Russia is looking for ways to influence coronavirus at the molecular level

MOSCOW, December 15 Scientists at SamSTU have for the first time obtained a computer model of the coronavirus helicase protein and are now looking for ways to influence it at the molecular level. In their opinion, this will help in the future to find an effective drug for the treatment of COVID-19. The study results were published in the journal Current Computer-Aided Drug Design.
Helicases are a class of enzymes found in all living organisms. Their main function is to separate two strands of a DNA molecule or intramolecular bonds in RNA. It is helicases that contribute to the spread of coronavirus in the body through replication.

Scientists at Samara State Technical University (SamSTU, Samara Polytechnic) studied the coronavirus helicase and turned to computer modeling to search for its inhibitors — substances that selectively inhibit the activity of the helicase.
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“An important aspect of the SARS-CoV-2 life cycle is the reproduction of the genetic material of the virus. Helicase is directly involved in this process, as it unwinds the RNA of the virus and allows other proteins (replicases) to “remove” the virus. its copy,” explained Vadim Shiryaev, associate professor of the Department of Organic Chemistry of Samara Polytechnic University.

In his opinion, understanding the mechanism of operation of this protein at the micro level will facilitate the search for potential effective drugs for the treatment of COVID-19.

The scientist also added that currently the only available “weapons” against coronaviruses with proven effectiveness are vaccines, some of which have a whole list of contraindications and side effects. Meanwhile, according to his estimates, the issue related to the effectiveness of existing chemotherapy drugs for treating already ill patients remains controversial.

The created virtual model of the helicase protein is simplified for studying the protein itself, but it helps to see the behavior of the helicase during the transition from the free state to binding to a small molecule inhibitor. According to the scientists, such models allow the use of computer calculations to predict the behavior of protein-ligand complexes at the molecular level.
«We have shown that the cavity of the protein being studied can bind to compounds that have a framework fragment resembling the structure of diamond. Such compounds have already are used to treat various diseases, and can become a starting point in the development of new drugs to combat coronaviruses,” said Yuri Klimochkin, head of the Department of Organic Chemistry at Samara Polytechnic University.

According to scientists, the proposed approach is suitable to create molecules that interact with other viral helicases.

The further task of the scientific team is to continue the search for inhibitors of SARS-CoV-2 replication. The research was supported by the Russian Science Foundation grant 21-73-20103.