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BofA Securities 2024 Health Care Conference

May 15, 2024

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

Calpain is important in ALS and other neurodegenerative diseases. There's been decades of literature supporting this as a target of interest. And probably importantly, too, calpain's long been associated with neurofilament biology.

We've seen that in our own hands as well. When you inhibit calpain-2 , you see a pretty, you know, notable drop in neurofilament, which makes for good clinical translation, you know, as we move into, hopefully, a clinical trial before the end of the year kicking off in a multiple ascending dose study in ALS. So probably went on longer, but that overview.

Speaker 5

Yeah.

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

Of where we stand.

Speaker 5

Yeah. Yeah. Let's start with Wolfram syndrome. So maybe give us a bit of the disease etiology, you know, kind of the standard of care today, and then maybe when you talk about, you know, the clinical studies.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Great. Thank you, Jeff. Yes, we're very excited about our Wolfram program. In particular, given the interim data that we saw where the hypothesis for our phase II study was slowing down progression or deterioration of the manifestations, and we actually saw improvements in beta cell function and in some individuals, modest improvement in vision. You asked about the disease and how it's treated currently.

As Josh mentioned, it's a monogenic disease, mutations in the WFS1 gene. It's been known since the 1930s, but to this day, there's no definitive treatment for it. It's managed by supportive care for the different manifestations and characteristics of the disease. The insulin-requiring diabetes, insulin for vision, not too much there except corrective lenses until people go blind. Hearing, sensorineural hearing loss, neurogenic bladder, self-catheterization.

There are other manifestations, brainstem manifestations, in which people forget to breathe. Their brainstem doesn't give that autonomic function. Actually, respiratory deterioration and decline is the main cause of death in the early 30s for these individuals.

Speaker 5

So similar to ALS in that respect.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Similar to ALS in that respect. Having said that, our studies have our study, but the non-clinical study, too, recapitulating in with our phase II, has. We do have biomarkers and pharmacodynamics to be able to tell us whether we're having an impact. Relatively soon, 12-week and 24-week improvements in C-peptide with a mixed meal challenge has been very helpful in guiding us to realize we're improving beta cell function, not just slowing the deterioration.

Speaker 5

Yeah. Maybe just to follow on that, just, you know, given, you know, GLP-1, I guess, kind of used in this population, just talk about I think that's those are some of the, the things you mentioned, you know, in terms of the rate of, kind of, background therapy with GLP-1 and how you think, kind of, the added benefit, you know, with the, AMX0035.

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Well, maybe I'd first start with Camille's point, which is that there's nothing improved for Wolfram syndrome. And, you know, GLP-1, I think people are hopeful that it may help with some of the diabetic complications. But Wolfram syndrome is not diabetes. Wolfram syndrome is a disease that WFS1 mutations cause stress, which causes mitochondrial dysfunction and then cell dysfunction and death. And I think what's nice from a translation perspective is you can see that in basically any cell type you study preclinically.

So we studied beta cells. We studied different neuron populations. And no matter how you look, it's the same thing. WFS1 mutations cause stress, mitochondrial dysfunction, cell dysfunction, and death. So then the question is, well, how do you target a disease like that? Well, we have a treatment that targets stress and mitochondrial dysfunction.

So, what you see in the disease etiology is the dysfunction in beta cells because I think they're probably a little less resistant to that pathophysiology, and then different neuron populations. And that's basically why you see the disease manifest as it does, starting with what looks like type 1 diabetes at age six, seven, eight, nine, then progressive vision loss, progressive hearing loss, ataxia, etc. So going back to your question, I think the real question is, can you target the root pathophysiology of the disease?

I think based on our preclinical studies, we were hopeful that we could because it's a great match of the mechanism of the drug to the mechanism of disease. And now what we're seeing clinically is, as Camille was saying, not even just slowing progression, but stabilization or even improvement over a relatively short period of time.

I think what we're hopeful is that we're indeed getting at the root cause of disease. That's why we're seeing efficacy across different organ systems rather than even just the diabetic complications, which are critical but not the whole disease.

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

And one other thing just to add that I think is important. In this study, we allowed, you know, diabetic medications. People are on insulin. People are on metformin. People are on all sorts of diabetic medications. GLPs have also been around for diabetes for a long time. They've been used in Wolfram for a long time. And Wolfram is still Wolfram. You know, so it's not that, you know, I do I don't think we should expect that GLPs are gonna, you know, dramatically, you know, change.

I think they'll, you know, help in the management of diabetes as they have, you know, elsewhere. In our particular trial, we did exclude, you know, the GLP-1s. The reason we did that was looking at the population. You know, there was a mix of people who were on them or not on them if we had just enrolled.

We didn't really want people to start the mid-study, you know, from a kind of, you know, statistics and otherwise perspective. But we don't, you know we don't think that that, you know, presents any particular challenge. Some of these people had been on GLPs before. Their diabetes was being managed as best as it possibly could by their endocrinologist. I feel pretty strongly that the clinician, you know, would not have taken them off therapies that they thought were working.

Speaker 5

Got it. So let me just, so these patients, the eight patients, are not on GLP-1 as part of the treatment with.

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

Correct.

Speaker 5

Got it. Okay. Then maybe just to think about, kind of, the upcoming data in the fall, you know, with 12 patients, 24 weeks, like, kind of, what's your expectation there? And maybe even a step further, you know, phase III redesign, right? Like, are you planning to include, you know, people with GLP-1 already on GLP-1 as background therapy or not?

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Well, maybe I'll start with, right now and then pass to Camille on some of the development plan. So I think the first thing is, for us to meet with FDA. I think, as Camille was saying, our original hypothesis going into the study, it's a progressive disease. Can we slow progression? We're seeing stabilization or even improvement. So that's, you know, exciting but very different than what we went into the study thinking.

So I think that's why with our current data, we're gonna meet with FDA to talk about the development plan. And I think what's nice, too, is that while Wolfram syndrome, there's nothing approved for Wolfram syndrome, everything we're measuring are very, very well-known outcomes. So I think in rare disease, you often get into this challenge of, well, how do you measure it? And if you measure this biomarker, does it matter?

You know, in this case, we're measuring C-peptide. We're measuring hemoglobin A1c. We're measuring visual acuity, CGIC and PGIC. These are all very, very well-known and things that FDA is very familiar with, too. Then maybe on the development plan, I'll, I'll pass to Camille a bit.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Sure. Thank you very much. Yes, we're very excited to meet with the agency to move the program forward. Before I do that, I did wanna respond to your question about what we expect in the fall. So as you said, all 12 individuals in the study 24 weeks will look at C-peptide and the other measures of glycemic control as well as visual acuity.

And some of the individuals, as you can imagine, some of those 8 individuals have now gone beyond 24 weeks. And we'll look at the totality of the data and also share, share what we know about those as well. And what we intend to do in meeting with the FDA is share the interim data that we have now.

We don't wanna wait to meet with them because this is a disease that leads to premature mortality, has tremendous unmet need. And we do believe that AMX0035 has a great role. Now, as Justin was saying, we're seeing tremendous responses with C-peptide. And that is a well-established objective measure.

So that's something that we certainly will be discussing with the agency in terms of, you know, how we can proceed in that regard in addition to the visual acuity and the global impression of change, which gets to the clinical benefit and measures of clinical benefit.

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

And maybe not to belabor this question, but the one other aspect I'd add, too, is one of the things that gives us particular confidence as we're moving forward in Wolfram is the translation story here. You know, it's a monogenic disease. And so the, you know, advantage is the preclinical models were WFS1 mutations in cells. And then a double knockout WFS1 mutation in mice where the groups were completely separated. You know, our p-value in the mice was less than 0.001.

You know, it was pretty unquestionable which mice were on drug and which mice were on placebo. And what's nice in a disease like Wolfram, for example, as compared to a disease like ALS, is you know that this gene is what's causing it.

And so when you're studying that preclinically, you're studying the same gene. Then you're studying the same gene in humans. It's a nice trend. Of course, there's no guarantee, but it's a nice translation story to be following that same gene throughout.

Speaker 5

Got it. And just given that, is there a way to build in some novelty to the phase III design looking at, you know, biomarkers, you know, and predictive of efficacy? That way, you know, obviously, even in the real world commercially, you could be able to, you know, maybe more easily identify, you know, patients and how the drug's working.

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Yeah. Absolutely. I think that's, you know, exactly why we wanna meet with FDA and talk about things. I mean, for example, in our current study, we enrolled people 17 years of age and up. In any disease like this, the earlier you treat, the better. So I think one of the things we're most excited about is we're seeing stabilization or improvement in adults. I mean, you know, you treat earlier. We can hope really fundamentally change the trajectory of the disease.

Then in terms of biomarkers and then longer-term clinical outcomes, that's why I think it's so nice using well-known, well-validated outcomes because I think there's, you know, potential for accelerated approval, following up with long-term, well-known clinical outcomes.

And then in terms of identifying patients commercially, so we think that there haven't been great estimates of population size in Wolfram syndrome. I think our best estimate is there's roughly 3,000 people with Wolfram in the U.S. But I think we definitely think it's underdiagnosed, which I think tends to happen when you have a rare disease with limited or no treatments available.

But I think what's nice is often in rare diseases, especially, you know, sometimes things called syndromes, you know, you're saying, "Well, how do we actually find these people? How do we actually identify them?" In this case, well, they present with what looks like type 1 diabetes. So that's already a population to look in. And it's, you know, caused by a single gene. And so there's already an ICD-10 code for Wolfram syndrome.

There's already genetic tests available. So it's really about, "Okay, look in this population, test for WFS1 mutations." And we think it should be relatively straightforward to identify people with Wolfram. And the last thing I'd say is, probably unsurprisingly, there are people with Wolfram globally. And you tend to find, you know, different sort of founder effects, in different places.

But everywhere you look, whether it's Japan or Sicily or Brazil or the U.S. or U.K., there are indeed people with Wolfram syndrome. So I think our hunch is that it's quite significantly underdiagnosed. But I think it's pretty easy, we hope, and pretty straightforward to get good estimates fogr the population.

Speaker 5

Post-type 1 diabetes, post that diagnosis, vision is the next thing to kind of break down. Is that?

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Yeah.

Speaker 5

Obviously, you guys could incorporate that, you know, in the phase redesign as well.

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Yeah. Absolutely. And I'd say it was a surprise but a nice surprise that in just six months' treatment, we're seeing stabilization or even improvement.

Speaker 5

Yeah.

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

In visual acuity. Good, you know, I don't think we wanna set this expectation. But, you know, one participant went from legally blind to not, which is really exciting. So I think there's many different outcomes we think we can look at in the phase III that we think will be really meaningful.

Speaker 5

Yep. Okay. Can we move to PSP, Charlie, I think?

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Yeah.

Speaker 5

Okay. So talk a little bit about, you know, PSP with 035, and, you know, just give us maybe some context for, you know, your development plans.

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

Sure. I'll maybe start and then pass to, to Camille pretty quickly. So maybe just reiterating, I think a lot of the excitement for PSP comes from we ran a 100-patient, roughly 100-patient, randomized placebo-controlled study in Alzheimer's disease and looked, among other things, at CSF biomarkers. And we saw a highly significant reduction in total tau and phospho-tau. And I think it's particularly interesting 'cause here we're using small molecules, which should hopefully be going intracellular.

We don't know of any extracellular action for these drugs. So you're really, you know, hopefully targeting tau, you know, at kind of the production or the early the early stage of where tau pathology is coming from.

So when we got those data, one of the questions we asked is, "What would be the main, you know, tauopathy that one might wanna target if you have a pretty potent effect on tau with a small molecule?" And PSP resoundingly came out as the tauopathy that you might wanna target. You know, the genetics strongly support, you know, a connection to tau. You look at the pathology in the brain.

You see tau pathology all over the brain. You know, so tau is clearly linked to this disease. So our trial, you know, is ongoing. You know, maybe I'll pass to Camille to talk a little bit about, you know, when we're gonna get data and how and everything like that.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Sure. Absolutely. Thank you, Josh. Yes. And thanks for the question. At the end of last year, we began enrolling in the pivotal study for our phase III study for PSP. And we had always planned an interim analysis to understand where we were with the program. And we're just moving that up a little bit.

So by mid-2025, we will have some interim data to share. And our plan is to look at the totality of the data, including the PSP Rating Scale as well as other measures of the disease, including biomarkers. And our plan is to look at the totality of the data for outcomes to be extra confident as we go into the second portion of the study.

Speaker 5

Gotcha. And when you think about the endpoints, phospho-tau, sort of a serum marker versus an imaging marker, like, is this.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Right.

Speaker 5

Is there a different level of sort of confidence or conviction when you compare those two?

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Sure. So actually, in the Alzheimer's study, it was CSF tau.

Speaker 5

Okay.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

We also will be looking at that in these individuals. There are imaging measures, MRI volume as well as a particular type of image that one sees because of the loss of the cortical.

Speaker 5

Right.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Other aspects. Both are, will be helpful in directionally telling us how we're doing.

Speaker 5

Yeah.

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Yeah. And I think what's nice is we're getting lumbar punctures at a few different time points in the study. And so we'll be able to look at a variety of different tau species, you know, if we think that's important. And I think, at least from the Alzheimer's field, I think the work that's been done recently showing which tau species in CSF correlate with tau imaging, I think, are very compelling. And actually, our global PI of the study.

Speaker 5

Mm-hmm.

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Günter Höglinger is one of the world experts in tau pathophysiology. So we'll be relying a lot on his expertise in terms of, you know, what do we think these particular tau species reductions mean? But I think, as Josh was saying, what's nice in PSP is that it's a very pure tauopathy.

So I think unlike in some cases like Alzheimer's or other tauopathies where I think we're still learning, "Okay, maybe this phospho-tau species tells us this. And this one correlates to amyloid. And this one correlates to brain degeneration." In PSP, it's pretty clear that it's a tau-driven neurodegenerative disease.

Charlie Yang
Senior Equity Research Analyst, BofA Securities

Right. Yeah. So, so I guess in, you know, in terms of the data that we expect to see, kind of what are, like, the subgroup analysis that you can do, you know, and are they, like, pre-specified, or are they going to be mostly kind of post-hoc analysis?

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

We haven't gone into detail yet. You know, I, we, we tend to be pretty rigorous in our analysis of things. This will be a very, you know, formal interim analysis. But I think, as Camille was saying, it's really gonna be the totality. It's not just utility but efficacy and looking at PSP Rating Scale, tau, MRI degeneration, you know, basically to give us confidence that we're seeing a meaningful effect here. Therefore, we wanna expand the size of the trial.

Charlie Yang
Senior Equity Research Analyst, BofA Securities

Got it.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

We'll have a statistical analysis.

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Yeah. Exactly.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Upfront before we do the analysis, for sure.

Charlie Yang
Senior Equity Research Analyst, BofA Securities

Yeah.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Yeah. It won't be post-hoc.

Charlie Yang
Senior Equity Research Analyst, BofA Securities

Got it. Okay. And maybe just on kind of maybe going, oh, just a step back in terms of kind of why you're kind of moving into phase III directly, like, kind of without kind of going through the typical kind of phase II study?

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

Sure. Yeah. So I think, one, I think by having the interim analysis, I think in a sense, you kind of do get a built-in phase II, you know, just to be totally frank. You get an early look where you can, you know, kind of look at the totality of the data, use that to, you know, design, modify, adjust, you know, going forward as needed or to, you know, double down and accelerate and everything like that.

So I guess we do, we kind of see that there effectively is a built-in, you know, phase II in how we design this. But what it does allow in building it this way is to be kind of operationally seamless, to allow you to, you know, presuming you see the effect there, to lose as little time as possible moving forward but you still have that moment built-in to kind of, you know, give an early look to decide, you know, how you're gonna move forward.

Speaker 5

Is there as much science? I know in Alzheimer's, you know, you have beta amyloid. You have oligomers. I mean, there's a lot of the correlation between that and cognitive decline is, it's a bit of a gray area. But in tau, though, you know, you're either, you know, it's sort of high, low. But the quality of the tau tangle, if you will, like, has not really been that characterized. Where are we in the science for PSP and sort of grading, you know, kind of the disease progression as it correlates to tau?

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

Yeah. I'd say it's advancing. There was just a good paper. I think it was in Brain that was looking also at tau seeding. You know, you may know about kind of the RT-QuIC assays and everything.

Speaker 5

Yep.

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

That have come for alpha-synuclein seeding. They've been doing the same for tau. They found a pretty dramatic signal in PSP. PSP also has peripheral tau as well, which, you know, is not seen in many of the other tauopathies. So you'll see it in, you know, in cranial nerves. You'll see it in kind of nerves outside of the CNS as well. So people have been looking for correlations there.

But I would say that the field is, like, there's, you know, quite a lot of tau pathology. So the field is, I think, still looking a little bit for the absolute best one to correlate with clinical progression. But I think the area of the field is in pretty firm agreement, especially with the strong genetic linkage, extremely strong genetic linkage of tau to the disease, is that this is a tauopathy.

Speaker 5

Right.

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

You know, so that, you know, tau and particular variants of tau can cause this disease. So how do we intervene in that, I think, is how the field thinks about it.

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Yeah. Which is where, too, we think, small molecule approach can be very compelling because, you know, for example, with antibodies, you know, you get incredulity questions of what part of tau are you targeting and where is it and how much actually gets in the brain and it's extracellular and these sorts of things.

Small molecules get everywhere. And so at least in our Alzheimer's study, when we looked, kind of no matter how you measured tau, whether just, you know, CSF, ELISA, different phospho species, or even proteomics, it was very dramatically lowered. And I think that's probably not surprising with a small molecule.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Yeah. I think that is an important point, Justin, just to reiterate that with AMX0035, it is intracellular as well. And that's, but not unexpectedly, an important characteristic.

Speaker 5

Right. Okay. Maybe if we switch gears to, kind of going back all the way back to ALS, you know, with your, antisense oligonucleotide 0114, maybe talk about kind of the mechanism and why you think, you know, this could be a, a good approach, you know, in this kind of difficult indication.

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

Sure. So AMX0114 is a 5-10-5 gapmer antisense oligonucleotide that inhibits, you know, downregulates calpain-2. So calpain-2 is a target, you know, I'd say generally at Amylyx, as we were in ALS, we spent a lot of time looking at the different targets that we might go after. And calpain-2 rose to the top as our kind of favorite target, to go after in ALS.

And I think that particularly arose out of you go through the literature, and there are years and years and years, really decades, of papers showing that calpain-2 is an essential protein in axonal degeneration. People have inhibited it in various, you know, neurodegenerative models, not just in ALS but MS, Parkinson's, Huntington's, etc., in vitro, in vivo. And you see a pretty consistent benefit from, you know, from inhibiting calpain-2. So we were really interested in the target in that regard.

The second thing that's nice is it's a protease. When you look work on a target that's a protease, it cleaves other proteins and leaves behind various unique fragments. So that makes it very easy to measure the activity.

One of the proteins that it cleaves is neurofilament light. In the literature, people have shown and we've actually shown in our preclinical experiments as well that when you inhibit calpain-2, you see a reduction, you know, in, in the kind of extracellular, you know, neurofilament light levels. I think all of that led to this being, I think, a pretty exciting target, where it translating this to clinic now, we hope to be in clinic before the end of the year, a multiple ascending dose study in ALS.

I think one big thing we'll have with this program that was probably more challenging with 35 is some real kind of biomarkers to focus on, both in terms of those proteolytic fragments that calpain-2 makes, but also neurofilament light itself, which we think that biology is, you know, very linked to, which should hopefully, you know, give us a really good target to measure even in an initial phase study.

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

And I'll just add to that. I think, you know, a question we often get is, well, if there's so much research on this, like, why has nobody targeted calpain-2 before? And I think it's, in our opinion, not just our opinion, from the literature also, you wanna very specifically inhibit calpain-2. So there are mutations in calpain-1 that cause forms of spastic paraplegia. There are calpain-3 mutations can cause form of limb-girdle muscular dystrophy. There's, you know, there's many, many different calpains.

So we wanna very specifically inhibit calpain-2. That's been challenging with other approaches. With an ASO, you're very certain that you knock down calpain-2 and not the other calpains. And with intrathecal administration, you're very certain that you're getting it into the CNS.

So I think it's why it's such a nice approach for a target that I think has been very well researched for decades, as Josh was saying, but hasn't been approached the right way. Maybe the last thing I'll say, Josh touched on it, but, we think there's, great evidence for, calpain activity being important in a number of different diseases.

From this trial, we'll get, I think, really robust information not just for ALS but what may support for other indications too, especially because we'll be getting, CSF in each cohort at multiple time points. And we'll be able to look at biomarkers, such as NFL that we think may, indicate not only that this might be an approach for ALS but for other diseases as well.

Speaker 5

In just the minute that we have, maybe just at a high level, what are you guys' thoughts about, you know, further in-licensing other, other compounds, you know, that, that balance with, you know, with sort of preserving cash levels or enough, enough to, to take these other programs forward?

Joshua Cohen
co-founder and Co-CEO, Amylyx Pharmaceuticals

Well, I mean, at first, I think we have a pretty strong cash position. Especially we swiftly restructured. So I think we have cash for, for quite a while, you know, well into 2026. And so we think we have an exciting pipeline.

So that's, that's, you know, focus area one, two, three. If there are things that complement that and that are that we think are excellent science, we'll certainly pursue that. But, you know, focus for now is certainly on, you know, three programs we have, which, you know, all have milestones coming up soon and I think are all really exciting.

Speaker 5

Yeah. Okay. Thanks, guys.

Camille Bedrosian
CMO, Amylyx Pharmaceuticals

Yeah. Thank you so much.

Justin Klee
co-founder and Co-CEO, Amylyx Pharmaceuticals

Thank you both.

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