<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.3 20210610//EN" "JATS-journalpublishing1-3.dtd">
<article article-type="research-article" dtd-version="1.3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xml:lang="ru"><front><journal-meta><journal-id journal-id-type="publisher-id">dan</journal-id><journal-title-group><journal-title xml:lang="ru">Доклады Национальной академии наук Беларуси</journal-title><trans-title-group xml:lang="en"><trans-title>Doklady of the National Academy of Sciences of Belarus</trans-title></trans-title-group></journal-title-group><issn pub-type="ppub">1561-8323</issn><issn pub-type="epub">2524-2431</issn><publisher><publisher-name>The Republican Unitary Enterprise Publishing House "Belaruskaya Navuka"</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.29235/1561-8323-2020-64-3-308-316</article-id><article-id custom-type="elpub" pub-id-type="custom">dan-885</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="ru"><subject>ХИМИЯ</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="en"><subject>CHEMISTRY</subject></subj-group></article-categories><title-group><article-title>Идентификация потенциальных ингибиторов коронавируса SARC-CoV-2 методами виртуального скрининга и молекулярного моделирования</article-title><trans-title-group xml:lang="en"><trans-title>Identification of potential inhibitors of coronavirus SARS-CoV-2 using the methods of virtual screening and molecular modeling</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Андрианов</surname><given-names>А. М.</given-names></name><name name-style="western" xml:lang="en"><surname>Andrianov</surname><given-names>A. M.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Андрианов Александр Михайлович – д-р хим. наук, гл. науч. сотрудник</p><p>ул. Купревича, 5/2, 220141, Минск </p></bio><bio xml:lang="en"><p>Andrianov Alexander M. – D. Sc. (Chemistry), Principal researcher</p><p>5/2, kuprevich Str., 220141, Minsk </p></bio><email xlink:type="simple">andrianov@iboch.by</email><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Корноушенко</surname><given-names>Ю. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Kornoushenko</surname><given-names>Yu. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Корноушенко Юрий Валерьевич – канд. хим. наук, ст. науч. сотрудник</p><p>ул. Купревича, 5/2, 220141, Минск </p></bio><bio xml:lang="en"><p>Kornoushenko Yuri V. – Ph. D. (Chemistry), Senior researcher</p><p>5/2, kuprevich Str., 220141, Minsk </p></bio><email xlink:type="simple">yurakorval@gmail.com</email><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Карпенко</surname><given-names>А. Д.</given-names></name><name name-style="western" xml:lang="en"><surname>Karpenko</surname><given-names>A. D.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Карпенко Анна Дмитриевна – аспирант</p><p>ул. Сурганова, 6, 220012, Минск </p></bio><bio xml:lang="en"><p>Karpenko Anna D. – Postgraduate student</p><p>6, Surganov Str., 220012, Minsk </p></bio><email xlink:type="simple">rfe.karpenko@gmail.com</email><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Тузиков</surname><given-names>А. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Tuzikov</surname><given-names>A. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Тузиков Александр Васильевич – член-корреспондент, д-р физ.-мат. наук, профессор, генеральный директор</p><p>ул. Сурганова, 6, 220012, Минск </p></bio><bio xml:lang="en"><p>Tuzikov Alexander V. – Corresponding Member, D. Sc. (Physics and Mathematics), Professor, General Director</p><p>6, Surganov Str., 220012, Minsk </p></bio><email xlink:type="simple">tuzikov@newman.bas-net.by</email><xref ref-type="aff" rid="aff-2"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru"><institution>Институт биоорганической химии Национальной академии наук Беларуси</institution></aff><aff xml:lang="en"><institution>Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus</institution></aff></aff-alternatives><aff-alternatives id="aff-2"><aff xml:lang="ru"><institution>Объединенный институт проблем информатики Национальной академии наук Беларуси</institution></aff><aff xml:lang="en"><institution>United Institute of Informatics Problems of the National Academy of Sciences of Belarus</institution></aff></aff-alternatives><pub-date pub-type="collection"><year>2020</year></pub-date><pub-date pub-type="epub"><day>09</day><month>07</month><year>2020</year></pub-date><volume>64</volume><issue>3</issue><fpage>308</fpage><lpage>316</lpage><permissions><copyright-statement>Copyright &amp;#x00A9; Андрианов А.М., Корноушенко Ю.В., Карпенко А.Д., Тузиков А.В., 2020</copyright-statement><copyright-year>2020</copyright-year><copyright-holder xml:lang="ru">Андрианов А.М., Корноушенко Ю.В., Карпенко А.Д., Тузиков А.В.</copyright-holder><copyright-holder xml:lang="en">Andrianov A.M., Kornoushenko Y.V., Karpenko A.D., Tuzikov A.V.</copyright-holder><license xml:lang="ru" license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>Данная работа распространяется под лицензией Creative Commons Attribution 4.0.</license-p></license><license xml:lang="en" license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>This work is licensed under a Creative Commons Attribution 4.0 License.</license-p></license></permissions><self-uri xlink:href="https://doklady.belnauka.by/jour/article/view/885">https://doklady.belnauka.by/jour/article/view/885</self-uri><abstract><p>С целью поиска низкомолекулярных соединений, способных имитировать структурно-функциональные свойства высокоаффинного лиганда X77 основной протеазы коронавируса SARS-CoV-2 – этиологического агента COVID-19, осуществлен виртуальный скрининг 9 молекулярных библиотек веб-сервера Pharmit, содержащих более 213,5 млн химических структур. С помощью методов молекулярного моделирования проведена оценка нейтрализующей активности идентифицированных молекул, в результате которой обнаружены 5 соединений-лидеров, перспективных для синтеза и тестирования на противовирусную активность. Показано, что эти соединения могут быть использованы в качестве базовых структур для разработки эффективных лекарственных препаратов для терапии коронавирусной инфекции нового типа.</p></abstract><trans-abstract xml:lang="en"><p>To find small-molecule compounds that can simulate the structural and functional properties of the high affinity X77 ligand of the main protease of SARS-CoV-2 - etiologic agent of COVID-19, the virtual screening of 9 molecular libraries of the Pharmit web server containing over 213.5 million chemical structures was performed. Using molecular modeling, the neutralizing activity of the identified molecules was evaluated, resulting in 5 leader compounds promising for synthesis and testing for antiviral activity. The data obtained indicate that these compounds may be used as basic structures for the development of effective drugs to treat the novel coronavirus infection.</p></trans-abstract><kwd-group xml:lang="ru"><kwd>коронавирус SARS-CoV-2</kwd><kwd>COVID-19</kwd><kwd>основная протеаза</kwd><kwd>ингибиторы SARS-CoV-2</kwd><kwd>виртуальный скрининг</kwd><kwd>молекулярный докинг</kwd><kwd>противовирусные препараты</kwd></kwd-group><kwd-group xml:lang="en"><kwd>coronavirus SARS-CoV-2</kwd><kwd>COVID-19</kwd><kwd>main protease</kwd><kwd>SARS-CoV-2 inhibitors</kwd><kwd>virtual screening</kwd><kwd>molecular docking</kwd><kwd>antiviral drugs</kwd></kwd-group></article-meta></front><back><ref-list><title>References</title><ref id="cit1"><label>1</label><citation-alternatives><mixed-citation xml:lang="ru">Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding / R. Lu [et al.] // Lancet. - 2020. - Vol. 395, N 10224. - P. 565–574. https://doi.org/10.1016/s0140-6736(20)30251-8</mixed-citation><mixed-citation xml:lang="en">Lu R., Zhao X., Li J., Niu P., yang B., Wu H., Wang W., Song H., Huang B., Zhu N., Bi y., Ma X., Zhan F., Wang L., Hu T., Zhou H., Hu Z., Zhou W., Zhao L., Chen J., Meng y., Wang J., Lin y., yuan J., Xie Z., Ma J., Liu W. J., Wang D., Xu W., Holmes E. C., Gao G. F., Wu G., Chen W., Shi W., Tan W. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet, 2020, vol. 395, no. 10224, pp. 565–574. https://doi.org/10.1016/s0140-6736(20)30251-8</mixed-citation></citation-alternatives></ref><ref id="cit2"><label>2</label><citation-alternatives><mixed-citation xml:lang="ru">A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster / J. F.-W. Chan [et al.] // Lancet. - 2020. - Vol. 395, N 10223. - P. 514–523. https://doi.org/10.1016/s0140-6736(20)30154-9</mixed-citation><mixed-citation xml:lang="en">Chan J. F.-W., yuan S., kok k.-H., To k. k.-W., Chu H., yang J., Xing F., Liu J., yip C. C.-y., Poon R. W.-S., Tsoi H.-W., Lo S. k.-F., Chan k.-H., Poon V. k.-M., Chan W.-M., Ip J. D., Cai J.-P., Cheng V. C.-C., Chen H., Hui C. k.-M., yuen k.-y. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet, 2020, vol. 395, no. 10223, pp. 514–523. https://doi.org/10.1016/s0140-6736(20)30154-9</mixed-citation></citation-alternatives></ref><ref id="cit3"><label>3</label><citation-alternatives><mixed-citation xml:lang="ru">SARS and MERS: recent insights into emerging coronaviruses / E. de Wit [et al.] // Nat. Rev. Microbiol. – 2016. – Vol. 14, N 8. – P. 523–534. https://doi.org/10.1038/nrmicro.2016.81</mixed-citation><mixed-citation xml:lang="en">de Wit E., van Doremalen N., Falzarano D., Munster V. J. SARS and MERS: recent insights into emerging coronaviruses. Nature Reviуws Microbiology, 2016, vol. 14, no. 8, pp. 523–534. https://doi.org/10.1038/nrmicro.2016.81</mixed-citation></citation-alternatives></ref><ref id="cit4"><label>4</label><citation-alternatives><mixed-citation xml:lang="ru">Chen, y. Emerging coronaviruses: genome structure, replication, and pathogenesis / y. Chen, Q. Liu, D. Guo // J. Med. Virology. – 2020. – Vol. 92, N 4. – P. 418–423. https://doi.org/10.1002/jmv.25681</mixed-citation><mixed-citation xml:lang="en">Chen y., Liu Q., Guo D. Emerging coronaviruses: genome structure, replication, and pathogenesis. Journal of Medical Virology, 2020, vol. 92, no. 4, pp. 418–423. https://doi.org/10.1002/jmv.25681</mixed-citation></citation-alternatives></ref><ref id="cit5"><label>5</label><citation-alternatives><mixed-citation xml:lang="ru">Structure of MPro from COVID-19 virus and discovery of its inhibitors / Z. Jin [et al.] // bioRxiv. – 2020. https://doi.org/10.1101/2020.02.26.964882</mixed-citation><mixed-citation xml:lang="en">Jin Z., Du X., Xu y., Deng y., Liu M., Zhao y., Zhang B., Li X., Zhang L., Peng C., Duan y., yu J., Wang L., yang k., Liu F., Jiang R., yang X., you T., Liu X., yang X., Bai F., Liu H., Liu X., Guddat L. W., Xu W., Xiao G., Qin C., Shi Z., Jiang H., Rao Z., yang H. Structure of MPro from COVID-19 virus and discovery of its inhibitors. bioRxiv, 2020. https://doi.org/10.1101/2020.02.26.964882</mixed-citation></citation-alternatives></ref><ref id="cit6"><label>6</label><citation-alternatives><mixed-citation xml:lang="ru">Liu, X. Potential inhibitors for 2019-nCoV coronavirus M protease from clinically approved medicines / X. Liu, X.-J. Wang // bioRxiv. – 2020. https://doi.org/10.1101/2020.01.29.924100</mixed-citation><mixed-citation xml:lang="en">Liu X., Wang X.-J. Potential inhibitors for 2019-nCoV coronavirus M protease from clinically approved medicines. bioRxiv, 2020. https://doi.org/10.1101/2020.01.29.924100</mixed-citation></citation-alternatives></ref><ref id="cit7"><label>7</label><citation-alternatives><mixed-citation xml:lang="ru">Therapeutic Drugs Targeting 2019-nCoV Main Protease by High-Throughput Screening / y. Li [et al.] // bioRxiv. – 2020. https://doi.org/10.1101/2020.01.28.922922</mixed-citation><mixed-citation xml:lang="en">Li y., Zhang J., Wang N., Li H., Shi y., Guo G., Liu k., Zeng H., Zou Q. Therapeutic Drugs Targeting 2019-nCoV Main Protease by High-Throughput Screening. bioRxiv, 2020. https://doi.org/10.1101/2020.01.28.922922</mixed-citation></citation-alternatives></ref><ref id="cit8"><label>8</label><citation-alternatives><mixed-citation xml:lang="ru">Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation / Z. Xu [et al.] // bioRxiv. – 2020. https://doi.org/10.1101/2020.01.27.921627</mixed-citation><mixed-citation xml:lang="en">Xu Z., Peng C., Shi y., Zhu Z., Mu k., Wang X., Zhu W. Nelfinavir was predicted to be a potential inhibitor of 2019- nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation. bioRxiv, 2020. https://doi.org/10.1101/2020.01.27.921627</mixed-citation></citation-alternatives></ref><ref id="cit9"><label>9</label><citation-alternatives><mixed-citation xml:lang="ru">Phylogenetic network analysis of SARS-CoV-2 genomes / P. Forster [et al.] // Proc. Natl. Acad. Sci. – 2020. – Vol. 117, N 17. – P. 9241–9243. https://doi.org/10.1073/pnas.2004999117</mixed-citation><mixed-citation xml:lang="en">Forster P., Forster L., Renfrew C., Forster M. Phylogenetic network analysis of SARS-CoV-2 genomes. Proceedings of the National Academy of Sciences, 2020, vol. 117, no. 17, pp. 9241–9243. https://doi.org/10.1073/pnas.2004999117</mixed-citation></citation-alternatives></ref><ref id="cit10"><label>10</label><citation-alternatives><mixed-citation xml:lang="ru">Sunseri, J. Pharmit: interactive exploration of chemical space / J. Sunseri, D. R. Koes // Nucl. Acids Res. – 2016. – Vol. 44, N W1. – P. W442–W448. https://doi.org/10.1093/nar/gkw287</mixed-citation><mixed-citation xml:lang="en">Sunseri J., Koes D. R. Pharmit: interactive exploration of chemical space. Nucleic Acids Research, 2016, vol. 44, no. W1, pp. W442–W448. https://doi.org/10.1093/nar/gkw287</mixed-citation></citation-alternatives></ref><ref id="cit11"><label>11</label><citation-alternatives><mixed-citation xml:lang="ru">Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings / C. A. Lipinski [et al.] // Adv. Drug Deliv. Rev. – 2001. – Vol. 46, N 1–3. – P. 3–26. https://doi.org/10.1016/s0169-409x(00)00129-0</mixed-citation><mixed-citation xml:lang="en">Lipinski C. A., Lombardo F., Dominy B. W., Feeney P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 2001, vol. 46, no. 1–3, pp. 3–26. https://doi.org/10.1016/s0169-409x(00)00129-0</mixed-citation></citation-alternatives></ref><ref id="cit12"><label>12</label><citation-alternatives><mixed-citation xml:lang="ru">Fast, accurate, and reliable molecular docking with QuickVina 2 / A. Alhossary [et al.] // Bioinformatics. – 2015. – Vol. 31, N 13. – P. 2214–2216. https://doi.org/10.1093/bioinformatics/btv082</mixed-citation><mixed-citation xml:lang="en">Alhossary A., Handoko S. D., Mu y., kwoh C. k. Fast, accurate, and reliable molecular docking with QuickVina 2. Bioinformatics, 2015, vol. 31, no. 13, pp. 2214–2216. https://doi.org/10.1093/bioinformatics/btv082</mixed-citation></citation-alternatives></ref><ref id="cit13"><label>13</label><citation-alternatives><mixed-citation xml:lang="ru">Durrant, J. D. BINANA: A novel algorithm for ligand-binding characterization / J. D. Durrant, J. A. McCammon // J. Mol. Graph. Model. – 2011. – Vol. 29, N 6. – P. 888–893. https://doi.org/10.1016/j.jmgm.2011.01.004</mixed-citation><mixed-citation xml:lang="en">Durrant J. D., McCammon J. A. BINANA: A novel algorithm for ligand-binding characterization. Journal of Molecular Graphics Modelling, 2011, vol. 29, no. 6, pp. 888–893. https://doi.org/10.1016/j.jmgm.2011.01.004</mixed-citation></citation-alternatives></ref><ref id="cit14"><label>14</label><citation-alternatives><mixed-citation xml:lang="ru">Durrant, J. D. NNScore 2.0: A neural-network receptor-ligand scoring function / J. D. Durrant, J. A. McCammon // J. Chem. Inf. Model. – 2011. – Vol. 51, N 11. – P. 2897–2903. https://doi.org/10.1021/ci2003889</mixed-citation><mixed-citation xml:lang="en">Durrant J. D., McCammon J. A. NNScore 2.0: A neural-network receptor-ligand scoring function. Journal of Chemical Information and Modeling, 2011, vol. 51, no. 11, pp. 2897–2903. https://doi.org/10.1021/ci2003889</mixed-citation></citation-alternatives></ref><ref id="cit15"><label>15</label><citation-alternatives><mixed-citation xml:lang="ru">Sharma, G. Thermodynamic analysis reveals a temperature-dependent change in the catalytic mechanism of Bacillus stearothermophilus tyrosyl-tRNA synthetase / G. Sharma, E. A. First // J. Biol. Chem. – 2009. – Vol. 284, N 7. – P. 4179–4190. https://doi.org/10.1074/jbc.m808500200</mixed-citation><mixed-citation xml:lang="en">Sharma G., First E. A. Thermodynamic analysis reveals a temperature-dependent change in the catalytic mechanism of Bacillus stearothermophilus tyrosyl-tRNA synthetase. Journal of Biological Chemistry, 2009, vol. 284, no. 7, pp. 4179– 4190. https://doi.org/10.1074/jbc.m808500200</mixed-citation></citation-alternatives></ref></ref-list><fn-group><fn fn-type="conflict"><p>The authors declare that there are no conflicts of interest present.</p></fn></fn-group></back></article>
