An Overview of Antiretroviral Agents for Treating HIV Infection in Paediatric Population

doi:10.2174/0929867325666180904123549
摘要

小儿获得性免疫缺陷综合症（AIDS）是威胁生命的传染病，其中人类免疫缺陷病毒（HIV）主要通过母婴传播（MTCT）在怀孕，分娩和分娩或母乳喂养期间传播。这篇综述概述了消除小儿HIV-1感染中全身性病毒复制的独特治疗方法。已经出现了许多种类的抗逆转录病毒药物作为治疗工具，用于下调HIV复制过程中的不同步骤。这些类别包括非核苷类似物逆转录酶抑制剂（NNRTIs），核苷/核苷酸类似物逆转录酶抑制剂（NRTIs / NtRTIs），整合酶抑制剂（INIs），蛋白酶抑制剂（PIs）和进入抑制剂（EIs）。某些抗逆转录病毒药物与药代动力学增强剂（PEs）并用可能会提高主要治疗剂的有效性。多种抗逆转录病毒药物疗法（高效抗逆转录病毒疗法-HAART）的组合目前是HIV感染的标准治疗方法。到目前为止，HAART的使用为延长和最大程度地抑制病毒以及保护HIV感染后的免疫系统提供了最佳机会。尽管如此，高剂量的多种药物的频繁给药，以足够的剂量不能有效地到达病毒库，耐药性的发展以及患者对患者依从性的缺乏都不利于完全消除HIV。基于纳米技术的药物递送系统的开发可以使抗逆转录病毒药物靶向性地以治疗浓度递送至难以接近的病毒库位置。此外，计算机辅助药物设计（CADD）方法的应用为开发具有良好药效学和药代动力学特性的抗HIV候选药物提供了有价值的工具。
关键词: 小儿HIV病毒，后天免疫机能丧失综合症（AIDS），抗逆转录病毒疗法，病毒库，药物设计，计算机辅助药物设计（CADD）。
« Previous Next »
[1] 
Centers for Disease Control (CDC). Unexplained immunodeficiency and opportunistic infections in infants-New York, New Jersey, California. MMWR Morb. Mortal. Wkly. Rep.,  1982, 31(49), 665-667.
[PMID:  6819445] 
[2] 
UNAIDS. World AIDS Day, 2017. Available at:. http://www.unaids.org/sites/default/files/media_asset/UNAI DS_FactSheet_en.pdf (Accessed: June 25, 2018)
[3] 
John, G.C.; Kreiss, J. Mother-to-child transmission of human immunodeficiency virus type 1. Epidemiol. Rev.,  1996, 18(2), 149-157.
[http://dx.doi.org/10.1093/oxfordjournals.epirev.a017922] [PMID:  9021309] 
[4] 
Tobin, N.H.; Aldrovandi, G.M. Immunology of pediatric HIV infection. Immunol. Rev.,  2013, 254(1), 143-169.
[http://dx.doi.org/10.1111/imr.12074] [PMID:  23772619] 
[5] 
Langford, S.E.; Ananworanich, J.; Cooper, D.A. Predictors of disease progression in HIV infection: a review. AIDS Res. Ther.,  2007, 4(1), 11.
[http://dx.doi.org/10.1186/1742-6405-4-11] [PMID:  17502001] 
[6] 
Van Dyke, R.B. Opportunistic infections in HIV-infected children. Semin. Pediatr. Infect. Dis.,  1995, 6(1), 10-16.
[http://dx.doi.org/10.1016/S1045-1870(05)80018-4] 
[7] 
Idele, P.; Hayashi, C.; Porth, T.; Mamahit, A.; Mahy, M. Prevention of mother-to-child transmission of HIV and paediatric HIV care and treatment monitoring: from measuring process to impact and elimination of mother-to-child transmission of HIV. AIDS Behav.,  2017, 21(1)(Suppl. 1), 23-33.
[http://dx.doi.org/10.1007/s10461-016-1670-9] [PMID:  28063074] 
[8] 
Simon, V.; Ho, D.D.; Abdool Karim, Q. HIV/AIDS epidemiology, pathogenesis, prevention, and treatment. Lancet,  2006, 368(9534), 489-504.
[http://dx.doi.org/10.1016/S0140-6736(06)69157-5] [PMID:  16890836] 
[9] 
Lu, K.; Heng, X.; Summers, M.F. Structural determinants and mechanism of HIV-1 genome packaging. J. Mol. Biol.,  2011, 410(4), 609-633.
[http://dx.doi.org/10.1016/j.jmb.2011.04.029] [PMID:  21762803] 
[10] 
German Advisory Committee Blood (Arbeitskreis Blut). Subgroup ‘Assessment of Pathogens Transmissible by Blood’. Human immunodeficiency virus (HIV). Transfus. Med. Hemother.,  2016, 43(3), 203-222.
[http://dx.doi.org/10.1159/000445852] [PMID:  27403093] 
[11] 
Haseltine, W.A. Molecular biology of the human immunodeficiency virus type 1. FASEB J.,  1991, 5(10), 2349-2360.
[http://dx.doi.org/10.1096/fasebj.5.10.1829694] [PMID:  1829694] 
[12] 
Thomson, M.M.; Nájera, R. Molecular epidemiology of HIV-1 variants in the global AIDS pandemic: an update. AIDS Rev.,  2005, 7(4), 210-224.
[PMID:  16425961] 
[13] 
Sharp, P.M.; Hahn, B.H. Origins of HIV and the AIDS pandemic. Cold Spring Harb. Perspect. Med.,  2011, 1(1) a006841
[http://dx.doi.org/10.1101/cshperspect.a006841] [PMID:  22229120] 
[14] 
Cohen, M.S.; Hellmann, N.; Levy, J.A.; DeCock, K.; Lange, J. The spread, treatment, and prevention of HIV-1: evolution of a global pandemic. J. Clin. Invest.,  2008, 118(4), 1244-1254.
[http://dx.doi.org/10.1172/JCI34706] [PMID:  18382737] 
[15] 
Campbell-Yesufu, O.T.; Gandhi, R.T. Update on human immunodeficiency virus (HIV)-2 infection. Clin. Infect. Dis.,  2011, 52(6), 780-787.
[http://dx.doi.org/10.1093/cid/ciq248] [PMID:  21367732] 
[16] 
Nyamweya, S.; Hegedus, A.; Jaye, A.; Rowland-Jones, S.; Flanagan, K.L.; Macallan, D.C. Comparing HIV-1 and HIV-2 infection: Lessons for viral immunopathogenesis. Rev. Med. Virol.,  2013, 23(4), 221-240.
[http://dx.doi.org/10.1002/rmv.1739] [PMID:  23444290] 
[17] 
Cicala, C.; Arthos, J.; Selig, S.M.; Dennis, G., Jr; Hosack, D.A.; Van Ryk, D.; Spangler, M.L.; Steenbeke, T.D.; Khazanie, P.; Gupta, N.; Yang, J.; Daucher, M.; Lempicki, R.A.; Fauci, A.S. HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Proc. Natl. Acad. Sci. USA,  2002, 99(14), 9380-9385.
[http://dx.doi.org/10.1073/pnas.142287999] [PMID:  12089333] 
[18] 
Balabanian, K.; Harriague, J.; Décrion, C.; Lagane, B.; Shorte, S.; Baleux, F.; Virelizier, J.L.; Arenzana-Seisdedos, F.; Chakrabarti, L.A. CXCR4-tropic HIV-1 envelope glycoprotein functions as a viral chemokine in unstimulated primary CD4+ T lymphocytes. J. Immunol.,  2004, 173(12), 7150-7160.
[http://dx.doi.org/10.4049/jimmunol.173.12.7150] [PMID:  15585836] 
[19] 
Haase, A.T. Population biology of HIV-1 infection: viral and CD4+ T cell demographics and dynamics in lymphatic tissues. Annu. Rev. Immunol.,  1999, 17(1), 625-656.
[http://dx.doi.org/10.1146/annurev.immunol.17.1.625] [PMID:  10358770] 
[20] 
Eckert, D.M.; Kim, P.S. Mechanisms of viral membrane fusion and its inhibition. Annu. Rev. Biochem.,  2001, 70, 777-810.
[http://dx.doi.org/10.1146/annurev.biochem.70.1.777] [PMID:  11395423] 
[21] 
Garg, H.; Blumenthal, R. Role of HIV Gp41 mediated fusion/hemifusion in bystander apoptosis. Cell. Mol. Life Sci.,  2008, 65(20), 3134-3144.
[http://dx.doi.org/10.1007/s00018-008-8147-6] [PMID:  18500445] 
[22] 
Wilen, C.B.; Tilton, J.C.; Doms, R.W. HIV: cell binding and entry. Cold Spring Harb. Perspect. Med.,  2012, 2(8) a006866
[http://dx.doi.org/10.1101/cshperspect.a006866] [PMID:   22908191] 
[23] 
Singh, K.; Marchand, B.; Kirby, K.A.; Michailidis, E.; Sarafianos, S.G. Structural aspects of drug resistance and inhibition of HIV-1 reverse transcriptase. Viruses,  2010, 2(2), 606-638.
[http://dx.doi.org/10.3390/v2020606] [PMID:  20376302] 
[24] 
Hu, W.S.; Hughes, S.H. HIV-1 reverse transcription. Cold Spring Harb. Perspect. Med.,  2012, 2(10) a006882
[http://dx.doi.org/10.1101/cshperspect.a006882] [PMID:  23028129] 
[25] 
Pommier, Y.; Johnson, A.A.; Marchand, C. Integrase inhibitors to treat HIV/AIDS. Nat. Rev. Drug Discov.,  2005, 4(3), 236-248.
[http://dx.doi.org/10.1038/nrd1660] [PMID:  15729361] 
[26] 
Craigie, R.; Bushman, F.D. HIV DNA integration. Cold Spring Harb. Perspect. Med.,  2012, 2(7) a006890
[http://dx.doi.org/10.1101/cshperspect.a006890] [PMID:  22762018] 
[27] 
Craigie, R. The molecular biology of HIV integrase. Future Virol.,  2012, 7(7), 679-686.
[http://dx.doi.org/10.2217/fvl.12.56] [PMID:  23024700] 
[28] 
Burniston, M.T.; Cimarelli, A.; Colgan, J.; Curtis, S.P.; Luban, J. Human immunodeficiency virus type 1 Gag polyprotein multimerization requires the nucleocapsid domain and RNA and is promoted by the capsid-dimer interface and the basic region of matrix protein. J. Virol.,  1999, 73(10), 8527-8540.
[http://dx.doi.org/10.1128/JVI.73.10.8527-8540.1999] [PMID:  10482606] 
[29] 
Brik, A.; Wong, C-H. HIV-1 protease: mechanism and drug discovery. Org. Biomol. Chem.,  2003, 1(1), 5-14.
[http://dx.doi.org/10.1039/b208248a] [PMID:  12929379] 
[30] 
Cihlar, T.; Fordyce, M. Current status and prospects of HIV treatment. Curr. Opin. Virol.,  2016, 18, 50-56.
[http://dx.doi.org/10.1016/j.coviro.2016.03.004] [PMID:  27023283] 
[31] 
Sierra, S.; Kupfer, B.; Kaiser, R. Basics of the virology of HIV-1 and its replication. J. Clin. Virol.,  2005, 34(4), 233-244.
[http://dx.doi.org/10.1016/j.jcv.2005.09.004] [PMID:  16198625] 
[32] 
Palella, F.J.J., Jr; Delaney, K.M.; Moorman, A.C.; Loveless, M.O.; Fuhrer, J.; Satten, G.A.; Aschman, D.J.; Holmberg, S.D. HIV Outpatient Study Investigators. Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. N. Engl. J. Med.,  1998, 338(13), 853-860.
[http://dx.doi.org/10.1056/NEJM199803263381301] [PMID:  9516219] 
[33] 
Vittinghoff, E.; Scheer, S.; O’Malley, P.; Colfax, G.; Holmberg, S.D.; Buchbinder, S.P. Combination antiretroviral therapy and recent declines in AIDS incidence and mortality. J. Infect. Dis.,  1999, 179(3), 717-720.
[http://dx.doi.org/10.1086/314623] [PMID:  9952385] 
[34] 
Mocroft, A.; Vella, S.; Benfield, T.L.; Chiesi, A.; Miller, V.; Gargalianos, P.; d’Arminio Monforte, A.; Yust, I.; Bruun, J.N.; Phillips, A.N.; Lundgren, J.D. Changing patterns of mortality across Europe in patients infected with HIV-1. EuroSIDA Study Group. Lancet,  1998, 352(9142), 1725-1730.
[http://dx.doi.org/10.1016/S0140-6736(98)03201-2] [PMID:  9848347] 
[35] 
Fischl, M.A.; Richman, D.D.; Grieco, M.H.; Gottlieb, M.S.; Volberding, P.A.; Laskin, O.L.; Leedom, J.M.; Groopman, J.E.; Mildvan, D.; Schooley, R.T.; Jackson, G.G.; Durack, D.T.; King, D. The efficacy of azidothymidine (AZT) in the treatment of patients with AIDS and AIDS-related complex. A double-blind, placebo-controlled trial. N. Engl. J. Med.,  1987, 317(4), 185-191.
[http://dx.doi.org/10.1056/NEJM198707233170401] [PMID:  3299089] 
[36] 
Young, F.E. The role of the FDA in the effort against AIDS. Public Health Rep.,  1988, 103(3), 242-245.
[PMID:  3131814] 
[37] 
Holec, A.D.; Mandal, S.; Prathipati, P.K.; Destache, C.J. Nucleotide reverse transcriptase inhibitors: a thorough review, present status and future perspective as HIV Therapeutics. Curr. HIV Res.,  2017, 15(6), 411-421.
[http://dx.doi.org/10.2174/1570162X15666171120110145] [PMID:  29165087] 
[38] 
Sarafianos, S.G.; Clark, A.D., Jr; Das, K.; Tuske, S.; Birktoft, J.J.; Ilankumaran, P.; Ramesha, A.R.; Sayer, J.M.; Jerina, D.M.; Boyer, P.L.; Hughes, S.H.; Arnold, E. Structures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA. EMBO J.,  2002, 21(23), 6614-6624.
[http://dx.doi.org/10.1093/emboj/cdf637] [PMID:  12456667] 
[39] 
Tuske, S.; Sarafianos, S.G.; Clark, A.D., Jr; Ding, J.; Naeger, L.K.; White, K.L.; Miller, M.D.; Gibbs, C.S.; Boyer, P.L.; Clark, P.; Wang, G.; Gaffney, B.L.; Jones, R.A.; Jerina, D.M.; Hughes, S.H.; Arnold, E. Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir. Nat. Struct. Mol. Biol.,  2004, 11(5), 469-474.
[http://dx.doi.org/10.1038/nsmb760] [PMID:  15107837] 
[40] 
Rhodes, D.I.; Peat, T.S.; Vandegraaff, N.; Jeevarajah, D.; Le, G.; Jones, E.D.; Smith, J.A.; Coates, J.A.; Winfield, L.J.; Thienthong, N.; Newman, J.; Lucent, D.; Ryan, J.H.; Savage, G.P.; Francis, C.L.; Deadman, J.J. Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design. Antivir. Chem. Chemother.,  2011, 21(4), 155-168.
[http://dx.doi.org/10.3851/IMP1716] [PMID:  21602613] 
[41] 
de Béthune, M-P. Non-nucleoside reverse transcriptase inhibitors (NNRTIs), their discovery, development, and use in the treatment of HIV-1 infection: a review of the last 20 years (1989-2009). Antiviral Res.,  2010, 85(1), 75-90.
[http://dx.doi.org/10.1016/j.antiviral.2009.09.008] [PMID:  19781578] 
[42] 
Kohlstaedt, L.A.; Wang, J.; Friedman, J.M.; Rice, P.A.; Steitz, T.A. Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science,  1992, 256(5065), 1783-1790.
[http://dx.doi.org/10.1126/science.1377403] [PMID:  1377403] 
[43] 
Spence, R.A.; Kati, W.M.; Anderson, K.S.; Johnson, K.A. Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors. Science,  1995, 267(5200), 988-993.
[http://dx.doi.org/10.1126/science.7532321] [PMID:  7532321] 
[44] 
Ren, J.; Milton, J.; Weaver, K.L.; Short, S.A.; Stuart, D.I.; Stammers, D.K. Structural basis for the resilience of efavirenz (DMP-266) to drug resistance mutations in HIV-1 reverse transcriptase. Structure, 2000, 8(10), 1089-1094. 26. Curr. Med. Chem.,  2020, 27(00) [Melo et al.].
[45] 
Lindberg, J.; Sigurdsson, S.; Löwgren, S.; Andersson, H.O.; Sahlberg, C.; Noréen, R.; Fridborg, K.; Zhang, H.; Unge, T. Structural basis for the inhibitory efficacy of efavirenz (DMP-266), MSC194 and PNU142721 towards the HIV-1 RT K103N mutant. Eur. J. Biochem.,  2002, 269(6), 1670-1677.
[http://dx.doi.org/10.1046/j.1432-1327.2002.02811.x] [PMID:  11895437] 
[46] 
Lansdon, E.B.; Brendza, K.M.; Hung, M.; Wang, R.; Mukund, S.; Jin, D.; Birkus, G.; Kutty, N.; Liu, X. Crystal structures of HIV-1 reverse transcriptase with etravirine (TMC125) and rilpivirine (TMC278): implications for drug design. J. Med. Chem.,  2010, 53(10), 4295-4299.
[http://dx.doi.org/10.1021/jm1002233] [PMID:  20438081] 
[47] 
Mouscadet, J-F.; Tchertanov, L. Raltegravir: molecular basis of its mechanism of action. Eur. J. Med. Res.,  2009, 14(Suppl. 3), 5-16.
[http://dx.doi.org/10.1186/2047-783X-14-S3-5] [PMID:  19959411] 
[48] 
Grobler, J.A.; Stillmock, K.; Hu, B.; Witmer, M.; Felock, P.; Espeseth, A.S.; Wolfe, A.; Egbertson, M.; Bourgeois, M.; Melamed, J.; Wai, J.S.; Young, S.; Vacca, J.; Hazuda, D.J. Diketo acid inhibitor mechanism and HIV-1 integrase: implications for metal binding in the active site of phosphotransferase enzymes. Proc. Natl. Acad. Sci. USA,  2002, 99(10), 6661-6666.
[http://dx.doi.org/10.1073/pnas.092056199] [PMID:  11997448] 
[49] 
Larson, K.B.; Wang, K.; Delille, C.; Otofokun, I.; Acosta, E.P. Pharmacokinetic enhancers in HIV therapeutics. Clin. Pharmacokinet.,  2014, 53(10), 865-872.
[http://dx.doi.org/10.1007/s40262-014-0167-9] [PMID:  25164142] 
[50] 
Clemente, J.C.; Coman, R.M.; Thiaville, M.M.; Janka, L.K.; Jeung, J.A.; Nukoolkarn, S.; Govindasamy, L.; Agbandje-McKenna, M.; McKenna, R.; Leelamanit, W.; Goodenow, M.M.; Dunn, B.M. Analysis of HIV-1 CRF_01 A/E protease inhibitor resistance: structural determinants for maintaining sensitivity and developing resistance to atazanavir. Biochemistry,  2006, 45(17), 5468-5477.
[http://dx.doi.org/10.1021/bi051886s] [PMID:  16634628] 
[51] 
Yedidi, R.S.; Maeda, K.; Fyvie, W.S.; Steffey, M.; Davis, D.A.; Palmer, I.; Aoki, M.; Kaufman, J.D.; Stahl, S.J.; Garimella, H.; Das, D.; Wingfield, P.T.; Ghosh, A.K.; Mitsuya, H. P2′ benzene carboxylic acid moiety is associated with decrease in cellular uptake: evaluation of novel nonpeptidic HIV-1 protease inhibitors containing P2 bis-tetrahydrofuran moiety. Antimicrob. Agents Chemother.,  2013, 57(10), 4920-4927.
[http://dx.doi.org/10.1128/AAC.00868-13] [PMID:  23877703] 
[52] 
Kim, E.; Baker, C.; Dwyer, M.; Murcko, M.; Rao, B.; Tung, R.; Navia, M. Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme. J. Am. Chem. Soc.,  1995, 117(3), 1181-1182.
[http://dx.doi.org/10.1021/ja00108a056] 
[53] 
Shen, C.H.; Wang, Y.F.; Kovalevsky, A.Y.; Harrison, R.W.; Weber, I.T. Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters. FEBS J.,  2010, 277(18), 3699-3714.
[http://dx.doi.org/10.1111/j.1742-4658.2010.07771.x] [PMID:  20695887] 
[54] 
Stoll, V.; Qin, W.; Stewart, K.D.; Jakob, C.; Park, C.; Walter, K.; Simmer, R.L.; Helfrich, R.; Bussiere, D.; Kao, J.; Kempf, D.; Sham, H.L.; Norbeck, D.W. X-ray crystallographic structure of ABT-378 (lopinavir) bound to HIV-1 protease. Bioorg. Med. Chem.,  2002, 10(8), 2803-2806.
[http://dx.doi.org/10.1016/S0968-0896(02)00051-2] [PMID:  12057670] 
[55] 
Reddy, G.S.; Ali, A.; Nalam, M.N.; Anjum, S.G.; Cao, H.; Nathans, R.S.; Schiffer, C.A.; Rana, T.M. Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2′ ligands in pseudosymmetric dipeptide isosteres. J. Med. Chem.,  2007, 50(18), 4316-4328.
[http://dx.doi.org/10.1021/jm070284z] [PMID:  17696512] 
[56] 
Kaldor, S.W.; Kalish, V.J.; Davies, J.F., II; Shetty, B.V.; Fritz, J.E.; Appelt, K.; Burgess, J.A.; Campanale, K.M.; Chirgadze, N.Y.; Clawson, D.K.; Dressman, B.A.; Hatch, S.D.; Khalil, D.A.; Kosa, M.B.; Lubbehusen, P.P.; Muesing, M.A.; Patick, A.K.; Reich, S.H.; Su, K.S.; Tatlock, J.H. Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease. J. Med. Chem.,  1997, 40(24), 3979-3985.
[http://dx.doi.org/10.1021/jm9704098] [PMID:  9397180] 
[57] 
Qian, K.; Morris-Natschke, S.L.; Lee, K-H. HIV entry inhibitors and their potential in HIV therapy. Med. Res. Rev.,  2009, 29(2), 369-393.
[http://dx.doi.org/10.1002/med.20138] [PMID:  18720513] 
[58] 
Briz, V.; Poveda, E.; Soriano, V. HIV entry inhibitors: mechanisms of action and resistance pathways. J. Antimicrob. Chemother.,  2006, 57(4), 619-627.
[http://dx.doi.org/10.1093/jac/dkl027] [PMID:  16464888] 
[59] 
Chen, R.Y.; Kilby, J.M.; Saag, M.S. Enfuvirtide. Expert Opin. Investig. Drugs,  2002, 11(12), 1837-1843.
[http://dx.doi.org/10.1517/13543784.11.12.1837] [PMID:  12457443] 
[60] 
Tan, Q.; Zhu, Y.; Li, J.; Chen, Z.; Han, G.W.; Kufareva, I.; Li, T.; Ma, L.; Fenalti, G.; Li, J.; Zhang, W.; Xie, X.; Yang, H.; Jiang, H.; Cherezov, V.; Liu, H.; Stevens, R.C.; Zhao, Q.; Wu, B. Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex. Science,  2013, 341(6152), 1387-1390.
[http://dx.doi.org/10.1126/science.1241475] [PMID:  24030490] 
[61] 
Xu, L.; Liu, H.; Murray, B.P.; Callebaut, C.; Lee, M.S.; Hong, A.; Strickley, R.G.; Tsai, L.K.; Stray, K.M.; Wang, Y.; Rhodes, G.R.; Desai, M.C. Cobicistat (GS-9350): A potent and selective inhibitor of human CYP3A as a novel pharmacoenhancer. ACS Med. Chem. Lett.,  2010, 1(5), 209-213.
[http://dx.doi.org/10.1021/ml1000257] [PMID:  24900196] 
[62] 
Sherman, E.M.; Worley, M.V.; Unger, N.R.; Gauthier, T.P.; Schafer, J.J. Cobicistat: review of a pharmacokinetic enhancer for HIV infection. Clin. Ther.,  2015, 37(9), 1876-1893.
[http://dx.doi.org/10.1016/j.clinthera.2015.07.022] [PMID:  26319088] 
[63] 
Sevrioukova, I.F.; Poulos, T.L. Structure and mechanism of the complex between cytochrome P4503A4 and ritonavir. Proc. Natl. Acad. Sci. USA,  2010, 107(43), 18422-18427.
[http://dx.doi.org/10.1073/pnas.1010693107] [PMID:  20937904] 
[64] 

AIDS info: Offering information on HIV/AIDS treatment,
prevention, and research, Available at:. https://aidsinfo.nih.gov/guidelines/html/2/pediatric-arv/512/ (Accessed: June 25, 2018).
[65] 
Ray, M.; Logan, R.; Sterne, J.A.; Hernández-Díaz, S.; Robins, J.M.; Sabin, C.; Bansi, L.; van Sighem, A.; de Wolf, F.; Costagliola, D.; Lanoy, E.; Bucher, H.C.; von Wyl, V.; Esteve, A.; Casbona, J.; del Amo, J.; Moreno, S.; Justice, A.; Goulet, J.; Lodi, S.; Phillips, A.; Seng, R.; Meyer, L.; Pérez-Hoyos, S.; García de Olalla, P.; Hernán, M.A. HIV-CAUSAL Collaboration. The effect of combined antiretroviral therapy on the overall mortality of HIV-infected individuals. AIDS,  2010, 24(1), 123-137.
[http://dx.doi.org/10.1097/QAD.0b013e3283324283] [PMID:  19770621] 
[66] 
Pirrone, V.; Thakkar, N.; Jacobson, J.M.; Wigdahl, B.; Krebs, F.C. Combinatorial approaches to the prevention and treatment of HIV-1 infection. Antimicrob. Agents Chemother.,  2011, 55(5), 1831-1842.
[http://dx.doi.org/10.1128/AAC.00976-10] [PMID:  21343462] 
[67] 
Desai, M.; Iyer, G.; Dikshit, R.K. Antiretroviral drugs: critical issues and recent advances. Indian J. Pharmacol.,  2012, 44(3), 288-298.
[http://dx.doi.org/10.4103/0253-7613.96296] [PMID:  22701234] 
[68] 
de Martino, M.; Tovo, P.A.; Balducci, M.; Galli, L.; Gabiano, C.; Rezza, G.; Pezzotti, P.; Osimani, P.; Di Bari, C.; Larovere, D.; Ruggeri, M.; Masi, M.; Specchia, F.; Battisti, L.; Duse, M.; Crispino, P.; Carrara, P.; Pintor, C.; Dedoni, M.; Dessì, C.; Loriano, D.; Anastasio, E.; Bezzi, T.; De Luca, M.; Farina, S.; Vierucci, A.; Bassetti, D.; Pontali, E.; Boni, S.; Marazzi, M.G.; Tasso, L.; Giovanettoni, C.; Salvini, F.; Pinzani, R.; Marchisio, P.; Viganò, A.; Tornaghi, R.; Zuccotti, G.V.; Riva, E.; Giovannini, M.; Lipreri, R.; Conio, S.; Ferraris, G.; Cellini, M.; Baraldi, C.; Guarino, A.; Canani, R.B.; Tarallo, L.; Giaquinto, C.; Ruga, E.; Rampon, O.; Nogare, E.R.D.; Sanfilippo, A.; Romano, A.; Benaglia, G.; Dodi, I.; Caselli, D.; Maccabruni, A.; Pacati, I.; Consolini, R.; Palla, G.; Cecchi, M.T.; Vecchi, V.; Anzidei, G.; Cerilli, S.; Chiodi, R.; Gattinara, G.C.; Krzysztofiak, A.; Bernardi, S.; Fundarò, C.; Genovese, O.; Colafati, G.S.; Catania, S.; Ajassa, C.; Mazza, A.; Garetto, S.; Riva, C.; Scolfaro, C. Italian Register for HIV Infection in Children and the Italian National AIDS Registry. Reduction in mortality with availability of antiretroviral therapy for children with perinatal HIV-1 infection. JAMA,  2000, 284(2), 190-197.
[http://dx.doi.org/10.1001/jama.284.2.190] [PMID:  10889592] 
[69] 
Fang, C.T.; Chang, Y.Y.; Hsu, H.M.; Twu, S.J.; Chen, K.T.; Lin, C.C.; Huang, L.Y.L.; Chen, M.Y.; Hwang, J.S.; Wang, J.D.; Chuang, C.Y. Life expectancy of patients with newly-diagnosed HIV infection in the era of highly active antiretroviral therapy. QJM,  2007, 100(2), 97-105.
[http://dx.doi.org/10.1093/qjmed/hcl141] [PMID:  17277317] 
[70] 
Pennings, P.S. HIV Drug Resistance: Problems and Perspectives. Infect. Dis. Rep.,  2013, 5(Suppl. 1) e5Available at:. https://www.ncbi.nlm.nih.gov/pmc/articles/ PMC3892620/ http://dx.doi.org/10.4081/idr.2013.s1.e5
[PMID:  24470969] 
[71] 
Amiji, M.M.; Vyas, T.K.; Shah, L.K. Role of nanotechnology in HIV/AIDS treatment: potential to overcome the viral reservoir challenge. Discov. Med.,  2006, 6(34), 157-162.
[PMID:  17234137] 
[72] 
Schrager, L.K.; D’Souza, M.P. Cellular and anatomical reservoirs of HIV-1 in patients receiving potent antiretroviral combination therapy. JAMA,  1998, 280(1), 67-71.
[http://dx.doi.org/10.1001/jama.280.1.67] [PMID:  9660366] 
[73] 
Blankson, J.N.; Persaud, D.; Siliciano, R.F. The challenge of viral reservoirs in HIV-1 infection. Annu. Rev. Med.,  2002, 53, 557-593.
[http://dx.doi.org/10.1146/annurev.med.53.082901.104024] [PMID:  11818490] 
[74] 
Tymchuk, C.N.; Currier, J.S. The safety of antiretroviral drugs. Expert Opin. Drug Saf.,  2008, 7(1), 1-4.
[http://dx.doi.org/10.1517/14740338.7.1.1] [PMID:  18171309] 
[75] 
Barry, M.; Mulcahy, F.; Merry, C.; Gibbons, S.; Back, D. Pharmacokinetics and potential interactions amongst antiretroviral agents used to treat patients with HIV infection. Clin. Pharmacokinet.,  1999, 36(4), 289-304.
[http://dx.doi.org/10.2165/00003088-199936040-00004] [PMID:  10320951] 
[76] 
Phelps, B.R.; Rakhmanina, N. Antiretroviral drugs in pediatric HIV-infected patients: pharmacokinetic and practical challenges. Paediatr. Drugs,  2011, 13(3), 175-192.
[http://dx.doi.org/10.2165/11587300-000000000-00000] [PMID:  21500872] 
[77] 
Sethi, A.K.; Celentano, D.D.; Gange, S.J.; Moore, R.D.; Gallant, J.E. Association between adherence to antiretroviral therapy and human immunodeficiency virus drug resistance. Clin. Infect. Dis.,  2003, 37(8), 1112-1118.
[http://dx.doi.org/10.1086/378301] [PMID:  14523777] 
[78] 
Dubrocq, G.; Rakhmanina, N.; Phelps, B.R. Challenges and opportunities in the development of HIV medications in pediatric patients. Paediatr. Drugs,  2017, 19(2), 91-98.
[http://dx.doi.org/10.1007/s40272-016-0210-4] [PMID:  28074348] 
[79] 
Onoue, S.; Yamada, S.; Chan, H-K. Nanodrugs: pharmacokinetics and safety. Int. J. Nanomedicine,  2014, 9, 1025-1037.
[http://dx.doi.org/10.2147/IJN.S38378] [PMID:  24591825] 
[80] 
Li, S.D.; Huang, L. Pharmacokinetics and biodistribution of nanoparticles. Mol. Pharm.,  2008, 5(4), 496-504.
[http://dx.doi.org/10.1021/mp800049w] [PMID:  18611037] 
[81] 
das Neves, J.; Amiji, M.M..; Bahia, M.F.; Sarmento, B. Nanotechnology-based systems for the treatment and prevention of HIV/AIDS. Adv. Drug Deliv. Rev.,  2010, 62(4-5), 458-477.
[http://dx.doi.org/10.1016/j.addr.2009.11.017] [PMID:  19914314] 
[82] 
Vyas, T.K.; Shah, L.; Amiji, M.M. Nanoparticulate drug carriers for delivery of HIV/AIDS therapy to viral reservoir sites. Expert Opin. Drug Deliv.,  2006, 3(5), 613-628.
[http://dx.doi.org/10.1517/17425247.3.5.613] [PMID:  16948557] 
[83] 
Shahiwala, A.; Amiji, M.M. Nanotechnology-based delivery systems in HIV/AIDS therapy. Future HIV Ther.,  2007, 1(1), 49-59.
[http://dx.doi.org/10.2217/17469600.1.1.49] 
[84] 
Muller, R.H.; Keck, C.M. Challenges and solutions for the delivery of biotech drugs-a review of drug nanocrystal technology and lipid nanoparticles. J. Biotechnol.,  2004, 113(1-3), 151-170.
[http://dx.doi.org/10.1016/j.jbiotec.2004.06.007] [PMID:  15380654] 
[85] 
Koo, O.M.; Rubinstein, I.; Onyuksel, H. Role of nanotechnology in targeted drug delivery and imaging: a concise review. Nanomedicine,  2005, 1(3), 193-212.
[http://dx.doi.org/10.1016/j.nano.2005.06.004] [PMID:  17292079] 
[86] 
Mahajan, S.D.; Aalinkeel, R.; Law, W-C.; Reynolds, J.L.; Nair, B.B.; Sykes, D.E.; Yong, K-T.; Roy, I.; Prasad, P.N.; Schwartz, S.A. Anti-HIV-1 nanotherapeutics: promises and challenges for the future. Int. J. Nanomedicine,  2012, 7, 5301-5314.
[http://dx.doi.org/10.2147/IJN.S25871] [PMID:  23055735] 
[87] 
Torchilin, V.P. Passive and active drug targeting: drug delivery to tumors as an example. Handb. Exp. Pharmacol.,  2010, 197(197), 3-53.
[http://dx.doi.org/10.1007/978-3-642-00477-3_1] [PMID:  20217525] 
[88] 
Roy, U.; Rodríguez, J.; Barber, P.; das Neves, J.; Sarmento, B.; Nair, M. The potential of HIV-1 nanotherapeutics: from in vitro studies to clinical trials. Nanomedicine (Lond.),  2015, 10(24), 3597-3609.
[http://dx.doi.org/10.2217/nnm.15.160] [PMID:  26400459] 
[89] 
Nair, M.; Jayant, R.D.; Kaushik, A.; Sagar, V. Getting into the brain: Potential of nanotechnology in the management of NeuroAIDS. Adv. Drug Deliv. Rev.,  2016, 103, 202-217.
[http://dx.doi.org/10.1016/j.addr.2016.02.008] [PMID:  26944096] 
[90] 
Bertrand, L.; Nair, M.; Toborek, M. Solving the blood-brain barrier challenge for the effective treatment of HIV replication in the central nervous system. Curr. Pharm. Des.,  2016, 22(35), 5477-5486.
[http://dx.doi.org/10.2174/1381612822666160726113001] [PMID:  27464720] 
[91] 
Reynolds, J.L.; Mahato, R.I. Nanomedicines for the treatment of CNS Diseases. J. Neuroimmune Pharmacol.,  2017, 12(1), 1-5.
[http://dx.doi.org/10.1007/s11481-017-9725-x] [PMID:  28150132] 
[92] 
Kirtane, A.R.; Langer, R.; Traverso, G. Past, present, and future drug delivery systems for antiretrovirals. J. Pharm. Sci.,  2016, 105(12), 3471-3482.
[http://dx.doi.org/10.1016/j.xphs.2016.09.015] [PMID:  27771050] 
[93] 
Baig, M.H.; Ahmad, K.; Roy, S.; Ashraf, J.M.; Adil, M.; Siddiqui, M.H.; Khan, S.; Kamal, M.A.; Provazník, I.; Choi, I. Computer aided drug design: success and limitations. Curr. Pharm. Des.,  2016, 22(5), 572-581.
[http://dx.doi.org/10.2174/1381612822666151125000550] [PMID:  26601966] 
[94] 
Jain, A. Computer aided drug design. J. Phys. Conf. Ser.,  2017, 884(1) 012072
[http://dx.doi.org/10.1088/1742-6596/884/1/012072] 
[95] 
Lemos, A.; Melo, R.; Moreira, I.S.; Cordeiro, M.N.D.S. Computational Modeling of Drugs Against Alzheimer’s Disease,  2018, 132, 61-106.
[http://dx.doi.org/10.1007/978-1-4939-7404-7_3] 
[96] 
Lemos, A.; Melo, R.; Preto, A.J.; Almeida, J.G.; Moreira, 1.S.; Cordeiro, M.N.D.S. In silico studies targeting Gprotein coupled receptors for drug research against parkinson’s disease. Curr. Neuropharmacol.,  2018, 16(6), 786-848.
[http://dx.doi.org/10.2174/1570159X16666180308161642] [PMID:  29521236] 
[97] 
Tan, J.J.; Cong, X.J.; Hu, L.M.; Wang, C.X.; Jia, L.; Liang, X.J. Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection. Drug Discov. Today,  2010, 15(5-6), 186-197.
[http://dx.doi.org/10.1016/j.drudis.2010.01.004] [PMID:  20096804] 
[98] 
Lounnas, V.; Ritschel, T.; Kelder, J.; McGuire, R.; Bywater, R.P.; Foloppe, N. Current progress in structure-based rational drug design marks a new mindset in drug discovery. Comput. Struct. Biotechnol. J.,  2013, 5 e201302011
[http://dx.doi.org/10.5936/csbj.201302011] [PMID:  24688704] 
[99] 
Turnbull, A.P.; Emsley, P. Studying protein-ligand interactions using X-ray crystallography. Methods Mol. Biol.,  2013, 1008, 457-477.
[http://dx.doi.org/10.1007/978-1-62703-398-5_17] [PMID:  23729263] 
[100] 
Huang, S-Y.; Zou, X. Efficient molecular docking of NMR structures: application to HIV-1 protease. Protein Sci.,  2007, 16(1), 43-51.
[http://dx.doi.org/10.1110/ps.062501507] [PMID:  17123961] 
[101] 
Kitchen, D.B.; Decornez, H.; Furr, J.R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Discov.,  2004, 3(11), 935-949.
[http://dx.doi.org/10.1038/nrd1549] [PMID:  15520816] 
[102] 
Meng, X-Y.; Zhang, H-X.; Mezei, M.; Cui, M. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des,  2011, 7(2), 146-157.
[http://dx.doi.org/10.2174/157340911795677602] [PMID:  21534921] 
[103] 
Ferreira, L.G.; Dos Santos, R.N.; Oliva, G.; Andricopulo, A.D. Molecular docking and structure-based drug design strategies. Molecules,  2015, 20(7), 13384-13421.
[http://dx.doi.org/10.3390/molecules200713384] [PMID:  26205061] 
[104] 
Lemos, A.; Leão, M.; Soares, J.; Palmeira, A.; Pinto, M.; Saraiva, L.; Sousa, M.E. Medicinal chemistry strategies to disrupt the p53-MDM2/MDMX interaction. Med. Res. Rev.,  2016, 36(5), 789-844.
[http://dx.doi.org/10.1002/med.21393] [PMID:  27302609] 
[105] 
McConkey, B.J.; Sobolev, V.; Edelman, M. The performance of current methods in ligand–protein docking. Curr. Sci.,  2002, 83(7), 845-856.
[106] 
Morris, G.M.; Huey, R.; Olson, A.J. Using AutoDock for ligand-receptor docking. Curr. Protoc. Bioinform,  2008, 24(1), 8.14.1-8.14.40.
[http://dx.doi.org/10.1002/0471250953.bi0814s24] [PMID:  19085980] 
[107] 
Trott, O.; Olson, A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem.,  2010, 31(2), 455-461.
[http://dx.doi.org/10.1002/jcc.21334] [PMID:  19499576] 
[108] 
Wu, G.; Robertson, D.H.; Brooks, C.L., III; Vieth, M. Detailed analysis of grid-based molecular docking: a case study of CDOCKER-A CHARMm-based MD docking algorithm. J. Comput. Chem.,  2003, 24(13), 1549-1562.
[http://dx.doi.org/10.1002/jcc.10306] [PMID:  12925999 ] 
[109] 
Allen, W.J.; Balius, T.E.; Mukherjee, S.; Brozell, S.R.; Moustakas, D.T.; Lang, P.T.; Case, D.A.; Kuntz, I.D.; Rizzo, R.C. DOCK 6: Impact of new features and current docking performance. J. Comput. Chem.,  2015, 36(15), 1132-1156.
[http://dx.doi.org/10.1002/jcc.23905] [PMID:  25914306] 
[110] 
Makino, S.; Ewing, T.J.; Kuntz, I.D. DREAM++: flexible docking program for virtual combinatorial libraries. J. Comput. Aided Mol. Des.,  1999, 13(5), 513-532.
[http://dx.doi.org/10.1023/A:1008066310669] [PMID:  10483532] 
[111] 
Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol.,  1996, 261(3), 470-489.
[http://dx.doi.org/10.1006/jmbi.1996.0477] [PMID:  8780787] 
[112] 
Verdonk, M.L.; Cole, J.C.; Hartshorn, M.J.; Murray, C.W.; Taylor, R.D. Improved protein-ligand docking using GOLD. Proteins,  2003, 52(4), 609-623.
[http://dx.doi.org/10.1002/prot.10465] [PMID:  12910460] 
[113] 
Repasky, M.P.; Shelley, M.; Friesner, R.A. Flexible ligand docking with Glide. Curr. Protoc. Bioinformatics,  2007, 18(1)
[http://dx.doi.org/10.1002/0471250953.bi0812s18] 
[114] 
Neves, M.A.; Totrov, M.; Abagyan, R. Docking and scoring with ICM: the benchmarking results and strategies for improvement. J. Comput. Aided Mol. Des.,  2012, 26(6), 675-686.
[http://dx.doi.org/10.1007/s10822-012-9547-0] [PMID:  22569591] 
[115] 
Rao, S.N.; Head, M.S.; Kulkarni, A.; LaLonde, J.M. Validation studies of the site-directed docking program LibDock. J. Chem. Inf. Model.,  2007, 47(6), 2159-2171.
[http://dx.doi.org/10.1021/ci6004299] [PMID:  17985863] 
[116] 
Bai, Q.; Shao, Y.; Pan, D.; Zhang, Y.; Liu, H.; Yao, X. Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations. PLoS One,  2014, 9(9) e107837
[http://dx.doi.org/10.1371%2Fjournal.pone.0107837] [PMID:  25229694] 
[117] 
Korb, O.; Stützle, T.; Exner, T.E. Empirical scoring functions for advanced protein-ligand docking with plants. J. Chem. Inf. Model.,  2009, 49(1), 84-96.
[http://dx.doi.org/10.1021/ci800298z] [PMID:  19125657] 
[118] 
Telvekar, V.N.; Chaudhari, H.K. 3D-QSAR and dockingbased combined in silico study on C-5 methyl substituted 4- arylthio and 4-aryloxy-3-iodopyridin-2-(1H)-one as HIV-1 RT inhibitors. Med. Chem. Res.,  2012, 21(8), 2032-2043.
[http://dx.doi.org/10.1007/s00044-011-9720-3] 
[119] 
Hsiou, Y.; Das, K.; Ding, J.; Clark, A.D., Jr; Kleim, J.P.; Rösner, M.; Winkler, I.; Riess, G.; Hughes, S.H.; Arnold, E. Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance. J. Mol. Biol.,  1998, 284(2), 313-323.
[http://dx.doi.org/10.1006/jmbi.1998.2171] [PMID:  9813120] 
[120] 
Zhang, Z.; Zheng, M.; Du, L.; Shen, J.; Luo, X.; Zhu, W.; Jiang, H. Towards discovering dual functional inhibitors against both wild type and K103N mutant HIV-1 reverse transcriptases: molecular docking and QSAR studies on 4,1-benzoxazepinone analogues. J. Comput. Aided Mol. Des.,  2006, 20(5), 281-293.
[http://dx.doi.org/10.1007/s10822-006-9050-6] [PMID:  16897578] 
[121] 
Chung, S.; Himmel, D.M.; Jiang, J-K.; Wojtak, K.; Bauman, J.D.; Rausch, J.W.; Wilson, J.A.; Beutler, J.A.; Thomas, C.J.; Arnold, E.; Le Grice, S.F.J. Synthesis, activity, and structural analysis of novel α-hydroxytropolone inhibitors of human immunodeficiency virus reverse transcriptase-associated ribonuclease H. J. Med. Chem.,  2011, 54(13), 4462-4473.
[http://dx.doi.org/10.1021/jm2000757] [PMID:  21568335] 
[122] 
Das, K.; Bauman, J.D.; Clark, A.D., Jr; Frenkel, Y.V.; Lewi, P.J.; Shatkin, A.J.; Hughes, S.H.; Arnold, E. High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations. Proc. Natl. Acad. Sci. USA,  2008, 105(5), 1466-1471.
[http://dx.doi.org/10.1073/pnas.0711209105] [PMID:  18230722] 
[123] 
Deng, B.L.; Cullen, M.D.; Zhou, Z.; Hartman, T.L.; Buckheit, R.W., Jr; Pannecouque, C.; De Clercq, E.; Fanwick, P.E.; Cushman, M. Synthesis and anti-HIV activity of new alkenyldiarylmethane (ADAM) non-nucleoside reverse transcriptase inhibitors (NNRTIs) incorporating benzoxazolone and benzisoxazole rings. Bioorg. Med. Chem.,  2006, 14(7), 2366-2374.
[http://dx.doi.org/10.1016/j.bmc.2005.11.014] [PMID:  16321539] 
[124] 
Ren, J.; Esnouf, R.; Garman, E.; Somers, D.; Ross, C.; Kirby, I.; Keeling, J.; Darby, G.; Jones, Y.; Stuart, D.; Stammers, D. High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Nat. Struct. Biol.,  1995, 2(4), 293-302.
[http://dx.doi.org/10.1038/nsb0495-293] [PMID:  7540934] 
[125] 
Barreca, M.L.; Rao, A.; De Luca, L.; Iraci, N.; Monforte, A.M.; Maga, G.; De Clercq, E.; Pannecouque, C.; Balzarini, J.; Chimirri, A. Discovery of novel benzimidazolones as potent non-nucleoside reverse transcriptase inhibitors active against wild-type and mutant HIV-1 strains. Bioorg. Med. Chem. Lett.,  2007, 17(7), 1956-1960.
[http://dx.doi.org/10.1016/j.bmcl.2007.01.025] [PMID:  17276064] 
[126] 
Lagos, C.F.; Caballero, J.; Gonzalez-Nilo, F.D.; David Pessoa-Mahana, C.; Perez-Acle, T. Docking and quantitative structure-activity relationship studies for the bisphenylbenzimidazole family of non-nucleoside inhibitors of HIV-1 reverse transcriptase. Chem. Biol. Drug Des.,  2008, 72(5), 360-369.
[http://dx.doi.org/10.1111/j.1747-0285.2008.00716.x] [PMID:  19012572] 
[127] 
Boechat, N.; Kover, W.B.; Bastos, M.M.; Romeiro, N.C.; Silva, A.S.C.; Santos, F.C.; Valverde, A.L.; Azevedo, M.L.G.; Wollinger, W.; Souza, T.M.L.; de Souza, S.L.O.; de Frugulhetti, I.C.P.P. Design, synthesis, and biological evaluation of new 3-hydroxy-2-oxo-3-trifluoromethylindole as potential HIV-1 reverse transcriptase inhibitors. Med. Chem. Res.,  2007, 15(9), 492-510.
[http://dx.doi.org/10.1007/s00044-007-9004-0] 
[128] 
Wan, Z.Y.; Yao, J.; Tao, Y.; Mao, T.Q.; Wang, X.L.; Lu, Y.P.; Wang, H.F.; Yin, H.; Wu, Y.; Chen, F.E.; De Clercq, E.; Daelemans, D.; Pannecouque, C. Discovery of piperidin-4-yl-aminopyrimidine derivatives as potent non-nucleoside HIV-1 reverse transcriptase inhibitors. Eur. J. Med. Chem.,  2015, 97, 1-9.
[http://dx.doi.org/10.1016/j.ejmech.2015.04.050] [PMID:  25935383] 
[129] 
Kertesz, D.J.; Brotherton-Pleiss, C.; Yang, M.; Wang, Z.; Lin, X.; Qiu, Z.; Hirschfeld, D.R.; Gleason, S.; Mirzadegan, T.; Dunten, P.W.; Harris, S.F.; Villaseñor, A.G.; Hang, J.Q.; Heilek, G.M.; Klumpp, K. Discovery of piperidin-4-yl-aminopyrimidines as HIV-1 reverse transcriptase inhibitors. N-benzyl derivatives with broad potency against resistant mutant viruses. Bioorg. Med. Chem. Lett.,  2010, 20(14), 4215-4218.
[http://dx.doi.org/10.1016/j.bmcl.2010.05.040] [PMID:  20538456] 
[130] 
Fan, N.; Zhang, S.; Sheng, T.; Zhao, L.; Liu, Z.; Liu, J.; Wang, X. Docking field-based QSAR and pharmacophore studies on the substituted pyrimidine derivatives targeting HIV-1 reverse transcriptase. Chem. Biol. Drug Des.,  2018, 91(2), 398-407.
[http://dx.doi.org/10.1111/cbdd.13086] [PMID:  28816417] 
[131] 
Hopkins, A.L.; Ren, J.; Esnouf, R.M.; Willcox, B.E.; Jones, E.Y.; Ross, C.; Miyasaka, T.; Walker, R.T.; Tanaka, H.; Stammers, D.K.; Stuart, D.I. Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors. J. Med. Chem.,  1996, 39(8), 1589-1600.
[http://dx.doi.org/10.1021/jm960056x] [PMID:  8648598] 
[132] 
Singh, A.; Yadav, D.; Yadav, M.; Dhamanage, A.; Kulkarni, S.; Singh, R.K. Molecular modeling, synthesis and biological evaluation of N-heteroaryl compounds as reverse transcriptase inhibitors against HIV-1. Chem. Biol. Drug Des.,  2015, 85(3), 336-347.
[http://dx.doi.org/10.1111/cbdd.12397] [PMID:  25055732] 
[133] 
Sweeney, Z.K.; Harris, S.F.; Arora, S.F.; Javanbakht, H.; Li, Y.; Fretland, J.; Davidson, J.P.; Billedeau, J.R.; Gleason, S.K.; Hirschfeld, D.; Kennedy-Smith, J.J.; Mirzadegan, T.; Roetz, R.; Smith, M.; Sperry, S.; Suh, J.M.; Wu, J.; Tsing, S.; Villaseñor, A.G.; Paul, A.; Su, G.; Heilek, G.; Hang, J.Q.; Zhou, A.S.; Jernelius, J.A.; Zhang, F.J.; Klumpp, K. Design of annulated pyrazoles as inhibitors of HIV-1 reverse transcriptase. J. Med. Chem.,  2008, 51(23), 7449-7458.
[http://dx.doi.org/10.1021/jm800527x] [PMID:  19007201] 
[134] 
Cheng, P.; Gu, Q.; Liu, W.; Zou, J.F.; Ou, Y.Y.; Luo, Z.Y.; Zeng, J.G. Synthesis of quinolin-2-one alkaloid derivatives and their inhibitory activities against HIV-1 reverse transcriptase. Molecules,  2011, 16(9), 7649-7661.
[http://dx.doi.org/10.3390/molecules16097649] [PMID:  21900867] 
[135] 
Dineshkumar, K.; Aparna, V.; Madhuri, K.Z.; Hopper, W. Biological activity of sporolides A and B from Salinispora tropica: in silico target prediction using ligand-based pharmacophore mapping and in vitro activity validation on HIV-1 reverse transcriptase. Chem. Biol. Drug Des.,  2014, 83(3), 350-361.
[http://dx.doi.org/10.1111/cbdd.12252] [PMID:  24165098] 
[136] 
Gomez, R.; Jolly, S.J.; Williams, T.; Vacca, J.P.; Torrent, M.; McGaughey, G.; Lai, M.T.; Felock, P.; Munshi, V.; Distefano, D.; Flynn, J.; Miller, M.; Yan, Y.; Reid, J.; Sanchez, R.; Liang, Y.; Paton, B.; Wan, B.L.; Anthony, N. Design and synthesis of conformationally constrained inhibitors of non-nucleoside reverse transcriptase. J. Med. Chem.,  2011, 54(22), 7920-7933.
[http://dx.doi.org/10.1021/jm2010173] [PMID:  21985673] 
[137] 
Goldgur, Y.; Craigie, R.; Cohen, G.H.; Fujiwara, T.; Yoshinaga, T.; Fujishita, T.; Sugimoto, H.; Endo, T.; Murai, H.; Davies, D.R. Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design. Proc. Natl. Acad. Sci. USA,  1999, 96(23), 13040-13043.
[http://dx.doi.org/10.1073/pnas.96.23.13040] [PMID:  10557269] 
[138] 
Safakish, M.; Hajimahdi, Z.; Zabihollahi, R.; Aghasadeghi, M.R.; Vahabpour, R.; Zarghi, A. Design, synthesis, and docking studies of new 2-benzoxazolinone derivatives as anti-HIV-1 agents. Med. Chem. Res.,  2017, 26(11), 2718-2726.
[http://dx.doi.org/10.1007/s00044-017-1969-8] 
[139] 
Hare, S.; Vos, A.M.; Clayton, R.F.; Thuring, J.W.; Cummings, M.D.; Cherepanov, P. Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Proc. Natl. Acad. Sci. USA,  2010, 107(46), 20057-20062.
[http://dx.doi.org/10.1073/pnas.1010246107] [PMID:  21030679] 
[140] 
Gao, P.; Zhang, L.; Sun, L.; Huang, T.; Tan, J.; Zhang, J.; Zhou, Z.; Zhao, T.; Menéndez-Arias, L.; Pannecouque, C.; Clercq, E.; Zhan, P.; Liu, X. 1-Hydroxypyrido[2,3-d]pyrimidin-2(1H)-ones as novel selective HIV integrase inhibitors obtained via privileged substructure-based compound libraries. Bioorg. Med. Chem.,  2017, 25(20), 5779-5789.
[http://dx.doi.org/10.1016/j.bmc.2017.09.006] [PMID:  28951095] 
[141] 
Hare, S.; Smith, S.J.; Métifiot, M.; Jaxa-Chamiec, A.; Pommier, Y.; Hughes, S.H.; Cherepanov, P. Structural and functional analyses of the second-generation integrase strand transfer inhibitor dolutegravir (S/GSK1349572). Mol. Pharmacol.,  2011, 80(4), 565-572.
[http://dx.doi.org/10.1124/mol.111.073189] [PMID:  21719464] 
[142] 
Tang, J.; Vernekar, S.K.V.; Chen, Y.L.; Miller, L.; Huber, A.D.; Myshakina, N.; Sarafianos, S.G.; Parniak, M.A.; Wang, Z. Synthesis, biological evaluation and molecular modeling of 2-Hydroxyisoquinoline-1,3-dione analogues as inhibitors of HIV reverse transcriptase associated ribonuclease H and polymerase. Eur. J. Med. Chem.,  2017, 133, 85-96.
[http://dx.doi.org/10.1016/j.ejmech.2017.03.059] [PMID:  28384548] 
[143] 
Su, H.P.; Yan, Y.; Prasad, G.S.; Smith, R.F.; Daniels, C.L.; Abeywickrema, P.D.; Reid, J.C.; Loughran, H.M.; Kornienko, M.; Sharma, S.; Grobler, J.A.; Xu, B.; Sardana, V.; Allison, T.J.; Williams, P.D.; Darke, P.L.; Hazuda, D.J.; Munshi, S. Structural basis for the inhibition of RNase H activity of HIV-1 reverse transcriptase by RNase H active site-directed inhibitors. J. Virol.,  2010, 84(15), 7625-7633.
[http://dx.doi.org/10.1128/JVI.00353-10] [PMID:  20484498] 
[144] 
Rostami, M.; Sirous, H.; Zabihollahi, R.; Aghasadeghi, M.R.; Sadat, S.M.; Namazi, R.; Saghaie, L.; Memarian, H.R.; Fassihi, A. Design, synthesis and anti-HIV-1 evaluation of a series of 5-hydroxypyridine-4-one derivatives as possible integrase inhibitors. Med. Chem. Res.,  2015, 24(12), 4113-4127.
[http://dx.doi.org/10.1007/s00044-015-1443-4] 
[145] 
Vyas, V.K.; Shah, S.; Ghate, M. Generation of new leads as HIV-1 integrase inhibitors: 3D QSAR, docking and molecular dynamics simulation. Med. Chem. Res.,  2017, 26(3), 532-550.
[http://dx.doi.org/10.1007/s00044-016-1772-y] 
[146] 
Srivastav, V.K.; Tiwari, M. QSAR and docking studies of coumarin derivatives as potent HIV-1 integrase inhibitors. Arab. J. Chem.,  2017, 10, S1081-S1094.
[http://dx.doi.org/10.1016/j.arabjc.2013.01.015] 
[147] 
Han, D.; Su, M.; Tan, J.; Li, C.; Zhang, X.; Wang, C. Structure- activity relationship and binding mode studies for a series of diketo-acids as HIV integrase inhibitors by 3DQSAR, molecular docking and molecular dynamics simulations. RSC Advances,  2016, 6(33), 27594-27606.
[http://dx.doi.org/10.1039/C6RA00713A] 
[148] 
Wielens, J.; Headey, S.J.; Rhodes, D.I.; Mulder, R.J.; Dolezal, O.; Deadman, J.J.; Newman, J.; Chalmers, D.K.; Parker, M.W.; Peat, T.S.; Scanlon, M.J. Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification? J. Biomol. Screen.,  2013, 18(2), 147-159.
[http://dx.doi.org/10.1177/1087057112465979] [PMID:  23139382] 
[149] 
Debnath, U.; Kumar, P.; Agarwal, A.; Kesharwani, A.; Gupta, S.K.; Katti, S.B. N-hydroxy-substituted 2-aryl acetamide analogs: a novel class of HIV-1 integrase inhibitors. Chem. Biol. Drug Des.,  2017, 90(4), 527-534.
[http://dx.doi.org/10.1111/cbdd.12974] [PMID:  28294572] 
[150] 
Wang, Y.; Rong, J.; Zhang, B.; Hu, L.; Wang, X.; Zeng, C. Design and synthesis of N-methylpyrimidone derivatives as HIV-1 integrase inhibitors. Bioorg. Med. Chem.,  2015, 23(4), 735-741.
[http://dx.doi.org/10.1016/j.bmc.2014.12.059] [PMID:  25618597] 
[151] 
Patel, S.B.; Patel, B.D.; Pannecouque, C.; Bhatt, H.G. Design, synthesis and anti-HIV activity of novel quinoxaline derivatives. Eur. J. Med. Chem.,  2016, 117, 230-240.
[http://dx.doi.org/10.1016/j.ejmech.2016.04.019] [PMID:  27105027] 
[152] 
Jianbo, T.; Pei, Z.; Simon, W.X.; Yingji, W. Quionolone carboxylic acid derivatives as HIV1 integrase inhibitors: Docking based HQSAR and topomer CoMFA analyses. J. Chemometr.,  2017, 31(12) e2934
[http://dx.doi.org/10.1002/cem.2934] [PMID:  29606793] 
[153] 
Aoki, M.; Hayashi, H.; Yedidi, R.S.; Martyr, C.D.; Takamatsu, Y.; Aoki-Ogata, H.; Nakamura, T.; Nakata, H.; Das, D.; Yamagata, Y.; Ghosh, A.K.; Mitsuya, H. C-5-modified tetrahydropyrano-tetrahydofuran-derived protease inhibitors (PIs) exert potent inhibition of the replication of HIV-1 variants highly resistant to various PIs, including Darunavir. J. Virol.,  2015, 90(5), 2180-2194.
[http://dx.doi.org/10.1128/JVI.01829-15] [PMID:  26581995] 
[154] 
Sroczynski, D.; Malinowski, Z.; Szczesniak, A.K.; Pakulska, W. New 1-(2H)-phthalazinone derivatives as potent nonpeptidic HIV-1 protease inhibitors: molecular docking studies, molecular dynamics simulation, oral bioavailability and ADME prediction. Mol. Simul.,  2016, 42(8), 628-641.
[http://dx.doi.org/10.1080/08927022.2015.1067808] 
[155] 
Nunthanavanit, P.; Ungwitayatorn, J. Molecular docking studies of chromone derivatives against wild type and mutant strains of HIV-1 protease. Med. Chem. Res.,  2014, 23(9), 4198-4208.
[http://dx.doi.org/10.1007/s00044-014-0992-2] 
[156] 
Bäckbro, K.; Löwgren, S.; Osterlund, K.; Atepo, J.; Unge, T.; Hultén, J.; Bonham, N.M.; Schaal, W.; Karlén, A.; Hallberg, A. Unexpected binding mode of a cyclic sulfamide HIV-1 protease inhibitor. J. Med. Chem.,  1997, 40(6), 898-902.
[http://dx.doi.org/10.1021/jm960588d] [PMID:  9083478] 
[157] 
Liu, F.; Boross, P.I.; Wang, Y.F.; Tozser, J.; Louis, J.M.; Harrison, R.W.; Weber, I.T. Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and G73S. J. Mol. Biol.,  2005, 354(4), 789-800.
[http://dx.doi.org/10.1016/j.jmb.2005.09.095] [PMID:  16277992] 
[158] 
Ala, P.J.; Huston, E.E.; Klabe, R.M.; McCabe, D.D.; Duke, J.L.; Rizzo, C.J.; Korant, B.D.; DeLoskey, R.J.; Lam, P.Y.; Hodge, C.N.; Chang, C.H. Molecular basis of HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with cyclic urea inhibitors. Biochemistry,  1997, 36(7), 1573-1580.
[http://dx.doi.org/10.1021/bi962234u] [PMID:  9048541] 
[159] 
Mahalingam, B.; Wang, Y.F.; Boross, P.I.; Tozser, J.; Louis, J.M.; Harrison, R.W.; Weber, I.T. Crystal structures of HIV protease V82A and L90M mutants reveal changes in the indinavir-binding site. Eur. J. Biochem.,  2004, 271(8), 1516-1524.
[http://dx.doi.org/10.1111/j.1432-1033.2004.04060.x] [PMID:  15066177] 
[160] 
Munshi, S.; Chen, Z.; Yan, Y.; Li, Y.; Olsen, D.B.; Schock, H.B.; Galvin, B.B.; Dorsey, B.; Kuo, L.C. An alternate binding site for the P1-P3 group of a class of potent HIV-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease. Acta Crystallogr. D Biol. Crystallogr.,  2000, 56(Pt 4), 381-388.
[http://dx.doi.org/10.1107/S0907444900000469] [PMID:  10739910] 
[161] 
Clemente, J.C.; Moose, R.E.; Hemrajani, R.; Whitford, L.R.; Govindasamy, L.; Reutzel, R.; McKenna, R.; Agbandje-McKenna, M.; Goodenow, M.M.; Dunn, B.M. Comparing the accumulation of active- and nonactive-site mutations in the HIV-1 protease. Biochemistry,  2004, 43(38), 12141-12151.
[http://dx.doi.org/10.1021/bi049459m] [PMID:  15379553] 
[162] 
Eakin, C.M.; Berman, A.J.; Miranker, A.D. A native to amyloidogenic transition regulated by a backbone trigger. Nat. Struct. Mol. Biol.,  2006, 13(3), 202-208.
[http://dx.doi.org/10.1038/nsmb1068] [PMID:  16491088] 
[163] 
Tong, J.; Wu, Y.; Bai, M.; Zhan, P. 3D-QSAR and molecular docking studies on HIV protease inhibitors. J. Mol. Struct.,  2017, 1129, 17-22.
[http://dx.doi.org/10.1016/j.molstruc.2016.09.052] 
[164] 
Wei, Y.; Li, J.; Chen, Z.; Wang, F.; Huang, W.; Hong, Z.; Lin, J. Multistage virtual screening and identification of novel HIV-1 protease inhibitors by integrating SVM, shape, pharmacophore and docking methods. Eur. J. Med. Chem.,  2015, 101, 409-418.
[http://dx.doi.org/10.1016/j.ejmech.2015.06.054] [PMID:  26185005] 
[165] 
King, N.M.; Prabu-Jeyabalan, M.; Bandaranayake, R.M.; Nalam, M.N.; Nalivaika, E.A.; Özen, A.; Haliloğlu, T.; Yilmaz, N.K.; Schiffer, C.A. Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease. ACS Chem. Biol.,  2012, 7(9), 1536-1546.
[http://dx.doi.org/10.1021/cb300191k] [PMID:  22712830] 
[166] 
Mohammadi, A.A.; Taheri, S.; Amouzegar, A.; Ahdenov, R.; Halvagar, M.R.; Sadr, A.S. Diastereoselective synthesis and molecular docking studies of novel fused tetrahydropyridine derivatives as new inhibitors of HIV protease. J. Mol. Struct.,  2017, 1139, 166-174.
[http://dx.doi.org/10.1016/j.molstruc.2017.03.029] 
[167] 
Krohn, A.; Redshaw, S.; Ritchie, J.C.; Graves, B.J.; Hatada, M.H. Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere. J. Med. Chem.,  1991, 34(11), 3340-3342.
[http://dx.doi.org/10.1021/jm00115a028] [PMID:  1956054] 
[168] 
Sethuvasan, S.; Sugumar, P.; Ponnuswamy, M.N.; Ponnuswamy, S. N-Benzyl-2,7-diphenyl-1,4-diazepan-5-one analogues: Synthesis, spectral characterization, stereochemistry, crystal structure and molecular docking studies. J. Mol. Struct.,  2016, 1121, 215-225.
[http://dx.doi.org/10.1016/j.molstruc.2016.05.065] 
[169] 
Bacilieri, M.; Moro, S. Ligand-based drug design methodologies in drug discovery process: an overview. Curr. Drug Discov. Technol.,  2006, 3(3), 155-165.
[http://dx.doi.org/10.2174/157016306780136781] [PMID:  17311561] 
[170] 
Dror, O.; Shulman-Peleg, A.; Nussinov, R.; Wolfson, H.J. Predicting molecular interactions in silico: a guide to pharmacophore identification and its applications to drug design. Curr. Med. Chem.,  2004, 11(1), 71-90.
[http://dx.doi.org/10.2174/0929867043456287] [PMID:  14754427] 
[171] 
Yang, S-Y. Pharmacophore modeling and applications in drug discovery: challenges and recent advances. Drug Discov. Today,  2010, 15(11-12), 444-450.
[http://dx.doi.org/10.1016/j.drudis.2010.03.013] [PMID:  20362693] 
[172] 
Golender, V.; Vesterman, B.; Eliyahu, O.; Kardash, A.; Kletzin, M.; Shokhen, M.; Vorpagel, E. Knowledge engineering approach to drug design and its implementation in the APEX-3D Expert System In: Proceedings of the 10th European Symposium on Structure-Activity Relationships, QSAR and Molecular Modeling; , 1995. 
[173] 
Patel, Y.; Gillet, V.J.; Bravi, G.; Leach, A.R. A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP. J. Comput. Aided Mol. Des.,  2002, 16(8-9), 653-681.
[http://dx.doi.org/10.1023/A:1021954728347] [PMID:  12602956] 
[174] 
Wolber, G.; Langer, T. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J. Chem. Inf. Model.,  2005, 45(1), 160-169.
[http://dx.doi.org/10.1021/ci049885e] [PMID:  15667141] 
[175] 
Chen, I-J.; Foloppe, N. Conformational sampling of druglike molecules with MOE and catalyst: implications for pharmacophore modeling and virtual screening. J. Chem. Inf. Model.,  2008, 48(9), 1773-1791.
[http://dx.doi.org/10.1021/ci800130k] [PMID:  18763758] 
[176] 
Harris, D.L.; Loew, G. Development and assessment of a 3D pharmacophore for ligand recognition of BDZR/GABAA receptors initiating the anxiolytic response. Bioorg. Med. Chem.,  2000, 8(11), 2527-2538.
[http://dx.doi.org/10.1016/S0968-0896(00)00185-1] [PMID:  11092538] 
[177] 
Dixon, S.L.; Smondyrev, A.M.; Knoll, E.H.; Rao, S.N.; Shaw, D.E.; Friesner, R.A. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: methodology and preliminary results. J. Comput. Aided Mol. Des.,  2006, 20(10-11), 647-671.
[http://dx.doi.org/10.1007/s10822-006-9087-6] [PMID:  17124629] 
[178] 
Clark, M.; Cramer, R.D.; Van Opdenbosch, N. Validation of the general purpose Tripos 5.2 force field. J. Comput. Chem.,  1989, 10(8), 982-1012.
[http://dx.doi.org/10.1002/jcc.540100804] 
[179] 
Mills, J.E.; de Esch, I.J.; Perkins, T.D.J.; Dean, P.M. SLATE: a method for the superposition of flexible ligands. J. Comput. Aided Mol. Des.,  2001, 15(1), 81-96.
[http://dx.doi.org/10.1023/A:1011102129244] [PMID:  11217921] 
[180] 
Distinto, S.; Esposito, F.; Kirchmair, J.; Cardia, M.C.; Gaspari, M.; Maccioni, E.; Alcaro, S.; Markt, P.; Wolber, G.; Zinzula, L.; Tramontano, E. Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint- and pharmacophore-based virtual screening approach. Eur. J. Med. Chem.,  2012, 50, 216-229.
[http://dx.doi.org/10.1016/j.ejmech.2012.01.056] [PMID:  22361685] 
[181] 
Barreca, M.L.; De Luca, L.; Iraci, N.; Rao, A.; Ferro, S.; Maga, G.; Chimirri, A. structure-based pharmacophore identification of new chemical scaffolds as non-nucleoside reverse transcriptase inhibitors. J. Chem. Inf. Model.,  2007, 47(2), 557-562.
[http://dx.doi.org/10.1021/ci600320q] [PMID:  17274611] 
[182] 
Keller, P.A.; Birch, C.; Leach, S.P.; Tyssen, D.; Griffith, R. Novel pharmacophore-based methods reveal gossypol as a reverse transcriptase inhibitor. J. Mol. Graph. Model.,  2003, 21(5), 365-373.
[http://dx.doi.org/10.1016/S1093-3263(02)00183-3] [PMID:  12543135] 
[183] 
Rani, P.; Kumar, V. Development of pharmacophore models for predicting HIV-1 reverse transcriptase inhibitory activity of pyridinone derivatives. Pharm. Chem. J.,  2011, 45(1), 36-42.
[http://dx.doi.org/10.1007/s11094-011-0556-4] 
[184] 
Reddy, K.K.; Singh, S.K.; Tripathi, S.K.; Selvaraj, C. Identification of potential HIV-1 integrase strand transfer inhibitors: in silico virtual screening and QM/MM docking studies. SAR QSAR Environ. Res.,  2013, 24(7), 581-595.
[http://dx.doi.org/10.1080/1062936X.2013.772919] [PMID:  23521430] 
[185] 
Reddy, K.K.; Singh, S.K. Combined ligand and structure-based approaches on HIV-1 integrase strand transfer inhibitors. Chem. Biol. Interact.,  2014, 218, 71-81.
[http://dx.doi.org/10.1016/j.cbi.2014.04.011] [PMID:  24792351] 
[186] 
Sangeetha, B.; Muthukumaran, R.; Amutha, R. Pharmacophore modelling and electronic feature analysis of hydroxamic acid derivatives, the HIV integrase inhibitors. SAR QSAR Environ. Res.,  2013, 24(9), 753-771.
[http://dx.doi.org/10.1080/1062936X.2013.792870] [PMID:  23710969] 
[187] 
Yadav, D.; Paliwal, S.; Yadav, R.; Pal, M.; Pandey, A. Identification of novel HIV 1-protease inhibitors: application of ligand and structure based pharmacophore mapping and virtual screening. PLoS One,  2012, 7(11) e48942https://dx.doi.org/10.1371%2Fjournal.pone.0048942
[188] 
Ravichandran, V.; Venkateskumar, K.; Shalini, S.; Harish, R. Exploring the structure–activity relationship of oxazolidinones as HIV-1 protease inhibitors - QSAR and pharmacophore modelling studies. Chemom. Intell. Lab. Syst.,  2016, 154, 52-61.
[http://dx.doi.org/10.1016/j.chemolab.2016.03.017] 
[189] 
Perkins, R.; Fang, H.; Tong, W.; Welsh, W.J. Quantitative structure-activity relationship methods: perspectives on drug discovery and toxicology. Environ. Toxicol. Chem.,  2003, 22(8), 1666-1679.
[http://dx.doi.org/10.1897/01-171] [PMID:  12924569] 
[190] 
Dudek, A.Z.; Arodz, T.; Gálvez, J. Computational methods in developing quantitative structure-activity relationships (QSAR): a review. Comb. Chem. High Throughput Screen.,  2006, 9(3), 213-228.
[http://dx.doi.org/10.2174/138620706776055539] [PMID:  16533155] 
[191] 
Cherkasov, A.; Muratov, E.N.; Fourches, D.; Varnek, A.; Baskin, I.I.; Cronin, M.; Dearden, J.; Gramatica, P.; Martin, Y.C.; Todeschini, R.; Consonni, V.; Kuz’min, V.E.; Cramer, R.; Benigni, R.; Yang, C.; Rathman, J.; Terfloth, L.; Gasteiger, J.; Richard, A.; Tropsha, A. QSAR modeling: where have you been? Where are you going to? J. Med. Chem.,  2014, 57(12), 4977-5010.
[http://dx.doi.org/10.1021/jm4004285] [PMID:  24351051] 
[192] 
Roy, K.; Kar, S.; Das, R.N. A primer on QSAR/QSPR modeling; Springer Briefs in Molecular Science, 2015. 
[193] 
Cramer, R.D.; Patterson, D.E.; Bunce, J.D. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc.,  1988, 110(18), 5959-5967.
[http://dx.doi.org/10.1021/ja00226a005] [PMID:  22148765] 
[194] 
Kubinyi, H. Handbook of Chemoinformatics: From Data to
Knowledge in 4 Volumes; ,  2008, pp. 1555-1574.
[http://dx.doi.org/10.1002/9783527618279.ch44d] 
[195] 
Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem.,  1994, 37(24), 4130-4146.
[http://dx.doi.org/10.1021/jm00050a010] [PMID:  7990113] 
[196] 
Moda, T.L.; Montanari, C.A.; Andricopulo, A.D. Hologram QSAR model for the prediction of human oral bioavailability. Bioorg. Med. Chem.,  2007, 15(24), 7738-7745.
[http://dx.doi.org/10.1016/j.bmc.2007.08.060] [PMID:  17870541] 
[197] 
Heidari, A.; Fatemi, M.H. Comparative molecular field analysis (CoMFA), topomer CoMFA, and hologram QSAR studies on a series of novel HIV-1 protease inhibitors. Chem. Biol. Drug Des.,  2017, 89(6), 918-931.
[http://dx.doi.org/10.1111/cbdd.12917] [PMID:  27933723] 
[198] 
Balaji, S.; Karthikeyan, C.; Moorthy, N.S.; Trivedi, P. QSAR modelling of HIV-1 reverse transcriptase inhibition by benzoxazinones using a combination of PVSA and pharmacophore feature descriptors. Bioorg. Med. Chem. Lett.,  2004, 14(24), 6089-6094.
[http://dx.doi.org/10.1016/j.bmcl.2004.09.068] [PMID:  15546736] 
[199] 
Vadivelan, S.; Deeksha, T.N.; Arun, S.; Machiraju, P.K.; Gundla, R.; Sinha, B.N.; Jagarlapudi, S.A.R.P. Virtual screening studies on HIV-1 reverse transcriptase inhibitors to design potent leads. Eur. J. Med. Chem.,  2011, 46(3), 851-859.
[http://dx.doi.org/10.1016/j.ejmech.2010.12.022] [PMID:  21272964] 
[200] 
Samee, W.; Ungwitayatorn, J.; Matayatsuk, C.; Pimthon, J. 3D-QSAR studies on phthalimide derivatives as HIV-1 reverse transcriptase inhibitors. Sci. Asia,  2010, 30, 81-88.
[http://dx.doi.org/10.2306/scienceasia1513-1874.2004.30.081] 
[201] 
Liu, X.; Chen, X.; Zhang, L.; Zhan, P.; Liu, X. 3D-QSAR and docking studies on piperidine-substituted diarylpyrimidine analogues as HIV-1 reverse transcriptase inhibitors. Med. Chem. Res.,  2015, 24(8), 3314-3326.
[http://dx.doi.org/10.1007/s00044-015-1381-1] 
[202] 
Patel, S.; Patel, B.; Bhatt, H. 3D-QSAR studies on 5- hydroxy-6-oxo-1,6-dihydropyrimidine-4- carboxamide derivatives as HIV-1 integrase inhibitors. J. Taiwan Inst. Chem. Eng.,  2016, 59, 61-68.
[http://dx.doi.org/10.1016/j.jtice.2015.07.024] 
[203] 
Ghasemi, G.; Nirouei, M.; Shariati, S.; Abdolmaleki, P.; Rastgoo, Z. A quantitative structure–activity relationship study on HIV-1 integrase inhibitors using genetic algorithm, artificial neural networks and different statistical methods. Arab. J. Chem.,  2016, 9(Suppl. 1), S185-S190.
[http://dx.doi.org/10.1016/j.arabjc.2011.03.006] 
[204] 
Nunthanavanit, P.; Anthony, N.G.; Johnston, B.F.; Mackay, S.P.; Ungwitayatorn, J. 3D-QSAR studies on chromone derivatives as HIV-1 protease inhibitors: application of molecular field analysis. Arch. Pharm. (Weinheim),  2008, 341(6), 357-364.
[http://dx.doi.org/10.1002/ardp.200700229] [PMID:  18442018] 
[205] 
Bhargava, S.; Adhikari, N.; Amin, S.A.; Das, K.; Gayen, S.; Jha, T. Hydroxyethylamine derivatives as HIV-1 protease inhibitors: a predictive QSAR modelling study based on Monte Carlo optimization. SAR QSAR Environ. Res.,  2017, 28(12), 973-990.
[http://dx.doi.org/10.1080/1062936X.2017.1388281] [PMID:  29072112] 
[206] 
Ioakimidis, L.; Thoukydidis, L.; Mirza, A.; Naeem, S.; Reynisson, J. Benchmarking the reliability of QikProp. Correlation between experimental and predicted values. QSAR Comb. Sci.,  2008, 27(4), 445-456.
[http://dx.doi.org/10.1002/qsar.200730051] 
[207] 
Yadav, G.; Ganguly, S.; Murugesan, S.; Dev, A. Synthesis, anti-HIV, antimicrobial evaluation and structure activity relationship studies of some novel benzimidazole derivatives. Antiinfect. Agents,  2015, 13(1), 65-77.
[http://dx.doi.org/10.2174/2211352512666141021002621] 
[208] 
Kashid, A.M.; Dube, P.N.; Alkutkar, P.G.; Bothara, K.G.; Mokale, S.N.; Dhawale, S.C. Synthesis, biological screening and ADME prediction of benzylindole derivatives as novel anti-HIV-1, anti-fungal and anti-bacterial agents. Med. Chem. Res.,  2013, 22(10), 4633-4640.
[http://dx.doi.org/10.1007/s00044-012-0463-6] 
[209] 
Pawar, V.S.; Lokwani, D.K.; Bhandari, S.V.; Bothara, K.G.; Chitre, T.S.; Devale, T.L.; Modhave, N.S.; Parikh, J.K. Design, docking study and ADME prediction of Isatin derivatives as anti-HIV agents. Med. Chem. Res.,  2011, 20(3), 370-380.
[http://dx.doi.org/10.1007/s00044-010-9329-y] 
[210] 
Pawar, V.; Lokwani, D.; Bhandari, S.; Mitra, D.; Sabde, S.; Bothara, K.; Madgulkar, A. Design of potential reverse transcriptase inhibitor containing Isatin nucleus using molecular modeling studies. Bioorg. Med. Chem.,  2010, 18(9), 3198-3211.
[http://dx.doi.org/10.1016/j.bmc.2010.03.030] [PMID:  20381364] 
[211] 
Belekar, V.; Shah, A.; Garg, P. High-throughput virtual screening of phloroglucinol derivatives against HIV-reverse transcriptase. Mol. Divers.,  2013, 17(1), 97-110.
[http://dx.doi.org/10.1007/s11030-012-9417-7] [PMID:  23338523] 
[212] 
Tripathi, S.K.; Selvaraj, C.; Singh, S.K.; Reddy, K.K. Molecular docking, QPLD, and ADME prediction studies on HIV-1 integrase leads. Med. Chem. Res.,  2012, 21(12), 4239-4251.
[http://dx.doi.org/10.1007/s00044-011-9940-6] 
[213] 
Frecer, V.; Berti, F.; Benedetti, F.; Miertus, S. Design of peptidomimetic inhibitors of aspartic protease of HIV-1 containing -Phe Psi Pro- core and displaying favourable ADME-related properties. J. Mol. Graph. Model.,  2008, 27(3), 376-387.
[http://dx.doi.org/10.1016/j.jmgm.2008.06.006] [PMID:  18678515] 
[214] 
Gupta, P.; Garg, P.; Roy, N. Identification of novel HIV-1 integrase inhibitors using shape-based screening, QSAR, and docking approach. Chem. Biol. Drug Des.,  2012, 79(5), 835-849.
[http://dx.doi.org/10.1111/j.1747-0285.2012.01326.x] [PMID:  22233531] 
[215] 
Khedkar, V.M.; Ambre, P.K.; Verma, J.; Shaikh, M.S.; Pissurlenkar, R.R.; Coutinho, E.C. Molecular docking and 3D-QSAR studies of HIV-1 protease inhibitors. J. Mol. Model.,  2010, 16(7), 1251-1268.
[http://dx.doi.org/10.1007/s00894-009-0636-5] [PMID:  20069323] 
[216] 
Markovic, I.; Clouse, K.A. Recent advances in understanding the molecular mechanisms of HIV-1 entry and fusion: revisiting current targets and considering new options for therapeutic intervention. Curr. HIV Res.,  2004, 2(3), 223-234.
[http://dx.doi.org/10.2174/1570162043351327] [PMID:  15279586] 
[217] 
Tilton, J.C.; Doms, R.W. Entry inhibitors in the treatment of HIV-1 infection. Antiviral Res.,  2010, 85(1), 91-100.
[http://dx.doi.org/10.1016/j.antiviral.2009.07.022] [PMID:  19683546] 
[218] 
Mehle, A.; Wilson, H.; Zhang, C.; Brazier, A.J.; McPike, M.; Pery, E.; Gabuzda, D. Identification of an APOBEC3G binding site in human immunodeficiency virus type 1 Vif and inhibitors of Vif-APOBEC3G binding. J. Virol.,  2007, 81(23), 13235-13241.
[http://dx.doi.org/10.1128/JVI.00204-07] [PMID:  17898068] 
[219] 
Cadima-Couto, I.; Goncalves, J. Towards inhibition of Vif-APOBEC3G interaction: which protein to target? Adv. Virol.,  2010, 2010649315
[http://dx.doi.org/10.1155/2010/649315] [PMID:  22347227] 
[220] 
Chiu, Y-L.; Soros, V.B.; Kreisberg, J.F.; Stopak, K.; Yonemoto, W.; Greene, W.C. Cellular APOBEC3G restricts HIV-1 infection in resting CD4+ T cells. Nature,  2005, 435(7038), 108-114.
[http://dx.doi.org/10.1038/nature03493] [PMID:  15829920] 
[221] 
Ciuffi, A.; Bushman, F.D. Retroviral DNA integration: HIV and the role of LEDGF/p75. Trends Genet.,  2006, 22(7), 388-395.
[http://dx.doi.org/10.1016/j.tig.2006.05.006] [PMID:  16730094] 
[222] 
Poeschla, E.M. Integrase, LEDGF/p75 and HIV replication. Cell. Mol. Life Sci.,  2008, 65(9), 1403-1424.
[http://dx.doi.org/10.1007/s00018-008-7540-5] [PMID:  18264802] 
[223] 
Christ, F.; Debyser, Z. The LEDGF/p75 integrase interaction, a novel target for anti-HIV therapy. Virology,  2013, 435(1), 102-109.
[http://dx.doi.org/10.1016/j.virol.2012.09.033] [PMID:  23217620] 
[224] 
Di Fenza, A.; Rocchia, W.; Tozzini, V. Complexes of HIV-1 integrase with HAT proteins: multiscale models, dynamics, and hypotheses on allosteric sites of inhibition. Proteins,  2009, 76(4), 946-958.
[http://dx.doi.org/10.1002/prot.22399] [PMID:  19306343] 
[225] 
Woodward, C.L.; Prakobwanakit, S.; Mosessian, S.; Chow, S.A. Integrase interacts with nucleoporin NUP153 to mediate the nuclear import of human immunodeficiency virus type 1. J. Virol.,  2009, 83(13), 6522-6533.
[http://dx.doi.org/10.1128/JVI.02061-08] [PMID:  19369352] 
[226] 
Luban, J. HIV-1 infection: going nuclear with TNPO3/Transportin-SR2 and integrase. Curr. Biol.,  2008, 18(16), R710-R713.
[http://dx.doi.org/10.1016/j.cub.2008.07.037] [PMID:  18727908] 
[227] 
Engelman, A. Host cell factors and HIV-1 integration. Future HIV Ther.,  2007, 1(4), 415-426.
[http://dx.doi.org/10.2217/17469600.1.4.415] 
[228] 
Thys, W.; Busschots, K.; McNeely, M.; Voet, A.; Christ, F.; Debyser, Z. LEDGF/p75 and transportin-SR2 are cellular cofactors of HIV integrase and novel targets for antiviral therapy. HIV Ther.,  2009, 3(2), 171-188.
[http://dx.doi.org/10.2217/17584310.3.2.171] 
[229] 
Rice, A.P. The HIV-1 Tat protein: mechanism of action and target for HIV-1 cure strategies. Curr. Pharm. Des.,  2017, 23(28), 4098-4102.
[http://dx.doi.org/10.2174/1381612823666170704130635] [PMID:  28677507] 
[230] 
Daelemans, D.; Pannecouque, C. HIV-1 Rev function as target for antiretroviral drug development. Curr. Opin. HIV AIDS,  2006, 1(5), 388-397.
[http://dx.doi.org/10.1097/01.COH.0000239851.22614.6a] [PMID:  19372838] 
[231] 
Coleman, S.H.; Day, J.R.; Guatelli, J.C. The HIV-1 Nef protein as a target for antiretroviral therapy. Expert Opin. Ther. Targets,  2001, 5(1), 1-22.
[http://dx.doi.org/10.1517/14728222.5.1.1] [PMID:  15992165] 
[232] 
Smithgall, T.E.; Thomas, G. Small molecule inhibitors of the HIV-1 virulence factor, Nef. Drug Discov. Today. Technol.,  2013, 10(4), e523-e529.
[http://dx.doi.org/10.1016/j.ddtec.2013.07.002] [PMID:  24451644] 
[233] 
Kogan, M.; Rappaport, J. HIV-1 accessory protein Vpr: relevance in the pathogenesis of HIV and potential for therapeutic intervention. Retrovirology,  2011, 8, 25.
[http://dx.doi.org/10.1186/1742-4690-8-25] [PMID:  21489275] 
[234] 
González, M.E. The HIV-1 Vpr Protein: A multifaceted target for therapeutic intervention. Int. J. Mol. Sci.,  2017, 18(1), 126.
[http://dx.doi.org/10.3390/ijms18010126] [PMID:  28075409] 
[235] 
Freed, E.O. HIV-1 gag proteins: diverse functions in the virus life cycle. Virology,  1998, 251(1), 1-15.
[http://dx.doi.org/10.1006/viro.1998.9398] [PMID:  9813197] 
[236] 
Pornillos, O.; Higginson, D.S.; Stray, K.M.; Fisher, R.D.; Garrus, J.E.; Payne, M.; He, G-P.; Wang, H.E.; Morham, S.G.; Sundquist, W.I. HIV Gag mimics the Tsg101-recruiting activity of the human Hrs protein. J. Cell Biol.,  2003, 162(3), 425-434.
[http://dx.doi.org/10.1083/jcb.200302138] [PMID:  12900394] 
[237] 
Freed, E.O. The HIV-TSG101 interface: recent advances in a budding field. Trends Microbiol.,  2003, 11(2), 56-59.
[http://dx.doi.org/10.1016/S0966-842X(02)00013-6] [PMID:  12598123] 
[238] 
Zhan, P.; Li, W.; Chen, H.; Liu, X. Targeting protein-protein interactions: a promising avenue of anti-HIV drug discovery. Curr. Med. Chem.,  2010, 17(29), 3393-3409.
[http://dx.doi.org/10.2174/092986710793176357] [PMID:  20712566] 
[239] 
Arhel, N.; Kirchhoff, F. Host proteins involved in HIV infection: new therapeutic targets. Biochim. Biophys. Acta,  2010, 1802(3), 313-321.
[http://dx.doi.org/10.1016/j.bbadis.2009.12.003] [PMID:  20018238] 
[240] 
Tavassoli, A. Targeting the protein-protein interactions of the HIV lifecycle. Chem. Soc. Rev.,  2011, 40(3), 1337-1346.
[http://dx.doi.org/10.1039/C0CS00092B] [PMID:  21152581] 
Rights & Permissions Print Cite
Article Metrics
21
Journal Information
For Authors
For Editors
For Reviewers
Explore Articles
Open Access
Open Access Articles
For Visitors
DOI https://dx.doi.org/10.2174/0929867325666180904123549	Print ISSN 0929-8673
Publisher Name Bentham Science Publisher	Online ISSN 1875-533X
当代药物化学

抗逆转录病毒药物治疗小儿艾滋病毒感染概述

摘要

当代药物化学

抗逆转录病毒药物治疗小儿艾滋病毒感染概述

摘要 Play Pause

Related Journals

Related Books

Related Articles

摘要
