RARE Daily

Bringing Aberrant Proteins Back into the Fold

May 21, 2021

In some diseases, such as lysosomal storage disorders, proteins are unable to serve their normal functions because they become misfolded. While some approaches, such as enzyme replacement therapies, have been used to treat these conditions, they can have significant limitations. Gain Therapeutics has developed a platform for using small molecule therapies to return proteins to their proper shape and restore their function. We spoke to Eric Richman, CEO of Gain Therapeutics, about its platform technology, how it works, and why it offers a compelling alternative to other approaches to treating lysosomal storage disorders.

Daniel Levine: Eric. Thanks for joining us.

Eric Richman: Thank you for having me. It’s a pleasure to be here.

Daniel Levine: We’re going to talk about Gain Therapeutics, protein misfolding, and the role this plays in a number of rare diseases, as well as Parkinson’s disease. We’re going to focus on the rare disease portion today, particularly lysosomal storage disorders. Perhaps we can begin with protein misfolding. Proteins are three-dimensional structures. What happens in the case of protein misfolding and what are its consequences?

Eric Richman: Good question. Protein misfolding is found in a variety of disorders and particularly in lysosomal storage disorders. Protein misfolding is the result of a genetic mutation or other stress factors, including anything, even aging. In the example of Parkinson’s disease, aging can cause protein misfolding. You find protein misfolding in a variety of diseases stemming from lysosomal storage disorders to oncology, metabolic diseases, cystic fibrosis, and many others. It’s a very important aspect of a cellular mechanism in that an enzyme has to be able to be free to act on a substrate. In a hereditary disease where there’s a mutation, an enzyme, and I use enzyme and protein interchangeably, may not be in the correct conformation. That means it’s misfolded. Because it’s misfolded, it can’t work on the substrate and it can’t move through the cell. The substrate then builds up and ends up in the recycling bin of the cell, which is the lysosome. Our technology is meant to stabilize that enzyme and push it back into the correct conformation. It can then flow through the cell and do what it needs to do with the substrate.

Daniel Levine: In the case of the diseases you’re pursuing, is the misfolded protein always an enzyme?

Eric Richman: First of all, let me take a step back and look at lysosomal storage disorders. There are approximately 70 to 80 lysosomal storage disorders that have been described in various publications, and of those, there’s only a handful that have any medicines whatsoever. Some lysosomal storage disorders that have treatments, and you’re familiar with some of those like Gaucher disease that has a product, Cerezyme, an enzyme replacement therapy. Those were very important products when they first came out because it was the first time there was anything to treat these lysosomal storage disorders. However, in the end, replacement therapy does not cross the blood-brain barrier because the molecules are too large. Our approach is different. We are creating small molecules that can stabilize the enzyme by crossing the blood-brain barrier. By doing so, we can treat the neuronal complications of the lysosomal storage disorders.

Daniel Levine: So again, in the case of the protein misfolding though, is the misfolded protein always an enzyme in the context of the diseases you’re pursuing?

Eric Richman: Yes, it is. Our starting point for identifying which diseases we can work on and which enzymes we can target starts with the 3-D crystal structure of the enzyme. That has to have been published in the literature as a starting point for us. Typically, we will only focus on diseases where there is a single mutation or a single protein that is misfolded. There may be other lysosomal storage disorders that are more complex that involve more than just a misfolded protein and those are lysosomal storage disorders and diseases that we’re not able to address at this time.

Daniel Levine: You mentioned the challenge of the blood-brain barrier. Traditional efforts to treat these conditions have been through the use of enzyme replacement therapies. How successful have these efforts been and what’s been the limitation of these approaches?

Eric Richman: As I mentioned earlier, it was truly a breakthrough when these products came out and we were able to replenish the enzyme that is defective. However, the neuronal complications are not addressed. Perhaps some of the symptoms of some of these lysosomal storage disorders can improve. Yet, the patient still is in a wheelchair. This is the focus and the goal of our treatments. By the way, we expect our small molecules could be combined with some of these other approaches, such as enzyme replacement therapy, and also, in the future, gene therapy. The way we see it is as another tool in the toolbox to be able to manage these diseases in patients that have different types or present at different times with these diseases.

Daniel Levine: Gain Therapeutics has developed a discovery platform it calls, See-TX. How does this work? And what’s the process for finding new therapeutics to target these conditions?

Eric Richman: The technology, SeeTX, stands for site directed enzyme enhancement therapy. This is a platform technology that was invented by one of the founders of computational biology as it meets super computers. It’s sort of the big data age of computational biology. This platform is highly efficient. It’s patented, and about a decade in the making. It’s very efficient at finding what’s called allosteric binding sites or binding hotspots. These are areas on the enzyme itself that when targeted by a small molecule the enzyme is stabilized. In other words, it’s locked into the proper conformation for the enzyme. How do we find these? Our approach is a target-based drug discovery approach. We start with the 3-D structure of the enzyme that’s responsible for the disease. Then through molecular simulations and molecular dynamics, we identify cavities that can be targeted. Yet, not all of those cavities are regulatory sites. Then we further apply molecular dynamics to look for free energy changes. Free energy changes predict which sites are regulatory and which sites can stabilize the enzyme. After identification of those allosteric sites, we then do a virtual screen to filter a pool of up to 10 million commercially available compounds to identify potential binders to that hotspot that would have a functional effect. Then what we do is rather common, in that we develop structural templates and traditional medicinal chemistry to continue to narrow the pool of enzymes that can facilitate correct folding to the enzyme and create scaffolds that stabilize the enzyme. So far, this process has been very efficient with the use of supercomputers, which makes it all possible. We can identify an allosteric site on an enzyme in five to six weeks, we can screen hits for some two to three weeks, and we can validate compounds in a couple of months. We’ve done this for all of the products in our portfolio and also in other areas outside of lysosomal storage disorders.

Daniel Levine: I think of allosteric binding sites being used to either activate or inactivate a molecule. What does it do to correct protein misfolding?

Eric Richman: The activation of the enzyme is by stabilizing it. If you can identify an allosteric site and design a small molecule to bind to that, then that has the potential to stabilize the enzyme and enhance its activity. What we have shown in some of the lysosomal storage disorders that we are targeting is, number one, we can find an allosteric binding site on an enzyme, two, we can target it and bind to it, three, that binding stabilizes the enzyme, and four, the enzyme’s activity is enhanced. So, what you look for there is depletion of toxic substrate and we see that in the relevant animal models.

Daniel Levine: This approach could provide an alternative to enzyme replacement therapies or gene therapies, which seek to correct the underlying mutation causing the disease. What might be the benefit of a small molecule approach compared to these other approaches?

Eric Richman: That’s a really good question. We have to look at them one by one. In the area of enzyme replacement therapy, as you know, it is a very inconvenient treatment for patients suffering from these diseases. It typically involves an infusion, which could be several hours to a full day every week or every other week, at a cost of somewhere between $250,000 and $350,000 a year. It’s a burden to the patients, a burden to the family, and, as discussed earlier, because it doesn’t penetrate the blood-brain barrier, it doesn’t even address the neuronal complications of the disease. So, adding in a small molecule approach is beneficial. A small molecule is easy to manufacture, it’s inexpensive, it’s oral, and that, in addition to enzyme replacement, potentially could address some of the neuronal complications of the disease that the enzyme replacement therapy does not address. In the area of gene therapy, I’m sure you’re aware that a lot of the gene therapy studies that are ongoing have various stages of clinical hold right now. Assuming all of that gets addressed, there are other issues that pop up. First of all, gene therapy is a very comprehensive treatment. There’s a lot of procedures that the patient has to go through before gene therapy. It can also be extremely expensive or projected to be extremely expensive. The gene therapy typically addresses a single homozygous mutation and therefore it’s limited. If there’s more than one misfolded protein or different mutations besides a single mutation, it may not have the ability to have any effect whatsoever in that patient. By combining it with our small molecule approach, there’s potential to have broader coverage of these various mutations on these genes.

Daniel Levine: The most advanced candidates in your pipeline are preclinical. What’s known about the ability of using this approach to restore function to enzymes?

Eric Richman: That’s a very important question and something that we’re generating the data on and are quite enthusiastic about. It’s a slow and long process to develop these types of treatments. What I can share with you is an example of Gaucher disease, where there is a very specific enzyme that is misfolded and it’s because of a mutated gene. That gene is also mutated in a form of Parkinson’s disease. What we have shown in our preclinical studies is that once we are able to target and identify the allosteric [site] and target it with a small molecule, we get enzyme stabilization in the patient-derived cells that have Gaucher disease. Then, in the area of Parkinson’s disease, we can actually show three different types of changes in biomarkers that you want to see. There’s an effect on depleting something called alpha synuclein, which is a marker for Parkinson’s. We also see improvement in dopaminergic neuron activity, that’s also a marker. Finally, in certain rat models, we can actually see an improvement in locomotion activity in certain tests that are given to these rats. All this together leads us to believe that identifying an allosteric site and targeted it with a small molecule and stabilizing that enzyme does have the potential to have an effect not only on the lysosomal storage disorder, but also potentially in areas like Parkinson’s disease.

Daniel Levine: Many of these diseases affect organs throughout the body, including the brain, although in some cases the neurological implications of these diseases take longer to develop. The problem with the enzyme replacement case of some of these conditions is that the therapy doesn’t get into the brain. What’s known about the ability of the oral therapy to address the CNS involvement of these conditions?

Eric Richman: It’s really premature for us to make any claims in this area and we wouldn’t do that. What we can do is tell you what we have observed in preclinical research. There, the small molecules penetrate various tissues and they do so in a dose dependent way, which leads you to believe that it can get into various areas of the brain depending on the dosage levels. Not only in the brain but also plasma and other tissue that is important for having a drug like effect. That’s something that we have seen and we’ve been able to repeat in our studies and it’s not the final answer, but it’s certainly encouraging.

Daniel Levine: Your lead candidate is in development to treat two different lysosomal storage disorders that both involve the same enzyme deficiency, this is GM1 gangliosidosis and Morquio B. What are they and how do they manifest themselves and progress?

Eric Richman: They are related. Morquio B and GM1 gangliosidosis both involve a gene called GLB1. The goal of a therapy is to stabilize that particular enzyme. Morquio B is relatively uncommon. The incidence is somewhere around one in every 250,000 to one in 1 million births. When there’s a mutation of that gene, the activity of the enzyme beta galactosidase is affected and that leads to an accumulation of a toxic substance called keratan sulphate. This is typically diagnosed in childhood. As the child grows, they notice a loss of nerve function, abnormal development, and hearing loss. There is no cure for this. This is a truly rare orphan type disease that needs new treatments. GM1 gangliosidosis is somewhat similar in that the enzyme beta galactosidase is responsible for breaking down GM1 ganglioside. An abundance of this results in neurodegeneration and neurological conditions. Again, this becomes apparent by six months and what’s observed is developmental regression, skeletal abnormalities, loss of vision, and even seizures. Again, there is no effective treatment and current approaches to treat the symptoms don’t really address the disease and don’t affect the progression.

Daniel Levine: What’s the prognosis for patients with the condition?

Eric Richman: Well, it’s very high morbidity and mortality for these patients. There’s really nothing suitable for them to turn to and that’s why it’s such an important disease to target.

Daniel Levine: What’s the development path forward?

Eric Richman: It’s continuing to do what we are doing, which is the preclinical research to identify a lead compound. Then taking that lead compound and making sure it does all the things that we expect it to do, including being available through oral administration and crossing the blood-brain barrier. Then entering to human clinical studies and being able to identify these patients early and be able to see if there’s an impact in managing these patients’ progression.

Daniel Levine: Is there a timeline you could offer at this point, if all goes well?

Eric Richman: If all goes well, we will be in the clinic next year, 2022.

Daniel Levine: Eric Richman, CEO of Gain Therapeutics, thanks so much for your time today.

Eric Richman: Thank you very much. My pleasure.


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