337
Views
2
CrossRef citations to date
0
Altmetric
Research Articles

Repurposing FDA-approved drugs as HIV-1 integrase inhibitors: an in silico investigation

, , ORCID Icon, , & ORCID Icon
Pages 2146-2159 | Received 29 Aug 2021, Accepted 08 Jan 2022, Published online: 22 Jan 2022

References

  • Agrawal, A., DeSoto, J., Fullagar, J. L., Maddali, K., Rostami, S., Richman, D. D., Pommier, Y., & Cohen, S. M. (2012). Probing chelation motifs in HIV integrase inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 109(7), 2251–2256. https://doi.org/10.1073/pnas.1112389109
  • Aljazzar, H., & Leue, S. K. (2011). A heuristic search algorithm for finding the k shortest paths. Artificial Intelligence, 175(18), 2129–2154. https://doi.org/10.1016/j.artint.2011.07.003
  • Andrake, M., Skalka, A., & Merkel, G. (2018). Inhibitors of HIV-1 integrase multimerization.
  • Anstett, K., Brenner, B., Mesplede, T., & Wainberg, M. A. (2017). HIV drug resistance against strand transfer integrase inhibitors. Retrovirology, 14(1), 36. https://doi.org/10.1186/s12977-017-0360-7
  • Bacchi, A., Carcelli, M., Compari, C., Fisicaro, E., Pala, N., Rispoli, G., Rogolino, D., Sanchez, T. W., Sechi, M., Sinisi, V., & Neamati, N. (2011). Investigating the role of metal chelation in HIV-1 integrase strand transfer inhibitors. Journal of Medicinal Chemistry, 54(24), 8407–8420. https://doi.org/10.1021/jm200851g
  • Barzegar, A., & Hamidi, H. (2017). Quantitative structure-activity relationships study of potent pyridinone scaffold derivatives as HIV-1 integrase inhibitors with therapeutic applications. Journal of Theoretical and Computational Chemistry, 16(5), 1750038. https://doi.org/10.1142/S0219633617500389
  • Brooks, K. M., Sherman, E. M., Egelund, E. F., Brotherton, A., Durham, S., Badowski, M. E., & Cluck, D. B. (2019). Integrase inhibitors: after 10 years of experience, is the best yet to come? Pharmacotherapy, 39(5), 576–598. https://doi.org/10.1002/phar.2246
  • Carswell, C. I., Plosker, G. L., & Jarvis, B. (2002). Rosuvastatin. Drugs, 62(14), 2075–2085. https://doi.org/10.2165/00003495-200262140-00008
  • Carter, G. C., Bernstone, L., Sangani, D., Bee, J. W., Harder, T., & James, W. (2009). HIV entry in macrophages is dependent on intact lipid rafts. Virology, 386(1), 192–202. https://doi.org/10.1016/j.virol.2008.12.031
  • CfsSubsetEval. (XXXX). CfsSubsetEval (weka-dev 3.9.5 API). https://weka.sourceforge.io/doc.dev/weka/attributeSelection/CfsSubsetEval.html.
  • Cheng, Z., Zhang, Y., & Fu, W. (2010). QSAR study of carboxylic acid derivatives as HIV-1 Integrase inhibitors. European Journal of Medicinal Chemistry, 45(9), 3970–3980. https://doi.org/10.1016/j.ejmech.2010.05.052
  • Chu, W.-T., Zhang, J.-L., Zheng, Q.-C., Chen, L., Xue, Q., & Zhang, H.-X. (2013). Insights into the drug resistance induced by the BaDHPS mutations: molecular dynamic simulations and MM/GBSA studies. Journal of Biomolecular Structure & Dynamics, 31(10), 1127–1136. https://doi.org/10.1080/07391102.2012.726529
  • Darnag, R., Minaoui, B., & Fakir, M. (2013). Pattern recognition system based on support vector machines: HIV-1 integrase inhibitors application. Control Theory Informatics, 3, 1–8.
  • del Real, G., Jiménez-Baranda, S., Mira, E., Lacalle, R. A., Lucas, P., Gómez-Moutón, C., Alegret, M., Peña, J. M., Rodríguez-Zapata, M., Alvarez-Mon, M., Martínez-A, C., & Mañes, S. (2004). Statins inhibit HIV-1 infection by down-regulating Rho activity. The Journal of Experimental Medicine, 200(4), 541–547. https://doi.org/10.1084/jem.20040061
  • Delaney, M. (2006). History of HAART – the true story of how effective multi-drug therapy was developed for treatment of HIV disease. Retrovirology, 3(S1), S6. https://doi.org/10.1186/1742-4690-3-S1-S6
  • Delelis, O., Carayon, K., Saïb, A., Deprez, E., & Mouscadet, J. F. (2008). Integrase and integration: biochemical activities of HIV-1 integrase. Retrovirology, 5, 114. https://doi.org/10.1186/1742-4690-5-114
  • Egan, M. F., Kost, J., Voss, T., Mukai, Y., Aisen, P. S., Cummings, J. L., Tariot, P. N., Vellas, B., van Dyck, C. H., Boada, M., Zhang, Y., Li, W., Furtek, C., Mahoney, E., Harper Mozley, L., Mo, Y., Sur, C., & Michelson, D. (2019). Randomized trial of verubecestat for prodromal Alzheimer's disease. The New England Journal of Medicine, 380(15), 1408–1420. https://doi.org/10.1056/NEJMoa1812840
  • Gavegnano, C., Detorio, M., Montero, C., Bosque, A., Planelles, V., & Schinazi, R. F. (2014). Ruxolitinib and tofacitinib are potent and selective inhibitors of HIV-1 replication and virus reactivation in vitro. Antimicrobial Agents and Chemotherapy, 58(4), 1977–1986.
  • Giguère, J.-F., & Tremblay, M. J. (2004). Statin compounds reduce Human Immunodeficiency Virus Type 1 replication by preventing the interaction between virion-associated host Intercellular Adhesion Molecule 1 and its natural cell surface ligand LFA-1. Journal of Virology, 78(21), 12062–12065. https://doi.org/10.1128/JVI.78.21.12062-12065.2004
  • González-Medina, M., & Medina-Franco, J. L. (2017). Platform for unified molecular analysis: PUMA. Journal of Chemical Information and Modeling, 57(8), 1735–1740. https://doi.org/10.1021/acs.jcim.7b00253
  • Gupta, P., Garg, P., & Roy, N. (2012). Identification of novel HIV-1 integrase inhibitors using shape-based screening, QSAR, and docking approach. Chemical Biology & Drug Design, 79(5), 835–849. https://doi.org/10.1111/j.1747-0285.2012.01326.x
  • Hajimahdi, Z., & Zarghi, A. (2016). Progress in HIV-1 integrase inhibitors: a review of their chemical structure diversity. Iranian Journal of Pharmaceutical Research: IJPR, 15(4), 595–628.
  • Hall, M., Frank, E., Holmes, G., Pfahringer, B., Reutemann, P., & Witten, I. H. (2009). The WEKA data mining software. ACM SIGKDD Explorations Newsletter, 11(1), 10–18. https://doi.org/10.1145/1656274.1656278
  • Hare, S., Vos, A. M., Clayton, R. F., Thuring, J. W., Cummings, M. D., & Cherepanov, P. (2010). Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Proceedings of the National Academy of Sciences of the United States of America, 107(46), 20057–20062. https://doi.org/10.1073/pnas.1010246107
  • Hightower, K. E., Wang, R., Deanda, F., Johns, B. A., Weaver, K., Shen, Y., Tomberlin, G. H., Carter, H. L., Broderick, T., Sigethy, S., Seki, T., Kobayashi, M., & Underwood, M. R. (2011). Dolutegravir (S/GSK1349572) exhibits significantly slower dissociation than raltegravir and elvitegravir from wild-type and integrase inhibitor-resistant HIV-1 integrase-DNA complexes. Antimicrobial Agents and Chemotherapy, 55(10), 4552–4559. https://doi.org/10.1128/AAC.00157-11
  • Ingale, K. B., & Bhatia, M. S. (2011). HIV-1 integrase inhibitors: a review of their chemical development. Antiviral Chemistry & Chemotherapy, 22(3), 95–105. https://doi.org/10.3851/IMP1740
  • Jacobson, K., & Ogbuagu, O. (2018). Integrase inhibitor-based regimens result in more rapid virologic suppression rates among treatment-naïve human immunodeficiency virus-infected patients compared to non-nucleoside and protease inhibitor-based regimens in a real-world clinical setting. Medicine, 97(43), e13016. https://doi.org/10.1097/MD.0000000000013016
  • Johns, B. A., Weatherhead, J. G., Hakogi, T., & Aoyama, Y. (2014). Chemical compounds used as HIV integrase inhibitors.
  • Klebe, G., Abraham, U., & Mietzner, T. (1994). Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. Journal of Medicinal Chemistry, 37(24), 4130–4146. https://doi.org/10.1021/jm00050a010
  • Ko, G. M. (2012). Differential evolution-binary particle swarm optimization algorithm for the analysis of aryl β-diketo acids for HIV-1 integrase inhibition [Paper presentation]. 2012 IEEE Congress on Evolutionary Computation, CEC 2012 https://doi.org/10.1109/CEC.2012.6256578
  • L, M. (2014). Stabilization of the integrase-DNA complex by Mg2+ ions and prediction of key residues for binding HIV-1 integrase inhibitors. Proteins, 82, 466–478.
  • Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/10.1021/ci200227u
  • Li, X., & Vince, R. (2006). Synthesis and biological evaluation of purine derivatives incorporating metal chelating ligands as HIV integrase inhibitors. Bioorganic & Medicinal Chemistry, 14(16), 5742–5755. https://doi.org/10.1016/j.bmc.2006.04.011
  • Markwick, P. R. L., & McCammon, J. A. (2011). Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Physical Chemistry Chemical Physics: PCCP, 13(45), 20053–20065.
  • Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011). Molecular docking: a powerful approach for structure-based drug discovery. Current Computer-Aided Drug Design, 7(2), 146–157. https://doi.org/10.2174/157340911795677602
  • Miller, B. R., McGee, T. D., 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. https://doi.org/10.1021/ct300418h
  • Miri, L., Bouvier, G., Kettani, A., Mikou, A., Wakrim, L., Nilges, M., & Malliavin, T. E. (2014). Stabilization of the integrase-DNA complex by Mg2+ ions and prediction of key residues for binding HIV-1 integrase inhibitors. Proteins Struct Proteins, 82(3), 466–478. https://doi.org/10.1002/prot.24412
  • Mouscadet, J. F., & Tchertanov, L. (2009). Raltegravir: molecular basis of its mechanism of action. European Journal of Medical Research, 14(Suppl 3), 5. https://doi.org/10.1186/2047-783X-14-S3-5
  • Neamati, N., Lin, Z., Karki, R. G., Orr, A., Cowansage, K., Strumberg, D., Pais, G. C. G., Voigt, J. H., Nicklaus, M. C., Winslow, H. E., Zhao, H., Turpin, J. A., Yi, J., Skalka, A. M., Burke, T. R., & Pommier, Y. (2002). Metal-dependent inhibition of HIV-1 integrase. Journal of Medicinal Chemistry, 45(26), 5661–5670. https://doi.org/10.1021/jm0201417
  • Neves, B. J., Braga, R. C., Melo-Filho, C. C., Moreira-Filho, J. T., Muratov, E. N., & Andrade, C. H. (2018). QSAR-based virtual screening: advances and applications in drug discovery. Frontiers in Pharmacology, 9, 1275. https://doi.org/10.3389/fphar.2018.01275
  • Oh, J. W., Oh, Y. T., Kim, D. J., & Shin, C. G. (1997). Characterization of mutants of human immunodeficiency virus type 1 integrase mutants expressed in Escherichia coli. Molecules and Cells, 7(5), 688–693.
  • Ono, A., & Freed, E. O. (2001). Plasma membrane rafts play a critical role in HIV-1 assembly and release. Proceedings of the National Academy of Sciences of the United States of America, 98(24), 13925–13930. https://doi.org/10.1073/pnas.241320298
  • Passos, D. O., Li, M., Jóźwik, I. K., Zhao, X. Z., Santos-Martins, D., Yang, R., Smith, S. J., Jeon, Y., Forli, S., Hughes, S. H., Burke, T. R., Craigie, R., & Lyumkis, D. (2020). Structural basis for strand-transfer inhibitor binding to HIV intasomes. Science (New York, NY), 367(6479), 810–814. https://doi.org/10.1126/science.aay8015
  • Passos, D. O., Li, M., Yang, R., Rebensburg, S. V., Ghirlando, R., Jeon, Y., Shkriabai, N., Kvaratskhelia, M., Craigie, R., & Lyumkis, D. (2017). Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Science (New York, NY), 355(6320), 89–92. https://doi.org/10.1126/science.aah5163
  • Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., DeBolt, S., Ferguson, D., Seibel, G., & Kollman, P. (1995). AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications, 91(1–3), 1–41. https://doi.org/10.1016/0010-4655(95)00041-D
  • Pennington, L. D., & Moustakas, D. T. (2017). The necessary Nitrogen atom: a versatile high-impact design element for multiparameter optimization. Journal of Medicinal Chemistry, 60(9), 3552–3579. https://doi.org/10.1021/acs.jmedchem.6b01807
  • Pierce, L. C. T., Salomon-Ferrer, R., de Oliveira, C. A. F., McCammon, J. A., & Walker, R. C. (2012). Routine access to millisecond time scale events with accelerated molecular dynamics. Journal of Chemical Theory and Computation, 8(9), 2997–3002. https://doi.org/10.1021/ct300284c
  • Rathi, L. G., Kashaw, S. K., Agrawal, R. K., & Mishra, P. (2001). Comparative Molecular Field Analysis (CoMFA): a modern approach towards drug design. Indian Journal of Pharmaceutical Sciences, 63, 367–370.
  • Rücker, C., Rücker, G., & Meringer, M. (2007). Y-randomization and its variants in QSPR/QSAR. Journal of Chemical Information and Modeling, 47(6), 2345–2357. https://doi.org/10.1021/ci700157b
  • Schroeder, M. A. (2020). A phase 1 trial of itacitinib, a selective JAK1 inhibitor, in patients with acute graft-versus-host disease. Blood Advances, 4, 1657–1669.
  • Svetnik, V., Liaw, A., Tong, C., Culberson, J. C., Sheridan, R. P., & Feuston, B. P. (2003). Random Forest: a classification and regression tool for compound classification and QSAR modeling. Journal of Chemical Information and Computer Sciences, 43(6), 1947–1958.
  • Trivedi, J., Mahajan, D., Jaffe, R. J., Acharya, A., Mitra, D., & Byrareddy, S. N. (2020). Recent advances in the development of integrase inhibitors for HIV treatment. Current HIV/AIDS Reports, 17(1), 63–75. https://doi.org/10.1007/s11904-019-00480-3
  • Tropsha, A. (2010). Best practices for QSAR model development, validation, and exploitation. Molecular Informatics, 29(6-7), 476–488. https://doi.org/10.1002/minf.201000061
  • Underwood, M. R., Johns, B. A., Sato, A., Martin, J. N., Deeks, S. G., & Fujiwara, T. (2012). The activity of the integrase inhibitor dolutegravir against HIV-1 variants isolated from raltegravir-treated adults. Journal of Acquired Immune Deficiency Syndromes (1999), 61(3), 297–301. https://doi.org/10.1097/QAI.0b013e31826bfd02
  • Veerasamy, R. (2011). Validation of QSAR models - strategies and importance. International Journal of Drug Design & Disocovery, 2, 511–519.
  • Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., … Wilson, M. (2018). DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Research, 46(D1), D1074–D1082. https://doi.org/10.1093/nar/gkx1037
  • Yan, A., Xuan, S., & Hu, X. (2012). Classification of active and weakly active ST inhibitors of HIV-1 integrase using a Support Vector Machine. Combinatorial Chemistry & High Throughput Screening, 15(10), 792–805. https://doi.org/10.2174/138620712803901108
  • Zakariazadeh, M., Barzegar, A., Soltani, S., & Aryapour, H. (2015). Developing 2D-QSAR models for naphthyridine derivatives against HIV-1 integrase activity. Medicinal Chemistry Research, 24(6), 2485–2504. https://doi.org/10.1007/s00044-014-1305-5

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.