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Melanie Cole (Host): As COVID-19 edges from pandemic to endemic status, there's a growing need for antiviral therapies. A multidisciplinary team of University of Florida researchers recently published a paper in Genome Medicine that has identified dozens of therapeutic targets that could feed the drug development pipeline. Welcome to UF Vet Med Voice with the University of Florida College of Veterinary Medicine. I'm Melanie Cole and joining me today is Dr. Chris Vulpe. He's a Professor in the Department of Physiological Sciences at the University of Florida College of Veterinary Medicine. Dr. Vulpe, it's a pleasure to have you with us today. As we get into this topic, help us to understand SARS COV2 and the host factors involved. Tell us a little bit about what the virus hijacks to grow in us.

Chris Vulpe, M.D., Ph.D. Guest): Sure. And thanks so much. Well, the SARS COV2 genome, like most viruses is very small and as you're probably aware, viruses can't grow or make copies of themselves on their own. Instead what they do is they infect other cells. In the case of SARS, they infect human cells and they hijack the normal cellular processes and proteins that they need in order to make copies of themselves. So that would include making RNA, what we call transcription, making protein or translation and most importantly, I guess, making copies of their genetic material, in order to make more copies of themselves. And we call these, cellular proteins, which the virus is using to make copies of itself; we call these host factors. And the virus can't replicate without these host factors. So, understanding and identifying these host factors is very important in developing ways to treat SARS COV 2. It turns out that every virus does this, hijacking a little differently. So you have to study every virus. separately to try to figure out what the host factors are that are involved. And once you identify those host factors, then you can try to develop drugs, which can target those host factors and prevent the virus from replicating.

Host: Well, thank you for telling us that and why it's so important to address the growing need for antiviral therapies. So before we talk about your study, tell us how the collaborative team got together. It's really a COVID tale in and of itself isnt it?

Dr. Vulpe: Yeah, it's actually kind of interesting. So like, many researchers, after COVID hit, there was a shut down of most or many universities that essentially prevented you from carrying on and carrying out the research that you were doing. And we were sent home and especially since I didn't work in virology, I was sitting at home thinking, well, is there anything useful that we could do to try to, help with this? And my lab was largely involved in doing these CRISPR genome wide screens, which we'll probably talk about later. So I thought, well, maybe they could be useful for helping us understand what's going on with the host factors involved in SARS COV2.

But of course I knew nothing, essentially squat about virology and I had not worked with any infectious agents before. So I reached out to the head of the Emerging Pathogens Institute here at UF and, he put me in touch with another researcher here, Mike Norris, who had experience with serious human pathogens, primarily bacterial human pathogens and was very familiar with how to deal with dangerous bugs. And at the same time, was also connected to a virologist, named Stephanie Karst who had also been wondering about how to do this. And she was a virologist, but, ha, not as much experience in genome-wide CRISPR screens. And so, essentially over Zoom, we, we're able to orchestrate a collaboration between our three groups, which, together had the necessary expertise to carry out this work, and pretty much starting right around when SARS COV2 hit, we were meeting weekly by Zoom and our teams, as well as several volunteers from our lab as well as other labs, came up with this plan. We were able to get a little bit of funding from UF to do it. And, anyway, so that's how it started and it's been a really wonderful collaboration.

Host: Dr Vulpe, as we get into your study, can you tell us a little bit about the CRISPR gene editing techniques to screen for genes that help coronaviruses replicate in humans? Tell us how that works.

Dr. Vulpe: Well, as you're probably aware of, CRISPR gene editing was discovered sometime ago by two scientists, Jennifer Doudna and Emmanuelle Charpentier. And more recently it was adapted to be able to target mammalian genes. And CRISPR allows you to disrupt the function of essentially any gene in the human genome or genome, and this is what we commonly call gene knockout. And so by using this technique, we can systematically test all the genes in the human genome to see which ones are important for SARS COV2 to grow in cells. And the approach that we use called genome-wide CRISPR screening, allows us to do this in a massively parallel way, where we put all the knockouts together in one pool of cells. So in this pool, every gene is knocked out. But just one gene is knocked out in each cell, but together the entire pool represents the whole genome. And so you can take this pool of gene knockouts and screen it to find the ones which prevents SARS COV2 growing. Essentially you just infect this pool and look for the cells with knockouts that prevent SARS COV2 from infecting and survive a SARS COV2 infection.

Host: So then expand for us doctor on your paper and your studies. Tell us a little bit about this as having broad spectrum antiviral therapies that target host specific processes would be so useful against COVID genetic variants that we've been seeing such as Omicron and Delta, which really are extending this pandemic.

Dr. Vulpe: Well, first of all, just with describing the paper, essentially the paper used this CRISPR screening approach to find host factors for SARS COV2 in comparison to a common cold virus called OC43. and using this technique, not surprisingly, we found a whole bunch of host genes involved, as you would probably expect, in all parts of the viral life cycle from viral entry, including the protein that you're probably familiar with ACE2, steps in viral protein synthesis, construction of the viral protein coat, to viral egress or getting the new viral particles out of the cell. And each of these host genes, and the corresponding protein represents a potential drug target. So these could be used to identify potential candidate drugs that could target these genes.

One problem with current drugs that target SARS COV2, for example, remdesivir which works against the SARS COV2 RNA polymerase, is that viruses can mutate very quickly and develop resistance. And in fact a SARS COV2 mutant resistant to remdesivir has already been identified. The advantage of drugs that target host factors is that they're not as susceptible to viral mutations. It's much harder for the virus to mutate to circumvent its need for a host factor than to just mutate to prevent a drug targeting a viral protein. As a result, drugs targeting host factors are much more difficult for viruses to develop resistance to.

We identified multiple host genes that were necessary for viral replication and for several of these host targets, there were already existing drugs that targeted that gene or corresponding protein. We therefore tested many of these candidate drugs targeting host factors to see if they were effective in preventing viral replication. Several of these were very promising. One of the most promising targets, a host protein called TBK BP1, and this drug is a already accepted drug called amlexanox. And this was quite effective in preventing the replication of SARS COV2. It's already being used, and is non toxic in people.

Host: These are very exciting developments. Dr. Vulpe, as we get ready to wrap, I'd like you to summarize for us what you see happening in the world of antiviral therapies, because there's certainly a growing need to combat these viruses as we're seeing them mutate and change. What would you like other providers and researchers to know about what you're doing at the University of Florida College of Veterinary Medicine?

Dr. Vulpe: Well, I think one of the urgent needs is trying to prepare for the next pandemic, as well as trying to effectively treat the ongoing pandemic. And for this, we're going to need effective antiviral drugs that will be able to treat, not only SARS COV2, but the next wave of corona viruses.

And so in order to do this, we need to identify pan coronavirus drugs, and if we can identify drugs, which could target coronaviruses in general, they could ultimately help or prevent or mitigate the next coronavirus pandemic, as well as the current one. So a lot of our effort is trying to identify host factors that are involved in the infection of not just SARS COV2 but of coronaviruses in general, and working on identifying the drugs, which could inhibit those host factors and prevent infection, not only by SARS COV2, but by any coronavirus. And we hope that we will have that ready sooner rather than later, so that we're ready for the next pandemic.

Host: Thank you so much Dr. Vulpe for joining us today and telling us about your study and the need for more antiviral therapies to combat the growing viruses that we're seeing. To learn more about the development of antiviral therapies for COVID-19 or to listen to more podcasts from the experts at the University of Florida College of Veterinary Medicine, please visit vetmed.ufl.edu/ufachievers.

That concludes today's episode of UF Vet Med Voice brought to you by the University of Florida College of Veterinary Medicine, advancing animal, human and environmental health. I'm Melanie Cole.