Search for new antibiotics

Konstantin Severinov, Post-science

As part of a joint project of Post-Science and Peter the Great St. Petersburg Polytechnic University, we are publishing a lecture by Konstantin Severinov, Doctor of Biological Sciences, dedicated to biologically active substances of bacteria.

The problem of resistance of pathogens of bacterial infections to antibiotics is now being heard. You can often read that a crisis is coming and soon doctors will not be able to treat diseases with the help of antibiotics available in their arsenal, which until recently we could cure thanks to some simple substances. And although antibiotics, of course, are very important substances, but, from the point of view of a fundamental biologist, it is not interesting how people use them to treat themselves, but rather the question of why bacteria need antibiotics at all, how they make them and what they use them for.

It turns out that antibiotics (a more general name is biologically active substances) are just a language with which bacteria communicate. Since they do not have a communication system like humans, they communicate with each other by chemical signals that allow one bacterium to give information to other bacteria that, for example, this place is occupied and one or another food source is present or absent here. Such chemical communication, the alphabet.

The bioorganic chemistry of those substances that are used for communication is very interesting. In nature, these substances are quite rare, and in order to make them, you need special enzymes, proteins that assemble complex molecules from simple precursors. With their help, you can exchange with each other and transmit some signals.

And I, as a biochemist, am interested in how such chemical structures arise. Another issue is the treatment thanks to these substances. For a bacterium-producer of anything – let's say it will be an antibiotic, that is, a substance capable of killing other bacteria – it is necessary to solve a number of tasks that do not seem simple at all. First, you need to be able to make this antibiotic. Secondly, you need to somehow not be killed by the antibiotic itself, which you produce, you need to somehow isolate it outside so that your neighbors can feel your presence, but at the same time maintain viability. By itself, this consideration immediately shows that the popular ideas of finding a magic bullet-an antibiotic that will cure and solve all the problems of bacterial resistance – is an unsolvable task.

Gene resistance to antibiotics is present in the very organisms that produce them. It's just the way nature works. In my laboratory, we are interested in trying to characterize as many antibiotics as possible. It is necessary that these are various antibiotics. We look at them precisely from the position of such chemical beauty and the biological mechanism of their action, how exactly this or that chemical substance is able to inhibit the growth of this or that microbe. After all, in order for this kind of oppression to occur, it is necessary that the substance that was produced by the producer gets inside the sensitive cell. There must be a special transport system.

By itself, this substance will not get inside the sensitive cell. Inside this sensitive cell, it must contact some target, with the components of some vital process, stop this process, as a result of which the sensitive cell will stop its growth. It turns out to be a rather difficult path. And we must understand that, since antibiotics are very diverse, their ways of action and mechanisms are also very diverse.

Only a very small number of antibiotics from all that are known today are actually used in practice. That is, we are talking about tens of thousands of known substances, of which literally several dozen are used. This does not mean that those substances that are not used are uninteresting. From the point of view of biology and evolution, they are worthy of attention. These are substances that for some reason have not yet found application in practice, and with the help of new methods that we have, we can create something more convenient to use.

The work we are doing is largely related to bioinformatic analysis. Recently, a huge number of DNA sequences containing the genes of certain microorganisms have appeared. Most of these microorganisms have never been handled by anyone. We have left the golden age of microbe hunters, when people, for example Zelman Waxman at the institute where I work in America, literally sent their employees to various places and asked them to cultivate bacteria from one or another soil sample in order to see if this cultured bacterium that grew on a Petri dish could, produce some toxic substance.

Nobody does that now. It turned out that the vast majority of bacteria simply cannot be cultured in our laboratory. We do not know what conditions of the nutrient medium should be created for a particular bacterium. This bacterium is there, but it just doesn't grow. Despite the fact that we cannot force or convince this bacterium to grow, we can use DNA sequence sequencing methods to determine the genes of this bacterium. There is no bacterium, but there are its genes, the genetic information necessary to create the products of the genes of this bacterium, in particular, for example, antibiotics. Antibiotics themselves are not encoded by genes, but are produced by the action of enzymes of proteins that are encoded by genes.

Such huge amounts of data, huge lengths of DNA sequences can be analyzed by special programs. They allow you to tell whether the product of a particular gene, a particular DNA sequence, is similar or not to something that could participate in the biosynthesis of some unique chemical group, whether the product of this or another gene can provide resistance to some antibiotic.

As a rule, antibiotic resistance is provided at the pump level. There is a pump on the cell membrane that throws some substance out. This is how you create resilience. We are actually making predictions: we look at the gene sequences and try to understand whether this or that gene or a complex of genes could be responsible for the synthesis of some new antibiotic. And if we decide that this is possible, the question arises of validation or experimental verification of the predictions we have made. Here we move on to the level of modern molecular genetics, molecular cloning, when a complex of genes, DNA sections, which, according to our considerations, may be responsible for the synthesis of one or another antibiotic, is transferred to the so-called surrogate host, that is, into a model organism, a model bacterium. We know very well how to cultivate it in the laboratory. A model bacterium is a so–called surrogate host, and in fact we are creating a transgenic organism. We inject into this bacterium, for example, into E. coli, the genes of an organism that may produce some kind of antibiotic.

We send letters to the most exotic places around the world where scientists have discovered such a bacterium, and ask them to send us a DNA sample. Often it is not even necessary to do this, because modern methods of chemical synthesis allow us to make really synthetic genes, that is, we can use the DNA sequence in the database to make a new chemical DNA molecule that contains all the information we believe is necessary for the synthesis of a new antibiotic.

Such DNA is introduced into a model cell, then we begin to conduct various physiological experiments to see if this cell has acquired a new property, whether it has begun to produce some new substance. At the same time, as a rule, we do not know what kind of substance it is. We can see if it has some kind of antibacterial activity, but it is not at all necessary that this will be the case. Very powerful analytical equipment is used, mass spectrometers, which allow weighing molecules with amazing accuracy and exceptional sensitivity and determining the exact molecular weight, and then using an electromagnetic field to break up such a molecule into its components, trying to determine what this molecule consisted of. This is such a solution to a puzzle-type problem, when we take a certain complex thing, break it into pieces, try to understand how these pieces then formed a whole together.

More often, of course, nothing happens. That is, the probability of our predictions being correct is somewhere 20-30%. But sometimes we manage to get new substances that have not been described before and were not known. And then the most interesting thing begins, namely, the study of how such substances are synthesized, how they are produced by producer cells and whether they act on any bacteria.

In itself, the effect on bacteria is not interesting to us from a medical point of view. We don't set out to cure someone of something. Very often, our new substances act on bacteria that are not pathogenic in themselves. But we are trying to go all the way from the production of a substance to its export outside, to its entry into a sensitive cell and interaction with a target.

The advantage of this work is that it is absolutely endless. The diversity of bacteria is gigantic, and there are many different bioactive substances that bacteria have learned to produce in the course of evolution. Newton said that he felt like a little kid on the seashore, who just picks up beautiful pebbles. We have a billion of these stones, and each of them can be beautiful.

Despite the fact that most of the time, of course, we are engaged in satisfying our own curiosity, our activity is not completely useless, because with some very small probability some of the new substances that we produce, or study, or discover may actually turn out to be future blockbusters. Another question: to find it, of course, you will need to turn over a lot of stones, the score should go not by tens, but by hundreds, maybe even thousands.

Because in order to become a valid antibiotic to be used in practice, it is not enough for a substance to have antibacterial activity, and it should be well tolerated by humans, it should not be toxic. Many early antibiotics were very toxic to humans. This substance can be obtained in large quantities, because sometimes we are talking about large-scale production.

There are a lot of restrictions that are not in our sphere of interests at all. But, as far as possible, we cooperate with people who are interested in the practical aspects of this kind of thing, and then, of course, our work simply boils down to the fact that, after the initial characterization of substances, we cooperate with doctors who are trying to check whether it may be that some of our substances really work for some pathogens that cause problems in the clinic. In one out of ten cases, our substances turn out to be somehow interesting to them.

At this stage, we part with our substances, because then it is not our sphere at all. Then someone else should try to bring them to the market, if you want, commercialize them. In fact, they are just conducting preclinical studies. This is a very expensive part of the work that requires a lot of time, it is extremely important, but it no longer applies to fundamental science.

About the author:
Konstantin Severinov is a Doctor of Biological Sciences, Professor at the Skolkovo Institute of Science and Technology (SkolTech), Professor at Rutgers University (USA), Head of the Laboratory of Molecular, Environmental and Applied Microbiology at Peter the Great SPbPU.

Portal "Eternal youth" http://vechnayamolodost.ru  26.05.2016