Good morning, everyone, and welcome everyone to the Prelude Therapeutics Investor Conference Call. Today's call is being recorded and is expected to last up to 45 minutes. At this time, I will now turn the call over to Prelude's Chief Financial Officer and Chief Legal Officer, Bryant Lim. Please go ahead.

Thank you, Operator. During today's call, we will make forward-looking statements based on current expectations, including statements concerning anticipated discovery, preclinical, and future clinical development activities for our product candidates, the potential safety, efficacy, benefits, and addressable market for our product candidates, and clinical trial results for our product candidates, together with other statements regarding our plans, prospects, and expectations. such statements represent our judgments as of today are not promises or guarantees and as you know may involve risks and uncertainties that may cause actual results to differ from the results discussed in the forward-looking statements please refer to our filings with the sec which are available through the investor relations section of our website for information concerning risk factors that may affect the company we undertake no obligation to update forward-looking statements, except as required by law. During this call, we will also be referring to certain slides from our corporate presentation that are available on the Investors section of our corporate website under Presentations and Events. Also on this call are Chris Vati, Prelude's Founder and Chief Executive Officer, as well as Peggy Shirley, our Chief Scientific Officer, and Sean Bruschi, our Chief Business Officer. I will now turn the call over to Chris to kick things off.

Thank you, Bryant, and good morning to everyone joining us today. Over the past quarter, we've made a series of strategic decisions designed to sharpen our R&D

focus, optimize our capital allocation, and align our business strategy with programs that we believe offer the highest probability of success. These steps strengthen our ability to deliver on our mission, to discover and develop transformative medicines that can meaningfully improve patient outcomes in cancer. Importantly, as part of these efforts, we've also enhanced our financial position, providing us with additional cash runway to advance our lead programs into clinical development. Looking ahead, our primary focus will be on rapidly advancing two development candidates that we believe represent compelling opportunities for our investors with both programs expected to enter the clinic in 2026. The first is a JAK2V617F selective inhibitor for myeloproliferative neoplasms, or NPNs. The second is a CAT6A selective degrader for ER-positive breast kits. Both of these programs target clinically validated pathways and have the potential to demonstrate efficacy and safety differentiation in early clinical development. In addition, we believe that these molecules significantly expand the clinical options over currently available treatments for cancers we are targeting. Meanwhile, our discovery team made significant progress in advancing next-generation ADCs called Degrader Antibody Conjugates, or DACs. Our early stage DAC program, targeting mutant caldeticulin, or MKLR, which is a very promising target in MPN, shows potential to drive deeper clinical and molecular responses in our preclinical studies. We look forward to presenting additional data from this program at the American Society of Hematology,

at our ASH meeting, annual meeting in December.

I'll begin this morning with an overview of our JAK2V617F selective inhibitor program, which will also be featured as an oral presentation at the upcoming ASH. Given that the content of our oral presentation is embargoed until ASH, I will limit my remarks to our approach and the opportunity we see targeting this mutation as a potential disease-modifying approach for a large subset of MDM patients. Peggy will then review the CAPS-6A selective degrader program with our lead candidate poised to enter the clinic in 2026. Our chief business officer, Sean Bruschi, will then provide an overview of the exclusive option agreement with Insight for the JAK program that we announced last week and future plans for our DAC program. And I'll return for closing comments before opening up the call for your questions. Let me draw your attention to the JAK-STAT pathway on slide seven alpha copper deck. One of the JAK enzymes called JAK2 plays a key role in a normal hematopoiesis by mediating growth factor signaling. These growth factors include erythropoietin for red blood cell production, thrombopoietin for platelet production, and GM-CSF for white blood cell production. In MPNs, an activating mutation in JAK2, called JAK2V617F, results in an unchecked activation of JAK-STAT signaling and hyperproliferation of myeloid and erythroid cells and platelets, which can lead to multiple forms of MPN, including polycythemia vera, or PV, D, essential thrombocytemia, or ET, and then even a more serious condition known as myelofibrosis or MS. Currently approved JAK2 inhibitors inhibit normal and mutant JAK2 similarly. This lack of selectivity results in inhibiting normal and abnormal bone marrow function equally and to a very narrow therapeutic window. Ruxolitinib, or JAKOFI, is the first approved JAK2 inhibitor for NPM. As the first targeted therapy to be approved for MF and the only JAK2 inhibitor approved for PV, Ruxolitinib has been absolutely transformative for many patients. It should be noted that several members of our team played significant roles in its discovery and development in our previous roles at INSIGHT. It was tremendously gratifying to see ruxolitinib become the gold standard in the treatment of MPN, especially in the spleen and symptom benefits it delivers to MPN patients with a debilitating disease. However, despite the clinical benefits it offers, ruxolitinib treatment is associated with high rates of anemia and thrombocytopenia that require dose modifications and often limit the use in patients that are anemic and or thrombocytopenic at baseline, along with the limitation of dosing for maximal efficacy. And because RUX does not specifically target V617 of mutated progenitor cells, molecular responses occur at very low rate and take years to achieve. Ever since the discovery of JAK2 V617F mutation in 2004, what we really wanted is an inhibitor that is selective for the mutant cells and one that does not interfere with normal bone marrow function. Such a molecule could provide the same transformative treatment for MPMs that BCR-ABLE inhibitors like Gleevec delivered for CML. We are excited about the possibility of finally achieving that goal by the breakthroughs in designing molecules that can directly target JAK2V617F. As shown on slide 9, the challenge had been that the mutation occurs in the part of the enzyme called the JH2 domain that is distinct from the catalytic kinase domain called the JH1 domain, where the current JAK2 inhibitors bind. Our scientists were able to design potent inhibitors of JAK2 that bind an allosteric JH2 binding site where the V617F mutation resides. We further achieve selectivity over normal JAK2 by directly targeting what we refer to as deep pocket, which contains three phenylalanine residues that include the third phenylalanine coming from the V617F mutation. By utilizing extra structure-based approaches, our chemists identified a novel series of compounds that can access the deep pocket to selectively target mutant JAK2 over wild type or normal JAK2 that is present in normal cells. Digging a bit more into the specifics of our lead development candidate, the picomolar JAK2-JH2 binder, with significant selectivity for mutant JAK2 over normal JAK2. In addition to the biochemical and cellular potency and selectivity,

our lead candidate has demonstrated that acquired physical chemical and pharmacokinetic properties

that enable achieving high levels of mutant JAK2 inhibition. In preclinical efficacy and toxicology studies, this molecule achieved better efficacy compared to toxalitinib without impacting wild-type JAK2 and normal bone marrow function. We look forward to providing additional preclinical data once it's presented at ASH in December, but I can inform you that we're well along with our IND enabling activities and we're planning to file an IND in the first quarter of 2026 and expect to initiate the phase one in the first half of 2026. In terms of prevalence, market size and opportunity, the target patient population include greater than 95% of TB patients, 50 to 60% of patients with MS and ET that are V617F positive. Collectively, more than 200,000 NPM patients in the U.S. alone could ultimately benefit from a JAK2 V617F selective inhibitor with a disease-modifying potential. We did announce last week, and Sean will provide more detail, that we entered into an exclusive option agreement with insight that provides them an opportunity to acquire the program during a defined time period as we aggressively drive forward the clinical development of our lead candidate and pre-clinical development as potential backup candidates during that option period. We look forward to sharing more details at ASH. I'll now turn the call over to Peggy to provide an overview of our Selective CAT 6A degraded program. Peggy? Thanks, Chris, and good morning, everyone.

Today, I wanted to summarize our efforts that led to the successful discovery of our first-in-class oral CAT-6A selective degrader and highlight how this is a differentiated approach to maximize the benefits of a clinically validated target in ER-positive breast cancer. Although multiple agents, including CDK4-6 inhibitors and oral SIRDs, have been developed for patients with ER-positive breast cancer. Resistance to these agents continues to occur. Thus, there remains an important need for additional treatment options that can complement the current therapies in the management of breast cancer. Recent data that Fidler presented on their CAT6-AB dual inhibitor suggests that targeting the CAT6 protein may provide a new avenue to address this important unmet need. As summarized in slide 14 in the corporate deck, the data Pfizer presented at ASCO earlier this year demonstrated that their CAT6-AB dual inhibitor in combination with filvestrin had impressive activity in a heavily pretreated population of ER-positive metastatic breast cancer patients, showing high response rates of greater than 30 percent and significant improvement in progression-free survival. Based on this, the program is now advancing into pivotal studies. Despite the promising efficacy, the safety and tolerability profile has left room for improvement as investigators noted rates of grade 3-4 neutropenia and also dyscusia in most patients. This has resulted in the majority of patients requiring dose reductions or modifications to address the neutropenia issues. These findings likely suggest that there will be challenges combining with standard-of-care CDK4-6 inhibitors and, as such, may initially be limited to second or third-line therapy. We believe that these safety and tolerability issues are the result of dual inhibition of CAT6A and CAT6B and that selective degradation of CAT6A provides a real opportunity for differentiation in the clinic. Slide 15 of our corporate deck automatically shows the rationale for selective degradation of CAT6A. CAT6A amplification and overexpression in cancer leads to its increased activity. And because CAT6A regulates the expression of the estrogen receptor, MYC, and other cell cycle genes, its increased activity drives ER-positive breast cancer growth. Although Cat6A overexpression drives cancer growth, both Cat6A and its related family member, Cat6B, are important in driving normal hematopoiesis, and preclinical data demonstrates that loss of both Cat6A and Cat6B results in bone marrow toxicity. Based on this, our approach of selectively degrading CAT6A has the potential to deliver differentiated safety and efficacy over non-selective CAT6AB inhibitors. As shown in slide 16, our lead compound is a highly potent degrader of CAT6A, with selectivity for cat 6a over cat 6b of greater than 1 000 fold as shown in the middle panel of the slide we've seen excellent oral pk across all species and compelling in vivo efficacy is monotherapy as shown in the graph on the right with complete regressions observed at well tolerated low once daily oral doses in a model of cat 6a amplified pr positive breast cancer As shown on slide 17, we also explored the in vivo activity of our CAT6A selective degraders in additional models that are more resistant to CAT6AB inhibitors. In the more resistant T47D model, we still have significant efficacy with complete regressions observed at well-tolerated doses. Importantly, as shown on the right panel, when we benchmarked against a dual inhibitor, we seemed to demonstrate much better efficacy as a monotherapy, even when compared to a CAT6AB dual inhibitor in combination with fulvestrin. Our preclinical data clearly demonstrates that selective CAT6A characterization shows robust efficacy in ER-positive breast cancer models. We next asked if selective CAT6A degradation could mitigate the neutropenia observed with dual CAT6AB inhibitors. As shown in slide 18 on the left, ex vivo experiments with human bone marrow cells demonstrated a reduction in these cells that give rise to neutrophils, whereas we see a very limited effect in this assay with our selective CAT6A degrader. On the right, we ran an in vivo experiment to confirm these results, and after 10 days of treatment, we see there is transient neutropenia in the mice treated with a dual CAT6AB inhibitor, but we have not observed significant neutropenia with our selective compounds. In summary, Prelude has discovered and developed multiple first-in-class, highly selected Cat 6A degraders, which in preclinical models show the potential to achieve best-in-class efficacy and to differentiate on safety and combinability early in clinical development. Our lead development candidate has completed dosing in non-GLP studies in rats and dogs and has a favorable tolerability profile and, importantly, no dose-dependent hematologic toxicities were observed with that as background we're excited to note that we're on track for an ind filing in mid-2026 with a phase one start expected in the second half of 2026 and with that i'll now turn the call over to sean to provide an update on our recent business development

activities thank you and good morning everyone today i wanted to provide an overview of the exclusive option agreement we entered into last week with INSIGHT and also discuss our plans as it relates to degrader antibody conjugates. The agreement with INSIGHT is a time-bound exclusive option agreement for the potential future purchase of our JAK2 B617 program assets. The option period commenced upon executing the deal and is structured so that INSIGHT has up to 15 months with potential for a three-month extension as needed to exercise its option, no more than 18 months in total. Importantly, INSIGHT has the ability to exercise its option at any point during the option period. If at the end of the option period, INSIGHT elects to not exercise its option, Prelude retains full ownership and global rights to the JAK program. At the outset of the option agreement, INSIGHT paid an upfront fee of $35 million and also purchased $25 million of Prelude non-voting common stock at a price of $4 per share, $60 million in total. If INSIGHT elects to exercise its option, an additional upfront payment of $100 million will be paid to Prelude upon closing of the asset purchase agreement plus additional downstream milestones and royalties in fact the deal includes up to 775 million in additional payments if certain clinical development and regulatory milestones are met plus single digit royalties on global sales as our jack 2 development candidates advance in total the deal can deliver up to 910 million in cash payments and future milestones to prelude next i'd like to to mention our business development work on degrader antibody conjugates. We've recently amended and expanded the scope of our existing collaboration with EbCellera. This agreement enables EbCellera to use Prelude's proprietary degrader payloads on additional undisclosed antibody targets of interest and, importantly, also enables Prelude to license our payloads to other potential partners. The DAC field is really taking off and degrader payload licensing arrangements have the potential to further expand the impact of this new technology while bringing in non-dilutive capital to support our ongoing R&D efforts as the field advances.

With that, I want to hand it back over to Chris. Thanks, Sean. So, before opening up the line for questions, I'd like to offer a few additional remarks related to our progress to date and where we expect to go moving forward. As I mentioned at the outset, today marks a transformative day for Prelude. We are a company that is rooted in science and discovery excellence with a mission to develop precision oncology medicines to transform the treatment landscape for patients with cancer. We are energized to be entering 2026 with two lead programs with highly differentiated development candidates, well understood and clinically validated mechanisms, and clear development paths. A strong and experienced team and the financial means to provide a runway for execution into 2027. We look forward to keeping your price of our progress and additional updates in the coming months. With that, I'll take some time to answer your question.

Thank you. As a reminder to ask a question, please press star 11 on your telephone and wait for your name to be announced. To withdraw your question, please press star 1-1 again. Please stand by while we compile the Q&A roster. Our first question comes from the line of Rennie Benjamin

from Citizens. Hey, good morning, guys. Thanks for taking the questions and congratulations on this deal with Insight and for kind of reorganizing the company to go after what I think are extremely well-validated targets. I have a couple of questions for you. I guess starting off, can you talk a little bit about how you're thinking about the clinical development of both the MUT-KEL-AR and the CAT-6 programs, especially given that you have, you know, competitors that are, call it a couple of years ahead of you in development, you know, how are you thinking about the clinical development of these assets? Do you want to be a fast follower into the same indications? Do you want to explore, you know, different indications? How should we be thinking

about the path forward? And I'm going to have a couple of follow-ups. Thanks, Ryan. This is Chris Wadi. So, you know, as we discussed in the call, our molecule is a very important and selective anterior object to the B617F right so as a result B617F positive NPMs that include myelofibrosis polycytinia vera and essential thrombocytemia are the three indications that we could look at as for in person human study you know myelofibrosis which is the most serious of the condition would be certainly the most of one of the most appropriate initial first-in-law studies that we start with. High-risk polycythemia vera or high-risk potential thrombocytemia are additional indications that could be added either from the beginning as part of the dose escalation, or once we demonstrate that we have, you know, a biologically or pharmacologically active dose. Those are the things that we're currently in the process of finalizing, and so, you know, hopefully we will be underway shortly, so we'll be able to talk about it in more detail. So, so, you actually answered, oh, sorry, go ahead. No, no, I was also going to comment on the CAT6 program, and then I'm, of course, happy to take any further follow-up questions. On the CAT6 program, again, our intent in developing a highly selective CAT6 A is to fundamentally ask the question in ER-positive breast cancer where we see a clear proof of concept and clinical validation from from Pfizer's molecules and the hypothesis we have a base and that's based on you know genetic data pre clinical data that if you can selectively use cat 6a you can reduce and avoid the hematological toxicity so we're going to be focused in the phase one development to initially obviously as a monotherapy but rapidly you know advances to other combinations and really asking the question do we see the differentiated profile that we're seeing in the preclinical studies in the clinic and if so rapidly move into the combinations with you know the backbone therapies in ER positive breast cancer so we are really going to be focused on

We have positive breast cancer for our CATS-A program.

Got it. And I guess just as a follow-up, you know, just to help us understand the prelude platform and the kind of preclinical work that you do, is the chemistry so differentiated that the preclinical models predict, for any of these molecules, by the way, does it predict a better efficacy, safety, or both? And as part of your preclinical testing, and I didn't get a chance to see the slides, but what tests do you run to give you the confidence that you have a best-in-class drug on your hands versus, let's say, a competitor like Pfizer, you know, that's already in the clinic?

So, let me just at a very high level start and just say that there are really good pre-clinical models for – I think that your question pertains to both programs for myeloprolioperative neoplasms and also your positive breast cancers that we can profile head-to-head against already, you know, approved agents are the ones that are moving in the clinical development. But for details, I will just turn the question over to Peggy to answer.

Sure. So in terms of the preclinical models, both in vitro and in vivo, we really established a robust number of those models to characterize the compounds. But I think it's more than just the in vivo and in vitro assays. We also spend a lot of time building in the 2K properties and really optimize those so that we know we have a molecule that will be optimal in the clinic in terms of covering the target and giving us the selectivity and the potency that we'll need to really target the pathway. So with CAT6-8 specifically, I think we have a number of differentiating features. We have CAT6-8 selectivity over the other family members, and we also took a degrader approach as opposed to an inhibitor approach. We thought that that would be a differentiating feature. We can eliminate the protein, as you know, through degradation, and it also helps us build in that selectivity that we think is really critical, the selectivity and the potency. So, in that, a very differentiated approach. Thank you very much. I'll jump back in the queue.

Thank you. One moment for our next question. Our next question comes from the line of Roger Song from Jefferies.

Okay, great. Thanks for taking my question. Thanks for sharing additional information around those two new the clinical program, interclinical program. So on Jack Chu, can you just remind us how the current mutation testing for this mutation currently performing in the clinical and then how likely you need to do the companion diagnosis as you continue the clinical development. And I have a question around the CAT-6 as well.

Yeah, absolutely. So, you know, V617F itself, now that we have multiple therapies in MPNs that are approved, and even prior to that has really become a sort of a standard of care diagnostic test for MPN. You know, in the case of PV, where greater than 95% of the patients are positive, so V617F, there is not a huge need for the test. However, in myelofidrosis that do not progress from PV to MS, there are primary myelofidrosis patients for whom it is somewhat critical. Currently approved therapies really are not specific to V617F positives, so they don't really require the testing. But in our case, we were going to be relying on routinely used QPCR type testing that is performed as standard of care for V617F.

Got it. And then regarding the CAS-6, given this is also a degrader approach, how do you differentiate this degrader approach versus your previous SMAC-2? And then what are the learnings you have applied from the previous degrader to CAS-6? And maybe just lastly, you're moving those two programs into the clinical in 2026 with current cash runway, how much clinical data release we should expect in 2026, and then what will be the value inflection point for those data results. Thank you.

Yeah, I'll let Peggy answer the first part of your question, and I'll come back to the second part.

Sure, so I think we learned a lot from our SMART-A2 program in terms of building in potency and selectivity and also building in, as I mentioned, all those really important PK properties like oral bioavailability into the CASCICS program. So we really learned a lot, I think, from the SMART-A program in terms of building in all those features that you need to optimize the compound to take it forward in the clinic, the activity for the capsic bay or protein, we utilized a lot of the knowledge and experience to generate what we believe are really optimized to greater...

With regard to your question on how far the cash takes, as we said, we are currently in that program in the early part of 26, and, you know, we will be in dose escalation. And until we get into the clinic, we have, you know, certain projections in terms of how many dose cohorts that it might take to get to the levels that we would, you know, we would expect the pharmacological activity, but, you know, I can't provide exact guidance until we actually start to enroll patients. So we think we'll be, you know, well underway in the phase one program, and we'll be keeping the street obviously, you know, updated with any progress we make. With regard to the CAP-6 program, again, the major milestone is really, you know, successfully completing the IND and doing studies and, you know, opening up the IND and starting to enroll patients. So in terms of actual clinical updates, we probably have to wait until 2027 to be providing them. But in terms of progress into the clinic, obviously we will update as we advance the 20 minutes.

Got it.

Yeah, thank you for giving the question. Thank you. One moment for our next question. Our next question comes from the line of Robert Burns from H.C. Wainwright.

Hey, guys. Thanks for taking my questions, and congrats on the deal with Insight. Just a few from me, if I may. So, obviously, the CAT 6, you know, competitive landscape, when we look at that, there's obviously numerous players with the space, not just 5s. They're obviously at B1 as well. And I see the differentiation with the selective CAT 6A degradation. So, you know, I'm just curious, for those more selective inhibitors or degraders that are in the landscape, how are you looking at them from a competitive landscape threat perspective. And then my second one would be, you know, obviously we're also seeing a lot of companies go straight from phase one when they see encouraging efficacy straight into phase three. Is that something that you would also consider? And are there ways that you could expedite the

development time of that compound? Thank you. Yeah. So I can start with that. I think in terms of the selectivity, the selective inhibitors that have been profiled, at least the ones that we've seen to date, they do show selectivity to mitigate some of the bone marrow toxicity that we also see. I'd say with the degrader approach, it really allowed us to have more robust efficacy compared to even the selective inhibitors. As we think that there is, you know, a different biology associated with degrading the protein because it is part of a complex than just inhibiting it and we think that's really beneficial from the efficacy point of view so I think there there will be differentiation from the selective inhibitors but I think they also provide additional abilities to to mitigate some of the bone marrow taxes

yeah I can just follow up on that you know again fundamentally the whole concept of degraders that are currently being developed across multiple targets is the idea that you just get much more deeper target engagement. And given the potency of our CAP6A molecule and the PK properties that the team has built into should allow us to very rapidly get to the levels of target inhibition that would differentiate our molecule versus others. I think that is a really important aspect of it, because the sooner you get there in the clinic, the faster we can move. And then the second part of this question. Would we advance rapidly? Yeah, so good question. So I think there's a lot of learning from, you know, from the data that's out there in terms of PD as well as combinations. We would be looking to actually do more combinations early in the development, because ultimately we want to get to earlier lines of therapy, which currently, you know, not being pursued by the existing clinical stage inhibitors. We would be looking to generate that data and to answer your question, yes, we would be looking for ways to advance rapidly, you know, to registrational stage programs once we confirm some of the preclinical hypotheses we have in the clinic.

Thank you. One moment for our next question. Our next question comes from the line of Rennie Benjamin from Citizens.

Hey, guys. Thanks for taking the follow-up. Can you just talk a little bit about the genesis of kind of why and how the deal with Insight took place, given that they have their own inhibitor already in the clinic? You know, is it something that was ongoing for a while? Is this something once the new CEO took over, the discussion started? Anything that would, you know, give us a clue as to how this came up, this nice deal came about?

Yes. Thanks, Ryan. so um you know as uh as we were thinking you know throughout 2025 and even 2024 in terms of um you know capitalizing the company and funding the programs that we had ongoing right so both jack 2 and cat 6 programs made significant advances uh and we were really anticipating that they would be moving into the IND enabling space in this career as well as marketing program that was moving forward in the clinic you know it's obviously companies of our size would always be looking at business development has you know one of the options to to basically fund this really important program so you know we've been in discussions with a number of number of companies for all the programs and you know obviously Insight is a leader in NPM space and there were several other companies that were very interested in the program as well so at the end of the

day when we look at you know all the options that the company had yeah you

know the the you know option agreement with insight actually was you know we believe was the best option to not only you know bring the capital that we need to the company but also put the program in the hands of a company for whom it is fundamentally a core strategic area and you know not only they would move aggressively through the clinical development but also you know will commercialize the product if we're fortunate to get to that point. So we're excited to be working with Insight in moving this program and with regard to another question about their own program and we really don't have any visibility into the program but you know we hope that that you know that our our novel chemical space that our scientists discovered to create our molecules, you know, would find a place ultimately in the Christian science and in the market.

Perfect. Thanks very much.

Thank you. At this time, I would now like to turn the conference back over to Chris Vaadhy for closing remarks.

Right. Thank you, everyone, for your time, and have a great day.

this concludes today's conference call thank you for participating you may now disconnect