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Research Articles

Analogue and structure based approaches for modelling HIV-1 integrase inhibitors

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Pages 11946-11956 | Received 27 May 2021, Accepted 25 Dec 2022, Published online: 03 Feb 2023

References

  • Abagyan, R., & Totrov, M. (2001). High-throughput docking for lead generation. Current opinion in Chemical Biology, 5(4), 375–382. https://doi.org/10.1016/S1367-5931(00)00217-9
  • Acar, M., Sutcu, M., Umur, O., Akturk, H., Torun, S. H., Tamay, Z., Salman, N., & Somer, A. (2017). Acquired immune deficiency syndrome in differential diagnosis of hyper-ige-immunoglobulinemia: Pediatric case report. Journal of Tropical Pediatrics, 63(1), 82–84. https://doi.org/10.1093/tropej/fmw053
  • Allen, M. P., & Tildesley, D. J. (1987). Computer simulation of liquids. Clarendon Press/Oxford University Press.
  • Artico, M., Di Santo, R., Costi, R., Novellino, E., Greco, G., Massa, S., Tramontano, E., Marongiu, M. E., De Montis, A., & La Colla, P. (1998). Geometrically and conformationally restrained cinnamoyl compounds as inhibitors of HIV-1 integrase: Synthesis, biological evaluation, and molecular modeling. Journal of Medicinal Chemistry, 41(21), 3948–3960. https://doi.org/10.1021/jm9707232
  • Bowen, E., DuVal, T., & Roche, V. (2017). Late diagnosis of human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS) in an older adult. Journal of the American Geriatrics Society, 65, S88–S89.
  • Bradley, T., Pollara, J., Santra, S., Vandergrift, N., Pittala, S., Bailey-Kellogg, C., Shen, X. Y., Parks, R., Goodman, D., Eaton, A., Balachandran, H., Mach, L. V., Saunders, K. O., Weiner, J. A., Scearce, R., Sutherland, L. L., Phogat, S., Tartaglia, J., Reed, S. G., … Haynes, B. F. (2017). Pentavalent HIV-1 vaccine protects against simian-human immunodeficiency virus challenge. Nature communications, 8, 15711. https://doi.org/10.1038/ncomms15711
  • Calvopina, M., Aguirre, C., Cevallos, W., Castillo, A., Abbasi, I., & Warburg, A. (2017). Case report: Coinfection of Leishmania guyanensis and human immunodeficiency virus-acquired immune deficiency syndrome: Report of a case of disseminated cutaneous leishmaniasis in Ecuador. The American Journal of Tropical Medicine and Hygiene, 96(5), 1151–1154.
  • Carugo, O., & Pongor, S. (2001). A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Science: A Publication of the Protein Society, 10(7), 1470–1473.
  • Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/10.1002/jcc.20290
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh ewald—An N.Log(N) method for ewald sums in large systems. Journal of Chemical Physics, 98, 10089–10092.
  • De Vivo, M., Masetti, M., Bottegoni, G., & Cavalli, A. (2016). Role of molecular dynamics and related methods in drug discovery. Journal of Medicinal Chemistry, 59(9), 4035–4061.
  • Dopke, M. F., Moultos, O. A., & Hartkamp, R. (2020). On the transferability of ion parameters to the TIP4P/2005 water model using molecular dynamics simulations. Journal of Chemical Physics, 152, 024501.
  • Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., & Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24(16), 1999–2012.
  • Durrant, J. D., & McCammon, J. A. (2011). Molecular dynamics simulations and drug discovery. BMC Biology, 9, 71.
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh ewald method. Journal of Chemical Physics, 103, 8577–8593.
  • Fatemi, M. H., Heidari, A., & Gharaghani, S. (2015). QSAR prediction of HIV-1 protease inhibitory activities using docking derived molecular descriptors. Journal of Theoretical Biology, 369, 13–22.
  • Frisch, M. J., Trucks, G., Schlegel, H. B., Scuseria, G. E., Robb, M. A., et al. (2009). Gaussian, Inc., Wallingford CT.
  • Grenier, P. O., & Auger, I. (2017). Acquired immune deficiency syndrome-associated Kaposi sarcoma in a child presenting as a solitary plantar hyperkeratotic plaque. Journal of Cutaneous Medicine and Surgery, 21, 348–350.
  • Harvey, M. J., & De Fabritiis, G. (2012). High-throughput molecular dynamics: The powerful new tool for drug discovery. Drug discovery Today, 17(19–20), 1059–1062.
  • Hong, H. X., Neamati, N., Wang, S. M., Nicklaus, M. C., Mazumder, A., Zhao, H., Burke, T. R., Pommier, Y., & Milne, G. W. A. (1997). Discovery of HIV-1 integrase inhibitors by pharmacophore searching. Journal of Medicinal Chemistry, 40(6), 930–936. https://doi.org/10.1021/jm960754h
  • Huang, M., Grant, G. H., & Richards, W. G. (2011). Binding modes of diketo-acid inhibitors of HIV-1 integrase: A comparative molecular dynamics simulation study. Journal of Molecular Graphics & Modelling, 29(7), 956–964.
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38.
  • Islam, M. A., & Pillay, T. S. (2016). Structural requirements for potential HIV-integrase inhibitors identified using pharmacophore-based virtual screening and molecular dynamics studies. Molecular bioSystems, 12(3), 982–993.
  • Ivetac, A., & McCammon, J. A. (2011). Molecular recognition in the case of flexible targets. Current pharmaceutical Design, 17(17), 1663–1671.
  • Iyer, M., & Hopfinger, A. J. (2007). Treating chemical diversity in QSAR analysis: Modeling diverse HIV-1 integrase inhibitors using 4D fingerprints. Journal of Chemical Information and Modeling, 47(5), 1945–1960.
  • Johnson, B. C., Metifiot, M., Pommier, Y., & Hughes, S. H. (2012). Molecular dynamics approaches estimate the binding energy of HIV-1 integrase inhibitors and correlate with in vitro activity. Antimicrobial Agents and Chemotherapy, 56(1), 411–419.
  • Jorgensen, W. L. (2004). The many roles of computation in drug discovery. Science (New York, N.Y.), 303(5665), 1813–1818. https://doi.org/10.1126/science.1096361
  • Karmon, S. L., & Markowitz, M. (2013). Next-generation integrase inhibitors where to after raltegravir? Drugs, 73(3), 213–228.
  • Liao, K. H., Chen, K. B., Lee, W. Y., Sun, M. F., Lee, C. C., & Chen, C. Y. (2014). Ligand-based and structure-based investigation for Alzheimer’s disease from traditional Chinese medicine. Evidence-Based Complementary and Alternative Medicine: eCAM, 2014, 364819.
  • Lin, Z. W., Neamati, N., Zhao, H., Kiryu, Y., Turpin, J. A., Aberham, C., Strebel, K., Kohn, K., Witvrouw, M., Pannecouque, C., Debyser, Z., De Clercq, E., Rice, W. G., Pommier, Y., & Burke, T. R. (1999). Chicoric acid analogues as HIV-1 integrase inhibitors. Journal of Medicinal Chemistry, 42(8), 1401–1414.
  • Lins, R. D., Briggs, J. M., Straatsma, T. P., Carlson, H. A., Greenwald, J., Choe, S., & McCammon, J. A. (1999). Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophysical journal, 76(6), 2999–3011.
  • Maiorov, V. N., & Crippen, G. M. (1994). Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins. Journal of Molecular Biology, 235(2), 625–634.
  • Makhija, M. T., & Kulkarni, V. M. (2001). Eigen value analysis of HIV-1 integrase inhibitors. Journal of Chemical Information and Computer Sciences, 41(6), 1569–1577.
  • Mehellou, Y., & De Clercq, E. (2010). Twenty-six years of anti-HIV drug discovery: Where do we stand and where do we go? Journal of Medicinal Chemistry, 53(2), 521–538.
  • Miller, B. R., 3rd, McGee, T. D., Jr., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321.
  • Neamati, N. (2001). Structure-based HIV-1 integrase inhibitor design: A future perspective. Expert opinion on Investigational Drugs, 10(2), 281–296. https://doi.org/10.1517/13543784.10.2.281
  • Neamati, N., Lin, Z. W., Karki, R. G., Orr, A., Cowansage, M., Strumberg, D., Pais, G. C. G., Voigt, J. H., Nicklaus, M. C., Winslow, H. E., Zhao, H., Turpin, J. A., Yi, J. Z., Skalka, A. M., Burke, T. R., & Pommier, Y. (2002). Metal-dependent inhibition of HIV-1 integrase. Journal of Medicinal Chemistry, 45(26), 5661–5670.
  • Neamati, N., Turpin, J. A., Winslow, H. E., Christensen, J. L., Williamson, K., Orr, A., Rice, W. G., Pommier, Y., Garofalo, A., Brizzi, A., Campiani, G., Fiorini, I., & Nacci, V. (1999). Thiazolothiazepine inhibitors of HIV-1 integrase. Journal of Medicinal Chemistry, 42(17), 3334–3341.
  • Nicklaus, M. C., Neamati, N., Hong, H. X., Mazumder, A., Sunder, S., Chen, J., Milne, G. W. A., & Pommier, Y. (1997). HIV-1 integrase pharmacophore: Discovery of inhibitors through three-dimensional database searching. Journal of Medicinal Chemistry, 40(6), 920–929.
  • Patel, S., Patel, B., & Bhatt, H. (2016). 3D-QSAR studies on 5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxamide derivatives as HIV-1 integrase inhibitors. Journal of the Taiwan Institute of Chemical Engineers, 59, 61–68.
  • Pommier, Y., Johnson, A. A., & Marchand, C. (2005). Integrase inhibitors to treat HIV/AIDS. Nature reviews. Drug Discovery, 4(3), 236–248.
  • Reva, B. A., Finkelstein, A. V., & Skolnick, J. (1998). What is the probability of a chance prediction of a protein structure with an RMSD of 6 A? Folding & Design, 3(2), 141–147.
  • Rice, P. A., & Baker, T. A. (2001). Comparative architecture of transposase and integrase complexes. Nature structural Biology, 8(5), 302–307.
  • Roe, D. R., & Cheatham, T. E. 3rd (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation. 9, 3084–3095.
  • Schluttig, J., Bachmann, M., & Janke, W. (2008). Comparative molecular dynamics and Monte Carlo study of statistical properties for coarse-grained heteropolymers. Journal of Computational Chemistry, 29(15), 2603–2612.
  • Shaik, B., Agrawal, V., Gupta, S. P., & Menon, U. (2017). Quantitative structure-activity relationship and docking studies on a series of oxadiazole and triazole substituted naphthyridines as HIV-1 integrase inhibitors. Letters in Drug Design & Discovery, 14, 10–27.
  • Sharma, J., Kumar Bhardwaj, V., Singh, R., Rajendran, V., Purohit, R., & Kumar, S. (2021). An in-silico evaluation of different bioactive molecules of tea for their inhibition potency against non structural protein-15 of SARS-CoV-2. Food chemistry, 346, 128933.
  • Sippl, W. (2002). Development of biologically active compounds by combining 3D QSAR and structure-based design methods. Journal of Computer-Aided Molecular Design, 16(11), 825–830. https://doi.org/10.1023/a:1023888813526
  • Srivastava, H. K., Choudhury, C., & Sastry, G. N. (2012). The efficacy of conceptual DFT descriptors and docking scores on the QSAR models of HIV protease inhibitors. Medicinal Chemistry, 8, 811–825.
  • Srivastava, H. K., & Sastry, G. N. (2012). Molecular dynamics investigation on a series of HIV protease inhibitors: Assessing the performance of MM-PBSA and MM-GBSA approaches. Journal of Chemical Information and Modeling, 52(11), 3088–3098.
  • Vernon, A., Fenimore, P., Strauss, C., Tung, C. S., Frenkel, D., & Terentjev, E. (2017). Using molecular dynamics simulations to understand pattern formation in polymers. Biophysical Journal, 112, 54a.
  • Vink, C., & Plasterk, R. H. A. (1993). The human-immunodeficiency-virus integrase protein. Trends in Genetics: TIG, 9(12), 433–438.
  • Walli, R., Herfort, O., Michl, G. M., Demant, T., Jager, H., Dieterle, C., Bogner, J. R., Landgraf, R., & Goebel, F. D. (1998). Treatment with protease inhibitors associated with peripheral insulin resistance and impaired oral glucose tolerance in HIV-1-infected patients. AIDS (London, England), 12(15), F167–F173.
  • Wang, J., & Hou, T. (2012). Develop and test a solvent accessible surface area-based model in conformational entropy calculations. Journal of Chemical Information and Modeling. 52, 1199–1212.
  • Zhao, H., Neamati, N., Hong, H. X., Mazumder, A., Wang, S. M., Sunder, S., Milne, G. W. A., Pommier, Y., & Burke, T. R. (1997a). Coumarin-based inhibitors of HIV integrase. Journal of Medicinal Chemistry, 40(2), 242–249.
  • Zhao, H., Neamati, N., Mazumder, A., Sunder, S., Pommier, Y., & Burke, T. R. (1997b). Arylamide inhibitors of HIV-1 integrase. Journal of Medicinal Chemistry, 40(8), 1186–1194.
  • Zouhiri, F., Mouscadet, J. F., Mekouar, K., Desmaele, D., Savoure, D., Leh, H., Subra, F., Bret, M. L., Auclair, C., & d‘Angelo, J. (2000). Structure-activity relationships and binding mode of styrylquinolines as potent inhibitors of HIV-1 integrase and replication of HIV-1 in cell culture. Journal of Medicinal Chemistry, 43(8), 1533–1540.

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