Alexey Vasilchenko: X-BIO is the perfect space for my research

Recent works conducted in the field of bacteriology by the University of Tyumen gained a wide press coverage. The discovery of an “antibiotics substitute” posed a special interest. The person behind the discovery – Alexey Vasilchenko, shares about his work process and found success in this interview.

– Alexey, are the headlines true and the excitement around your work is justified?

– In general, media loves to eksaduarate. Once something exiting is announced it is put through a media cycle, going from source to source... And the further it goes the more various details are added. Therefore, it is hard to judge what was said about our work.

As for the news about antibiotics substitute...  Peptides have long been considered an alternative to the so-called conventional antibiotics, which are prescribed by doctors. By the way, an interesting fact: the well-known, British bacteriologist Alexander Fleming, before his penicillin discovery, was actively studying the antimicrobial protein lysozyme, which is contained in biological fluids of animals.

– Is your work concentrated on making a breakthrough or piecing together preexisting data?

– In science, it makes no sense to waste time on problems that have long been analyzed and described. It is akin to trying to reinvent the bicycle; you can redesign it but you cannot add something fundamentally new. If you want to be successful, you have to do start over, make something completely new. If your work appears secondary, no decent journal would publish an article about it.

– You have discovered some new properties of peptides, correct?

– Our latest work that gained media traction was about a new structure found in peptides. It was bacteriocin, an antimicrobial peptide that is synthesized by bacteria, and it had a number of unusual properties not previously seen among similar peptides. This counts as a new discovery from the point of view of fundamental science.

– Would you explain the gist of what are peptides and bacteriocins?

– All living things, from the most primitive unicellular ones to, for example, elephants and humans, produce protective molecules – antimicrobial peptides and proteins. Protective molecules have certain properties that allow them to interact with bacterial cells, killing or inhibiting their growth. The production of protective peptides is probably one of the most evolutionarily ancient factors of the innate immunity of organisms. And bacteria, like any other living organisms have these molecules, which are called bacteriocins. By the way, each group of peptides has its own specific name.

– What is the next step? Are you trying to find new properties of peptides? Maybe apply that knowledge for practical use?

– One of the directions of our current work is the search for bacterial strains-producers of antimicrobial peptides. If we are able to find a molecule that is new in structure and properties, this already will be a big achievement. Another direction we want to take is conducting a comprehensive study of already known peptides, using new methods. For example, it is known that peptides can kill bacterial (and cancer) cells, but in order for this process to transpire, a certain effective concentration should be in place. In the natural environment, peptides are diluted, once the concentration becomes weak the non-lethal, so-called subinhibitory effects of these substances, become active (the same mechanism works in conventional antibiotics).

Thus, penicillin molecules, once diluted, no longer can kill bacteria, but work as signaling molecules for the quorum sensing (a phenomenon that describes the collective behavior of bacteria), which can increase the aggressiveness of the microbe. If antimicrobial molecules do not kill the bacteria, then they provoke it to respond. It may result in resistance to the antimicrobial molecules, and then it can escalate to developing an enhanced synthesis of various toxins or a transition to a persistence mode, and so on. In general, very few works have been devoted to the study of the subinhibitory effects of antibiotics, and even more so antimicrobial peptides. This is definitely worth investigating.

– Do you want to find a way to prevent these peptides from becoming diluted?

– First of all, we want to understand how a particular bacterial strain will react to small doses of antimicrobial substances. Ensuring that antimicrobial substances are stable and delivered immediately in the right concentration and to the right place is a slightly different task that we hope to tackle in the future.

– Some publications on this topic claim that there are advantages of peptides over traditional pesticides. If antimicrobial peptides have been known to be beneficial, why aren’t we using them now? Are they insufficiently researched or too expensive?

– Yes, all of these complications pose a challenge. The problem of antimicrobial peptides applications is that they are insufficiently researched and expensive to issue on an industrial scale. That is why it is necessary to develop new approaches for the production and purification of peptides.

The most common use of peptides is for plant protection. The transgenic plants are created by introducing a gene of the corresponding antimicrobial peptide. However, not all countries allow the use of transgenic plants.

– So, are you deciding to postpone the research?

– Not at all. We are primarily engaged in the development of agriculture, and the aligning problems. Subsequently, we are also working on solving the complex issue outlined above.

– Let's change the direction of the conversation then. You made quite a name for yourself in this field. How did you start out?

– My PhD work was related to the study of the microbial cells reactions to various substances using atomic force microscopy. Coincidently, one of these substances was a peptides agent from human platelets ... This was the most intriguing part of the research, thus I decided to investigate peptides and their effect on bacterial cells.

After graduation, I worked at the Institute of Cellular and Intracellular Symbiosis of the Ural Branch of the Russian Academy of Sciences in the Laboratory of Dysbiosis, where I could study a large collection of bacteria, including those that produce bacteriocins. Throughout the years, we collaborated with Evgeny Rogozhin, a specialist from the Institute of Bioorganic Chemistry of the Russian Academy of Sciences, whose focus of study is plant antimicrobial peptides. Over time, a certain research bassline formed, which made it possible to develop this topic further. For the last six months, I have been working at University of Tyumen to develop it even further.

– Why University of Tyumen?

– One of the graduates of my alma mater, Orenburg State University, is now a postgraduate student at University of Tyumen State. They shared about their great experience at the university, further career prospects and how good it is to live in Tyumen in general. This raving review and a combination of other factors inspired me to move to Tyumen. One of the biggest factors was the fact that my research in Orenburg fit well with the newly established Institute of Environmental and Agricultural Biology (X-BIO) tasks. Another deciding aspect was that my wife was hired too.

– You work a lot with your wife Anastasia Vasilchenko. Is “Family Contracting” Effective in Science?

– My wife is engaged in soil science. She wants to work with biopesticides as well, monitoring them in soils. The plant and the soil are viewed as one system here. Previously, our scientific interests did not overlap, I mean microbiology and soil science, but here, at the X-BIO Institute, certain points of contact have appeared.

– Do you collaborate with other scientists or organizations? 

– Back in Orenburg, there are still colleagues who work on similar projects; I keep in touch with them. There are also contacts with the Kazan State University. We value the connection with the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (Moscow) – the largest Russian center for the study of peptides and proteins, including antimicrobial ones.

Of course, we mainly collaborate with University of Tyumen. For example, we consult with the colleges at the Center of Collective Usage for Chemical Analysis and Identification Of Substances (in our research we use methods of analytical chemistry).

– Let’s circle back. Will we see a replacement for debilitating antibiotics and toxic pesticides in the near future?

– Sure. Whatever the commercial interests of pharmaceutical giants in the creation of new drugs, bacteria are not playing along. According to the World Health Organization, general antibiotic resistance poses a great threat. Therefore, a replacement or alternative to outdated antibiotics should be developed. A lot of research is dedicated to this cause. In principle, everything is ready to make a breakthrough; perhaps, the root of the problem is some political and economic issues.

– Last question. How are you finding Tyumen and UTMN? What do you enjoy in addition to science? What are your plans for the future?

– We moved here back in October 2017. Tyumen is good, hospitable, neat and clean. As for the university, at first I was somewhat surprised that the buildings are widely scattered throughout the city. However, in general, this is a normal occurrence in Russia.

I love to work out. I do karate. I fell in love with it almost ten years ago, when I was in graduate school. I put my best efforts into raising my son; he is two years and four months old. It turns out that this is a tougher task than it seems. 

My plans are to develop the existing groundwork for my research further and to build a laboratory for it, which is already in the works...