ITMO’s Master’s Student Karina Pats: Why Writing About Research Is No Less Interesting Than Doing Research

Karina Pats, master’s student at ITMO’s Department of Intelligent Technologies in Humanities, published (available in Russian) the results of her research in the Laboratory of Structural Bioinformatics, under the supervision of the laboratory head Yuri Porozov, on the popular science portal "Biomolecule" (an educational portal, created and maintained by the staff of the Institute of Biochemistry at the Russian Academy of Sciences). In this article dated November 2017 she told us about such promising area as immuno-oncology. The student described an interesting area, such as immuno-oncology, and also highlighted the most interesting part of her research - the experiment on the molecular dynamics of the protein target. At the end of the year the Biomolecule portal summarized the results of an open competition for articles on biology and biomedicine topics in several categories. All of it resulted in Karina winning a prize in one of the categories, thus immediately receiving several awards and offers for collaboration

You won the open competition of the popular scientific portal "Biomolecule", dedicated to the molecular foundations of modern biology and practical applications of scientific achievements in medicine and biotechnology, in the category "My work". Tell us, what does your new status of prize-winner give you?

I received a diploma in the general competition in the category "My work", but there were other awards and offers for collaboration as well. For example, my article was separately noted and received a prize in the category "The Editor's Choice". The article itself will be published in the Russian Academy of Sciences’ journal "Priroda" (“Nature” - Rus.). In addition to that, I was offered to continue writing various materials for the portal. An official group was created on Facebook for the authors of the portal where they can exchange ideas and other information. Also as part of cooperation with "Biomolecule" you can review various popular science books or offer your ideas for any future materials.

Generally, I’m very interested in the field of science communication. When I entered ITMO for a Master's Degree, I knew that there was a Master’s Program for Science Communication at the university. However, I still decided to move along my own professional track, while the interest in scientific communication did not vanish. I think that in the nearest future I might take up writing my next text if the portal offers suggestions for it.

You have received a prize for a text (available in Russian) based on the results of your own research. What do you think is more interesting for you: to write a text based on your own scientific works or describe scientific achievements in principle, regardless of the authorship of the research? What areas are you interested in?

This is my first experience. However, I’ve had a keen interest in writing from school, and I'm trying to develop my skills in the liberal arts. Cooperation with such portals and the opportunity to write articles is one of the ways to develop in our professional field, combining it with a hobby. It would be interesting for me to concentrate on bioinformatics and chemoinformatics, attracting the interest of the general public to these promising areas. Since I received my Bachelor's Degree at the St. Petersburg State Chemical and Pharmaceutical Academy, I am extremely interested in the design of medicines. I have entered my Master’s at ITMO specifically for chemoinformatics, as I want to further develop in this field.

How did you get acquainted with ITMO, in particular with the International laboratory of structural bioinformatics and its Head, your supervisor, Yuri Porozov?

I studied industrial biotechnology at the St. Petersburg State Chemical and Pharmaceutical Academy. However, literally in the middle of my freshman year, I got acquainted with bioinformatics which interested me much more. So, I tried to get as far as possible into this area. My thesis I already wrote together with the Laboratory of Structural Bioinformatics at ITMO. And my scientific adviser was Yuri Porozov. The fact is, that during the training at the academy - in the last year - all students are sent to work in various laboratories and research institutes. And that's how I got to the laboratory at ITMO, where I completed my thesis project. So, I had two scientific advisors for my thesis: one from the academy and the second one - namely, Yuri Porozov. My article at "Biomolecule" is, in fact, the result of the work I have done during my last year at the academy, a significant part of which I have conducted research at ITMO’s lab.

Yuri Porozov

Was the experiment described in the article the main focus of your thesis? Tell us more: what is it all about?

Yes, I tried to introduce the reader to the general design of the experiment in an adapted format. As I understand that not everyone is familiar with this area or research, and reading its scientific details could be rather boring. I tried to write it so, that even an unprepared reader would understand: how the experiment on creating a biologically active substance is done on a computer. I tried writing about what to start with, what strategies could be applied - and I also tried covering some other issues.

Our experiment was conducted in the field of pharmaceutical oncology. We studied a fairly new promising target - the CIS protein, trying to find a suitable match for it: a small molecule that could block this protein. The article describes the mechanism of the protein’s action: namely, why it should be blocked, what it does, as well as some other interesting parameters. Our article also describes an interesting experiment on molecular dynamics in detail. That is, calculations of the behavior of this protein in a medium with water - for a certain, given time, which is predominant for our body. The article compares the inhibitor (blocking substance) developed by us and the reference compound, which binds with the CIS protein in our body by default. Our task was to develop an inhibitor that would bind with the protein more strongly than the reference compound. Accordingly, the article has colorful illustrations which clearly show the substance developed by us and the reference substance. There are some shortcomings in this work. However, for a one year research paper the results are quite impressive.

Why did you start your ITMO lab work by studying the CIS protein?

When I first came to the lab, I was offered several options to choose from. For example, one of the research topics was related to the development of new antibiotics. But it was the topic connected to the study of the CIS protein that I chose. Overall, immuno-oncology seemed to me more interesting because I was always close to the topic of developing new drugs in the field of oncology. And what’s more, immuno-oncology is a very promising area today.

Oncological pharmacology. Source:

At what stage is your project right now? And what are you doing in the lab currently?

This project got transferred to one senior Bachelor's student from the Chemical and Pharmaceutical Academy. Like me, she was assigned to the Laboratory of Structural Bioinformatics at ITMO. Today she is developing this project I started. It will be interesting to see what happens to it next. My focus has shifted to artificial intelligence and machine learning, as these two areas are quite relevant today. The idea of my current project has grown on the basis of the first project described in the article - automatic selection by machine learning of molecules suitable for different proteins according to the key-lock principle, which will be well connected with the protein. It is important that the molecules are valid in terms of chemistry: they should not be toxic, and they need to be synthesized. The global idea is to train the neural network to recognize the active protein center and on the basis of the data on which the network is trained, to select possible chemical compounds to the protein.

Where can this new development be applied?

This is a universal development for pharmaceutical manufacturers because so many classes of drugs, not only from the field of oncology, are aimed at blocking some protein target. Often the incorrect functioning of proteins causes the development of a disease. That is why it is important to be able to select an inhibitor that will firmly and selectively bind to a given protein in order to achieve the ultimate goal - to change the function of the protein by preventing or stopping the progression of the disease. And the effect that we expect to receive from this development is quite universal.

Are there any analogues that you rely on in your work?

Well, there is Insilico Medicine which has many branches around the world, including in Russia. The company is engaged in a similar task and also uses machine learning, but the company's employees are still generating different molecules for now, when we want to focus specifically on the fact that the molecules are selected for the active center of the protein, a specific target and its active center. This is especially important, because for inhibitors there are two significant parameters - affinity and selectivity. The first feature is the ability of the compound to bind firmly to the protein, the second is the ability not to affect any targets other than the initial target. High values of these parameters can be achieved by selecting a molecule suitable for the active center of a particular protein. The more the active center is studied, the more chances we have to construct a molecule that is suitable for this protein. This is one of our major tasks: to teach the neural network to accurately identify active centers.

Tell us, what would you like to do after the completion of your project, after you graduate from your Master's program?

There are two ways: PhD program and work in science or work in industry. So far, I'm inclined to go into the industry. I am interested in the development of medicines, after the academy I clearly understood that this area is of particular interest to me. I came to ITMO in order to learn how to program and apply this skill in my professional field, as this is a fundamental skill in the fields of bio and chemo-informatics. While at my academy there was no such department where students would be taught programming in the pharmaceutical field.

Antibodies battle cancer cells. Source:

Speaking about bioinformatics in general, it is quite a popular field. However, due to the fact that it is not taught at the academy, many students have knowledge in this area generated at the level of individual interest. I was lucky to get acquainted with this area because Elena Fedorova, the former head of the department of research work at the academy, was actively engaged in it. It was she who, knowing my interest in the field, "transferred" me into the hands of Yuri Porozov after she left the academy.

In your opinion, how different is the training in a classical academy and the training at ITMO, the first non-classical university?

The differences are quite noticeable. Of course, it is important to take into account that the Bachelor's and Master's Degrees are basically different. However, a student is given more freedom at ITMO. In addition to that, everything is less formal. For example, at the academy all lectures are strictly written, teachers dictate when, how and what to record, where to highlight. While at ITMO you set yourself the task of learning to highlight and record the most important information.

Do you already have any ideas for your future publications?

It seems to me that at the initial stages it is easier to write about your research. Now I'm researching a new topic - and the area is new to me also. Therefore, as soon as I have some ideas on the current topic, I will try to come up with written material. The topic I’m currently working on is rather promising. So, it is important to talk about it because so far it is fairly new and undeveloped in our country

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