References
- Wang H.B., Mo Q.H., Yang Z. HIV vaccine research: The challenge and the way forward. J. Immunol. Res. 2015;2015. Article ID 503978. doi: 10.1155/2015/503978
- Mann J.K., Ndung’u T. HIV-1 vaccine immunogen design strategies. Virol. J. 2015;12(3). doi: 10.1186/s12985-014-0221-0
- Corti D., Lanzavecchia A. Broadly neutralizing antiviral antibodies. Ann. Rev. Immunol. 2013;31:705–742. doi: 10.1146/annurev-immunol-032712-095916
- Arts E.J., Hazuda D.J. HIV-1 antiretroviral drug therapy. Cold Spring Harb. Perspect. Med. 2012;2:a007161. doi: 10.1101/cshperspect.a007161
- Kumari G., Singh R.K. Highly active antiretroviral therapy for treatment of HIV/AIDS patients: current status and future prospects and the Indian scenario. HIV & AIDS Rev. 2012;11:5–14. doi: 10.1016/j.hivar.2012.02.003
- MacArthur R.D., Novak R.M. Maraviroc: The first of a new class of antiretroviral agents. Clin. Infect. Dis. 2008;47:236–241. doi: 10.1086/589289
- Matthews T., Salgo M., Greenberg M., Chung J., DeMasi R., Bolognesi D. Enfuvirtide: The first therapy to inhibit the entry of HIV-1 into host CD4 lymphocytes. Nat. Rev. Drug Discov. 2004;3:215–225. doi: 10.1038/nrd1331
- Bettiker R.L., Koren D.E., Jacobson J.M. Ibalizumab. Curr. Opin. HIV AIDS. 2018;13(4):354–358. doi: 10.1097/COH.0000000000000473
- Rizza S.A., Bhatia R., Zeuli J., Temesgen Z. Ibalizumab for the treatment of multidrug-resistant HIV-1 infection. Drugs Today (Barc). 2019;55(1):25–34. doi: 10.1358/dot.2019.55.1.2895651
- Blair H.A. Ibalizumab: A Review in multidrug-resistant HIV-1 infection. Drugs. 2020;80(2):189–196. doi: 10.1007/s40265-020-01258-3
- Kozal M., Aberg J., Pialoux G., Cahn P., Thompson M., Molina J.-M., Grinsztejn B., Diaz R., Castagna A., Kumar P., Latiff G., DeJesus E., et al., for the BRIGHTE Trial Team. Fostemsavir in adults with multidrug-resistant HIV-1 infection. N. Engl. J. Med. 2020;382:1232–1243. doi: 10.1056/NEJMoa1902493
- Chahine E.B. Fostemsavir: The first oral attachment inhibitor for treatment of HIV-1 infection. Am. J. Health Syst. Pharm. 2021;78(5):376–388. doi: 10.1093/ajhp/zxaa416
- Lai Y.-T. Small molecule HIV-1 attachment inhibitors: Discovery, mode of action and structural basis of inhibition. Viruses. 2021;13:843. doi: 10.3390/v13050843
- Kwong P.D., Mascola J.R., Nabel G.J. The changing face of HIV vaccine research. J. Int. AIDS Soc. 2012;15:17407. doi: 10.7448/IAS.15.2.17407
- Huang J., Ofek G., Laub L., Louder M.K., Doria-Rose N.A., Longo N.S., Imamichi H., Bailer R.T., Chakrabarti B., Sharma S.K., Alam S.M., Wang T., Yang Y., Zhang B., Migueles S.A., Wyatt R., Haynes B.F., Kwong P.D., Mascola J.R., Connors M. Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature. 2012;491:406–412. doi: 10.1038/nature11544
- Kashyn I.A., Tuzikov A.V., Andrianov A.M. Identification of Novel Potential Inhibitors of the HIV-1 gp41 Protein by Virtual Screening and Molecular Modeling Methods. Mathematical Biology and Bioinformatics. 2015;10(2):325–343. doi: 10.17537/2015.10.325
- Andrianov A.M., Kashyn I.A., Tuzikov A.V. Potential HIV-1 fusion inhibitors mimicking gp41-specific broadly neutralizing antibody 10E8: In silico discovery and prediction of antiviral potency. J. Bioinform. Comput. Biol. 2018;4(4):1022. doi: 10.1142/S0219720018400073
- Xiao T., Frey G., Fu Q., Lavine C.L., Scott D. A., Seaman M.S., Chou J.J., Chen B. HIV-1 fusion inhibitors targeting the membrane-proximal external region of Env spikes. Nat. Chem. Biol. 2020;16:529–537. doi: 10.1038/s41589-020-0496-y
- Kolb H.C., Finn M.G., Sharpless K.B. Click chemistry: Diverse chemical function from a few good reactions. Angew. Chemie Int. Ed. 2001;40(11):2004–2021. doi: 10.1002/1521-3773(20010601)40:11<2004::AID-ANIE2004>3.0.CO;2-5
- Sander T., Freyss J., von Korff M., Rufener C. DataWarrior: An open-source program for chemistry aware data visualization and analysis. J. Chem. Inf. Model. 2015;55(2):460–473. doi: 10.1021/ci500588j
- Sterling T., Irwin J.J. ZINC 15–ligand discovery for everyone. J. Chem. Inf. Model. 2015;55(11):2324–2337. doi: 10.1021/acs.jcim.5b00559
- Durrant J.D., McCammon J.A. AutoClickChem: Click chemistry in silico. PLoS Comput. Biol. 2012;8:e1002397. doi: 10.1371/journal.pcbi.1002397
- 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. Adv. Drug Deliv. Rev. 2001;46:3–26.
- Alhossary A., Handoko S.D., Mu Y., Kwoh C.K. Fast, accurate, and reliable molecular docking with QuickVina 2. Bioinformatics. 2015;31(13):2214–2216. doi: 10.1093/bioinformatics/btv082
- Wójcikowski M., Ballester P.J., Siedlecki P. Performance of machine-learning scoring functions in structure-based virtual screening. Sci. Rep. 2017;7. Article No. 46710. doi: 10.1038/srep46710
- Shen C., Hu Y., Wang Z., Zhong H., Zhang H., Zhong H., Wang G., Yao X., Xu L., Cao D., Hou T. Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions. Brief. Bioinf. 2021;22(1):497–514. doi: 10.1093/bib/bbz173
- Case D.A., Belfon K., Ben-Shalom I.Y., Brozell S.R., Cerutti D.S., Cheatham III T.E., Kollman P.A. AMBER 2020. University of California, 2020.
- Genheden S., Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinity. Expert Opin. Drug Discov. 2015;10(5):449–461. doi: 10.1517/17460441.2015.1032936
- Ryckaert J.P., Ciccotti G., Berendsen H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977;23(3):327–341. doi: 10.1016/0021-9991(77)90098-5
- Stewart J.J.P. Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters. J. Mol. Model. 2013;19:1–32. doi: 10.1007/s00894-012-1667-x
- Sulimov A.V., Kutov D.C., Katkova E.V., Sulimov V.B. Combined docking with classical force field and quantum chemical semiempirical method PM7. Adv. Bioinf. 2017;5:1–6. doi: 10.1155/2017/7167691
- Klamt A. COSMO-RS: From quantum chemistry to fluid phase thermodynamics and drug design, 1st ed. Boston, MA, USA: Elsevier, 2005. 246 p.
- Klamt A., Schüürmann G. COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc. Perkin Transac. 1993;2:799–805. doi: 10.1039/P29930000799
- Durrant J.D., McCammon J.A. BINANA: A novel algorithm for ligand-binding characterization. J. Mol. Graph. Model. 2011;29(6):888–893. doi: 10.1016/j.jmgm.2011.01.004
- Durrant J.D., McCammon J.A. NNScore 2.0: A neural-network receptor–ligand scoring function. J. Chem. Inf. Model. 2011;51(11):2897–2903. doi: 10.1021/ci2003889
- Daina A., Michielin O., Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep. 2017;7. Article No. 42717. doi: 10.1038/srep42717
- Salzwedel K., West J.T., Hunter E.A. 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. 1999;73(3):2469–2480. doi: 10.1128/JVI.73.3.2469-2480.1999
- Bellamy-McIntyre A.K., Lay C.-S., Bar S., Maerz A.L., Gert H., Talbo G.H., Heidi E., Drummer H.E., Poumbourios P. 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. 2007;282:23104–23116. doi: 10.1074/jbc.M703485200
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