Title

Presentation

Codexis, Inc. misses on earnings expectations. Reported EPS is $-0.25 EPS, expectations were $-0.2.

Operator: Greetings and welcome to the Codexis First Quarter 2025 Earnings Conference Call and webcast. At this time, all participants are in a listen-only mode. [Operator Instructions] As a reminder, this conference is being recorded. It’s now my pleasure to turn the call over to your host, Carrie McKim, Director of Investor Relations. Carrie, please go ahead.

Carrie McKim: Thank you, operator. With me today are Dr. Stephen Dilly, Codexis’ Chairman and Chief Executive Officer; Georgia Erbez, Chief Financial Officer and Dr. Stefan Lutz, Senior Vice President of Research. During this call, management 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 the beliefs and expectations of management as of the statement date May 14, 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 Carrie and thanks everyone for joining. Before we begin our comments today, you’ll notice that Chief Operating Officer Kevin Norritt isn’t on this call. That’s because he’s busy at an on site visit with an important Codexis customer. But he will be available for follow up questions later this week and will also present during our Tides USA investor recap call next Thursday. Starting on Slide 2, we’ve delivered a first quarter largely in line with our expectations. Crucially, we preserved a strong financial position, maintaining our runway to cash flow positivity by the end of 2026. The Q1 revenue guidance we outlined in February included a $2.5 million one time payment from a Pharma Biocatalysis customer, which then shifted into April.

Had we received payment on the timeline originally communicated by our customer, we would have come in at the top of our Q1 range. That said, we’ve since received the order and we’re confident in reiterating our 2025 guidance and the current range of published analyst estimates. That confidence is underscored by the meaningful progress we’ve made across both core businesses so far in 2025, which sets us up for a substantial revenue ramp in the second half of the year. On slide 3 in Pharma Biocatalysis, our product mix is changing and we’re driving margin improvement. We also have a nice bench of new customers, particularly within the mid tier pharma segment. While drugs in phase 1 and 2 clinical trials aren’t significant revenue generators today, we’re positioning this business for a steady growth trajectory as some of those assets enter later stage trials and commercialization in the years to come.

Already this year we’ve also executed on several key commercial milestones with our ecosynthesis platform. In March, we signed our first revenue generating ECO Contract representing the inaugural project to enter our innovation map. Furthermore, our double-stranded RNA ligase business is growing. We delivered our first order to a large Pharma customer in Q1, with additional orders expected and we’ve secured an initial ligase order from a second drug innovator. We’re also very much looking forward to the TIDES meeting in San Diego next week. There will be at least six presentations showcasing the ECO platform and including three by Codexis and three by our collaborators. The presentations will cover a wide range of topics, including the intrinsic scalability and sustainability of the core ECO process and our emerging capability to fully control chirality, which can influence the biological activity specificity and potency of each molecule.

We’ll also be presenting on our groundbreaking machine learning capabilities for improved ligase selection and fragment design. Possibly the most validating event will be presentations from three of our CDMO collaborators describing the superior performance of our ligases in their hands. Stefan will share more on each of those presentations shortly and we plan to host a tight recap call for investors to dive into detail following the meeting. Moving to slide 4, many companies are finding the current macro environment to be a challenge. However, it’s become increasingly clear that several of these external factors could play in our favor and actually create a positive environment for our ecosystem platform.Let me tell you how. First, the siRNA field is evolving exactly as we’d hoped and planned for.

In March alone, there was a label expansion of Alnylam’s drug Vutrisiran to address ATTR amyloidosis with cardiomyopathy. And Sanofi and Alnylam’s Fitusiran became the seventh siRNA therapeutic to gain FDA approval. Eli Lilly also shared promising Phase II data on nepotisiran showing that the asset significantly reduced levels of a genetically inherited cardiovascular risk factor that impact nearly a quarter of the world’s population. This momentum clearly points to the coming demand for these RNA based therapeutics, particularly given the potential impact across both rare orphan and widespread disease indications. You’ve also probably seen recent pressure on companies to onshore their production. That’s good news for Codexis. Not only can our ecosynthesis technology offer the scalability and flexibility that customers need, but it also enables on shoring with greatly reduced capital expenditure and could be built out on an expedited timeline.

Taking things one step further, we’ve previously shared that we’re working to develop an enzymatic supply of raw materials for our ECO process. This would help customers diversify their source of input materials and it would reduce their dependence on uncertain foreign supply chains, particularly China. The big picture is coming together nicely for our ecosynthesis platform. Shifting to slide 5, let me recap the commercial landscape for ECO. Here you can see our three core customer segments Small siRNA Drug Innovators, Large siRNA drug innovators, and oligo CDMOs. While we have momentum across all three categories, particularly with our Ligase offering, we’re currently gaining the most traction with CDMOs. That’s because small drug innovators are interested in our technology but tend to be cash strapped.

Especially today, larger drug innovators are the opposite. They’re interested, but are largely focused on addressing a demand problem that’s two to three years away, meaning they can watch where the industry goes before making any decisions. CDMOs, on the other hand, are an ideal first mover for ecosynthesis. They know exactly how long it takes to ramp up capacity and they want to build out infrastructures today so they’re ready when customers come looking for siRNA manufacturing slots. They also generally have an existing network of customers that we can tap into to build new relationships. In fact, we’ve already been in situations where a CDMO collaborator has introduced us to their drug innovator clients who are looking for innovative siRNA manufacturing solutions.

Importantly, that dynamic benefits both Codexis and the CDMO as we’ll funnel our drug innovator customers to the CDMO as part of the commercial scale up process. The beauty of this model is it sets us up for a consistent flow of customers and we can provide them with a clear route to GMP grade material in the near term. It also gives us time to thoughtfully determine the best path forward for a potential Codexis GMP manufacturing facility. As we said in the past, executing on a market penetration strategy takes time. Fortunately, we know that from here on out, driving adoption of ecosynthesis is a matter of execution, not invention. We’ve already shown that we have the tools and the technical know how. Now it’s about taking a few finite steps to demonstrate to customers that we can develop a reproducible scalable process for their assets.

As it happens, that’s what our Tides USA presentations next week are all about. So let me pass it over to Stefan for a preview of what’s to come.

Stefan Lutz: Thanks Stephen. Moving to Slide 6. As Stephen mentioned, Codexis has an exciting lineup of presentations at the TIDES U.S. meeting next week. Last fall at TIDES Europe, we showcased technical validation demonstrating that we can use enzymes to successfully synthesize complete siRNA therapeutic assets, including the attachment of a tissue targeting moiety. Our upcoming presentations represent the next critical step, showing customers that our ecosynthesis processes can repeatedly create high quality siRNA products and reliably manufacture their assets at larger scale. Codexis oral presentation on the main stage will demonstrate the consistency and reproducibility of our enzymatic siRNA manufacturing process using inclisiran as an example.

Our data also showcases the quality of RNA fragments synthesized by the ECO platform and with it the possibility to simplify manufacturing processes. Finally, the talk will highlight impurity profiles and enzyme control, two crucial aspects of an effective GMP scale up process. We will also present a poster focusing on how we are improving the success rate of assembly of siRNA drug substance by ligation. Two months ago we launched a proprietary machine learning tool for the optimized pairing of our highly engineered ligases and RNA fragment designs. Already successfully deployed on multiple assets, the new tool shortens process development time and lowers the cost for our customers. As a bonus, three of our CDMO collaborators are presenting on the use of our ligases and to combine short RNA fragments.

This includes a joint presentation between Codexis and Bachem. At TIDES EU last November, we shared a ligase case study featuring work that we had done on behalf of Bachem. This time the ligations were performed by their team in house. Similarly, the other two CDMOs successfully tested our proprietary enzymes in their own facilities. This demonstrates that our process can easily be transferred and the benefits across yield, purification and impurity control can be replicated in our customers hands. Finally, our second oral presentation showcases continuous improvements and innovation around RNAI manufacturing by introducing a new feature currently under development for the ecosynthesis technology, the ability to stereo control during oligonucleotide synthesis.

RNAi therapeutic assets contain sulfur modifications in the phosphate backbone which helps to modulate the asset’s safety, stability and efficacy. However, the sulfur also adds extra complexity as it introduces chirality, creating mirror images of the oligonucleotide strands. In sharp contrast to existing chemical manufacturing solutions that have little control over this process and produce a mixture of mirror images, our enzymatic approach gives us a high degree of control over chirality. In turn, that ability gives our customers a choice to define the composition of the oligo products, potentially boosting their assets Therapeutic Potency and its market position. We plan to host a public investor conference call next Thursday, May 22nd at 8am Eastern to review these landmark presentations in more detail and share insights from the ground at TIDES.

Access details are already available on our investor website, so be sure to tune in. With that, I will now turn the call over to Georgia for a discussion of our financial results for the first quarter of 2025.

Georgia Erbez: Thanks, Stefan. Good afternoon everyone. Starting on slide 7, I will provide a brief overview of our financial results here on the call and will invite you to review our 10-Q filed today for a more detailed discussion. Total revenue for the first quarter ended March 31, 2025 was $7.5 million compared to $17.1 million in the first quarter of 2024. As you may recall, our Q1 revenue last year was higher than normal, largely due to two factors. First, we recognized $6 million in revenue related to a one time agreement with Roche for an exclusive global license to our double stranded DNA ligase. Second, we received 2 sizable customer orders that came in during Q1. Our strong first quarter last year was then followed by a lower revenue in Q2, again underscoring the variability of our clients ordering patterns.

Clearly, our revenue can be impacted by the unpredictability of large orders, as was the case with the $2.5 million pharma biocatalysis order that Stephen mentioned earlier. Here, a delay of a few weeks caused an unexpected change in our Q1 results. However, despite this lumpiness, the significant commercial interest we are seeing across our businesses reinforce our confidence that 2025 guidance range that we’ve set. Product gross margin was 55% for the first quarter of 2025. This was up from 49% in Q1 2024, largely due to the shifts in sales to more profitable products and declines in less profitable legacy products. Turning to operating expenses, research and development expenses for the first quarter of 2025 were $12.9 million compared to $11.2 million last year, largely driven by an increase in costs associated with salaries and employee costs and higher lab expenses.

Selling, General and Administrative expenses were $12.4 million compared to $12.9 million in the first quarter of 2024. The decrease was primarily due to lower legal fees and lower stock-based compensation expense. The net loss for the first quarter 2025 was $20.7 million compared to $11.5 million for the first quarter 2024. Finally, we are reiterating our 2025 guidance. As a reminder, we guided to a range of $64 million to $68 million for 2025, with revenue more heavily weighted towards the back half of this year. We are comfortable with the current consensus estimates for the second quarter. We ended the quarter in a strong cash position with $59.8 million in cash, cash equivalents and investments which we expect will be sufficient to fund our planned operations through achieving cash flow positivity by the end of 2026.

With that, I will now turn the call back over to Stephen.

Stephen Dilly: Thank you Georgia. Before I hand it over to Q&A, I want to briefly comment on why this all matters to customers. Looking at slide 8, you can see the enormous impact of ecosynthesis. Our modeling indicates that this technology enables five times bigger batches, is 50% faster and costs 70% less to stand up than phosphoramide chemistry. As more and more siRNA pipeline assets progress through clinical trials and require significant volumes of material, particularly for larger disease indications, these impacts become incredibly meaningful to customers and in many cases without a technology like ecosynthesis, the scale and CapEx limitations will prohibit drug innovators from going after certain disease areas at all.

The cherry on the top is that we can do certain things that aren’t feasible with phosphoramadite chemistry, such as controlling chirality at scale. Between three CDMOs asking to use our logo in their TIDES presentations next week. External tailwinds towards onshoring production and supply chain dynamics playing in our favor we’re in a very different place than we were at this time last year. We believe the market is realizing how our technology will act as an essential enabler of this emerging therapeutic class and it’s why the future for Codexis is very bright. Now, we’d be happy to take your questions. Operator?

Operator: Thank you. [Operator Instructions] Our first question today is coming from Kristen Kluska from Cantor Fitzgerald. Your line is now live.

Kristen Kluska: Hi, good afternoon, everyone. Thanks for taking the questions. And it was very nice to see a pretty sizable deal in the siRNA development candidates earlier this morning as well. Just wanted to ask a question about how you think about the three core customer segments. Understand CDMOS might be the ones that are willing to take the leaps a little bit earlier, but what do you think it’s really going to take to get the small and large siRNA drug innovators to want to be interested more on the earlier side of preparation?

Stephen Dilly: Well, thanks for the question. Yes, we noticed the big deal this morning as well, and that was in our constellation of conversations as well. So the beautiful thing about the CDMOS is their reach, right? They’re having to think forward, they’re having to plan. They’ve got multiple customers. And one of the things that we’ve noticed is it’s a very much easier conversation for a CDMO to talk to an existing customer. They’re supplying a molecule to and say, hey, we’ve got this better process. And they’re a trusted partner and there’s just a lower barrier to acceptance to that. However, all of this is what we keep now saying is block and tackling. Once we’ve done the first and the second and the third of these molecules successfully, then the barrier to entry will be that much lower.

There’ll be the validation. What do we have to show? We have to show that we move from mathematical modeling to really demonstrating the performance of scale. We have to show that our production time is shorter because that is incredibly important to people. And that’s all related to the efficiency of the cycling of the enzyme. We have to actually demonstrate that you can stand up a GMP facility quicker and way cheaper than you could with an alternative technology. It’s that kind of stuff. And then it’s the thing around the reproducibility of the impurity profile, demonstrating that our stuff acts in biological systems just the same as the chemically synthesized version. It’s all of that kind of thing that we’re doing this year. As I said in my sort of pre prepared comments, it’s great that it’s execution now.

We’re not having to invent anything to get people over the hump. It’s just show me, show me, show me.

Operator: Thank you. Our next question is coming from Tycho Peterson from Jefferies. Your line is now live.

Tycho Peterson: Hey, thanks. Just wondering if you could talk a little more on the second half ramp and maybe, how much of that is coming from new products order activity and maybe a little bit more color on the pharma pipeline for the RNA ligase orders would be helpful to.

Georgia Erbez: Sure. We do expect that the ramp is going to be because of these new contracts with ecosynthesis. So that’s why we’ve always said more towards the back half and just looking at the timelines that it takes to negotiate these deals. So yes, the growth will be coming from that segment.

Operator: Thank you. Next question is coming from Allison Bratzel from Piper Sandler. Your line is now live.

Allison Bratzel: Hey team, good afternoon and thanks for taking the question. Could you just walk us through the assumptions on that year end 2026 cash flow positivity guidance and just, if there’s any scenarios, development, partnerships, things like that that could pull it forward or conversely if investment in an internal GMP facility could push that out and just, you know, related to that, when is the right time to make the investment in a Conexis GMP facility? Would just be great to get your current thinking on that. Thanks.

Stephen Dilly: So let’s lay out the guardrails really clearly. So we are projecting flipping to cash flow positive end of 2026 and that’s based on organic evolution of the pipeline that we’ve got. And the revenue ramp that we’re projecting, it does not include the GMP facility. The GMP facility is seen as an accelerator of really getting to major revenues, but that would be funded out with a current means so that one way or another we need to finance that. It’s not a massive spend. And I’ll let Georgia go into as much detail as she wants to on that.

Georgia Erbez: Sure. When we’re looking at the spend on that, it’s broken both into the capital side and the operating side. But both of those, the capital side is really more weighted much more heavily towards 2026. So we’re spending a little bit this year on that, but not a whole lot. And then the operating side of that will even come a little bit later than that. So more towards the end of 2026 and into 2027, so we’re looking at more like 18 months to two years to have this be, a fully operational type of facility once you get the equipment in and then you get it validated. So when we’re looking at financing a project like that, we’re looking at doing it in stages and in small increments along the way. So we’re not looking to fund it all up front.

Stephen Dilly: Right. And we want to be. If and when we’re funding it, we want to be doing that based on a flow of orders that we can show people so that when we build it, they will come. And, one of the obvious sort of things is now we’ve got three CDMOs as well as us talking about our Ligase platform. That’s really important in terms of, of the ramp there. Now we’ve started to get orders in, in terms of programs in the Innovation Lab. That gives us a line of sight to when people are going to be needing GMP material and allows us to plan accordingly. So we’re trying to build just in time here and not too far ahead of the curve.

Allison Bratzel: Got it. Thank.

Operator: Thank you. [Operator Instructions] Our next question is coming from Dan Arias from Stifel. Your line is now live.

Dan Arias: Hi, guys. Thanks for the questions here. Maybe just on the orders that you have in hand for the Ligase, the large farm and then the other innovator. Can you share anything in terms of how much you’re providing to them and then what is the way in which we should think about them becoming steady customers? I guess first is your expectation that they would become a repeat customer. And then what, if anything, are sort of the stipulations that are tied to subsequent orders.

Stephen Dilly: We absolutely expect each of those to become repeat customers and steady orders. One of the important things is the phase of the medicines that they’re supporting. They tend to be moving into significant bulk now from sort of phase 2 to phase 3. Three is the time of adoption, because that’s really when people need to optimize their process. The beautiful thing about that is it’s a shorter timeline than we’ve traditionally seen with pharma manufacturing, where people have been adopting our enzymes even preclinically. And yet in the old days, it was taking us 7 to 10 years to get to peak. This is more like 3 to 5 to get to peak. And I think the cadence of our first order is interesting. We supply this year, we’ll probably get the second order either at the end of this year or early next and so on, as they scale and they ramp and they increase batch size.

And similarly, we’re talking about starting off with grams or tens of grams, then moving to 50 grams or 100 grams and then at steady state, several hundred grams sort of annually to support a modest size siRNA product. So these look very good in comparison to our traditional pharma manufacturing enzymes.

Dan Arias: Okay, thank you.

Operator: Thank you. Next question today is coming from Matt Hewitt from Craig-Hallum. Your line is now live.

Matthew Hewitt: Good afternoon. Thanks for taking the questions. Maybe first up with the three different CDMO collaborators that are presenting at TIDES. And I think you touched on this a little bit. But is the key there that they’re each bringing different customers to the table with you, or is there more to it that maybe one or the other have different skill sets or different areas of focus? I’m just curious, what is there a key with the three different collaborators?

Stephen Dilly: Matt, it’s kind of all of the above. So first of all, it’s that there are three different CDMOs, all of whom have had success with our ligase in their hands. One of them back end, which we’ve been public about, we’ve been working with them sort of, we’ve done the experiment in house, we’ve shown them, we’ve kind of coached them all the rest of it. The other two, we didn’t have that kind of relationship. They picked it up, they did it themselves and they were successful. And so that really says a lot about the transferability of our technology into other people’s hands without massive sort of training and coaching. And each one of those is building a ligation platform to service multiple customers. So it’s us currently one to three and then those three to many. And so this is how we can actually make a scalable platform for the ligation technology. So we’re super excited about that.

Matthew Hewitt: Makes sense. And one follow up here. You’ve done a good job filling out your team here in the first quarter. Are there any other roles that you would like to maybe add before the end of the year? Or do you feel like you’ve got the right team in place at this point? Thank you.

Stephen Dilly: Teams coming together really, really nicely. We’ve got the vast majority of folks in place for the next phase, both at the executive level and the VP level. We continue to evolve our focus. We’ve moved from being a research organization to becoming now a development organization and a development commercialization organization. A lot of the sort of increased effort is in process scale up, process development, that kind of science. Well, we need to add a little bit more expertise, but we’re in good shape and we’re overall looking at keeping our headcount about flat this year while we do more. We’re driving efficiency constantly and yes, we think that’s the right thing to do.

Matthew Hewitt: Got it. All right, thank you.

Operator: Thank you. Next question today is coming from Brendan Smith with TD Cowen. Your line is now live.

Brendan Smith: Great. Thanks for taking the questions, guys, and congrats on progress. I actually wanted to ask if you could expound a bit more on the machine learning capabilities that you mentioned, maybe just without getting ahead of the TIDE meeting too much. Just wondering how widely you’re expecting to integrate some of these capabilities or which areas of the business you see as especially ripe for that kind of tech and maybe what you think that could potentially mean for operating burn moving forward.

Stephen Dilly: Yes, great question. So, one of the things that we say at Codexis is, we really are the OGs in terms of machine learning and artificial intelligence. We’ve been doing it since before it was called that. But what we’ve learned is it’s really, really good if it’s applied to tractable problems. And the ligase is a beautiful example of that. What we learned with ligation is that there are a finite set of variables that define the performance of the enzyme that were actually of a complexity scale that you could address them with a machine learning algorithm. And the challenge here is to identify the ideal enzyme from a large library for a specific nick in a specific molecule to do the ligation as close to perfectly as we can.

And what you will be seeing at TIDES next week is evidence that we’re not just talking about it. It actually works. And that’s kind of cool because that was from Ideation to launch in a year or less, which is in this industry. That’s pretty cool. Then what we’re looking at is the application of broadly data science and artificial intelligence to our core technology as well to making our core code evolver technology better. And Stefan, do you want to talk about that?

Stefan Lutz: Yes. Machine learning is on everybody’s mind these days. Codexis, as Stephen pointed out, has been leveraging these tools very effectively for, gosh, close to two decades now. And there’s by no means we’re not done, in fact, expanding this beyond just the enzyme engineering, thinking about opportunities on the manufacturing side of things is highly attractive and will help us to further build out a differentiated product offering for our customers.

Stephen Dilly: So let’s just drill down for a couple of things there. One of them is in the enzyme engineering. It’s predicting the impact of different mutations and then having the ability to check that experimentally and move faster and evolve faster in the process stuff the manufacturing, it’s about looking for trends and things that are defining those trends and driving the efficiency of the process. And so we think that can accelerate our optimization of the process for each individual siRNA molecule. So yes, very much an area of focus, but grounded in real experiments and real science.

Stefan Lutz: And it might also be worth pointing out that this machine learning, like the one that we are deploying now for ligation reaction, it’s not just working in our hands. We’ve actually started, as was mentioned in the recording, we’ve deployed this on customer assets and our partners, our collaborators have tested it in their hands and it controls consistently has performed exceptionally well, which causes reason for good lots of enthusiasm.

Brendan Smith: Got it. Sounds great. Thanks guys.

Operator: Thank you. We reached the end of our question-and-answer session. I’d like to turn the floor back over for any further closing comments.

Stephen Dilly: Well, thank you again for joining us today. As you heard, we’re slated for an exciting Tides USA next week. So don’t forget, if you can’t go to the meeting to tune into our investor recap, call at 8am Eastern Time next Thursday, May 22nd to hear all the updates coming out of that meeting. Operator?

Operator: Thank you. That does conclude today’s teleconference and webcast. You may disconnect your lines at this time and have a wonderful day. We thank you for your participation today.