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Research Articles

Expediting the drug discovery for ideal leads against SARS-CoV-2 via molecular docking of repurposed drugs

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Pages 7949-7965 | Received 19 Aug 2021, Accepted 17 Sep 2022, Published online: 27 Sep 2022

References

  • Ahmad, S., Abbasi, H. W., Shahid, S., Gul, S., & Abbasi, S. W. (2021). Molecular docking, simulation and MM-PBSA studies of nigella sativa compounds: A computational quest to identify potential natural antiviral for COVID-19 treatment. Journal of Biomolecular Structure & Dynamics, 39(12), 4225–4233. https://doi.org/10.1080/07391102.2020.1775129
  • Ahmed, M. Z., Muteeb, G., Khan, S., Alqahtani, A. S., Somvanshi, P., Alqahtani, M. S., Ameta, K. L., & Haque, S. (2021). Identifying novel inhibitor of quorum sensing transcriptional regulator (SdiA) of Klebsiella pneumoniae through modelling, docking and molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics, 39(10), 3594–3604. https://doi.org/10.1080/07391102.2020.1767209
  • Baroody, F. M., & Naclerio, R. M. (2000). Antiallergic effects of H1-receptor antagonists. Allergy, 55, 17–27. https://doi.org/10.1034/j.1398-9995.2000.00803.x
  • Brown, E. S., Park, J., Marx, C. E., Hynan, L. S., Gardner, C., Davila, D., Nakamura, A., Sunderajan, P., Lo, A., & Holmes, T. (2014). A randomized, double-blind, placebo-controlled trial of pregnenolone for bipolar depression. Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology, 39(12), 2867–2873. https://doi.org/10.1038/npp.2014.138
  • Chen, B., Tian, E. K., He, B., Tian, L., Han, R., Wang, S., Xiang, Q., Zhang, S., Arnaout, T. E., & Cheng, W. (2020a). Overview of lethal human coronaviruses. Signal Transduction and Targeted Therapy, 5(1), 89.
  • Chen, C., Zhang, Y., Huang, J., Yin, P., Cheng, Z., Wu, J., Chen, S., Zhang, Y., Chen, B., Lu, M., Luo, Y., Ju, L., Zhang, J., & Wang, X. (2020b). Favipiravir versus arbidol for COVID-19: A randomized clinical trial. medRxiv, 2020.03.17.20037432.
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
  • Ennis, M., & Tiligada, K. (2021). Histamine receptors and COVID-19. Inflammation Research: Official Journal of the European Histamine Research Society. [et al.], 70(1), 67–75. https://doi.org/10.1007/s00011-020-01422-1
  • Gao, X., Zhu, K., Qin, B., Olieric, V., Wang, M., & Cui, S. (2021). Crystal structure of SARS-CoV-2 Orf9b in complex with human TOM70 suggests unusual virus-host interactions. Nature Communications, 12(1), 2843. https://doi.org/10.1038/s41467-021-23118-8
  • Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., … Rao, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science (New York, N.Y.), 368(6492), 779–782. https://doi.org/10.1126/science.abb7498
  • Gaunt, H. J., Vasudev, N. S., & Beech, D. J. (2016). Transient receptor potential canonical 4 and 5 proteins as targets in cancer therapeutics. European Biophysics Journal, 45(7), 611–620. https://doi.org/10.1007/s00249-016-1142-1
  • Glebov, O. O. (2020). Understanding SARS-CoV-2 endocytosis for COVID-19 drug repurposing. The FEBS Journal, 287(17), 3664–3671. https://doi.org/10.1111/febs.15369
  • Jiang, H. W., Zhang, H. N., Meng, Q. F., Xie, J., Li, Y., Chen, H., Zheng, Y. X., Wang, X. N., Qi, H., Zhang, J., Wang, P. H., Han, Z. G., &, Tao, S. C. (2020). SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. Cellular & Molecular Immunology, 17(9), 998–1000. https://doi.org/10.1038/s41423-020-0514-8
  • Haviernik, J., Stefanik, M., Fojtikova, M., Kali, S., Tordo, N., Rudolf, I., Hubalek, Z., Eyer, L., & Ruzek, D. (2018). Arbidol (umifenovir): A broad-spectrum antiviral drug that inhibits medically important arthropod-borne flaviviruses. Viruses, 10(4), 184. https://doi.org/10.3390/v10040184
  • Hoffmann, M., Kleine-Weber, H., Schroeder, S., Kruger, N., Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N. H., Nitsche, A., Muller, M. A., Drosten, C., & Pohlmann, S. (2020). SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell, 181(2), 271–280 e8. https://doi.org/10.1016/j.cell.2020.02.052
  • Hu, X., Zhou, Z., Li, F., Xiao, Y., Wang, Z., Xu, J., Dong, F., Zheng, H., & Yu, R. (2021). The study of antiviral drugs targeting SARS-CoV-2 nucleocapsid and spike proteins through large-scale compound repurposing. Heliyon, 7(3), e06387. https://doi.org/10.1016/j.heliyon.2021.e06387
  • Huang, Y., Yang, C., Xu, X. F., Xu, W., & Liu, S. W. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica, 41(9), 1141–1149. https://doi.org/10.1038/s41401-020-0485-4
  • Kang, S., Yang, M., Hong, Z., Zhang, L., Huang, Z., Chen, X., He, S., Zhou, Z., Zhou, Z., Chen, Q., Yan, Y., Zhang, C., Shan, H., & Chen, S. (2020). Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites. Acta Pharmaceutica Sinica B, 10(7), 1228–1238. https://doi.org/10.1016/j.apsb.2020.04.009
  • Kaur, M., Sharma, A., Kumar, S., Singh, G., & Barnwal, R. P. (2021). SARS-CoV-2: Insights into its structural intricacies and functional aspects for drug and vaccine development. International Journal of Biological Macromolecules, 179, 45–60. https://doi.org/10.1016/j.ijbiomac.2021.02.212
  • Kern, D. M., Sorum, B., Hoel, C. M., Sridharan, S., Remis, J. P., Toso, D. B., & Brohawn, S. G. (2020). Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs, bioRxiv.
  • Kim, Y., Jedrzejczak, R., Maltseva, N. I., Wilamowski, M., Endres, M., Godzik, A., Michalska, K., & Joachimiak, A. (2020). Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2. Protein Science: A Publication of the Protein Society, 29(7), 1596–1605. https://doi.org/10.1002/pro.3873
  • Kingsmore, K. M., Grammer, A. C., & Lipsky, P. E. (2020). Drug repurposing to improve treatment of rheumatic autoimmune inflammatory diseases. Nature Reviews Rheumatology, 16(1), 32–52. https://doi.org/10.1038/s41584-019-0337-0
  • Kushwaha, P. P., Singh, A. K., Bansal, T., Yadav, A., Prajapati, K. S., Shuaib, M., & Kumar, S. (2021). Identification of natural inhibitors against SARS-CoV-2 drugable targets using molecular docking, molecular dynamics simulation, and MM-PBSA approach. Frontiers in Cellular and Infection Microbiology, 11, 730288. https://doi.org/10.3389/fcimb.2021.730288
  • Lu, S., Ye, Q., Singh, D., Cao, Y., Diedrich, J. K., Yates, J. R., III, Villa, E., Cleveland, D. W., & Corbett, K. D. (2021). The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein. Nature Communications, 12(1), 502. https://doi.org/10.1038/s41467-020-20768-y
  • Meltzer-Brody, S., & Kanes, S. J. (2020). Allopregnanolone in postpartum depression: Role in pathophysiology and treatment. Neurobiology of Stress, 12, 100212. https://doi.org/10.1016/j.ynstr.2020.100212
  • Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639–1662. https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
  • Mukherjee, S., Dasgupta, S., Adhikary, T., Adhikari, U., & Panja, S. S. (2021). Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: Inhibitor modelling study through molecular docking and MD-simulation study. Journal of Biomolecular Structure & Dynamics, 39(18), 7322–7334. https://doi.org/10.1080/07391102.2020.1804458
  • Nizamudeen, Z. A., Xu, E. R., Karthik, V., Halawa, M., Arkill, K. P., Jackson, A. M., Bates, D. O., & Emsley, J. (2021). Structural assessment of SARS-CoV2 accessory protein ORF7a predicts LFA-1 and Mac-1 binding potential. Biosci Rep, 41(1), BSR20203837.
  • Panchapakesan, U., & Pollock, C. (2018). Drug repurposing in kidney disease. Kidney International, 94(1), 40–48. https://doi.org/10.1016/j.kint.2017.12.026
  • Paranjpe, M. D., Taubes, A., & Sirota, M. (2019). Insights into computational drug repurposing for neurodegenerative disease. Trends in Pharmacological Sciences, 40(8), 565–576. https://doi.org/10.1016/j.tips.2019.06.003
  • Paraskevis, D., Kostaki, E. G., Magiorkinis, G., Panayiotakopoulos, G., Sourvinos, G., & Tsiodras, S. (2020). Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infection, Genetics and Evolution : journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 79, 104212. https://doi.org/10.1016/j.meegid.2020.104212
  • Paridaens, R. J., Dirix, L. Y., Beex, L. V., Nooij, M., Cameron, D. A., Cufer, T., Piccart, M. J., Bogaerts, J., & Therasse, P. (2008). Phase III study comparing exemestane with tamoxifen as first-line hormonal treatment of metastatic breast cancer in postmenopausal women: The European Organisation for Research and Treatment of Cancer Breast Cancer Cooperative Group. Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology, 26(30), 4883–4890. https://doi.org/10.1200/JCO.2007.14.4659
  • Paul, S. M., Pinna, G., & Guidotti, A. (2020). Allopregnanolone: From molecular pathophysiology to therapeutics. A historical perspective. Neurobiology of Stress, 12, 100215. https://doi.org/10.1016/j.ynstr.2020.100215
  • Periwal, N., Rathod, S. B., Pal, R., Sharma, P., Nebhnani, L., Barnwal, R. P., Arora, P., Srivastava, K. R., & Sood, V. (2021). In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/10.1080/07391102.2021.1908170
  • Pinna, G. (2021). Sex and COVID-19: A protective role for reproductive steroids. Trends in Endocrinology and Metabolism, 32(1), 3–6. https://doi.org/10.1016/j.tem.2020.11.004
  • Pushpakom, S., Iorio, F., Eyers, P. A., Escott, K. J., Hopper, S., Wells, A., Doig, A., Guilliams, T., Latimer, J., McNamee, C., Norris, A., Sanseau, P., Cavalla, D., & Pirmohamed, M. (2019). Drug repurposing: Progress, challenges and recommendations. Nature Reviews Drug Discovery, 18(1), 41–58. https://doi.org/10.1038/nrd.2018.168
  • Ren, Y., Shu, T., Wu, D., Mu, J., Wang, C., Huang, M., Han, Y., Zhang, X. Y., Zhou, W., Qiu, Y., & Zhou, X. (2020). The ORF3a protein of SARS-CoV-2 induces apoptosis in cells. Cellular & Molecular Immunology, 17(8), 881–883. https://doi.org/10.1038/s41423-020-0485-9
  • Rhee, J.-Y. (2021). A review of the possibility of nafamostat mesylate in COVID-19 treatment. Journal of Cellular Immunology, 3(1), 1–7.
  • Rogstam, A., Nyblom, M., Christensen, S., Sele, C., Talibov, V. O., Lindvall, T., Rasmussen, A. A., André, I., Fisher, Z., Knecht, W., & Kozielski, F. (2020). Crystal structure of non-structural protein 10 from severe acute respiratory syndrome Coronavirus-2. International Journal of Molecular Sciences, 21(19), 7375. https://doi.org/10.3390/ijms21197375
  • Rut, W., Lv, Z., Zmudzinski, M., Patchett, S., Nayak, D., Snipas, S. J., Oualid, F. E., Huang, T. T., Bekes, M., Drag, M., & Olsen, S. K. (2020). Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design, bioRxiv.
  • Shah, S. B. (2021). COVID–19 and progesterone: Part 2. Unraveling high severity, immunity patterns, immunity grading, progesterone and its potential clinical use. Endocrine and Metabolic Science, 5, 100110. https://doi.org/10.1016/j.endmts.2021.100110
  • Shivanika, C., Kumar, S. D., Ragunathan, V., Tiwari, P., Sumitha, A., & Devi, P. B. (2022). Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease. Journal of Biomolecular Structure & Dynamics, 40(2), 585–611. https://doi.org/10.1080/07391102.2020.1815584
  • Subissi, L., Imbert, I., Ferron, F., Collet, A., Coutard, B., Decroly, E., & Canard, B. (2014). SARS-CoV ORF1b-encoded nonstructural proteins 12–16: Replicative enzymes as antiviral targets. Antiviral Research, 101, 122–130. https://doi.org/10.1016/j.antiviral.2013.11.006
  • Tatar, G., Ozyurt, E., & Turhan, K. (2021). Computational drug repurposing study of the RNA binding domain of SARS-CoV-2 nucleocapsid protein with antiviral agents. Biotechnology Progress, 37(2), e3110. https://doi.org/10.1002/btpr.3110
  • Theoharides, T. C., Antonopoulou, S., & Demopoulos, C. A. (2020). Coronavirus 2019, microthromboses, and platelet activating factor. Clinical Therapeutics, 42(10), 1850–1852. https://doi.org/10.1016/j.clinthera.2020.08.006
  • Touret, F., Gilles, M., Barral, K., Nougairède, A., van Helden, J., Decroly, E., de Lamballerie, X., & Coutard, B. (2020). In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication. Scientific Reports, 10(1), 1–8. https://doi.org/10.1038/s41598-020-70143-6
  • Villalaín, J. (2010). Membranotropic effects of arbidol, a broad anti-viral molecule, on phospholipid model membranes. The Journal of Physical Chemistry B, 114(25), 8544–8554. https://doi.org/10.1021/jp102619w
  • Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281–292.e6. https://doi.org/10.1016/j.cell.2020.02.058
  • Wong, P., Chang, C. C. R., Marx, C. E., Caron, M. G., Wetsel, W. C., & Zhang, X. (2012). Pregnenolone rescues schizophrenia-like behavior in dopamine transporter knockout mice. Plos One, 7(12), e51455. https://doi.org/10.1371/journal.pone.0051455
  • Yamamoto, M., Kiso, M., Sakai-Tagawa, Y., Iwatsuki-Horimoto, K., Imai, M., Takeda, M., Kinoshita, N., Ohmagari, N., Gohda, J., Semba, K., Matsuda, Z., Kawaguchi, Y., Kawaoka, Y., & Inoue, J-i (2020). The anticoagulant nafamostat potently inhibits SARS-CoV-2 infection in vitro: An existing drug with multiple possible therapeutic effects. bioRxiv, 2020.04.22.054981.
  • Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science (New York, N.Y.), 367(6485), 1444–1448. https://doi.org/10.1126/science.abb2762
  • Yu, R., Chen, L., Lan, R., Shen, R., & Li, P. (2020). Computational screening of antagonists against the SARS-CoV-2 (COVID-19) coronavirus by molecular docking. International Journal of Antimicrobial Agents, 56(2), 106012. https://doi.org/10.1016/j.ijantimicag.2020.106012
  • Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science (New York, N.Y.), 368(6489), 409–412. https://doi.org/10.1126/science.abb3405
  • Zhu, Z., Lu, Z., Xu, T., Chen, C., Yang, G., Zha, T., Lu, J., & Xue, Y. (2020). Arbidol monotherapy is superior to lopinavir/ritonavir in treating COVID-19. Journal of Infection, 81(1), e21–e23. https://doi.org/10.1016/j.jinf.2020.03.060
  • Zucchini, G., Geuna, E., Milani, A., Aversa, C., Martinello, R., & Montemurro, F. (2015). Clinical utility of exemestane in the treatment of breast cancer. International Journal of Women’s Health, 7, 551–563. https://doi.org/10.2147/IJWH.S69475

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