Laboratory of Big Data Analysis for Digital Pharmacology
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Andrei A. Kashirin
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Viktoria M. Lusina
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The laboratory was established in 2024 for the purpose of studies within the framework of the research "Big data analysis of medical virology for the search of effective and safe antiviral compounds and optimization of therapy of infectious diseases" supported by the Program of Basic Scientific Research in the Russian Federation for the long-term period (2021-2030) (№124050800018-9).
THE PURPOSES OF THE LABORATORY
THE MAIN DIRECTIONS OF RESEARCH
Development of computer methods and software tools for automated extraction, integration and analysis of large chemical and biomedical data. The methods for extraction, integration and analysis of biomedical data are based on the application of machine learning methods.
- Development of a data organisation scheme within the system "Chemical сompound - molecular target - pharmacological and toxic cffects - disease".
- To develop and improve algorithms to analyse text data and automatically extract associations between objects (biological and chemical molecules).
- Compilation of training sets and building of machine learning models to estimate the effects of antiviral compounds, including side effects and toxicity.
- Development and improvement of algorithms for network analysis of intermolecular interactions for a comprehensive understanding of the mechanisms of side effects and toxicity of pharmacologically active antiviral compounds.
- Development of an information and computing platform for data selection of known effects of antiviral compounds and computational prediction of pharmacological, adverse and toxic effects.
The head of the laboratory, O.A. Tarasova, PhD is the author/co-author of more than forty articles, 38 are indexed by Web of Science Core Collection (WoS H-index 13), 40 are indexed by Scopus (Scopus h-index 14); more than 70 scientific papers indexed by RSCI (RSCI h-index 12). In 2024 O.A. Tarasova was awarded the Prize for the best scientific work of the first degree at the Forum of Young Scientists dedicated to the 300th anniversary of the Russian Academy of Sciences and the 80th anniversary of the Academy of Medical Sciences of the USSR (RAMS) "Medical Science: yesterday, today, tomorrow". The prize was awarded for the study "Analysis of HIV-host interaction using bioinformatics methods" in the section "Innovative methods and technologies".
O.A. Tarasova in 2016-2022 was the head of the projects supported by RFBR: 16-34-60187, "Fighting drug resistance to HIV-1 reverse transcriptase inhibitors" and RSF: 17-75-10187, "Analysis of HIV resistance mechanisms to HIV reverse transcriptase and protease inhibitors using bio- and chemoinformatics approaches"; 19-75-10097, "Analysis of the interactions between HIV and human organism considering prescribed HIV/AIDS therapy".
The laboratory research studies are conducted in collaboration with the Laboratory of Structure-Function Drug Design, headed by Corresponding Member of the Russian Academy of Sciences, Prof. V.V. Poroikov. The laboratory collaborates with the M.P. Chumakov Federal Scientific Center for Research and Development of Immunobiological Drugs of the Russian Academy of Sciences and FBIS Central Research Institute of Epidemiology of Rospotrebnadzor.
The staff of the laboratory has established stable cooperation with Federal State Budgetary Educational Institution of Further Professional Education "Russian Medical Academy of Continuous Professional Education" of the Ministry of Healthcare of the Russian Federation. In particular, computer models developed by researchers of the laboratory were used in studies of clinical pharmacologists and were described in the following publications: [Ivashchenko D.V. et al., 2018, DOI: 10.1515/dmpt-2017-003630], [Otdelenov V.A. et al., 2020, DOI: 10.37489/2588-0519-2020-S4-103-105], [Kiselev Y.Y. et al., 2020, DOI: 10.37489/2588-0519-2020-S4-75-80].
The laboratory's researchers carry out collaborative studies with researchers from the Federal University of Alfenas, Brazil.
Bitencourt-Ferreira G., Villarreal M.A., Quiroga R., Biziukova N., Poroikov V., Tarasova O., de Azevedo Junior W.F. (2024) Exploring Scoring Function Space: Developing Computational Models for Drug Discovery, Current Medicinal Chemistry, 31(17), 2361-2377. DOI:10.2174/0929867330666230321103731
Paremskaia A.I., Rudik A.V., Filimonov D.A., Lagunin A.A., Poroikov V.V., Tarasova O.A. (2023) Web Service for HIV Drug Resistance Prediction Based on Analysis of Amino Acid Substitutions in Main Drug Targets, Viruses, 15(11), 2245. DOI:10.3390/v15112245
Pikalyova K., Orlov A., Lin A., Tarasova O., Marcou G., Horvath D., Poroikov V., Varnek A. (2022) HIV-1 drug resistance profiling using amino acid sequence space cartography, Bioinformatics, 38(8), 2306-2314. DOI:10.1093/bioinformatics/btac090
Rhee S.-Y., Boehm M., Tarasova O., Di Teodoro G., Abecasis A.B., Sönnerborg A., Bailey A.J., Kireev D., Zazzi M., the EuResist Network Study Group, Shafer R.W. (2022) Spectrum of Atazanavir-Selected Protease Inhibitor-Resistance Mutations, Pathogens, 11(5), 546. DOI:10.3390/pathogens11050546
Khandazhinskaya A.L., Maslova A.A., Matyugina E.S., Kukhanova M.K., Kochetkov S.N., Mercurio V., Ñahui Palomino R.A., Margolis L., Vanpouille C., Novikov M.S., Paramonova M.P., Fedorova N.E., Yurlov K.I., Kushch A.A., Tarasova O. (2021) Dual-targeted anti-CMV/anti-HIV-1 heterodimers, Biochimie, 189, 169-180. DOI:10.1016/j.biochi.2021.06.011
Tarasova O.A., Biziukova N.Y., Rudik A.V., Dmitriev A.V., Filimonov D.A., Poroikov V.V. (2021) Extraction of Data on Parent Compounds and Their Metabolites from Texts of Scientific Abstracts, Journal of Chemical Information and Modeling, 61(4), 1683-1690. DOI:10.1021/acs.jcim.0c01054
Tarasova O.A., Rudik A.V., Ivanov S.M., Lagunin A.A., Poroikov V.V., Filimonov D.A. (2021) Machine Learning Methods in Antiviral Drug Discovery, Topics in Medicinal Chemistry, 37, 245-279. DOI:10.1007/7355_2021_121
Tarasova O., Rudik A., Kireev D., Poroikov V. (2021) RHIVDB: A freely accessible database of HIV amino acid sequences and clinical data of infected patients, Frontiers in Genetics, 12, 679029. DOI:10.3389/fgene.2021.679029
Ivanov S., Filimonov D., Tarasova O. (2021) A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression, Computational and Structural Biotechnology Journal, 19, 2447-2459. DOI:10.1016/j.csbj.2021.04.056
Бизюкова Н.Ю., Тарасова О.А., Рудик А.В., Филимонов Д.А., Поройков В.В. (2020) Автоматическое распознавание названий химических соединений в текстах научных публикаций, Научно-техническая информация. Серия 2: Информационные процессы и системы, (11), 36-46. DOI:10.36535/0548-0027-2020-11-5
Tarasova O., Biziukova N., Kireev D., Lagunin A., Ivanov S., Filimonov D., Poroikov V. (2020) A Computational Approach for the Prediction of Treatment History and the Effectiveness or Failure of Antiretroviral Therapy, International Journal of Molecular Sciences, 21(3), 748. DOI:10.3390/ijms21030748
Tarasova O., Ivanov S., Filimonov D.A., Poroikov V. (2020) Data and Text Mining Help Identify Key Proteins Involved in the Molecular Mechanisms Shared by SARS-CoV-2 and HIV-1, Molecules, 25(25), 2944-2944. DOI:10.3390/molecules25122944
Ivanov S., Lagunin A., Filimonov D., Tarasova O. (2020) Network-Based Analysis of OMICs Data to Understand the HIV-Host Interaction, Frontiers in Microbiology, 11, 1314. DOI:10.3389/fmicb.2020.01314
Biziukova N., Tarasova O., Ivanov S., Poroikov V. (2020) Automated Extraction of Information From Texts of Scientific Publications: Insights Into HIV Treatment Strategies, Frontiers in Genetics, 11, 618862. DOI:10.3389/fgene.2020.618862
Tarasova O.A., Biziukova N.Yu., Filimonov D.A., Poroikov V.V., Nicklaus M.C. (2019) Data mining approach for extraction of useful information about biologically active compounds from publications, Journal of Chemical Information and Modeling, 59(9), 3635-3644. DOI:10.1021/acs.jcim.9b00164