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It is well-known that mathematical and computational methods play a significant role in modern biological research. They help to understand biological processes better and are widely used in such global projects as decoding the human genome, drug design, simulation of epidemic spread and environmental consequences analysis for zones of industrial facilities (to name but a few). Such topical research will be held at NSU and supported by funds of the Project 5-100.

One of the priorities is to study the molecular structure and mechanisms of forming amyloid fibrils, which are proteins that build up in the brains of patients with Alzheimer's, killing brain cells. Bioinformatics research in the area together with structural analysis may shed some light on how Alzheimer's appears and develops. Scientists are expected to discover methods of early detection and effective treatment of such a wide-spread disease causing senile dementia. Furthermore, the researchers are going to use computer modeling to create proteins which may be able to block HIV, the virus that causes AIDS, as well as other viruses causing dangerous diseases. The scientific supervisor of the Laboratory is a visiting scientist, Dr. Andrey Kajava, who holds a position of Director of Research at the Centre National de la Recherche Scientifique (CNRS) in France.

‘One of our focus areas is amyloid fibrils formation,’ says the researcher. ‘The fact is that amyloid fibrils appear in the process of several neurodegenerative diseases, including Alzheimer, Parkinson and Hungtington diseases. However, an understanding of the structure and mechanism of amyloid fibril formation remains elusive, as well as whether such proteins cause the above diseases or are just a consequence. We are going to study the molecular basis of the Alzheimer disease, why ordinary molecules suddenly begin to aggregate and form the fibrils. If we understand this, we can generate some ideas how to inhibit, suppress such processes.’ Anastasia Bakulina, who works at NSU and SRC VB "VECTOR" and will head the Laboratory at NSU, agrees with her colleague, ‘The situation with Alzheimer's is now even worse than that with cancer. We are chugging along to our goal of fighting the latter, but the treatment of neurodegenerative diseases is far behind. Neurodegenerative diseases are considered incurable, resulting in progressive degeneration and/or death of neuron cells. There are some drugs going through clinical trials, but they fail to prove their efficiency. Thus, Alzheimer's proves a hard nut to crack.’

The researchers plan to identify proteins that could serve as targets for new drugs and vaccines against different diseases.

‘The most labor-intensive thing about pharmaceutical solutions is to find appropriate target proteins for new drugs. We’re going to take it up,’ says Andrey Kajava.

Another plan is to use the instruments of bioinformatics and work toward an AIDS vaccine. ‘This infection does not have an effective vaccine yet,’ explains Anastasia Bakulina. ‘We cannot come up with a ready vaccine, but we can take a piece of HIV molecule, analyze it and make a prediction for the development of a drug.’

Such research is going to be useful for many other new viruses, for instance SARS, which killed many people in Vietnam and China in 2003. Researchers say that they don’t have enough time to create vaccines for emerging viruses. One of recent examples is Ebola virus disease, which Anastasia dealt with by analyzing mutations in this virus glycoprotein.

‘The traditional way of developing a vaccine takes a lot of time. If we, at the Laboratory, find an appropriate variant fast enough, and "VECTOR" synthesizes it and then tries it on laboratory animals, we’ll have a real technology allowing to make vaccines quickly,’ says Anastasia.

After decoding the human genome sequence, scientists got a great deal of information about humans, and they say it accumulates faster than it can be analyzed.

‘It is essential to work out programs that could analyze protein sequences and identify their biological roles,’ says Andrey Kajava. ‘Bioinformatics has an additional advantage of being not so expensive in comparison to traditional molecular biology experiments, which require costly equipment, reagents, cell cultures, test animals, etc. Instead of doing experiments, we use computers to systematize the accumulated data, create databases and analyze them, which lets us discover some relations and phenomena that researchers could not see in the laboratory. Moreover, our discoveries may eliminate the need to do an experiment, which will save time and money.’

The researchers are inviting colleagues to join their team, especially biologists and programmers interested in the research area. Applicants may work on a part-time basis in addition to their main job. You are welcome to send your applications and inquiries to Anastasia Bakulina at bakulina@gmail.com.

In order to introduce some ideas, the researchers invite young scientists to attend a school on computer modeling for biomolecule structure and dynamics, which is to be held in November, 2015. They also plan to organize bioinformatics hackathon and give students an opportunity to apply for a Master’s level program.