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Research Articles

Hit identification and drug repositioning of potential non-nucleoside reverse transcriptase inhibitors by structure-based approach using computational tools (part II)

, , , , , & ORCID Icon show all
Pages 3772-3789 | Received 16 Jun 2019, Accepted 27 Aug 2019, Published online: 17 Sep 2019

References

  • Anantram, A., Kundaikar, H., Degani, M., & Prabhu, A. (2019). Molecular dynamic simulations on an inhibitor of anti-apoptotic Bcl-2 proteins for insights into its interaction mechanism for anti-cancer activity. Journal of Biomolecular Structure and Dynamics, 37(12), 3109–3121. doi:10.1080/07391102.2018.1508371
  • Ashburn, T. T., & Thor, K. B. (2004). Drug repositioning: Identifying and developing new uses for existing drugs. Nature Reviews Drug Discovery, 3(8), 673–683. doi:10.1038/nrd1468
  • Cheson, B. D., Levine, A. M., Mildvan, D., Kaplan, L. D., Wolfe, P., Rios, A., … Hawkins, M. J. (1987). Suramin therapy in AIDS and related disorders. Report of the US Suramin Working Group. JAMA: The Journal of the American Medical Association, 258(10), 1347–1351. doi:10.1001/jama.1987.03400100081025.
  • Coffin, J. M., & Fan, H. (2016). The discovery of reverse transcriptase. Annual Review of Virology, 3(1), 29–51. doi:10.1146/annurev-virology-110615-035556
  • Cutinho, P. F., Roy, J., Anand, A., Ravishankar, C., Murahari, M., & Venkataramana Chimatapu, H. S. (2019). Design of metronidazole derivatives and flavonoids as potential non-nucleoside reverse transcriptase inhibitors using combined ligand- and structure-based approaches. Journal of Biomolecular Structure and Dynamics, 1–23. doi:10.1080/07391102.2019.1614094
  • De Clercq, E. (1987). Suramin in the treatment of AIDS: Mechanism of action. Antiviral Research, 7(1), 1–10. doi:10.1016/0166-3542(87)90034-9
  • De Clercq, E. (1995). Antiviral therapy for human immunodeficiency virus infections. Clinical Microbiology Reviews, 8(2), 200–239. doi:10.1128/CMR.8.2.200
  • Fatima, S., Sharma, A., Saxena, R., Tripathi, R., Shukla, S. K., Pandey, S. K., … Tripathi, R. P. (2012). One pot efficient diversity oriented synthesis of polyfunctional styryl thiazolopyrimidines and their bio-evaluation as antimalarial and anti-HIV agents. European Journal of Medicinal Chemistry, 55, 195–204. doi:10.1016/j.ejmech.2012.07.018
  • GNS, H. S., GR, S., Murahari, M., & Krishnamurthy, M. (2019). An update on drug repurposing: Re-written saga of the drug’s fate. Biomedicine & Pharmacotherapy, 110, 700–716. doi:10.1016/j.biopha.2018.11.127
  • Hosseinipour, M. C., Gupta, R. K., Van Zyl, G., Eron, J. J., & Nachega, J. B. (2013). Emergence of HIV drug resistance during first- and second-line antiretroviral therapy in resource-limited settings. The Journal of Infectious Diseases, 207(suppl_2), S49–S56. doi:10.1093/infdis/jit107
  • Hu, Y., Zhou, L., Zhu, X., Dai, D., Bao, Y., & Qiu, Y. (2019). Pharmacophore modeling, multiple docking, and molecular dynamics studies on Wee1 kinase inhibitors. Journal of Biomolecular Structure and Dynamics, 37(10), 2703–2715. doi:10.1080/07391102.2018.1495576
  • Ismail, M. A. H., Tratrat, C., & Haroun, M. G. (2013). Molecular modelling design, synthesis and cytotoxic evaluation of certain substituted 2-(3,4,5-triacetoxybenzoylamino)benzo[d]thiazole and 2-(galloylamino)benzo[d]thiazole derivatives having potential topoisomerase-I inhibitory activity. Journal of Enzyme Inhibition and Medicinal Chemistry, 28(6), 1331–1345. doi:10.3109/14756366.2012.716835
  • Keri, R. S., Budagumpi, S., Pai, R. K., & Balakrishna, R. G. (2014). Chromones as a privileged scaffold in drug discovery: A review. European Journal of Medicinal Chemistry, 78, 340–374. doi:10.1016/j.ejmech.2014.03.047
  • Koes, D. R., & Camacho, C. J. (2018). ZINCPharmer: Pharmacophore search of the ZINC database, Nucleic Acids Research, 40(August), 409–414. doi:10.1093/nar/gks378.
  • Koes, D. R., Pabon, N. A., Deng, X., & Phillips, M. A. (2015). A Teach-Discover-Treat application of ZincPharmer: An online interactive pharmacophore modeling and virtual screening tool. PLoS One, 10, e0134697. https://doi.org/doi:10.1371/journal.pone.0134697.
  • Li, T., Cui, Y., & Wu, B. (2019). Molecular dynamics investigations of structural and functional changes in Bcl-2 induced by the novel antagonist BDA-366. Journal of Biomolecular Structure and Dynamics, 37(10), 2527–2537. doi:10.1080/07391102.2018.1491424
  • Murahari, M., Kharkar, P. S., Lonikar, N., & Mayur, Y. C. (2017). Design, synthesis, biological evaluation, molecular docking and QSAR studies of 2,4-dimethylacridones as anticancer agents. European Journal of Medicinal Chemistry, 130, 154. doi:10.1016/j.ejmech.2017.02.022
  • Murahari, M., Mahajan, V., Neeladri, S., Kumar, M. S., & Mayur, Y. C. (2019). Ligand based design and synthesis of pyrazole based derivatives as selective COX-2 inhibitors. Bioorganic Chemistry, 86(January), 583–597. doi:10.1016/j.bioorg.2019.02.031
  • Murahari, M., Prakash, K. V., Peters, G. J., & Mayur, Y. C. (2017). Acridone-pyrimidine hybrids- design, synthesis, cytotoxicity studies in resistant and sensitive cancer cells and molecular docking studies. European Journal of Medicinal Chemistry, 139, 961. doi:10.1016/j.ejmech.2017.08.023
  • Namasivayam, V., Vanangamudi, M., Kramer, V. G., Kurup, S., Zhan, P., Liu, X., … Byrareddy, S. N. (2019). The journey of HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) from lab to clinic. Journal of Medicinal Chemistry, 62(10), 4851–4883. doi:10.1021/acs.jmedchem.8b00843
  • Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. doi:10.1021/acs.jmedchem.5b00104
  • Schrödinger Release 2018-3. (2018a). Desmond Molecular Dynamics System, D. E. Shaw Research, New York, NY.
  • Schrödinger Release 2018-3. (2018b). Glide, Schrödinger, LLC, New York, NY.
  • Schrödinger Release 2018-3. (2018c). LigPrep, Schrödinger, LLC, New York, NY.
  • Schrödinger Release 2018-3. (n.d.). Maestro, Schrödinger, LLC, New York, NY.
  • Schrödinger Release 2018-3. (2018d). Phase, Schrödinger, LLC, New York, NY.
  • Schrödinger Release 2018-3. (2018e). Prime, Schrödinger, LLC, New York, NY.
  • Sharma, H., Patil, S., Sanchez, T. W., Neamati, N., Schinazi, R. F., & Buolamwini, J. K. (2011). Bioorganic & medicinal chemistry synthesis, biological evaluation and 3D-QSAR studies of 3-keto salicylic acid chalcones and related amides as novel HIV-1 integrase inhibitors. Bioorganic & Medicinal Chemistry, 19(6), 2030–2045. doi:10.1016/j.bmc.2011.01.047
  • Ungwitayatorn, J., Wiwat, C., Samee, W., Nunthanavanit, P., & Phosrithong, N. (2011). Synthesis, in vitro evaluation, and docking studies of novel chromone derivatives as HIV-1 protease inhibitor. Journal of Molecular Structure, 1001(1-3), 152–161. doi:10.1016/j.molstruc.2011.06.035
  • Vasavi, C. S., Ramasamy, T., & Munusami, P. (2019). Exploring the drug resistance mechanism of active site, non-active site mutations and their cooperative effects in CRF01_AE HIV-1 protease: Molecular dynamics simulations and free energy calculations. Journal of Biomolecular Structure and Dynamics, 37(10), 2608–2626. doi:10.1080/07391102.2018.1492459
  • Vora, J., Patel, S., Sinha, S., Sharma, S., Srivastava, A., Chhabria, M., & Shrivastava, N. (2019). Structure based virtual screening, 3D-QSAR, molecular dynamics and ADMET studies for selection of natural inhibitors against structural and non-structural targets of Chikungunya. Journal of Biomolecular Structure and Dynamics, 37(12), 3150–3161. doi:10.1080/07391102.2018.1509732
  • Zhou, P., Takaishi, Y., Duan, H., Chen, B., Honda, G., Itoh, M., … Lee, K.-H. (2000). Coumarins and bicoumarin from Ferula sumbul: Anti-HIV activity and inhibition of cytokine release. Phytochemistry, 53(6), 689–697. doi:10.1016/S0031-9422(99)00554-3

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