentially 3 things. There’s — the scaling the ligase at ISO quality standards, so we can be in clinical and even commercial products. Then making the core enzymes and reagents for customers that are going to end up doing this themselves and essentially giving us a royalty of the final product. And then there’s the capability of making siRNA in our own facility. And the beautiful thing about the place we’re just about to sign Alison, can do all of those things in a very modular way. So we’re well set whichever way the market moves.

Operator: Your next question comes from Matt Hewitt with Craig-Hallum Capital Group.

Tollef Kohrman: This is Tollef Kohrman for Matt Hewitt. Can you please describe the unique capabilities or advantages Nitto brings to its evaluation agreement that Proton doesn’t currently offer, particularly in terms of scalability, manufacturing expertise or technology integration?

Britton Jimenez: Yes. No problem. This is Britton here. Yes, Nitto is a great partner, and we’re very excited about the agreement that we have in place with them. And as you know, if you look at back at Nitto Avecia, they’re one of the market leaders in the CDMO marketplace. And they’re going to be able to help us scale our technology into the larger batch sizes that are going to be needed in the Phase II, Phase III and commercial production. So it’s one of the pieces in our strategy that we’ve been working on that we’ve been discussing over the past year, and we’re going to continue to push forward with Nitto Avecia and others in the marketplace that can continue to support our strategy.

Operator: [Operator Instructions] Your next question comes from Chad Wiatrowski with TD Cowen.

Chad Wiatrowski: Just want to dig on — you mentioned 11 revenue-generating contracts in hand today. Could you speak a little bit about the contribution of that siRNA revenue in the product revenue segment? And I know you haven’t guided to 2026, but can we expect that to help offset some of the decline in maybe the legacy small molecule biocatalyst sales? Or will it not quite offset fully the strategic refocus?

Georgia Erbez: Yes. So the contracts that we have right now are all in the service area. They’re not in the product area. So that’s where you’ll see these new contracts come into the financials. And it is — we do expect the service revenue to be relatively consistent from year-to-year. It’s just the — where we’re getting it is shifting. And we have expected this shift for quite some time.

Chad Wiatrowski: Got it. And then anything you want to highlight just with TIDES EU coming up next week. What can we expect to see out of those presentations? And how impactful could that be for the commercial progress?

Alison Moore: Yes. So we’re really excited about TIDES next week. What we promised we would talk about was how is our technology scaling — and we’ve been basically working all year on that, and we’re really proud to show our data around the performance of our platform at scale. In addition, when we talked with the FDA earlier this year about our platform, they were particularly interested in our ability to be able to analyze product during the production process, so having an in-process control. And we will also have a presentation about the opportunity of in-process analytics using the ECO Synthesis platform. So we think that both of these presentations are first-in-class presentations for the siRNA therapeutic developers and that particular market in general.

Operator: And ladies and gentlemen, there are no further questions at this time. So I’ll hand the floor back to Alison Moore for closing remarks.

Alison Moore: Thank you, everybody. Thanks for calling in today. We have a lot more to talk about with respect to our excitement related to ECO Synthesis. I will have a lot more to say going forward. I am so excited to have the privilege of my new role. And thank you for listening in today.

Operator: Thank you. And with that, we conclude today’s conference call. All parties may now disconnect. Have a good day.