Bioinformatics for biomedicine

Marina Moskalenko, NSU Press Service 

A laboratory of structural bioinformatics and molecular modeling is being opened at the Faculty of Natural Sciences of Novosibirsk State University. The new scientific division will analyze the structure of biological macromolecules, as well as solve fundamental and applied problems using existing computer modeling methods and develop its own algorithms and programs for predicting the spatial structure of biopolymers. The results of the scientists' research can be used in materials science, bio- and nanotechnology and medicine.

The ideologists of the project are Anastasia Bakulina and Andrey Kayava. Photo of the NSU press service

Mathematical and computer methods occupy an important place in modern biological research. They contribute to the understanding of biological processes, and without them it would be impossible to carry out such global projects as decoding the human genome, computer modeling of new effective drugs ("drag design") and simulation of the spread of epidemics, analysis of the environmental consequences of industrial facilities, and much more. Now such an urgent direction will be developed at NSU with the funds of the 5-100 Project. 

Among the priority tasks of scientists is the study of the molecular structure and mechanisms of formation of amyloid plaques, pathological formations in the brain that appear with the progression of Alzheimer's disease. Bioinformatic and structural studies in this area can shed light on the emergence and development of such a disease and contribute to finding methods for early diagnosis and treatment of this common ailment that leads to senile dementia. In addition, the laboratory staff is engaged in computer modeling of proteins on the basis of which it is possible to create a vaccine against HIV infection, as well as the search for targets to fight other diseases. The new NSU laboratory will be headed by a visiting scientist, Candidate of Biological Sciences Andrey Kayava, who is currently both the head of the Structural bioinformatics and Molecular Modeling group, and the Director of Science at the National Center for Scientific Research (CNRS) of France.

– One of our future directions will be working on the problems of amyloid plaques, – says the scientific director of the project. – It is still unknown for sure whether such proteins are the cause or consequence of Alzheimer's and other neurodegenerative diseases. In the laboratory, we will try to understand the molecular basis of the disease: why do normal molecules spontaneously begin to aggregate and form plaques at some point? Accordingly, if we understand this, it will be possible to think about how to inhibit, suppress such processes.

The head of the new laboratory Anastasia Bakulina, Candidate of Biological Sciences, lecturer at NSU and part-time employee of the State Scientific Center of Virology and Biotechnology "Vector", agrees with her colleague: 

– The situation with Alzheimer's disease is actually worse now than with cancer. If we can confidently say that we are conducting a slow offensive on all fronts against him, then everything is bad with neurodegenerative diseases. Some medications have been developed, but the test results have shown that they are not effective. That is, Alzheimer's is such a thing that it is not clear at all how to deal with it. 

Scientists also intend to identify proteins that may be targets for drugs for other diseases. 

– The most time–consuming part in pharmaceutical development is to find good target proteins for new drugs. And we will do it, – says Andrey Kayava.

In addition, the researchers plan to use bioinformatics tools in the search for solutions for an HIV vaccine. 

– There is still no vaccine for such an infection, – Anastasia Bakulina explains. – We can't immediately give out a ready-made vaccine, but we have the opportunity to take some separate piece of protein from the human immunodeficiency virus molecule, analyze it and make a prediction necessary for the further creation of the drug.

Research in this area will be useful for many other new viruses, for example, SARS (SARS, which claimed many lives in Vietnam and China in 2003). After all, according to the researchers, now scientists simply do not have time to make vaccines quickly for many viruses. A recent example is the Ebola virus. Anastasia Bakulina was engaged in the analysis of mutations in the protein of this virus. 

– Traditional vaccine preparation technologies are very long. If we quickly find an option, a solution, and, let's say, Vector will synthesize it quickly, test it on animals, then we may have a real technology that allows us to make vaccines very quickly," says the head of the laboratory.

After decoding the genome, scientists have become aware of a lot of information about a person, and, according to researchers, it accumulates faster than they manage to understand it.

– Therefore, it is important to develop programs that will analyze protein sequences and talk about what biological role these molecules have, – says Andrey Kayava. – Also in favor of bioinformatics is its relative cheapness: in traditional molecular biology, experiments are usually used that require expensive equipment, reagents, cell cultures, experimental animals, and the like. We do not do experiments, but, sitting at computers, systematize the already accumulated data, create databases of this data, analyze them, and this allows us to discover some relationships and phenomena that people in laboratories could not do themselves. In addition, we can often make a discovery that will make the experiment unnecessary, which will save time and money.

Now scientists are at the stage of attracting researchers to work in a group. They invite all interested biologists and programmers to cooperate (candidates who already have a main job and are ready to work part-time are also considered). For all questions, you can write to the head of the laboratory bakulina@gmail.com .

In addition, in November, the researchers will hold a school for young scientists on computer modeling of the structure and dynamics of biomolecules. They also plan to organize a bioinformatic hackathon and create a specialized master's degree.

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21.09.2015