В.В. Поройков

Savosina P., Druzhilovskiy D., Filimonov D., Poroikov V, WWAD: The most comprehensive small molecule World Wide Approved Drug database of therapeutics. Frontiers in Pharmacology, 2024, 15, 1473279. DOI: 10.3389/fphar.2024.1473279.

de Azevedo WF Jr, Quiroga R, Villarreal MA, da Silveira NJF, Bitencourt-Ferreira G, da Silva AD, Veit-Acosta M, Oliveira PR, Tutone M, Biziukova N, Poroikov V, Tarasova O, Baud S.SAnDReS 2.0: Development of Machine-Learning Models to Explore the Scoring Function Space. Journal of Computational Chemistry, 2024, 45(27), 2333-2346. DOI: 10.1002/jcc.27449

Medvedeva S.M., Petrou A., Fesatidou M., Gavalas A., Geronikaki A.A., P.I. Savosina, Druzhilovskiy D.S., Poroikov V.V., Shikhaliev K.S., Kartsev V.G. Anti-inflammatory action of new hybrid N-acyl-[1,2]dithiolo-[3,4-c]quinoline-1-thione, SAR and QSAR in Environmental Research, 2024, 35(5), 343-366, DOI: 10.1080/1062936X.2024.2347965.

Stolbova E.A., Stolbov L.A., Filimonov D.A., Poroikov V.V., Tarasova O.A. Quantitative Prediction of Human Immunodeficiency Virus Drug Resistance. Viruses, 2024, 16, 1132. DOI: 10.3390/v16071132.

Ilyin N., Nabiullin A., Kozlova A., Kupriyanova O., Shevyrin V., Gloriozova T., Filimonov D., Lagunin A., Galstyan D., Kolesnikova T., Mor M., Efimova E., Poroikov V., de Abreu M., Demin K.A., Kalueff A. Chronic behavioral and neurochemical effects of four novel N-benzyl-2-phenylethylamine derivatives recently identified as ‘psychoactive’ in adult zebrafish screens. ACS Chemical Neuroscience, 2024, 15, 10, 2006–2017. DOI: 10.1021/acschemneuro.4c00017.

Pogodin P.V., Salina E.G., Semenov V.V., Raihstat M.M., Druzhilovskiy D.S., Filimonov D.A., Poroikov V.V. Ligand-based virtual screening and biological evaluation of inhibitors of Mycobacterium tuberculosis H37Rv. SAR and QSAR in Environmental Research, 2024, 35(1), 53-69, DOI: 10.1080/1062936X.2024.2304803.

Schimunek J., Seidl P., Elez K., Hempel T., Le T., Noé F., Olsson S., Raich L., Winter R., Gokcan H., Gusev F., Gutkin E.M., Isayev O., Kurnikova M.G., Narangoda C.H., Zubatyuk R., Bosko I.P., Furs K.V., Karpenko A.D., Kornoushenko Y.V., Shuldau M., Yushkevich A., Benabderrahmane M.B., Bousquet-Melou P., Bureau R., Charton B., Cirou B.C., Gil G., Allen W.J., Sirimulla S., Watowich S., Antonopoulos N.A., Epitropakis N.E., Krasoulis A.K., Pitsikalis V.P., Theodorakis S.T., Kozlovskii I., Maliutin A., Medvedev A., Popov P., Zaretckii M., Eghbal-Zadeh H., Halmich C., Hochreiter S., Mayr A., Ruch P., Widrich M,. Berenger F., Kumar A., Yamanishi Y., Zhang K.Y.J., Bengio E., Bengio Y., Jain M.J., Korablyov M., Liu C.H., Marcou G., Glaab E., Barnsley K., Iyengar S.M., Ondrechen M.J., Haupt V.J., Kaiser F., Schroeder M., Pugliese L., Albani S.., Athanasiou C., Beccari A., Carloni P., D'Arrigo G., Gianquinto E., Goßen J., Hanke A., Joseph B.P., Kokh D..B, Kovachka S., Manelfi C., Mukherjee G., Muñiz-Chicharro A., Musiani F., Nunes-Alves A., Paiardi G., Rossetti G., Sadiq S.K., Spyrakis F., Talarico C., Tsengenes A., Wade R.C., Copeland C., Gaiser J., Olson D.R., Roy A., Venkatraman V., Wheeler T.J., Arthanari H., Blaschitz K., Cespugli M., Durmaz V., Fackeldey K., Fischer P.D., Gorgulla C., Gruber C., Gruber K., Hetmann M., Kinney J.E., Padmanabha Das K.M., Pandita S., Singh A., Steinkellner G., Tesseyre G., Wagner G., Wang Z.F., Yust .RJ., Druzhilovskiy D.S., Filimonov D.A., Pogodin P.V., Poroikov V., Rudik A.V., Stolbov L.A., Veselovsky A.V., De Rosa M., De Simone G., Gulotta M.R., Lombino J., Mekni N., Perricone U., Casini A., Embree A., Gordon D.B., Lei D., Pratt K., Voigt C.A., Chen K.Y., Jacob Y., Krischuns T., Lafaye P., Zettor A., Rodríguez M.L., White K.M., Fearon D., Von Delft F., Walsh M.A., Horvath D., Brooks C.L. 3rd, Falsafi B., Ford B., García-Sastre A., Yup Lee S., Naffakh N., Varnek A., Klambauer G., Hermans T.M. A community effort in SARS-CoV-2 drug discovery. Molecular Informatics, 2024, 43, e202300262.. DOI: 10.1002/minf.202300262.

Bitencourt-Ferreira G., Villarreal M.A., Quiroga R., Biziukova N., Poroikov V., Tarasova O., de Azevedo Junior W.F. Exploring scoring function space: Developing computational models for drug discovery. Current Medicinal Chemistry, 2024, 31(17), 2361-2377.  DOI: 10.2174/0929867330666230321103731.

Поройков В.В., Дмитриев А.В., Дружиловский Д.С., Иванов С.М., Лагунин А.А., Погодин П.В., Рудик А.В., Савосина П.И., Тарасова О.А., Филимонов Д.А. Оценка безопасности фармакологически активных веществ in silico c применением методов машинного обучения: Обзор. Безопасность и риск фармакотерапии, 2023, 11(4), 372-389. DOI: 10.30895/2312-7821-2023-11-4-372-389.

Rudik A.V., Dmitriev A.V., Lagunin A.A., Filimonov D.A., Poroikov V.V. MetaTox 2.0: Estimating the Biological Activity Spectra of Drug-Like Compounds Taking into Account Probable Biotransformations. ACS Omega, 2023, 8, 45774−45778. DOI: 10.1021/acsomega.3c06119.

Ivanov S.M., Tarasova O.A., Poroikov V.V. Transcriptome-based analysis of human peripheral blood reveals regulators of immune response in different viral infections. Frontiers in Immunology, 2023, 14, 1199482. DOI: 10.3389/fimmu.2023.1199482.

Paremskaia A.I., Rudik A.V., Filimonov D.A., Lagunin A.A., Poroikov V.V., Tarasova O.A. Web Service for HIV Drug Resistance Prediction Based on Analysis of Amino Acid Substitutions in Main Drug Targets. Viruses, 2023, 15, 2245. DOI: 10.3390/v15112245.

Ionov N., Druzhilovskiy D., Filimonov D., Poroikov V. Phyto4Health: Database of Phytocomponents from Russian Pharmacopoeia Plants. Journal of Chemical Information and Modeling, 2023, 63 (7), 1847–1851. DOI: 10.1021/acs.jcim.2c01567

Filimonov D., Dmitriev A., Rudik A., Poroikov V. Assessment of the Xenobiotics Toxicity Taking into Account Their Metabolism. In: Machine Learning and Deep Learning in Computational Toxicology, Computational Methods in Engineering & the Sciences, H. Hong (Ed.), Springer Nature, 2023, P. 21-51. DOI: 10.1007/978-3-031-20730-3_2.

Поройков В.В. Цифровая фармакология: совместные усилия дадут лучшие результаты. В кн.: Научно-технологическое и инновационное сотрудничество стран БРИКС: Материалы международной научно-практической конференции. Вып. 1 / РАН. ИНИОН. Отд. науч. сотрудничества; отв. ред. В.И. Герасимов. – М., 2023, с. 487-490. ISBN 978-5-248-01057-8.

Lagunin A.A., Rudik A.V., Pogodin P.V., Savosina P.I., Tarasova O.A., Dmitriev A.V., Ivanov S.M., Biziukova N.Y., Druzhilovskiy D.S., Filimonov D.A., Poroikov V.V.. CLC-Pred 2.0: A Freely Available Web Application for In Silico Prediction of Human Cell Line Cytotoxicity and Molecular Mechanisms of Action for Druglike Compounds. International Journal of Molecular Sciences, 2023, 24 (2), 1689. DOI: 10.3390/ijms24021689.

Tarasova O.A., Biziukova N.Yu., Shemshura A.B., Filimonov D.A., Kireev D.E., Pokrovskaya A.V., Poroikov V.V. Identification of molecular mechanisms involved into viral in-fection progression based on text-mining: case study for HIV-infection. International Journal of Molecular Sciences, 2023, 24 (2), 1465. DOI: 10.3390/ijms24021465.

Bocharova O.A., Ionov N.S., Kazeev I.V., Shevchenko V.E., Bocharov E.V., Karpova R.V., Sheychenko O.P., Aksenov A.A., Chulkova S.V., Kucheryanu V.G., Revishchin A.V., Pavlova G.V., Kosorukov V.S., Filimonov D.A., Lagunin A.A., Matveev V.B., Pyatigorskaya N.V., Stilidi I.S., Poroikov V.V. Computer-Aided Evaluation of Polyvalent Medications’ Pharmacological Potential. Multiphytoadaptogen as a Case Study. Molecular Informatics, 2023, 41, 2200176. DOI: 10.1002/minf.202200176.

Tarasova O.A., Rudik A.V., Biziukova N.Yu., Filimonov D.A., Poroikov V.V. Chemical named entity recognition in the texts of scientific publications using the naïve Bayes classifier approach. Journal of Cheminformatics, 2022, 14, 55. DOI: 10.1186/s13321-022-00633-4.

Stolbov L.A., Filimonov D.A., Poroikov V.V. SAR based on Self Consistent Classifier. SAR and QSAR in Environmental Research. 2022, 33 (10), 793-804. DOI: 10.1080/1062936X.2022.2139751.

Panina S.B., Pei J., Baran N., Tjahjono E., Patel S., Alatrash G., Konoplev S.N., Stolbov L.A., Poroikov V.V., Konopleva M., Kirienko N.V. Novel mitochondria-targeting compounds selectively kill human leukemia cells. Leukemia, 2022, 36 (7), 2009–2021.. DOI: 10.1038/s41375-022-01614-0

Pikalyova K., Orlov A., Lin A., Tarasova O., Marcou G., Horvath D., Poroikov V., Varnek A. HIV-1 drug resistance profiling using amino acid sequence space cartography. Bioinformatics, 2022, 38(8), 2307-2314. DOI: 10.1093/bioinformatics/btac090

Zernov N., Veselovsky A.V., Poroikov V.V., Melentieva D., Bolshakova A., Popugaeva E. New Positive TRPC6 Modulator Penetrates Blood–Brain Barrier, Eliminates Synaptic Deficiency and Restores Memory Deficit in 5xFAD Mice. International Journal of Molecular Sciences, 2022, 23, 13552. DOI: 10.3390/ijms232113552.

Karasev D.A., Sobolev B.N., Lagunin A.A., Filimonov D.A., Poroikov V.V. The method predicting interaction between protein targets and small-molecular ligands with the wide applicability domain. Computational Biology and Chemistry, 2022, 98, 107674. DOI: 10.1016/j.compbiolchem.2022.107674.

Ivanov S., Lagunin A., Filimonov D., Poroikov V. Relationships between the structure and severe drug-induced liver injury for low, medium and high doses of drugs. Chemical Research in Toxicology, 2022, 2022, 35 (3), 402–411. DOI: 10.1021/acs.chemrestox.1c00307

Medvedeva S.M., Shikhaliev K.S., Geronikaki A.A., Savosina P.I., Druzhilovsky D.S., Poroikov V.V. Computer-aided discovery of pleiotropic effects: Anti-inflammatory action of dithioloquinolinethiones as a case study. SAR and QSAR in Environmental Research, 2022, 33 (4), 273-287. DOI: 1062936X.2022.2064547

Horishny М., Geronikaki A., Kartsev V., Matiychuk V., Petrou A., Pogodin P., Poroikov V., Papadopoulou T.A., Vizirianakis I.S., Kostic M., IvanovM., Sokovic M. Synthesis, biological evaluation and molecular docking studies of 5-indolylmethylen-4-oxo-2-thioxothiazolidine derivatives. Molecules, 2022, 27, 1068. DOI: 10.3390/molecules27031068

Бочарова О.А., Казеев И.В., Шевченко В.Е., Шейченко О.П., Поройков В.В., Бочаров Е.В., Карпова Р.В., Ионов Н.С., Кучеряну В.Г., Косоруков В.С., Матвеев В.Б., Стилиди И.С. Возможности стандартизации мультифитоадаптогена: тандемная масс-спектрометрия для анализа биологически активных веществ родиолы розовой. Химико-фармацевтический журнал, 2022, 56 (1), 32-38. DOI: 10.30906/0023-1134-2022-56-1-32-38

Muratov E.N., Amaro R., Andrade C.H., Brown N., Ekins S., Fourches D., Isayev O., Kozakov D., Medina-Franco J., Merz K.M., Oprea T.I., Poroikov V., Schneider G., Todd M.H., Varnek A., Winkler D.A., Zakharov A., Cherkasov A., Tropsha A. A critical overview of computational approaches employed for COVID-19 drug discovery. Chemical Society Reviews, 2021, 50, 9121-9151. DOI: 10.1039/d0cs01065k

Madugula S.S., John L., Nagamani S., Gaur A.S., Poroikov V.V., Sastry G.N. Molecular descriptor analysis of approved drugs using unsupervised learning for drug repurposing. Computers in Biology and Medicine, 2021, 138, 104856. DOI: 10.1016/j.compbiomed.2021.104856

Costa R., Lucena L., Silva L., Zocolo G., Herrera-Acevedo C., Scotti L., Da Costa F., Ionov N., Poroikov V., Muratov E., Scotti M. SistematX: Web portal of natural products. Journal of Chemical Information and Modeling, 2021, 61(6), 2516–2522. DOI: 10.1021/acs.jcim.1c00083.

Tarasova O., Rudik A., Kireev D., Poroikov V. RHIVDB: A freely accessible database of HIV amino acid sequences and clinical data of infected patients. Frontiers in Genetics, 2021, 12, 679029. DOI: 10.3389/fgene.2021.679029.

Zveaghintseva M., Stingaci E., Pogrebnoi S., Smetanscaia A., Valica V., Uncu L., Kravtsov V., Melnik E., Petrou A., Glamočlija J., Soković M., Carazo A., Mladěnka P., Poroikov V., Geronikaki A., Macaev F. Chromenol derivatives as novel antifungal agents. Synthesis, in silico and in vitro evaluation. Molecules, 2021, 26, 4304. DOI: 10.3390/molecules26144304

Dmitriev A.V., Rudik A.V., Karasev D.A., Pogodin P.V., Lagunin A.A., Filimonov D.A., Poroikov,V.V. In silico prediction of drug–drug interactions mediated by cytochrome P450 isoforms. Pharmaceutics, 2021, 13, 538. https://doi.org/10.3390/pharmaceutics13040538

Tarasova O., Poroikov V. Machine learning in discovery of new antivirals and optimization of viral infections therapy. Current Medicinal Chemistry, 2021, 28, 7840-7861. DOI: 10.2174/0929867328666210504114351

Dembitsky V.M., Gloriozova T.A., Poroikov V.V. Antitumor profile of carbon-bridged steroids (CBS) and triterpenoids. Marine Drugs, 2021, 19, 324. DOI: 10.3390/md19060324

Tarasova O.A., Biziukova N.Yu., Rudik A.V., Dmitriev A.V., Filimonov D.A., Poroikov V.V. Extraction of data on parent compounds and their metabolites from texts of scientific abstracts. Journal of Chemical Information and Modeling, 2021,  61 (4), 1683–1690. DOI: 10.1021/acs.jcim.0c01054,

Kamoutsis C., Fesatidou M., Petrou A., Geronikaki A., Poroikov V., Ivanov M., Sokovic M., Ciric A., Carazo A., Mladenka P. Triazolo based-thiadiazole derivatives. Synthesis, biological evaluation and molecular docking studies. Antibiotics, 2021, 10, 804. DOI: 10.3390/antibiotics10070804

Dmitriev A.V., Rudik A.V., Karasev D.A., Pogodin P.V., Lagunin A.A., Filimonov D.A., Poroikov V.V. In silico prediction of drug–drug interactions mediated by cytochrome P450 isoforms. Pharmaceutics, 2021, 13, 538. DOI: 10.3390/pharmaceutics13040538.

Rudik A., Dmitriev A., Lagunin A., Filimonov D., Poroikov V. MetaPASS: a web application for analyzing the biological activity spectrum of organic compounds taking into account their biotransformation. Molecular Informatics, 2021, 40 (4), 2000231 DOI: 10.1002/minf.202000231.

Ionov N., Pogodin P., Poroikov V. Assessing the Prediction Quality of the Anti-SARS-CoV-2 Activity Using the D3Targets-2019-nCoV Web Service. Biomedical Chemistry: Research and Methods, 2021, 3(4), e00140. DOI: 10.18097/BMCRM00140

Поройков В.В. Компьютерное конструирование лекарств: от поиска новых фармакологических веществ до системной фармакологии. Биомедицинская химия, 2020, 66 (1), 30-41. DOI: 10.18097/PBMC20206601030. / Poroikov V.V. Computer-aided drug design: from discovery of novel pharmaceutical agents to systems pharmacology. Biochemistry (Moscow), Supplement Series B: Biomedical Chemistry, 2020, 14 (3), 216–227. DOI: 10.1134/S1990750820030117

Lloyd K., Papoutsopoulou S., Smith E., Stegmaier P., Bergey F., Morris L., Kittner M., England H., Spiller D., White M.H.R., Duckworth C.A., Campbell B.J., Poroikov V., Martins dos Santos V.A.P., Kel A., Muller W., Pritchard D.M., Probert C., Burkitt M.D., the SysmedIBD consortium. Using systems medicine to identify a therapeutic agent with potential for repurposing in inflammatory bowel disease. Disease Models & Mechanisms, 2020,13, dmm044040. DOI: 10.1242/dmm.044040

Biziukova N., Tarasova O., Ivanov S., Poroikov V. Automated extraction of information from texts of scientific publications: insights into HIV treatment strategies. Frontiers in Genetics, 2020, 11, 618862. DOI: 10.3389/fgene.2020.618862

Ermolenko E., Imbs A., Gloriozova T., Poroikov V.V., Sikorsky T., Dembitsky V. Chemical diversity of soft coral steroids and their determined and potential pharmacological activities. Marine Drugs, 2020, 18, 613. DOI: 10.3390/md18120613

Druzhilovskiy D.S., Stolbov L.A., Savosina P.I., Pogodin P.V., Filimonov D.A., Veselovsky A.V., Stefanisko K., Tarasova N.I., Nicklaus M.C., Poroikov V.V. Computational approaches to identify a hidden pharmacological potential in large chemical libraries. Supercomputing Frontiers and Innovations, 2020, 7 (3), 57-76. DOI: 10.14529/jsfi200306

Lagunin A., Povydysh M., Ivkin D., Luzhanin V., Krasnova M., Okovityi S., Nosov A., Titova M., Tomilova S., Filimonov D., Poroikov V. Antihypoxic action of Panax Japonicus, Tribulus Terrestris and Dioscorea Deltoidea cell cultures: in silico and animal studies. Molecular Informatics, 2020, 39, 2000093. DOI: 10.1002/minf.202000093

Filimonov D.A., Rudik A.V., Dmitriev A.V., Poroikov V.V. Computer-aided estimation of biological activity profiles of drug-like compounds taking into account their metabolism in human body. International Journal of Molecular Sciences, 2020, 21, 7492; DOI: 10.3390/ijms21207492

Филимонов Д.А., Рудик А.В., Дмитриев А.В., Лагунин А.А., Поройков В.В. Компьютерная оценка вероятности образования метаболитов ксенобиотиков в организме человека. Биофизика, 2020, 65 (6), 1203-1210. DOI: 10.31857/S0006302920060204

Tarasova O., Ivanov S., Filimonov D.A., Poroikov V. Data and text mining help identify key proteins involved in the molecular mechanisms shared by SARS and HIV. Molecules, 2020, 25, 2944.  DOI: 10.3390/molecules25122944

Dembitsky V.M., Gloriozova T.A., Poroikov V.V. Pharmacological profile of natural and synthetic compounds with rigid adamantane-based scaffolds as potential agents for the treatment of neurodegenerative diseases. Biochem. Biophys. Res. Communs., 2020, 529 (2020) 1225-1241. DOI: 10.1016/j.bbrc.2020.06.123

Muratov E.N., Bajorath J., Sheridan R.P., Tetko I., Filimonov D., Poroikov V., Oprea T., Baskin I.I., Varnek A., Roitberg A., Isayev O., Curtalolo S., Fourches D., Cohen Y., Aspuru-Guzik A., Winkler D.A., Agrafiotis D., Cherkasov A., Tropsha A. QSAR Without Borders. Chemical Society Reviews, 2020, 49, 3525-3564. DOI: 10.1039/d0cs00098a

Mansouri K., Kleinstreuer N., Abdelaziz A.M., Alberga D., Alves V.M., Andersson P.L., Andrade C.H., Bai F., Balabin I., Ballabio D., Benfenati E., Bhhatarai B., Boyer S., Chen J., Consonni V., Farag S., Fourches D., García-Sosa A.T., Gramatica P., Grisoni F., Grulke C.M., Hong H., Horvath D., Hu X., Huang R., Jeliazkova N., Li J., Li X., Liu H., Manganelli S., Mangiatordi G.F., Maran U., Marcou G., Martin T., Muratov E., Nguyen D.-T., Nicolotti O., Nikolov N.G., Norinder U., Papa E., Petitjean M., Piir G., Pogodin P., Poroikov V., Qiao X., Richard A.M., Roncaglioni A., Ruiz P., Rupakheti C., Sakkiah S., Sangion A., Schramm K.-W., Selvaraj C., Shah I., Sild S., Sun L., Taboureau O., Tang Y., Tetko I.V., Todeschini R., Tong W., Trisciuzzi D., Tropsha A., Van Den Driessche G., Varnek A., Wang Z., Wedebye E.B., Williams A.J., Xie H., Zakharov A.V., Zheng Z., Judson R.S. CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity, Environmental Health Perspectives, 2020, 128 (2), 027002-1 - 027002-17. DOI: 10.1289/EHP5580.

Stolbov L., Druzhilovskiy D., Rudik A., Filimonov D., Poroikov V., Nicklaus M. AntiHIV-Pred: Web-resource for in silico prediction of anti-HIV/AIDS activity. Bioinformatics, 2020,  36 (3), 978–979. DOI: 10.1093/bioinformatics/btz638

Поройков В.В. Прогнозирование свойств фармакологических веществ in silico. В кн.: Промышленная фармация. Путь создания продукта / Под ред. А.Л. Хохлова и Н.В. Пятигорской. – М.: Из-во РАН, 2019, с.44-86.

Зефирова О.Н., Балакин К.В., Красавин М.Ю., Палюлин В.А., Поройков В.В., Радченко Е.В., Салахутдинов Н.Ф., Спасов А.А., Фисенко В.П., Бачурин С.О. Глоссарий русскоязычных терминов в медицинской химии. Известия Академии наук. Серия химическая, 2019, № 12, 2381-2395.

Поройков В.В., Филимонов Д.А., Глориозова Т.А., Лагунин А.А., Дружиловский Д.С., Рудик А.В., Столбов Л.А., Дмитриев А.В., Тарасова О.А., Иванов С.М., Погодин П.В. Компьютерный прогноз спектров биологической активности органических соединений: возможности и ограничения. Известия Академии наук. Серия химическая, 2019, № 12, 2143-2154.

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