Keeping Hijackers at Bay: Novel Targets for Antivirals

Guy S. Salvesen, PhD; Sumit K. Chanda, PhD


November 07, 2012

Editorial Collaboration

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Guy S. Salvesen, PhD: Hello. I am Dr. Guy Salvesen, Program Director of the NCI-designated Cancer Center at Sanford-Burnham Medical Research Institute. Welcome to this segment of Developments to Watch from Sanford-Burnham and Medscape.

Joining me today is my colleague Dr. Sumit Chanda, Associate Professor of the Infectious and Inflammatory Disease Center. Today's program will focus on key research efforts in identifying novel targets for antiviral therapies and how this research will affect clinical practice.

Thank you for joining us, Sumit.

Sumit K. Chanda, PhD: Thank you for having me.

Dr. Salvesen: Of the many millions of microbes in the environment, just a handful affects humans. I understand that part of the reason is immunity, but certain microbes have targeted the host machinery, and your research is focused on the interaction between microbes and host cell machinery. Can you tell us a bit about that?

Dr. Chanda: If you think of the recent pandemics -- HIV, influenza -- they come from different species, either swine or nonhuman primates, and jump species into humans. That interaction or interface between the virus and the host is critical in determining how the virus becomes virulent and pathogenic within a given organism.

Traditionally, we focused on studying our responses to the virus or on the virus itself, but there has been limited knowledge on that actual interface -- where the virus enters the host and takes advantage of host cellular proteins to propagate its replication cycle.

If you imagine a virus, which typically contains 10-20 genes, and our cells, which have about 20,000 genes -- the viruses have a very minimal survival rate, and so they have to live off the land. They have to use our cellular machinery. What that machinery is is largely unknown and represents a potential treasure trove of novel targets that extend beyond just the virus, which is what we have traditionally done.

Dr. Salvesen: Viruses, as you point out, have a limited ability to reproduce on their own. They require the host cell.

Dr. Chanda: Absolutely.

Dr. Salvesen: Which major pathways does a host use to organize itself that are hijacked by the virus, and what does that hijacking do?

Dr. Chanda: Very little was known about this until recently, but there are various processes that the virus needs to enter the cell, to reproduce its genome, and then to exit the cell. All of these rely on facets of our normal cellular function. Things like endocytosis, genome replication, or budding are used by nearly all viruses to replicate within our bodies -- and targeting those without driving toxic effects may be a powerful strategy in developing novel antivirals.

One of the advantages of this approach is that, traditionally, when we throw a drug at a virus, the virus mutates its genome quite rapidly and becomes resistant. But if you target our own proteins, the virus doesn't have the ability to mutate around that as readily. So one of the key advantages is to be able to circumvent the issues of drug resistance that we see when we are treating diseases, such as HIV and influenza.

Dr. Salvesen: Would this be true for all viruses or only a subset of viruses? Is there common host machinery that all viruses must use and that we might target?

Dr. Chanda: If we found a target that we didn't need for a short time but that the virus did, I think that would be the Holy Grail. But we are finding that there are large subsets of viruses that use common cellular machinery. I don't think there is a silver bullet, but there is a possibility of developing broad-spectrum antivirals that span multiple viral classes. One of the advantages of that is that it obviates the need for expensive diagnostic tests to determine which infection you have.

For example, if you come to the doctor's office with a respiratory infection, it could be influenza, respiratory syncytial virus (RSV), or any number of infections. Once you rule out a bacterial component, if you find an antiviral that has this kind of broad-spectrum activity you don't need to send out for a test and wait 2 to 3 days for the results to come back. You can just prescribe a broad-spectrum antiviral that will target most viruses suspected of causing that kind of infection.

Dr. Salvesen: I think you used the numbers 20 viral proteins and 20,000 host proteins. I might even guess 200,000 host proteins with all of the posttranslation modifications.

Dr. Chanda: Yes, absolutely.

Dr. Salvesen: What kind of technology is required to drill down to the point where you know which of the pathways you need to target?

Dr. Chanda: A confluence of a number of different events has enabled us to ask and answer these questions.

First and foremost, the sequencing of the human genome gave us the parts list -- the number of genes in our genome -- and we applied to that a technology called RNA interference (RNAi), for whose discovery Drs. Andy Fire and Craig Mello won a Nobel Prize a couple of years ago. Essentially, RNAi allows you to introduce a synthetic RNA molecule into a cell and ablate the function of a specific gene.

We have taken that approach and scaled it up, using automation typically employed by the pharmaceutical industry to knock out or inhibit 1 gene at a time, but across the entire human genome.

The experimental setup is actually quite simple and elegant. You knock out 1 gene at a time, introduce the virus into the cells, and then ask the question, "Can this virus still replicate?" If it can't, then you can extrapolate that the virus needs that gene (or the protein that is encoded by that gene) to sustain its replication in the cell.

We have been applying this to a number of different viruses -- HIV, influenza, dengue, West Nile -- to identify components that are both shared and unique to each virus that it uses to facilitate replication and that are encoded in our own genomes.[1]

Dr. Salvesen: Has this systems-wide approach given you any insight into the common points of viruses? You already said that there is no silver bullet.

Dr. Chanda: Right.

Dr. Salvesen: Does it give you any insight into the common points that all viruses rely on in the host system?

Dr. Chanda: There are some common points. Right now, we are focusing on replication of the viral genome.

All viruses are composed of nucleic acids, with the possible exception of prions, and those viruses need to replicate their genomes, whether they are RNA-based or DNA-based. That is a step where the viruses implicitly rely on the host machinery, such as nucleotides or proteins that are lying around our cells and that we typically use to replicate our own cells. The virus hijacks those. That is a common mechanism that most viruses will exploit to facilitate replication.

As we have seen with cancer therapies that target these kinds of steps, our body can do without them for a short period but the viruses can't. So when we introduce this small molecule that inhibits this process, we are finding that it inhibits not only influenza, but also RSV and HIV. We even have some data on Ebola. In almost every class of virus that we have been able to assay in our labs, inhibiting this pathway with a small molecule has had a profound effect on viral replication.

Dr. Salvesen: Does targeting multiple viruses in this way rely on structural biology approaches, or systems biology approaches? Do you bring many approaches to bear on this? What is the most successful way of doing it?

Dr. Chanda: It is a true integrative strategy. Systems biology as a field is only about a decade old, and the innovations just keep coming. The field has had its growing pains and there have been some false starts, but we've found that an integrative approach, combining RNAi, which is a genetic approach, with a biochemical approach, works best.

We have been working with a collaborator at the University of California, San Francisco, Dr. Nevan Krogan, who has been able to look at the host-pathogen interface on a physical level by evaluating the biochemical interactions that occur between the host and the virus.[2] If we integrate that with our genetic data, the RNAi data, we get a real 3-dimensional understanding of what the host-pathogen interface looks like. That allows us to use our intuition and biological knowledge to zero in on targets that we think are going to be the most tractable and amenable to therapeutic modulation.

Again, the key here is to go after targets that are not toxic to us in the short-term. One of the advantages of going after the virus is that it encodes proteins that we don't have in our bodies, and so the chances for toxic side effects become smaller. We've talked about the disadvantages of going after that approach, but the disadvantage of going after our own proteins is that it can also make us sick. The challenge now is to catalogue these proteins and put together 3-dimensional maps to find appropriate targets that are also safe to target.

You can parallel it to getting a fever. We get sick, we feel uncomfortable, but the microbe really doesn't like it, and it flushes the microbe out. We can tolerate high fevers for a short time, whereas the pathogen can't. If we can do this therapeutically with a small molecule, we can flush the virus out while limiting the toxicity to ourselves.

Dr. Salvesen: Following up on toxicities, one of the issues that has perplexed clinicians for many years now is development of resistance toward therapy, toward drugs, and so on. Clearly, if you are targeting the host system, there is less chance of that. The host doesn't mutate as much.

Dr. Chanda: Right.

Dr. Salvesen: What are the issues with that? Is that an issue of concern to scientists who are using these kinds of approaches?

Dr. Chanda: Well, it is not that the virus can't mutate around the host, they just can’t do it as readily. So what we envision is that these might be part of some sort of combination therapy, which, as we have seen with HIV, has been immensely successful. If you add a host-targeting component to the mix, I think you will come up with a much more powerful cocktail. In fact, some of these have been tried with HIV -- there are now entry inhibitors that block the receptor for HIV.[3] So I think that we are starting along that path.

But to answer your question, I think the major concern is that whenever you target your own body's functions, there are going to be toxicities that we can't predict and don't understand. A number of careful safety studies need to be done as we move forward. But if we can find a protein or proteins that we can do without -- at least for acute therapy, like for influenza or RSV, whose treatment regimens span about 2 weeks --but that the virus can't, I think that is where the sweet spot is in this kind of therapeutic approach.

Dr. Salvesen: You mentioned that there are already attempts at combination therapy with small molecules -- for example, with drugs that target the entry system to the host. What are the next steps? Where do you see us going with this kind of approach? Do you think there are certain host mechanisms that are vital to target?

Dr. Chanda: Host entry targeting is a very powerful strategy, but unfortunately different viruses use different receptors to enter the host.

So the other strength of our approach is that once you have catalogued all of the different proteins that these different viruses use, you can zero in on the ones that are shared by most viruses. It is probably not going to be the receptor, because we already know which receptor is used by most viruses.

But there are components, such as the replication machinery, that are shared, and we are finding they are commonly used by multiple viruses. So we feel that intracellular targets -- using small molecules that can enter the cell and disrupt the function -- will give you this kind of broad-spectrum activity.

With this, we can start to move away from the "1 bug, 1 drug" paradigm and enter an era of broad-spectrum therapeutics. The 2 approaches have risk-benefit profiles that are complementary to each other, which is why I think the cocktail strategy could be a powerful way to boost the efficacy of treatment of antivirals.

The other advantage of the broad-spectrum approach is that when a virus jumps species and undergoes zoonotic transmission, say from a pig to a human, or wherever the next pandemic may come from, if you have a drug that we know works on viruses of certain classes, there is no need to go back and start over to develop an antiviral therapy. We will have drugs stockpiled and at the ready for new and emerging viruses that threaten the global population.

Dr. Salvesen: Looking forward to what clinicians can expect in the next few years, which populations would be most likely to benefit from these therapies?

Dr. Chanda: These could be applied globally. They could be used alongside front-line treatments and current antiviral regimens, and will be part of the armamentarium that clinicians have at their disposal to combat these viruses.

Because this is such a radical and new way of treating viral infections, we think they may not jump to the front line immediately, but as their safety is borne out with longer-term use, they could become the therapeutic regimen of choice for combating viral infections.

Dr. Salvesen: It sounds like a very promising future therapy, but how far downstream are we at this time? Are we close, or is there lots of fundamental work that still needs to be done to provide such therapy to clinicians?

Dr. Chanda: The basic biology is coming along rapidly, and we have a better understanding of new targets and new therapeutic strategies. The hurdle now is a regulatory one. As I mentioned, safety is a major concern, so we anticipate that there will be some stringent safety requirements that the US Food and Drug Administration will need to be fulfilled before it approves this kind of therapy for use in a general population. I would anticipate that, within a 5- to 7-year horizon, these drugs will start entering the market.

Dr. Salvesen: That was a very interesting topic. Thanks very much for participating in this program, Sumit.

Dr. Chanda: Thank you.

Dr. Salvesen: And thank to all of you for joining us today. I hope you will join us for additional programs in the Developments to Watch series on Medscape.