Voir la notice de l'article provenant de la source Math-Net.Ru
@article{MBB_2021_16_a2, author = {A. M. Andrianov and A. M. Yushkevich and I. P. Bosko and A. D. Karpenko and Yu. V. Kornoushenko and K. V. Furs and A. V. Tuzikov}, title = {Design and identification of potential {HIV-1} entry inhibitors using {\emph{In} silico} click chemistry and molecular modeling methods}, journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika}, pages = {317--334}, publisher = {mathdoc}, volume = {16}, year = {2021}, language = {ru}, url = {http://geodesic.mathdoc.fr/item/MBB_2021_16_a2/} }
TY - JOUR AU - A. M. Andrianov AU - A. M. Yushkevich AU - I. P. Bosko AU - A. D. Karpenko AU - Yu. V. Kornoushenko AU - K. V. Furs AU - A. V. Tuzikov TI - Design and identification of potential HIV-1 entry inhibitors using \emph{In silico} click chemistry and molecular modeling methods JO - Matematičeskaâ biologiâ i bioinformatika PY - 2021 SP - 317 EP - 334 VL - 16 PB - mathdoc UR - http://geodesic.mathdoc.fr/item/MBB_2021_16_a2/ LA - ru ID - MBB_2021_16_a2 ER -
%0 Journal Article %A A. M. Andrianov %A A. M. Yushkevich %A I. P. Bosko %A A. D. Karpenko %A Yu. V. Kornoushenko %A K. V. Furs %A A. V. Tuzikov %T Design and identification of potential HIV-1 entry inhibitors using \emph{In silico} click chemistry and molecular modeling methods %J Matematičeskaâ biologiâ i bioinformatika %D 2021 %P 317-334 %V 16 %I mathdoc %U http://geodesic.mathdoc.fr/item/MBB_2021_16_a2/ %G ru %F MBB_2021_16_a2
A. M. Andrianov; A. M. Yushkevich; I. P. Bosko; A. D. Karpenko; Yu. V. Kornoushenko; K. V. Furs; A. V. Tuzikov. Design and identification of potential HIV-1 entry inhibitors using \emph{In silico} click chemistry and molecular modeling methods. Matematičeskaâ biologiâ i bioinformatika, Tome 16 (2021), pp. 317-334. http://geodesic.mathdoc.fr/item/MBB_2021_16_a2/
[1] H. B. Wang, Q. H. Mo, Z. Yang, “HIV vaccine research: The challenge and the way forward”, J. Immunol. Res, 2015 (2015), 503978 <ext-link ext-link-type='doi' href='https://doi.org/10.1155/2015/503978'>10.1155/2015/503978</ext-link>
[2] J. K. Mann, T. Ndung'u, “HIV-1 vaccine immunogen design strategies”, Virol. J, 12:3 (2015) <ext-link ext-link-type='doi' href='https://doi.org/10.1186/s12985--014--0221--0'>10.1186/s12985--014--0221--0</ext-link>
[3] D. Corti, A. Lanzavecchia, “Broadly neutralizing antiviral antibodies”, Ann. Rev. Immunol, 31 (2013), 705–742 <ext-link ext-link-type='doi' href='https://doi.org/10.1146/annurev-immunol-032712--095916'>10.1146/annurev-immunol-032712--095916</ext-link>
[4] E. J. Arts, D. J. Hazuda, “HIV-1 antiretroviral drug therapy”, Cold Spring Harb. Perspect. Med., 2 (2012), a007161 <ext-link ext-link-type='doi' href='https://doi.org/10.1101/cshperspect.a007161'>10.1101/cshperspect.a007161</ext-link>
[5] G. Kumari, R. K. Singh, “Highly active antiretroviral therapy for treatment of HIV/AIDS patients: current status and future prospects and the Indian scenario”, HIV & AIDS Rev, 11 (2012), 5–14 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/J.HIVAR.2012.02.003'>10.1016/J.HIVAR.2012.02.003</ext-link>
[6] R. D. MacArthur, R. M. Novak, “Maraviroc: The first of a new class of antiretroviral agents”, Clin. Infect. Dis., 47 (2008), 236–241 <ext-link ext-link-type='doi' href='https://doi.org/10.1086/589289'>10.1086/589289</ext-link>
[7] T. Matthews, M. Salgo, M. Greenberg, J. Chung, R. DeMasi, D. Bolognesi, “Enfuvirtide: The first therapy to inhibit the entry of HIV-1 into host CD4 lymphocytes”, Nat. Rev. Drug Discov, 3 (2004), 215–225 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/nrd1331'>10.1038/nrd1331</ext-link>
[8] R. L. Bettiker, D. E. Koren, Jacobson J. M., “Ibalizumab”, Curr. Opin. HIV AIDS, 13:4 (2018), 354–358 <ext-link ext-link-type='doi' href='https://doi.org/10.1097/COH.0000000000000473'>10.1097/COH.0000000000000473</ext-link>
[9] S. A. Rizza, R. Bhatia, J. Zeuli, Z. Temesgen, “Ibalizumab for the treatment of multidrug-resistant HIV-1 infection”, Drugs Today (Barc), 55:1 (2019), 25–34 <ext-link ext-link-type='doi' href='https://doi.org/10.1358/dot.2019.55.1.2895651'>10.1358/dot.2019.55.1.2895651</ext-link>
[10] H. A. Blair, “Ibalizumab: A Review in multidrug-resistant HIV-1 infection”, Drugs, 80:2 (2020), 189–196 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/s40265--020--01258--3'>10.1007/s40265--020--01258--3</ext-link>
[11] M. Kozal, J. Aberg, G. Pialoux, P. Cahn, M. Thompson, J. M. Molina, B. Grinsztejn, R. Diaz, A. Castagna, P. Kumar, G. Latiff, E. DeJesus et al, for the BRIGHTE Trial Team, “Fostemsavir in adults with multidrug-resistant HIV-1 infection”, N. Engl. J. Med, 382 (2020), 1232–1243 <ext-link ext-link-type='doi' href='https://doi.org/10.1056/NEJMoa1902493'>10.1056/NEJMoa1902493</ext-link>
[12] E. B. Chahine, “Fostemsavir: The first oral attachment inhibitor for treatment of HIV-1 infection”, Am. J. Health Syst. Pharm, 78:5 (2021), 376–388 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/ajhp/zxaa416'>10.1093/ajhp/zxaa416</ext-link>
[13] Y. T. Lai, “Small molecule HIV-1 attachment inhibitors: Discovery, mode of action and structural basis of inhibition”, Viruses, 13 (2021), 843 <ext-link ext-link-type='doi' href='https://doi.org/10.3390/v13050843'>10.3390/v13050843</ext-link>
[14] P. D. Kwong, J. R. Mascola, G. J. Nabel, “The changing face of HIV vaccine research”, J. Int. AIDS Soc, 15 (2012), 17407 <ext-link ext-link-type='doi' href='https://doi.org/10.7448/IAS.15.2.17407'>10.7448/IAS.15.2.17407</ext-link>
[15] J. Huang, G. Ofek, L. Laub, M. K. Louder, N. A. Doria-Rose, N. S. Longo, H. Imamichi, R. T. Bailer, B. Chakrabarti, S. K. Sharma, S. M. Alam, T. Wang, Y. Yang, B. Zhang, S. A. Migueles, R. Wyatt, B. F. Haynes, P. D. Kwong, J. R. Mascola, M. Connors, “Broad and potent neutralization of HIV-1 by a gp41-specific human antibody”, Nature, 491 (2012), 406–412 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/nature11544'>10.1038/nature11544</ext-link>
[16] I. A. Kashin, A. V. Tuzikov, A. M. Andrianov, “Identifikatsiya novykh potentsialnykh ingibitorov belka gp41 VICh-1 metodami virtualnogo skrininga i molekulyarnogo modelirovaniya”, Matematicheskaya biologiya i bioinformatika, 10:2 (2015), 325–343 <ext-link ext-link-type='doi' href='https://doi.org/10.17537/2015.10.325'>10.17537/2015.10.325</ext-link>
[17] A. M. Andrianov, I. A. Kashyn, A. V. Tuzikov, “Potential HIV-1 fusion inhibitors mimicking gp41-specific broadly neutralizing antibody 10E8: In silico discovery and prediction of antiviral potency”, J. Bioinform. Comput. Biol, 4:4 (2018), 1022
[18] T. Xiao, G. Frey, Q. Fu, C. L. Lavine, D. A. Scott, M. S. Seaman, J. J. Chou, B. Chen, “HIV-1 fusion inhibitors targeting the membrane-proximal external region of Env spikes”, Nat. Chem. Biol, 16 (2020), 529–537 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/s41589--020--0496-y'>10.1038/s41589--020--0496-y</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=4450510'>4450510</ext-link>
[19] H. C. Kolb, M. G. Finn, K. B. Sharpless, “Click chemistry: Diverse chemical function from a few good reactions”, Angew. Chemie Int. Ed, 40:11 (2001), 2004–2021 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/1521-3773(20010601)40:11<2004::AID-ANIE2004>3.0.CO;2-5'>10.1002/1521-3773(20010601)40:11<2004::AID-ANIE2004>3.0.CO;2-5</ext-link>
[20] T. Sander, J. Freyss, M. von Korff, C. Rufener, “DataWarrior: An open-source program for chemistry aware data visualization and analysis”, J. Chem. Inf. Model, 55:2 (2015), 460–473 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ci500588j'>10.1021/ci500588j</ext-link>
[21] T. Sterling, J. J. Irwin, “ZINC 15-ligand discovery for everyone”, J. Chem. Inf. Model, 55:11 (2015), 2324–2337 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/acs.jcim.5b00559'>10.1021/acs.jcim.5b00559</ext-link>
[22] J. D. Durrant, J. A. McCammon, “AutoClickChem: Click chemistry in silico”, PLoS Comput. Biol., 8 (2012), e1002397 <ext-link ext-link-type='doi' href='https://doi.org/10.1371/journal.pcbi.1002397'>10.1371/journal.pcbi.1002397</ext-link>
[23] C. A. Lipinski, F. Lombardo, B. W. Dominy, P. J. Feeney, “Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings”, Adv. Drug Deliv. Rev, 46 (2001), 3–26 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0169-409X(00)00129-0'>10.1016/S0169-409X(00)00129-0</ext-link>
[24] A. Alhossary, S. D. Handoko, Y. Mu, Kwoh C. K., “Fast, accurate, and reliable molecular docking with QuickVina 2”, Bioinformatics, 31:13 (2015), 2214–2216 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/bioinformatics/btv082'>10.1093/bioinformatics/btv082</ext-link>
[25] M. Wojcikowski, P. J. Ballester, P. Siedlecki, “Performance of machine-learning scoring functions in structure-based virtual screening”, Sci. Rep., 7 (2017) <ext-link ext-link-type='doi' href='https://doi.org/10.1038/srep46710'>10.1038/srep46710</ext-link>
[26] C. Shen, Y. Hu, Z. Wang, H. Zhong, H. Zhang, H. Zhong, G. Wang, X. Yao, L. Xu, D. Cao, T. Hou, “Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions”, Brief. Bioinf, 22:1 (2021), 497–514 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/bib/bbz173'>10.1093/bib/bbz173</ext-link>
[27] D. A. Case, K. Belfon, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, T. E. Cheatham III, P. A. Kollman, AMBER 2020, University of California, 2020
[28] S. Genheden, U. Ryde, “The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinity”, Expert Opin. Drug Discov, 10:5 (2015), 449–461 <ext-link ext-link-type='doi' href='https://doi.org/10.1517/17460441.2015.1032936'>10.1517/17460441.2015.1032936</ext-link>
[29] J. P. Ryckaert, G. Ciccotti, H. J.C. Berendsen, “Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes”, J. Comput. Phys, 23:3 (1977), 327–341 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0021--9991(77)90098--5'>10.1016/0021--9991(77)90098--5</ext-link>
[30] J. J.P. Stewart, “Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters”, J. Mol. Model, 19 (2013), 1–32 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/s00894--012--1667-x'>10.1007/s00894--012--1667-x</ext-link>
[31] A. V. Sulimov, D. C. Kutov, E. V. Katkova, V. B. Sulimov, “Combined docking with classical force field and quantum chemical semiempirical method PM7”, Adv. Bioinf, 5 (2017), 1–6 <ext-link ext-link-type='doi' href='https://doi.org/10.1155/2017/7167691'>10.1155/2017/7167691</ext-link>
[32] Klamt A., COSMO-RS: From quantum chemistry to fluid phase thermodynamics and drug design, 1st ed., Elsevier, Boston, MA, USA, 2005, 246 pp.
[33] A. Klamt, G. Schuurmann, “COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient”, J. Chem. Soc. Perkin Transac, 2 (1993), 799–805 <ext-link ext-link-type='doi' href='https://doi.org/10.1039/P29930000799'>10.1039/P29930000799</ext-link>
[34] J. D. Durrant, J. A. McCammon, “BINANA: A novel algorithm for ligand-binding characterization”, J. Mol. Graph. Model, 29:6 (2011), 888–893 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/j.jmgm.2011.01.004'>10.1016/j.jmgm.2011.01.004</ext-link>
[35] J. D. Durrant, J. A. McCammon, “NNScore 2.0: A neural-network receptor-ligand scoring function”, J. Chem. Inf. Model., 51:11 (2011), 2897–2903 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ci2003889'>10.1021/ci2003889</ext-link>
[36] A. Daina, O. Michielin, V. Zoete, “SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules”, Sci. Rep, 7 (2017), 42717 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/srep42717'>10.1038/srep42717</ext-link>
[37] K. Salzwedel, J. T. West, E. A. Hunter, “A conserved tryptophan-rich motif in the membrane-proximal region of the human immunodeficiency virus type 1 gp41 ectodomain is important for Env-mediated fusion and virus infectivity”, J. Virol, 73:3 (1999), 2469–2480 <ext-link ext-link-type='doi' href='https://doi.org/10.1128/JVI.73.3.2469--2480.1999'>10.1128/JVI.73.3.2469--2480.1999</ext-link>
[38] A. K. Bellamy-McIntyre, C. S. Lay, S. Bar, A. L. Maerz, H. Gert, G. H. Talbo, E. Heidi, H. E. Drummer, P. Poumbourios, “Functional links between the fusion peptide-proximal polar segment and membrane-proximal region of human immunodeficiency virus gp41 in distinct phases of membrane fusion”, J. Biol. Chem, 282 (2007), 23104–23116 <ext-link ext-link-type='doi' href='https://doi.org/10.1074/jbc.M703485200'>10.1074/jbc.M703485200</ext-link>