Overcoming Antibiotic Resistance

Guy S. Salvesen, PhD; Andrei Osterman, PhD

Disclosures

June 29, 2012

Editorial Collaboration

Medscape &

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Guy S. Salvesen, PhD: Hello. I am Dr. Guy Salvesen, Program Director in the NCI-Designated Cancer Center at the 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. Andrei Osterman, Professor at the Infectious and Inflammatory Disease Center. Today's program will focus on key research in identifying and understanding mechanisms behind the development of antibiotic resistance and how this research will affect clinical practice. Thank you for joining us today, Andrei.

Andrei Osterman, PhD: Thanks for inviting me.

Dr. Salvesen: One of the things that scientists and clinicians are very worried about is the development of resistance to commonly used therapeutics that target microorganisms, pathogens, and so on. What do you think the major hurdles are and the major issues are in that particular area?

Dr. Osterman: Development of resistance in microbes started millions of years ago. Essentially, most of our antibiotics today, as you know, are natural products that were developed by other cohabitants of the environmental niche, such as fungi and plants to fight bacteria. Essentially, we took some of them, modified them, and are using them now in clinical practice, which is a wonderful and great thing to do. We were fortunate for many years.

But the resistance existed in bacteria. In some sense, what we're seeing now is the uprising of bacteria that already had some elements of resistance and are just fine-tuning it to address the most common derivatives of traditional antibiotics.

Dr. Salvesen: What are the global health consequences of the development of resistance to drugs and bacteria -- or the selection for it, as you just explained to us?

Dr. Osterman: Development, or the propagation, of resistance takes place because of unwise use of antibiotics for clinical infections. What happens is that the resistance is propagating. We are essentially running out of means to fight bacteria.[1] Our pipelines are drying up because most of the antibiotics are just variations on very few themes.

In my opinion, the global consequence is that at some point, we may run out of them completely and some infection can cause devastation, as happened in the 15th and 16th centuries. Hopefully this will not happen if we continue our research.

Dr. Salvesen: Clearly, we need some new approaches here. Your research is focused on understanding the central pathways to program the metabolism within bacterial cells. How does that research give us some new ideas and new approaches that may overcome drug resistance and replace some of the current therapeutics?

Dr. Osterman: Our thinking is actually not necessarily even replacing, but instead expanding, our pipeline, using the approaches that for some reason were not explored by nature -- or at least we don't have evidence of the exploration of these paths in nature. They were certainly not explored by pharma. This means targeting a different set of novel targets -- instead of going on and on about several very well-established targets, choose new ones that can be used for developing completely new molecules.

This can happen largely because of genomics, because of our ability to sequence multiple genomes. We can look at the genomes of bacteria, the genetic information, and tell which genes or which enzymes encoded by them are absolutely conserved, essential for life of bacteria. We select those genes or enzymes as new targets and develop, using our chemical genomics approach, medicinal chemistry, a completely new class of molecules that is not derivative of natural products.

The premise here is that bacteria didn't get a chance to develop resistance to them yet over millions of years, so we're attacking novel targets. Also, these targets were not compromised by unwise use of antibiotics in clinical practice, so there is no preexisting propagated resistance to these molecules. That's essentially the idea.

Dr. Salvesen: You think your research is going to be targeting central, conserved mechanisms of metabolism within many different bacterial species? Maybe you could start off by telling me how many bacterial genomes we know the sequence of right now.

Dr. Osterman: The number of bacterial genomes is growing exponentially. At this point, we have more than 1000 genomes in the public domain and, in reality, a lot more are sequenced. What is also important is that we're now sequencing for variations, for various clinical isolates. We can actually say what the variation is, even within the same species. The amount of genomic information is growing, and this is critical and instrumental for these developments.

Dr. Salvesen: From the genomics point of view, does that tell you that there are specific targets that are shared between bacterial species that you should go for? Or are there individual targets within bacterial subtypes that would be good to exploit therapeutically?

Dr. Osterman: Both strategies are reasonable. For example, we are focusing our research in a very central component -- really, the central machinery. The idea here, again, is to find something that is completely essential and target it, which is not a bad strategy if you have such a bad enemy facing you. Of course, some people are focusing on more niche-specific targets because bacteria are also very diverse.

Again, in our approach, we are looking for conserved elements that are implicated by genomes, but we are also looking for their biochemical and physiologic importance. We don't want to target the gene just because it's conserved. We want to target it because we understand why it is so important for bacteria. That's the kind of science that I'm working in.

Dr. Salvesen: I know that you have a broad interest in this topic -- biochemical pathways from both the structural level and the biochemical and genetic levels. Do you think that the systems-level approach is giving us tools that we didn't have in the past that could lead toward identifying good targets, or do you think we need other tools as well?

Dr. Osterman: I think at this point, we are very well set with tools as far as dealing with microbial infection because of the genomes, physiologic tools, and our ability to analyze the transcriptome or a set of metabolites. Our knowledge of major pathogens, including genomic knowledge, is very profound today. I think at this point the focus is on actual development. Again, we have multiple examples of research projects, which are already well advanced, based on this knowledge.

Dr. Salvesen: Is there a chance that -- I'm sort of setting up here, I know there will be a chance -- but give me the level of chance for the targets you're looking at. If targets and therapeutics are made available, what will become of the bacteria that express these targets? Can they develop resistance as well? Whatever drug we have, will resistance be developed? Or are there some central conserved pathways against which you think you might be able to develop small molecules, drugs, and therapeutics that will target areas that cannot evolve and therefore cannot develop antibiotic resistance?

Dr. Osterman: Bacteria are so resourceful, which we know because of comparing genomes. Essentially, every target is a matter of chance and time. We are trying to increase the probability that resistance will not be affecting this particular pathway or target. We also understand it will take time. I think what is critically important is to have a pipeline to address multiple targets and have multiple means.

But you're right. When we're choosing the target, we're trying to take something for which there is less chance to develop resistance. As you know, there are multiple mechanisms of resistance.[2] For example, one mechanism of resistance may come from redundancy in certain metabolic and regulatory networks where bacteria can simply shut down the system that is targeted. We're trying to avoid this approach by targeting only those enzymes or those pathways that are completely indispensable.

The other possibility is to develop resistance and to develop a local mutation in your target enzyme and resist the drug. To avoid that, we are trying to target the active site of the enzyme, a place where changes are not likely because they will also affect the function of the enzyme itself.

Finally, a very important mechanism of resistance is efflux -- when bacteria essentially pump out the foreign molecules coming in. That's probably the hardest to fight. The idea is to use metabolic enzymes, chemical molecules that resemble more normal metabolites and may not be recognized by pumps as invaders -- these will have a better chance of being sustained within the cell.

Dr. Salvesen: Do you think that, looking at it from that perspective, there will always be a need to develop more and more drugs? Eventually, one cannot overcome the ability of the pathogen or the bacterium to avoid the drug by one of these mechanisms. You're always going to need a pipeline that you've talked about.

Dr. Osterman: I'm absolutely certain.

Dr. Salvesen: So, clinicians can look forward to new generations of existing drugs and new drugs completely. Eventually, as we keep using these molecules to combat disease, there will be a need to keep the research going in that area.

Dr. Osterman: You're absolutely right about that.

Dr. Salvesen: We can't overcome resistance. There's no way of completely overcoming it, but there are some areas that you can target to minimize the bacteria's ability to become resistant.

Dr. Osterman: I think we cannot overcome 2 things. First, resistance. Second, diversity. What's happening today is that we have drugs that are killing the major foes, the major pathogens, but the small one that was sitting in the niche and that was not really competitive now becomes competitive. Haemophilus influenzae is one example.

Some of these bacteria are intrinsically resistant for their existence. It's not that they developed resistance, but rather have intrinsic resistance to current antibiotics. They get a chance, when everything else is killed, to come up and rise. I think the need to keep the pipeline is to overcome the growing resistance, which will be always happening, but also the diversity of microbes.

Dr. Salvesen: Do you want to tell us about an example that you are working on that you think is a good target?

Dr. Osterman: We obviously think that the target we are working on is extremely good, and it took a number of years to select this target. I started choosing this target looking at the genomes about a dozen years ago.

We first identified a particular pathway of interest. It produced the molecule NAD, which is an essential redox cofactor.[3] Without going into details, at least 10%-15% of all the biochemical reactions in any organism are essentially dependent on this cofactor. This is not a protein; it is a small molecule, and this small molecule has to be produced by a set of enzymes inside of the organs. It cannot be taken up from the outside because of the limitations of transport for such a molecule.

All bacteria have machinery to synthesize this molecule, NAD, from its precursors, from the smaller blocks. Our inference was that the enzymes that are involved in the last stage of synthesis of this molecule may become a potential drug target. At that point, it was a hypothesis based on comparing genomes and doing some genetic experiments. I would say that at this point, it's a proven fact, owing to the work of others and our work: Essentially, we proved over many years that you can develop small molecules that can block synthesis of this essential cofactor by targeting particular enzymes. That would lead to the suppression of growth and killing of the microbes.

Dr. Salvesen: It's a great target, the enzyme systems that generate NAD. Of course, I guess we generate NAD in our bodies as well. What are the likely toxicity issues for using such compounds that would target that system?

Dr. Osterman: You're absolutely right. If we step back for a second and look at classic antibiotics, they are typically targeting a component of machinery that is not shared between us and bacteria. I think that nature was lazy, and it just went for the low-hanging fruit and developed what was easy. One would start to think why such antibiotics did not evolve themselves.

I think with the science that we have now, we can go about this problem rationally because our enzymes that make the same molecules are actually quite different; I should even say very different. At least, they're different enough that the inhibitors that would develop against the bacterial form of the enzyme do not affect our enzyme in a bad way.

We know that because we essentially perform this work in parallel. We have the human enzyme that performs the same reaction, and the bacterial enzyme. We compared them structurally and functionally, and when we look for inhibitors, we immediately test them for cross-reactivity. I think as long as we are conscious about this problem, we have a lesser chance to see toxicity -- although, of course, toxicity is a general problem.

Dr. Salvesen: We've been talking in fairly general terms. What sort of specific pathogens or specific diseases would you suggest we target with the novel therapies that you're working on?

Dr. Osterman: If we think about the importance for our society -- multidrug-resistant Staphylococcus aureus is a clinical infection, and Streptococcus pyogenes and S pneumoniae, which are affecting children and newborns. There are also bad infections in hospitals. These are probably the key major targets for this society. Obviously, multiresistant Mycobacterium tuberculosis is another problem. We're trying to look at these organisms.

There is a growing list of new pathogens coming. Day after day, we hear about outbreaks of Escherichia coli, which you and I use in our laboratories, There is quite a spectrum. The National Institutes of Health (NIH) and National Institute of Allergy and Infectious Diseases (NIAID) composed a list of pathogens and classified them as A, B, and C with respect to their potential importance.[4]

There is another aspect of the problem, which is not discussed too much these days. It is the potential of using microbes as agents of biological warfare. We know that they exist and are still stockpiled in certain parts of the world, and I think we should be also alerted to this possibility. That's the group of organisms that we are looking at.

Dr. Salvesen: It's something that is unpleasant to think about, but I think we need to be prepared.

What sort of human populations would benefit most from these novel therapies? I am assuming hospital patients, for example.

Dr. Osterman: Yes, hospital patients.

Dr. Salvesen: And for a more general population?

Dr. Osterman: A more general population, too, as a follow-up for, say, a flu epidemic, where there is always a bacterial infection you have to deal with. There is definitely a hospital population of elderly people with reduced immune resistance to bacteria, while in the whole world, definitely in less developed countries -- it's not only a compassion issue, but new strains can develop that can propagate to the rest of the world. There are no boundaries for infection, as you know, in the global economy and in the modern world.

Dr. Salvesen: It seems like this approach that we have discussed is very promising, but what can clinicians look forward to in the coming years? Are there going to be any stumbling blocks in generating and approving this new therapeutic strategy? How long down the road are we looking at before drugs become available for prescription, for example?

Dr. Osterman: I'm very hopeful, but at the same time, if we think about today, there are not many new drugs that were developed from genomics -- although there was a lot of expectation and a lot of enthusiasm, which is still ongoing, I wouldn't say too many drugs came out of this sort of de novo, rational approach. Most of the drugs that we're seeing today are still variations on the previous themes. I am hopeful there will be new drugs coming that will be developed. I know about the efforts in big pharmaceutical companies -- we collaborate with some of them -- that are trying to explore new targets.

It will definitely take time. There is a process of developing a drug, as you know; it takes a lot of time, and it's very costly. There is also a process with regulatory authorities and the US Food and Drug Administration (FDA). But I'm hopeful that within maybe a decade, clinicians will see a whole new generation of antibiotics.

My other hope for clinicians is that they will be able to use them more rationally once they start using genome analysis as a diagnostic tool. What we're seeing in capability today, I have no doubt that it's going to happen very, very soon. The clinician will be able to identify precisely what type of infection is ongoing in this particular patient and then go the shelf and pick the right drugs against the right bugs. That may change the picture entirely.

Dr. Salvesen: Andrei, you've explained to us a little bit about the process by which one identifies targets. Having identified a target using a combination of techniques, where do you take it next? For example, in your research, where are you going with it?

Dr. Osterman: Starting from this moment, when the target was actually identified through genomic discovery, we have to reduce it to practice, if you will. Essentially, we start and get it to the point where industry would be interested enough to pursue these small molecules and take them all the way to the FDA and to the pharmacy.

What we need to do, first of all, is to characterize these target proteins from representative microbial pathogens. We already did that for a number of them: Mycobacterium, Staphylococcus, and Streptococcus.

We also characterized the countertarget, the human enzyme that can be a potential victim of not-too-specific drugs. We characterized these proteins using crystallography -- we have a crystal structure so that we can actually identify which part of the active site would represent the most difference between the human enzyme and bacterial target.

We also performed high-throughput screening to identify small molecules that are already weak initial inhibitors -- "hit" compounds. That work was performed in the Sanford-Burnham Drug Screening Center.

Now we're currently working with chemists at our institute to improve these small molecules and make them more specific, with a higher affinity to make them biologically active in these cells. I think at this point we're pretty much advanced, but we still have a ways to go before the pharmaceutical industry will be interested enough to take them and develop them into actual drugs.

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

Dr. Osterman: My pleasure, Guy.

Dr. Salvesen: We would like to thank you for joining us today. I hope you will be able to join for additional programs in the Developments to Watch series on Medscape.

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