{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T10:28:47Z","timestamp":1762252127338},"reference-count":67,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2014,9,26]],"date-time":"2014-09-26T00:00:00Z","timestamp":1411689600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"name":"OpenEye Scientific Software, Inc."},{"name":"Russian Foundation for Basic Research","award":["14-03-00851","14-03-31566"],"award-info":[{"award-number":["14-03-00851","14-03-31566"]}]},{"name":"iScalare laboratory at MIPT"},{"name":"Government of the Russian Federation"},{"name":"Lomonosov Moscow State University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecular Informatics"],"published-print":{"date-parts":[[2014,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Flaviviral diseases, including dengue fever, West Nile fever, yellow fever, tick\u2010borne encephalitis, Omsk haemorrhagic fever, and Powassan encephalitis, threaten human health all over the world. Lack of effective antivirals targeting replication cycle of flaviviruses makes the search of such compounds a challenging task. Recently we have identified a reproduction inhibitor effective against tick\u2010borne encephalitis virus and Powassan virus (POWV) (<jats:italic>ACS Med. Chem. Lett.<\/jats:italic>, <jats:bold>2013<\/jats:bold>, <jats:italic>4<\/jats:italic>, 869\u2013874). To enable using this inhibitor as a template for 3D pharmacophore search, a biologically active conformation of this molecule should have been established. Here we performed molecular dynamics simulations of the complexes between the different enantiomers of the inhibitor and POWV envelope (E) proteins, putative targets of the inhibitor, in the different protonation states corresponding to the different stages of membrane fusion process. Several stable conformations of the inhibitor were identified, opening routes for further design of more advanced molecules.<\/jats:p>","DOI":"10.1002\/minf.201300185","type":"journal-article","created":{"date-parts":[[2014,9,26]],"date-time":"2014-09-26T08:56:58Z","timestamp":1411721818000},"page":"695-708","source":"Crossref","is-referenced-by-count":14,"title":["Interaction of Flaviviruses with Reproduction Inhibitors Binding in \u03b2\u2010OG Pocket: Insights from Molecular Dynamics Simulations"],"prefix":"10.1002","volume":"33","author":[{"given":"Evgenia V.","family":"Dueva","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dmitry I.","family":"Osolodkin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liubov I.","family":"Kozlovskaya","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir A.","family":"Palyulin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir M.","family":"Pentkovski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikolay S.","family":"Zefirov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2014,9,26]]},"reference":[{"key":"e_1_2_7_1_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrd703"},{"key":"e_1_2_7_2_2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules16010221"},{"key":"e_1_2_7_3_2","doi-asserted-by":"publisher","DOI":"10.1517\/13543776.2011.550876"},{"key":"e_1_2_7_4_2","doi-asserted-by":"publisher","DOI":"10.1517\/17460441.2012.673579"},{"key":"e_1_2_7_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.1456"},{"key":"e_1_2_7_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.febslet.2007.01.093"},{"key":"e_1_2_7_7_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.82210-0"},{"key":"e_1_2_7_8_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00726-009-0370-4"},{"key":"e_1_2_7_9_2","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.200806081"},{"key":"e_1_2_7_10_2","doi-asserted-by":"publisher","DOI":"10.1002\/rmv.712"},{"key":"e_1_2_7_11_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.011437-0"},{"key":"e_1_2_7_12_2","first-page":"1419","volume":"161","author":"Gholam B. I. A.","year":"1999","journal-title":"Can. Med. Assoc. J."},{"key":"e_1_2_7_13_2","doi-asserted-by":"publisher","DOI":"10.1089\/vbz.2008.0022"},{"key":"e_1_2_7_14_2","doi-asserted-by":"publisher","DOI":"10.1186\/1756-0500-5-594"},{"key":"e_1_2_7_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(10)61120-8"},{"key":"e_1_2_7_16_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0000428"},{"key":"e_1_2_7_17_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0832193100"},{"key":"e_1_2_7_18_2","doi-asserted-by":"publisher","DOI":"10.1021\/cb800176t"},{"key":"e_1_2_7_19_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm800412d"},{"key":"e_1_2_7_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01148-08"},{"key":"e_1_2_7_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.antiviral.2009.09.007"},{"key":"e_1_2_7_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmc.2011.04.041"},{"key":"e_1_2_7_23_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002627"},{"key":"e_1_2_7_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2009.12.012"},{"key":"e_1_2_7_25_2","first-page":"42","volume":"27","author":"Kozlovskaya L. I.","year":"2013","journal-title":"Med. Virol."},{"key":"e_1_2_7_26_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbapap.2011.09.012"},{"key":"e_1_2_7_27_2","doi-asserted-by":"publisher","DOI":"10.1042\/BST0360043"},{"key":"e_1_2_7_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2006.07.011"},{"key":"e_1_2_7_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2010.04.024"},{"key":"e_1_2_7_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrc.2012.07.069"},{"key":"e_1_2_7_31_2","doi-asserted-by":"publisher","DOI":"10.1021\/ml400226s"},{"key":"e_1_2_7_32_2","first-page":"13","volume":"51","author":"Kislenko G. S.","year":"1982","journal-title":"Med. Parazitol. (Mosk.)"},{"key":"e_1_2_7_33_2","doi-asserted-by":"publisher","DOI":"10.1038\/375291a0"},{"key":"e_1_2_7_34_2","doi-asserted-by":"publisher","DOI":"10.1006\/viro.1993.1247"},{"key":"e_1_2_7_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm404"},{"key":"e_1_2_7_36_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1993.1626"},{"key":"e_1_2_7_37_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340170404"},{"key":"e_1_2_7_38_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889892009944"},{"key":"e_1_2_7_39_2","unstructured":"Tripos International 1699 South Hanley Rd. St. Louis Missouri 63144 USA."},{"key":"e_1_2_7_40_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540100804"},{"key":"e_1_2_7_41_2","unstructured":"\u00a0"},{"key":"e_1_2_7_42_2","unstructured":"OMEGA version 2.4.6 OpenEye Scientific Software Inc. Santa Fe NM USA www.eyesopen.com 2010;"},{"key":"e_1_2_7_43_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci100031x"},{"key":"e_1_2_7_44_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199604)17:5\/6<520::AID-JCC2>3.0.CO;2-W"},{"key":"e_1_2_7_45_2","unstructured":"QUACPAC Version 1.5.0 OpenEye Scientific Software Inc. Santa Fe NM USA 2010; www.eyesopen.com."},{"key":"e_1_2_7_46_2","unstructured":"\u00a0"},{"key":"e_1_2_7_47_2","unstructured":"FRED version 2.2.5 OpenEye Scientific Software Inc. Santa Fe NM USA 2010; www.eyesopen.com;"},{"key":"e_1_2_7_48_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-012-9584-8"},{"key":"e_1_2_7_49_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1008158231558"},{"key":"e_1_2_7_50_2","doi-asserted-by":"publisher","DOI":"10.1002\/bip.10207"},{"key":"e_1_2_7_51_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1007996124545"},{"key":"e_1_2_7_52_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm0003992"},{"key":"e_1_2_7_53_2","unstructured":"D.\u2005A. Case T.\u2005A. Darden T.\u2005E. Cheatham III C.\u2005L. Simmerling J. Wang R.\u2005E. Duke R. Luo R.\u2005C. Walker W. Zhang K.\u2005M. Merz B. Roberts B. Wang S. Hayik A. Roitberg G. Seabra I. Kolossv\u00e1ry K.\u2005F. Wong F. Paesani J. Vanicek J. Liu X. Wu S.\u2005R. Brozell T. Steinbrecher H. Gohlke Q. Cai X. Ye J. Wang M.\u2010J. Hsieh G. Cui D.\u2005R. Roe D.\u2005H. Mathews M.\u2005G. Seetin C. Sagui V. Babin T. Luchko S. Gusarov A. Kovalenko P.\u2005A. Kollman AMBER 11 University of California San Francisco2010."},{"key":"e_1_2_7_54_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21123"},{"key":"e_1_2_7_55_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20035"},{"key":"e_1_2_7_56_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.10128"},{"key":"e_1_2_7_57_2","doi-asserted-by":"publisher","DOI":"10.1016\/0021-9991(77)90098-5"},{"key":"e_1_2_7_58_2","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1002\/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E","volume":"56","author":"Tsui V.","year":"2001","journal-title":"Biopolymers (Nucleic Acids Sci.)."},{"key":"e_1_2_7_59_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20660"},{"key":"e_1_2_7_60_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21123"},{"key":"e_1_2_7_61_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(02)73940-4"},{"key":"e_1_2_7_62_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(97)78851-9"},{"key":"e_1_2_7_63_2","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"e_1_2_7_64_2","doi-asserted-by":"publisher","DOI":"10.1021\/ct400341p"},{"key":"e_1_2_7_65_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01735-06"},{"key":"e_1_2_7_66_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01125-06"},{"key":"e_1_2_7_67_2","doi-asserted-by":"publisher","DOI":"10.1038\/497443a"}],"container-title":["Molecular Informatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fminf.201300185","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fminf.201300185","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/minf.201300185","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T23:19:37Z","timestamp":1700608777000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/minf.201300185"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,9,26]]},"references-count":67,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2014,10]]}},"alternative-id":["10.1002\/minf.201300185"],"URL":"https:\/\/doi.org\/10.1002\/minf.201300185","archive":["Portico"],"relation":{},"ISSN":["1868-1743","1868-1751"],"issn-type":[{"value":"1868-1743","type":"print"},{"value":"1868-1751","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,9,26]]}}}