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Research Articles

Investigation of novel indole-based HIV-1 protease inhibitors using virtual screening and text mining

Pages 3638-3648 | Received 31 Mar 2020, Accepted 06 May 2020, Published online: 17 Jun 2020

References

  • Agrawal, L., Lu, X., Jin, Q., & Alkhatib, G. (2006). Anti-HIV therapy: Current and future directions. Current Pharmaceutical Design, 12(16), 2031–2055. https://doi.org/10.2174/138161206777442100
  • Bandini, M. (2013). Electrophilicity: ole chemistry” dark-side” of indole. Organic & Biomolecular Chemistry, 11(32), 5206–5212. https://doi.org/10.1039/c3ob40735g
  • Banks, J. L., Beard, H. S., Cao, Y., Cho, A. E., Damm, W., Farid, R., Felts, A. K., Halgren, T. A., Mainz, D. T., Maple, J. R., Murphy, R., Philipp, D. M., Repasky, M. P., Zhang, L. Y., Berne, B. J., Friesner, R. A., Gallicchio, E., & Levy, R. M. (2005). Integrated Modeling Program, Applied Chemical Theory (IMPACT). Journal of Computational Chemistry, 26(16), 1752–1780. https://doi.org/10.1002/jcc.20292
  • Bathula, R., Lanka, G., Muddagoni, N., Dasari, M., Nakkala, S., Bhargavi, M., Somadi, G., Sivan, S. K., & Rajender Potlapally, S. (2020). Identification of potential Aurora kinase-C protein inhibitors: An amalgamation of energy minimization, virtual screening, prime MMGBSA and AutoDock. Journal of Biomolecular Structure & Dynamics, 38(8), 2314–2325. https://doi.org/10.1080/07391102.2019.1630318
  • Berendsen, H. J. C., Postma, J. P. M., Gunsteren, W. F. v., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. In Intermolecular Forces: Proceedings of the Fourteenth Jerusalem Symposium on Quantum Chemistry and Biochemistry Held in Jerusalem, Israel, April 13–16, 1981 (pp. 331–342). Springer Netherlands. https://doi.org/10.1007/978-94-015-7658-1_21
  • Bourinbaiar, A. S. (2009). New developments in drug and vaccine discoveries. Current Pharmaceutical Design, 15(11), 1157–1158. https://doi.org/10.2174/138161209787846810
  • Bozzette, S. A., Ake, C. F., Tam, H. K., Chang, S. W., & Louis, T. A. (2003). Cardiovascular and cerebrovascular events in patients treated for human immunodeficiency virus infection. The New England Journal of Medicine, 348(8), 702–710. https://doi.org/10.1056/NEJMoa022048
  • Campiani, G., Ramunno, A., Maga, G., Nacci, V., Fattorusso, C., Catalanotti, B., Morelli, E., & Novellino, E. (2002). Non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors: Past, present, and future perspectives. Current Pharmaceutical Design, 8(8), 615–657. https://doi.org/10.2174/1381612024607207
  • Condra, J. H., Schleif, W. A., Blahy, O. M., Gabryelski, L. J., Graham, D. J., Quintero, J. C., Rhodes, A., Robbins, H. L., Roth, E., & Shivaprakash, M. (1995). Apr). In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors. Nature, 374(6522), 569–571. https://doi.org/10.1038/374569a0
  • Cutinho, P. F., Roy, J., Anand, A., Cheluvaraj, R., Murahari, M., & Chimatapu, H. S. V. (2020). Design of metronidazole derivatives and flavonoids as potential non-nucleoside reverse transcriptase inhibitors using combined ligand- and structure-based approaches. Journal of Biomolecular Structure & Dynamics, 38(6), 1626–1648. https://doi.org/10.1080/07391102.2019.1614094
  • Deng, J., Dayam, R., Al-Mawsawi, L. Q., & Neamati, N. (2007). Design of second generation HIV-1 integrase inhibitors. Current Pharmaceutical Design, 13(2), 129–141. https://doi.org/10.2174/138161207779313687
  • Desmond. (2011). version 4.9, Schrodinger, LLC, New York.
  • Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/10.1021/jm0306430
  • Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/10.1021/jm051256o
  • Gottlinger, H. G., Sodroski, J. G., & Haseltine, W. A. (1989). Role of capsid precursor processing and myristoylation in morphogenesis and infectivity of human immunodeficiency virus type 1. Proceedings of the National Academy of Sciences of the United States of America, 86(15), 5781–5785. https://doi.org/10.1073/pnas.86.15.5781
  • Hoover, W. G. (1985). Canonical dynamics: Equilibrium phase-space distributions. Physical Review. A, General Physics, 31(3), 1695–1697. https://doi.org/10.1103/physreva.31.1695
  • Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82. https://doi.org/10.1021/ci100275a
  • Hruz, P. W. (2008). HIV protease inhibitors and insulin resistance: Lessons from in-vitro, rodent and healthy human volunteer models. Current Opinion in HIV and Aids, 3(6), 660–665. https://doi.org/10.1097/COH.0b013e3283139134
  • Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J. F., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all-atom protein loop prediction. Proteins, 55(2), 351–367. https://doi.org/10.1002/prot.10613
  • Kakarala, K. K., Jamil, K., & Devaraji, V. (2014). Structure and putative signaling mechanism of Protease activated receptor 2 (PAR2) – A promising target for breast cancer. Journal of Molecular Graphics & Modelling, 53, 179–199. https://doi.org/10.1016/j.jmgm.2014.07.012
  • Klumpp, K., & Mirzadegan, T. (2006). Recent progress in the design of small molecule inhibitors of HIV RNase H. Current Pharmaceutical Design, 12(15), 1909–1922. https://doi.org/10.2174/138161206776873653
  • Kotler, D. P. (2008). HIV and antiretroviral therapy: Lipid abnormalities and associated cardiovascular risk in HIV-infected patients. Journal of Acquired Immune Deficiency Syndromes, 49(2), 79–85.
  • Krallinger, M., & Valencia, A. (2005). Text-mining and information-retrieval services for molecular biology. Genome Biology, 6(7), 224.
  • Kumar, A., Rathi, E., & Kini, S. G. (2020). Identification of potential tumour-associated carbonic anhydrase isozyme IX inhibitors: Atom-based 3D-QSAR modelling, pharmacophore-based virtual screening and molecular docking studies. Journal of Biomolecular Structure and Dynamics 38(7), 2156–2170. https://doi.org/10.1080/07391102.2019.1626285
  • Li, J., Abel, R., Zhu, K., Cao, Y., Zhao, S., & Friesner, R. A. (2011). The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling. Proteins, 79(10), 2794–2812. https://doi.org/10.1002/prot.23106
  • Louis, J. M., Ishima, R., Torchia, D. A., & Weber, I. T. (2007). HIV-1 protease: Structure, dynamics, and inhibition. Advances in Pharmacology (San Diego, Calif.).), 55, 261–298. https://doi.org/10.1016/S1054-3589(07)55008-8
  • Lv, Z., Chu, Y., & Wang, Y. (2015). HIV protease inhibitors: A review of molecular selectivity and toxicity. HIV/AIDS (Auckland, N.Z.).), 7, 95–104. https://doi.org/10.2147/HIV.S79956
  • Ma, Z., & Tuckerman, M. (2010). Constant pressure ab initio molecular dynamics with discrete variable representation basis sets. The Journal of Chemical Physics, 133(18), 184110. https://doi.org/10.1063/1.3499812
  • MarvinSketch 18.30.0, chemaxon. (2018).
  • Matthews, B. W. (1975). Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochimica et Biophysica Acta, 405(2), 442–451. https://doi.org/10.1016/0005-2795(75)90109-9
  • Menendez-Arias, L., Matamoros, T., & Cases-Gonzalez, C. E. (2006). Insertions and deletions in HIV-1 reverse transcriptase: Consequences for drug resistance and viral fitness. Current Pharmaceutical Design, 12(15), 1811–1825. https://doi.org/10.2174/138161206776873608
  • N. C. for. HIV/AIDS. (2019). Estimated HIV incidence and prevalence in the United States, 2010–2016. (Vol. 24, Tech. Rep.). Center for Desease Control and Prevetion.
  • Panda, S. K., Saxena, S., & Guruprasad, L. (2020). Homology modeling, docking and structure-based virtual screening for new inhibitor identification of Klebsiella pneumoniae heptosyltransferase-III. Journal of Biomolecular Structure & Dynamics, 38(7), 1887–1902. https://doi.org/10.1080/07391102.2019.1624296
  • Protein Preparation. (2011). Version 2.5, Schrodinger, LLC, New York.
  • Raha, K., & Merz, K. M. (2004). A quantum mechanics-based scoring function: Study of zinc ion-mediated ligand binding. Journal of the American Chemical Society, 126(4), 1020–1021. https://doi.org/10.1021/ja038496i
  • Rather, M. A., Dutta, S., Guttula, P. K., Dhandare, B. C., Yusufzai, S. I., & Zafar, M. I. (2020). Structural analysis, molecular docking and molecular dynamics simulations of G-protein-coupled receptor (kisspeptin) in fish. Journal of Biomolecular Structure & Dynamics, 38(8), 2422–2439. https://doi.org/10.1080/07391102.2019.1633407
  • Roy, S., Kumar, A., Baig, M. H., Masařík, M., & Provazník, I. (2015). Virtual screening, ADMET profiling, molecular docking and dynamics approaches to search for potent selective natural molecules based inhibitors against metallothionein-III to study Alzheimer's disease. Methods (San Diego, Calif.).), 83, 105–110. https://doi.org/10.1016/j.ymeth.2015.04.021
  • Sahin, K. S., D. (2020). Identifying new piperazine-based PARP1 inhibitors using text mining and integrated molecular modeling approaches. Journal of Biomolecular Structure and Dynamics, https://doi.org/10.1080/07391102.2020.1715262.
  • Sahin, K., Zengin Kurt, B., Sonmez, F., & Durdagi, S. (2019). Novel AChE and BChE inhibitors using combined virtual screening, text mining and in vitro binding assays. Journal of Biomolecular Structure and Dynamics, 1–17. https://doi.org/10.1080/07391102.2019.1660218
  • Saikia, S., & Bordoloi, M. (2019). Molecular docking: Challenges, advances and its use in drug discovery perspective. Current Drug Targets, 20(5), 501–521. https://doi.org/10.2174/1389450119666181022153016
  • Sastry, G. M., Dixon, S. L., & Sherman, W. (2011). Rapid shape-based ligand alignment and virtual screening method based on atom/feature-pair similarities and volume overlap scoring. Journal of Chemical Information and Modeling, 51(10), 2455–2466. https://doi.org/10.1021/ci2002704
  • Shelley, J. C., Cholleti, A., Frye, L. L., Greenwood, J. R., Timlin, M. R., & Uchimaya, M. (2007). Epik: A software program for pK(a) prediction and protonation state generation for drug-like molecules. Journal of Computer-Aided Molecular Design, 21(12), 681–691. https://doi.org/10.1007/s10822-007-9133-z
  • Shen, C. H., Wang, Y. F., Kovalevsky, A. Y., Harrison, R. W., & Weber, I. T. (2010). Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters. The FEBS Journal, 277(18), 3699–3714. https://doi.org/10.1111/j.1742-4658.2010.07771.x
  • Śledź, P., & Caflisch, A. (2018). Protein structure-based drug design: From docking to molecular dynamics. Current Opinion in Structural Biology, 48, 93–102. https://doi.org/10.1016/j.sbi.2017.10.010
  • Soontornniyomkij, V., Umlauf, A., Chung, S. A., Cochran, M. L., Soontornniyomkij, B., Gouaux, B., Toperoff, W., Moore, D. J., Masliah, E., Ellis, R. J., Grant, I., & Achim, C. L. (2014). HIV protease inhibitor exposure predicts cerebral small vessel disease. AIDS (London, England)), 28(9), 1297–1306. https://doi.org/10.1097/QAD.0000000000000262
  • Subhani, S., Jayaraman, A., & Jamil, K. (2015). Homology modelling and molecular docking of MDR1 with chemotherapeutic agents in non-small cell lung cancer. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 71, 37–45. https://doi.org/10.1016/j.biopha.2015.02.009
  • Taber, D. F., & Tirunahari, P. K. (2011). Indole synthesis: A review and proposed classification. Tetrahedron, 67(38), 7195–7210. https://doi.org/10.1016/j.tet.2011.06.040
  • Todeschini, R., Ballabio, D., & Grisoni, F. (2016). 10). Beware of Unreliable Q2! A Comparative Study of Regression Metrics for Predictivity Assessment of QSAR Models. Journal of Chemical Information and Modeling, 56(10), 1905–1913. https://doi.org/10.1021/acs.jcim.6b00277
  • Tozser, J. (2001). HIV inhibitors: Problems and reality. Annals of the New York Academy of Sciences, 946, 145–159.
  • Tripathi, S. K., Muttineni, R., & Singh, S. K. (2013). Extra precision docking, free energy calculation and molecular dynamics simulation studies of CDK2 inhibitors. Journal of Theoretical Biology, 334, 87–100. https://doi.org/10.1016/j.jtbi.2013.05.014
  • Walker, B. D., & Burton, D. R. (2008). Toward an AIDS vaccine. Science (New York, N.Y.).), 320(5877), 760–764. https://doi.org/10.1126/science.1152622
  • Wlodawer, A., & Erickson, J. W. (1993). Structure-based inhibitors of HIV-1 protease. Annual Review of Biochemistry, 62, 543–585. https://doi.org/10.1146/annurev.bi.62.070193.002551
  • Yeung, K.-S., Qiu, Z., Yin, Z., Trehan, A., Fang, H., Pearce, B., Yang, Z., Zadjura, L., D'Arienzo, C. J., Riccardi, K., Shi, P.-Y., Spicer, T. P., Gong, Y.-F., Browning, M. R., Hansel, S., Santone, K., Barker, J., Coulter, T., Lin, P.-F., Meanwell, N. A., & Kadow, J. F. (2013). Inhibitors of HIV-1 attachment. Part 8: The effect of C7-heteroaryl substitution on the potency, and in vitro and in vivo profiles of indole-based inhibitors. Bioorganic & Medicinal Chemistry Letters, 23(1), 203–208. https://doi.org/10.1016/j.bmcl.2012.10.117
  • Zhang, M. Z., Chen, Q., & Yang, G. F. (2015). A review on recent developments of indole-containing antiviral agents. European Journal of Medicinal Chemistry, 89, 421–441. https://doi.org/10.1016/j.ejmech.2014.10.065
  • Zhao, F., Wang, J.-L., Ming, H.-Y., Zhang, Y.-N., Dun, Y.-Q., Zhang, J.-H., & Song, Y.-B. (2020). Insights into the binding mode and functional components of the analgesic-antitumour peptide from Buthus martensii Karsch to human voltage-gated sodium channel 1.7 based on dynamic simulation analysis. Journal of Biomolecular Structure & Dynamics, 38(6), 1868–1879. https://doi.org/10.1080/07391102.2019.1620126

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