Good day, and welcome everyone to the Aprea Therapeutics KOL event featuring presentations by esteemed key opinion leaders Dr. Joseph Vacca, a medicinal chemistry expert, and Dr. Eric J. Brown, professor from the University of Pennsylvania and a member of the Abramson Family Cancer Research Institute. We will also hear from Dr. Nadeem Mirza, Chief Medical Officer at Aprea, and Dr. Oren Gilad, the company's President and Chief Executive Officer. Dr. Gilad is a pioneer in the field of cancer research, having authored several scientific publications during his 13-year academic career, including on the ATR pathway. Dr. Gilad also brings extensive experience across multiple phases of drug development. All speakers will be available for a Q&A session following the formal presentations. Also, I would like to note that this call is being recorded on the date of today's event, June 24, 2024. A replay will be made available on Aprea's corporate website. Now, I would like to turn the call over to Dr. Oren Gilad, who will begin today's event with an overview of the company and agenda. Oren?
Thank you, Tara, and welcome everyone to our event today. It is a pleasure to be here to discuss APR-1051, our highly selective oral WEE1 inhibitor, as well as recent developments in the field. As you will see, we're very excited about the opportunity for this key program. Hopefully, by the end of the event, you will have a good appreciation of the work conducted by our scientists to create a molecule that is differentiated, potentially best-in-class. Next slide, please. Forward-looking statements. So, as described here on slide two, we will be making forward-looking statements in today's webinar. They're based on certain assumptions and are subject to a number of risks and uncertainties.
The risks, uncertainties, and assumptions that affect these forward-looking statements include risks that are included in the company's SEC report, including our Form 10-K for the fiscal year ended the 31 December 2020 and Form 10-Q for the first fiscal quarter of 2024. We qualify all of our forward-looking statements by these caution statements and expect, as required by law, we assume no responsibility for updating any forward-looking statements. In addition, with respect to all of our forward-looking statements, we claim the protection of the safe harbor for forward-looking statements. Next slide, please. So, let me first introduce the speakers on our call today. We provide a quick overview of our company. In addition to Dr. Nadeem Mirza, our Chief Medical Officer, we are honored to have two esteemed key opinion leaders in the field, Dr. Joseph Vacca and Dr. Eric J. Brown. Dr.
Mirza has been with Aprea since February 2023. He brings over 30 years of clinical and development experience in solid tumors and hematologic malignancies. In the past, Dr. Mirza served on multiple leadership roles, including global head hematology and solid tumors at AbbVie Oncology, where he oversaw the global launch of Venclexta. He was also Vice President, Head of Oncology, North American Medical Affairs, and North Oncology, where he was responsible for a medical affairs program that supported 12 products across several oncology indications. Dr. Mirza also has leadership roles in medical affairs and clinical development at Genzyme, Sanofi, Onyx Pharmaceuticals, Abraxis Oncology, and Verastem Oncology. We are honored to have him on our team. Dr. Vacca is a medicinal chemistry expert and a consultant to Aprea Therapeutics. Dr.
Vacca spent approximately 30 years at Merck and made major contributions to several approved lifesaving drugs, including the HIV protease inhibitor, Crixivan, the HCV protease inhibitor, Victrelis, and combination product Zepatier, and certainly a recently approved second-generation HIV NNRTI inhibitor, doravirine. Dr. Vacca has over 100 publications and patents and is the holder of many awards, including Merck Director Award, PhRMA Discoverers Award , National Inventor of the Year Award, European Inventor of the Year, and the ACS Award for Creative Invention. He was also appointed to the American Chemical Society Medicinal Chemistry Hall of Fame and was also named Hero of Chemistry along with his research team for his role in the discovery and development of the HIV integrase inhibitor, Isentress. Lastly, Dr. Brown is a consultant to Aprea, a professor at the University of Pennsylvania, and a member of the Abramson Family Cancer Research Institute.
He was the first to clone mTOR and the first to demonstrate that ATR loss causes genomic instability. His laboratory demonstrated that the DNA replication abnormalities caused by oncogenic stress is synthetic lethal with ATR suppression. This body of work I should know something about because he and I published this paper together. His laboratory focus has been on how to customize clinical use of DDR inhibitors to aid in better identifying the best treatment for patients with specific genetic mutations. Next, thank you. So, what's on the agenda today? Dr. Nadeem Mirza is going to give us, provide us with a clinical overview of neutropenia and sepsis for other WEE1 inhibitors. Then Dr. Joseph Vacca is going to tell us about the approach that Aprea took in generating the selective and potent WEE1 inhibitor, APR-1051, which is also the focus of our call today, followed by Dr. Eric Brown, who is going to tell us how the chemistry provided by Joseph Vacca has been translated to biology and how the approach that we are taking there.
After a quick summary, we will open the floor for Q&A. Next slide, please. So, Aprea is a biopharmaceutical company that is focusing on developing drugs for synthetic lethality by targeting the DNA damage response pathway. We have an outstanding team, and please go on our website and look at the caliber of the team that are involved in the team. Our programs are designed to address significant medical needs. Next slide, please. Each program is designed to have a single-agent activity, but also work in combination with the other programs in our portfolio.
Our ATR inhibitor is the first macrocyclic ATR inhibitor that is currently in the clinic in the dose escalation portion of the study. The WEE1 inhibitor, 1051, that's the focus of this call today, that entered the clinic recently. Announcement was made. The third undisclosed DDR inhibitor came from our platform, Repli-Biome, and we will disclose the target once the patent is filed. Next slide, please. What are today's take-home messages? We actually narrow it down to four take-home messages. The first one is that WEE1 is a clinically validated target. You're going to see that we have a drug that is differentiated, structurally differentiated molecule. Same target, but a different drug. When it comes to the efficacy, there's not much differences in efficacy between our molecule and the others. When it comes to safety, that's where we start to see differentiation.
We have been focusing on the PLK family of this. So, we have been spending a lot of time developing a molecule that is selective and does not inhibit the PLK, as we identified as a liability. So, therefore, when you put the whole package together, our IND has been cleared, patient has been dosed recently, and FDA did not raise any concerns about sepsis. Next slide, please. So, as we were working on developing the program and developing the drug, we identified PLK inhibition to be a critical area of improvement if we want our WEE1 molecule to potentially have success in the clinic. We've been looking at published work, and we saw that both the two other molecules in the field, two of them have liabilities associated with PLK1, 2, and 3. Next slide, please. Now, without any further delay, it is my pleasure to turn the call to Dr. Nadeem Mirza, who is going to give us a clinical overview of neutropenia and sepsis of other WEE1 inhibitors.
Thank you, Oren. Good morning. I will present a clinical overview on neutropenia and sepsis observed with other WEE1 inhibitors. Last week, Zentalis announced that FDA had placed a partial clinical hold on three clinical trials with azenosertib monotherapy. These trials include phase 1 monotherapy in advanced solid tumors, phase 2 monotherapy in patients with uterine serous carcinoma, also known as TETON study, and a phase 2 monotherapy trial in patients with platinum-resistant ovarian cancer, also known as Denali study. This partial clinical hold was a result of two drug-related deaths presumed due to sepsis during the first half of this year in the Denali study. Zentalis also provided information on three additional drug-related deaths in two other solid tumor studies. Neutropenia and sepsis have been observed in clinical trials with azenosertib monotherapy. This table summarizes the incidence of neutropenia leading to sepsis.
The first trial investigated adavosertib monotherapy in advanced solid tumors in phase 1 setting. In this trial, neutropenia was observed in 40% of patients, with 16% of patients having grade 3 or higher neutropenia. 4% of patients developed febrile neutropenia, and one fatal case of sepsis was reported in the setting of grade 4 hematologic toxicities. This patient also had developed febrile neutropenia and aspiration pneumonia. In the second trial, also known as Ignite study, in which patients with recurrent high-grade serous ovarian cancer received monotherapy, 45% of patients required dose reductions due to neutropenia or diarrhea, and three cases of fatal sepsis were reported. In the third trial, in which uterine serous carcinoma patients received monotherapy in phase 2 setting, 21% of patients developed grade 3 or higher neutropenia. In this study, seven cases of sepsis were reported, with two being fatal and associated with grade 4 neutropenia. Both azenosertib and adavosertib inhibit WEE1 and PLK1. So, is there a concern with PLK1 inhibition? This slide summarizes the PLK1 inhibitors associated with severe neutropenia and sepsis.
Boehringer Ingelheim PLK1 inhibitor, volasertib, has shown high incidence of severe neutropenia in phase 1 trial in patients with advanced solid tumors. 65% of patients developed grade 3 or higher neutropenia. In a phase 3 trial in AML patients, the incidence of neutropenia and febrile neutropenia was approximately double, while sepsis was approximately three times more among patients who received volasertib when compared to those who did not. Additionally, adverse events leading to death were higher in the volasertib plus low-dose Ara-C arm compared to placebo plus low-dose Ara-C arm. Merck's PLK1 inhibitor, also known as MK-1496, in a phase 1 trial with advanced solid tumors observed grade 3 or higher neutropenia among 35% of patients. The publication stated that neutropenia caused by MK-1496 is a mechanism-based effect of PLK1 inhibition. In summary, azenosertib and adavosertib both inhibit WEE1 and PLK1. PLK1 inhibition causes severe neutropenia that may lead to sepsis, often fatal. Thank you. Now, I would like to invite Dr. Joe Vacca to present his work on medicinal chemistry design for APR-1051 WEE1 inhibitor. Joe?
Thanks, Nadim. So, I'd like to talk about our design of our compound 1051. When we start a program, a medicinal chemistry program, we usually look in the literature to see what other compounds have come before us, what some of the issues are, and how we might improve those compounds. The compound WEE1 inhibitor that was best known in the literature is shown on the left, AZD1775. That compound was a good WEE1 inhibitor with an IC50 against the enzyme of 3.9 nanomolar. It was also reported in their publication that it had a similar activity to PLK1 at 3 nanomolar. So, we took this compound and computationally modeled it into the WEE1 kinase to see how it fit in and what interactions it had with the enzyme.
One of the things we saw that there was an important interaction between an OH group, which is pointed to by a small arrow, and an asparagine group in the back of the WEE1 site. It looked like an important interaction. We also then modeled it into a PLK1 active site, and we saw a similar interaction with that hydroxyl group to the back of an aspartic acid in the PLK1 site. A few years later, Zentalis published their structure shown on the right-hand side, ZN-c3. This compound is almost the same compound as AZD1775, except for two carbon atoms. You can see on the right-hand side where I say small difference, that's the only spot where there's a change in the molecule between the two. Zentalis compound had similar activity against WEE1 at 3.2 nanomolar. Their design was better, though.
It had a PLK IC50 of about 92.1 nanomolar. And if you look at their crystal structure that they reported in the WEE1 active site, that hydroxyl binds in the area of the asparagine 431. And if you model it into the PLK1 site, it also has a similar interaction to the aspartic acid. So, what we wanted to do when we first set out, knowing the background of the AZD1775, we decided to try a different series of compounds that had also been reported in the literature. This compound on the top left was reported by AbbVie to have potent activity against WEE1. It's a different structural series, and you can see it does not have a hydroxyl group on the right-hand side, which would bind to PLK1. So, we started working in this series of molecules and eventually came up with APR-1051 shown on the right side.
We haven't published our full structure yet, so I had to put in some groups to represent pieces that we have. But this compound is not the same as compound 36. It also doesn't have any hydroxyl group that combined to the back-end site of PLK1. And as expected, when we tested it against PLK1, it hardly bound at all, almost 16,000 nanomolar, and still had great activity against the WEE1 IC50 of about 1.8 nanomolar. So, from that, we pushed the compound forward. And I'd like to hand over the presentation to Dr. Eric Brown to talk more about 1051.
Thank you, Dr. Vacca. First off, I would just like to note that based on all available data, Dr. Vacca's strategy to create a highly potent WEE1 inhibitor that does not substantially off-target PLK1, 2, or 3 was successful. I'm going to review the data that demonstrates this. Just to take a step back, I wanted to talk a little bit about how WEE1 inhibition works as a cancer therapy. WEE1 inhibition causes the premature activation of a kinase known as CDK1, which promotes premature entry into mitosis, which catastrophically kills cancer cells. In particular, what is interesting about WEE1 inhibition is that it can also deactivate a kinase known as CDK2. And so, by activating CDK2 in combination with overexpression of cyclin E, that causes premature S phase entry.
By two different mechanisms, WEE1 inhibition can force cyclin E overexpressing cancer cells into S phase and then further into mitosis, leading to under-replicated DNA to enter into the next phase of the cell cycle, thus causing cancer cell death. APR-1051 has all the expected effects on cells. In its ability to inhibit WEE1, off to the left-hand portion is its in vitro biochemical inhibition of WEE1 represented. And secondly, its ability to prematurely activate CDK1, as indicated by a loss of phosphorylation of CDK1, and also its ability to kill cancer cells at relatively low concentrations. However, most importantly, as presented by Dr. Vacca, one of the main goals in identifying this particular WEE1 inhibitor is the ability of this inhibitor to not off-target PLK1, 2, and 3, which we see as a significant liability.
On the right-hand side, you can see APR-1051's in vitro biochemical activity compared to Zentalis. In this case, you can see that APR-1051 is very potent with an IC50 of 1.8 nanomolar, compared to Zentalis, which was run in parallel from a commercially available source at 3.2 nanomolar. So, that's a good control that matches very closely with Zentalis's reported IC50 for their WEE1 inhibitor. In contrast, you can see that APR-1051 does not significantly inhibit PLK1, 2, or 3 with an IC50 of 15,000 nanomolar, 1,800 nanomolar, and 31,600 nanomolar. This is a difference of 8,000, 1,000, and 17,000 compared to the ability of APR-1051 to inhibit WEE1. However, if you were to look at Zentalis's ability to inhibit WEE1 at 3.2 nanomolar, it also inhibits PLK1 at approximately 91 nanomolar, PLK2 at 32 nanomolar, and PLK3 at 52 nanomolar.
This is a difference of only 29-fold, 10-fold, and 16-fold compared to its ability to inhibit WEE1. This represents a possible liability for the compound in that it's inhibiting WEE1 at only a moderately lower IC50 compared to its ability to inhibit three key PLK family kinases. I should also note that PLK2 and 3 have overlapping functions in regulating the cell cycle. So, some level of inhibition of PLK1, 2, and 3 could pose a risk. That's a risk that APR-1051 does not have. Another aspect of inhibiting the PLK family has recently been reported in several studies shown here that in addition to the ability of PLK inhibition to cause neutropenia, which is strongly related to sepsis, it's been shown that PLK inhibition can also cause a dysregulation of intestinal barrier function in combination with sepsis.
So, if you think about it this way, PLK1 inhibition can cause sepsis through a defect in generating neutrophils. But separately, it can also cause an impairment of recovery of the intestinal barrier under conditions of sepsis that could lead to a positive feedback loop of leading to sepsis and then causing a loss of intestinal barrier function, which has been known to lead to the invasion of bacteria from the intestines into the bloodstream and therefore exacerbating it. That could actually be a significant problem in inhibiting PLK1 and its effects on causing sepsis. That is summarized here, showing that the intestine plays, number one, an important role in the pathophysiology of sepsis. The intestinal barrier prevents the entry of bacteria and toxins into the circulation. And maintenance of the intestinal barrier is critical for limiting the effects of sepsis.
PLK1 inhibition slows the recovery of the intestinal barrier function, causing decreased survival. The reports that I showed in the previous slide have further demonstrated that overexpression of PLK1 can increase barrier function. That really pinpoints PLK1 as a key regulator of intestinal barrier function under conditions of sepsis. Looking at APR-1051, one would expect that if there was a loss of intestinal barrier function, then animals that were treated with 1051 would undergo a rapid loss of body weight. The reason for that is that mice drink about 20% of their body weight per day. Intestinal barrier dysfunction causes a rapid loss of body weight. In this xenograft model, what you can see is that APR-1051 completely suppresses the growth of a cyclin E overexpressing ovarian cancer tumor model dosed every day at 30 mg per kg.
However, very little loss of body weight was observed in these animals, indicating that this compound does not cause significant loss of the ability of these animals to drink and further suggesting that there is no loss of intestinal barrier function in these animals, also consistent with the possibility that not off-targeting the PLK family is preventing some of the effects that have been observed previously with other compounds, including PLK1 inhibition directly. With that, I'd like to turn it back over to Dr. Oren Gilad.
Thank you, Eric. I hope that today's discussion has given you a better understanding on why our WEE1 program is differentiated. We do believe that the work conducted by our chemists will potentially solve the major problem associated with the other WEE1 inhibitors in the field. We will continue to update on our clinical program. Hopefully, we will update in the future. Here is the summary slide. We covered all of it, and everything I said hopefully came across. I think that with that, it is now my pleasure to open the call for our Q&A session. Tara?
Great. Thank you, Oren. So, as a reminder to our audience on the webcast, if you'd like to submit a question, you may do so by using the Q&A text box at the bottom of the webcast player. So, our first question comes from Jason McCarthy at Maxim. Please go ahead, Jason.
Hi, guys. Thanks for taking the questions. Great presentation. Can you just elaborate a little bit more on what Zentalis had gone through with their IND? Because if it was known at the time with the other PLK1 inhibitors, volasertib and the Merck compound, that there are issues with PLK1, how did Zentalis kind of get as far as it did with its molecule?
Thank you, Jason. We don't have access to their IND. We don't have access to any IND. And it's customary that people do not, or companies do not share data from IND and interaction with the FDA. So, we really don't know.
Got it. As part of the WEE1 trial, will there be specific attention paid to maintenance of the intestinal lining given what's now been published?
Nadeem?
No, thank you. It's a great question. As mentioned earlier, when we did the IND submission to FDA, we provided them the whole IND package. There were no concerns raised by FDA. As you recall, part of the IND package includes histopathology of the animal tox data. Unfortunately, we are not at liberty to discuss or disclose that. But there were no concerns raised from FDA, and we are not concerned either. We dosed the patient last week, and we will continue to monitor those patients closely.
Just a last quick question, kind of building on that. As you look at some of the safety data that comes out of the ongoing phase 1 trial, will there be particular attention in how high you push the dose and the level of sepsis or lack of sepsis? Is that something that you'd focus on? Or are there going to be other adverse events that you would expect that will get you to your maximum tolerated dose, but it's not going to be sepsis where Zentalis seems to have been tripped up?
So, great question. As mentioned earlier, our drug is a differentiated molecule from others. And so, we don't anticipate or expect such adverse events that have been observed with other WEE1 inhibitors. However, we continue to monitor those patients carefully. So, as you know, in phase 1, there are certain assessments being done on a regular basis. So, we will continue to do that. And as I mentioned earlier, during the interaction with FDA on our clinical protocol, there were no concerns raised by FDA whatsoever on what we have put in place at the moment.
Great. Thank you for taking the questions. I'll jump back in the queue.
Thank you.
Thanks for the questions, Jason. Our next question comes from Robert Driscoll at Wedbush. Please go ahead, Robert.
Great. Thanks. Good morning, guys. And thanks for taking the questions here. Just the first one. So, obviously, I think there's pretty clear evidence here that you presented that the PLK1 inhibition does appear to be associated with a significant heme tox. I was wondering if inhibition of PLK1 contributes to the efficacy of these early-generation, current-generation WEE1 inhibitors at all, in your opinion, I guess.
Thank you, Robert. Yeah, Eric, please.
I'd be happy to answer that because I think you'll be fascinated with the answer. The truth of the matter is that PLK1 inhibition actually counteracts some of the effects of WEE1 inhibition. And that's because PLK1 and WEE1 actually have opposing effects in the cell cycle, with WEE1 stopping the cells from going into mitosis and PLK1 driving the cells into mitosis. So, by inhibiting WEE1, you're actually counteracting what one would want to cause by inhibiting WEE1 and driving cells into mitosis prematurely. And it's really kind of a bad mix because you're counteracting the mechanism of action of WEE1 inhibition, but at the same time, you're getting overlapping toxicity with WEE1 and PLK1 inhibition combined.
Got it. That makes sense. And then just with this potentially differentiated toxicity profile, how are you thinking about the potential for combinations here? There's arguably clinical validation for the chemotherapy combinations and obviously a number of options open in the targeted therapy space as well.
Yeah, that's a great question. Something that we're thinking about right now. Clearly, there's a lot of data out there to indicate you can combine WEE1 with IO. That has been demonstrated for head and neck cancers as being a very promising area. Also, you can imagine that with a lower toxicity profile, we could even combine with other agents that could have an overlapping tox with something else like PARP inhibition, for instance. That's also been tested in the clinic. Targeted agents, I think, are favorable, but also combinations with chemotherapies like gemcitabine are also a possibility. Nadim, would you like to add anything to that?
Well, we have an ATR inhibitor that's quite safe. We can potentially look at a combination within our own pipeline.
Brilliant. Thanks a lot, guys. Appreciate the insights today. Thank you.
Thanks for your questions, Robert. Our next question comes from Joe Pantginis at H.C. Wainwright. Please go ahead, Joe.
Hi, everybody. Thanks for taking the questions. Thanks for all the details today. First, I wanted to focus a little bit more on the medicinal chemistry approach. Obviously, you talked about the importance of the hydroxy group. And I was just curious, and you obviously have some more confidential aspects of the chemical structure. Is it based primarily on the structure, on the reduced off-target activity? That seems obviously the key thing. Or are there other potential factors at play? That's what I wanted to touch on first.
Yeah, it always comes into a couple of things. One is potency against the target. And we ran a lot of our assays in cell-based assays to look for potency and how they compare to other compounds. And then it comes into play pharmacokinetics of the compound. You want to be able to make a pill out of the compound and give it orally to patients. And then it also has to do with off-target toxicity. So, we would follow PLK1 occasionally with a series of compounds just to spot check it. But you also look at other kinases in this big panel. And there's also other off-targets that you look at. So, it usually takes two or three years to go through a drug discovery program before you decide to pick your final compound based on a series of.
Oh, sorry.
Of assays.
Sorry. Yep, absolutely. So, thanks for that. And just as an addendum to that, obviously, you mentioned other kinases. Is there anything of note that you can disclose with regard to anything else on the kinome tree that you are hitting or aren't hitting of note?
I think there are other kinases we are hitting, but there was really nothing to be worried about, I think, from what we looked at. We also tested IC50s against some of the other kinases. Eric, do you have anything else to add on that?
No, nothing to add. Thank you.
Got it. So, and also, I guess, looking at the entire landscape right now for this approach and mechanism, I guess, have you talked to the FDA? Has the FDA come to you? Is there any body language yet of increased monitoring or anything that the FDA might have said to you with regard to safeguards? Just approaching it from, are you being put into a basket that you necessarily shouldn't be put in? Nadim, can you address that?
Yes. Thank you for the question. We have not received any communication from FDA so far. As mentioned earlier, during our interaction with FDA earlier this year for the IND, there were no concerns raised by FDA on our clinical program. As you recall, we received our IND, we were cleared in March, and we just dosed our patient last week. Between, I would say, March and this, as of today, we have not received any communication. I don't anticipate any such communication because our package of data that was submitted to FDA, the preclinical package, did show that it is differentiated from other WEE1 inhibitors. Again, in the phase 1, we have certain measures in place. We will obviously monitor those patients carefully. But the short answer to your question is, no, we haven't received any communication from FDA.
Got it. Very helpful and encouraging. Thanks a lot.
Thanks for the questions, Joe. I'll now turn it over to Mike Moyer of LifeSci Advisors to read the remainder of the questions from the webcast.
Great. Thank you, Tara. Just going to pull up the written questions here. Yeah, there was a question just regarding the history of the compound. How long, generally speaking, did it take to design APR-1051?
Joe?
Yeah. Probably, I'd say less than a year to actually come up with the molecule. We had started with some earlier designs before that and then came up with that compound. Then you always try to beat your compound. We kept coming up with the 1051 as being the best compound. I think it took at least another 1.5 years to go past that and make other compounds. Probably 2.5 years, I would say.
Great. Yeah, the next question. What are expected timelines for this current dose escalation study? And how have the recent events altered investigator interest?
So, we expect a clinical update in Q4 this year. Regarding your second question, the recent events actually have led to greater enthusiasm about our program from investigators, given the fact that it is a differentiated molecule and potentially best-in-class safety and efficacy-wise. Our investigators are looking forward to advancing the trial.
Great. And then just one last question. I think Dr. Brown addressed most of this, but did you see anything in preclinical tox that supports the differentiated mechanism of action and molecule related to expected or unexpected neutropenic or GI adverse events?
I'll take this question. We have not disclosed any specifics related to GLP tox, but we can share that FDA had raised no concerns related to our IND package. As I mentioned earlier, we initiated our phase 1 trial, and we dosed our patient last week.
Great. Those are all the written questions. I'll turn it back over to Oren.
Thank you, Mike. So, thank you, everyone, for joining us today. We appreciate your support and look forward to continuing to develop and update you on all of our programs. Thank you.