Algorithm to boost search for new antibiotics by Russian and American scientists

The study was carried out by Aleksei Gurevich, Alla Mikheenko, Aleksandr Shlemov, Anton Korobeinikov, and Hosein Mohimani and published in the Nature Microbiology.

The algorithm VarQuest can allow us to compare two data bases: chemical structures of the biologically active natural products and mass spectrum of the substances that the micro-organisms under study produce, says SPbU Associate Professor, Candidate of Physics and mathematics Anton Korobeinikov.

“Each data base has ten thousands of compounds, and our algorithm are quick in finding the similar ones, — said the researcher. — The scientists can find a new compound that is similar to the known biologically active substance and examine it methodically and in detail. Presumably, the new substance would be more pharmacologically effective than its known analogues in the data bases”.

Established in the late 2014 at SPbU, the laboratory “Centre for Algorithmic Biotechnology” is headed by Candidate of Physics and Mathematics, Professor Pavel Pevzner from the University of California. A real breakthrough the laboratory has achieved is a Genome Assembly Algorithm SPAdes (Saint Petersburg Assembler) that is used by the thousands of experts in genomics worldwide. The article that describes how the assembler works have been cited in about 300 papers, according to the Google Scholar, and become one of the most cited works in Russia for the last 5 years.

The VarQuest is especially useful in medicine, says the first author is a junior research fellow Aleksei Gurevich at the Laboratory. “The scientists raise the global alarm that the bacterial pathogens have become antibiotic resistant and we therefore have to develop new drugs, — he said. — A new drug on the market implies two stages: search for biologically active natural product that will be incorporated into the drug and testing the drug on people and animals. We cannot make the second stage go quicker as it will harm people, while we can do it with the first stage. Most antibiotics are based on natural products. If we want to find the compounds with the pre-determined properties, we need computational methods to process big experimental data bases. Our algorithm ensures we can reduce the time necessary to find new antibiotics”.

The biggest data base of the natural products is collected by the scientists worldwide and has more than a billion of mass spectra. It is on the GNPS Spectral Libraries (The Global Natural Product Social Molecular Networking). If you a registered user, you can use it, just as VarQuest.

The research is a real breakthrough in reviving antibiotics production in Russia. In 1960s, the Soviet Union was at the forefront of the research in the sphere. In 1985, the USSR produced 2,300 tones of antibiotics, while in 2005 Russia completely stopped the antibiotics production. The VarQuest may as well revive our antibiotics industry, thus helping the scientists  sequence the genomes of the bacteria and fungi that produce natural antibiotics.

The VarQuest is part of the research that is financed by the Russian Science Foundation and American National Institute of Health.