Repurposing of anticancer phytochemicals for identifying potential fusion inhibitor for SARS-CoV-2 using molecular docking and molecular dynamics (MD) simulations

References

• Adnan, M., Rasul, A., Hussain, G., Shah, M. A., Zahoor, M. K., Anwar, H., Sarfraz, I., Riaz, A., Manzoor, M., Adem, Ş., & Selamoglu, Z. (2020). Ginkgetin: A natural biflavone with versatile pharmacological activities. Food and Chemical Toxicology : An International Journal Published for the British Industrial Biological Research Association, 145, 111642. https://doi.org/10.1016/j.fct.2020.111642
   PubMed Web of Science ®Google Scholar
• Arya, R., Das, A., Prashar, V., & Kumar, M. (2020). Potential inhibitors against papain-like protease of novel coronavirus (SARS-CoV-2) from FDA approved drugs.
   Google Scholar
• Bhardwaj, V. K., & Purohit, R. (2020). Targeting the protein-protein interface pocket of Aurora-A-TPX2 complex: Rational drug design and validation. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1772109
   Google Scholar
• Bhardwaj, V. K., Singh, R., Sharma, J., Rajendran, V., Purohit, R., & Kumar, S. (2020). Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1766572
   Google Scholar
• Chen, Y., Guo, Y., Pan, Y., & Zhao, Z. J. (2020). Structure analysis of the receptor binding of 2019-nCoV. Biochemical and Biophysical Research Communications, 525(1), 135–140. https://doi.org/10.1016/j.bbrc.2020.02.071
   Google Scholar
• Chen, X., Li, R., Pan, Z., Qian, C., Yang, Y., You, R., Zhao, J., Liu, P., Gao, L., Li, Z., Huang, Q., Xu, L., Tang, J., Tian, Q., Yao, W., Hu, L., Yan, X., Zhou, X., Wu, Y., … Ye, L. (2020). Human monoclonal antibodies block the binding of SARS-CoV-2 spike protein to angiotensin converting enzyme 2 receptor. Cell Mol Immunol, 17 (6), 647–649. https://doi.org/10.1038/s41423-020-0426-7
   PubMed Web of Science ®Google Scholar
• Chiang, C. T., Way, T. D., Tsai, S. J., & Lin, J. K. (2007). Diosgenin, a naturally occurring steroid, suppresses fatty acid synthase expression in HER2-overexpressing breast cancer cells through modulating Akt, mTOR and JNK phosphorylation. FEBS Letters, 581(30), 5735–5742. https://doi.org/10.1016/j.febslet.2007.11.021
   PubMed Web of Science ®Google Scholar
• de Oliveira, O. V., Rocha, G. B., Paluch, A. S., & Costa, L. T. (2020). Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1772885
   Google Scholar
• Fenclova, M., Novakova, A., Viktorova, J., Jonatova, P., Dzuman, Z., Ruml, T., Kren, V., Hajslova, J., Vitek, L., & Stranska-Zachariasova, M. (2019). Poor chemical and microbiological quality of the commercial milk thistle-based dietary supplements may account for their reported unsatisfactory and non-reproducible clinical outcomes. Scientific Reports, 9(1), 11118. https://doi.org/10.1038/s41598-019-47250-0
   PubMedGoogle Scholar
• Ganguly, B., Chaudhary, A., Dakhar, H., Singh, I. P., & Chatterjee, A. (2019). Methanolic extract of Potentilla fulgens root and its ethyl-acetate fraction delays the process of carcinogenesis in mice. Scientific Reports, 9(1), 1–11. https://doi.org/10.1038/s41598-019-53747-5
   PubMedGoogle Scholar
• Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., Zhang, L., Fan, G., Xu, J., Gu, X., Cheng, Z., Yu, T., Xia, J., Wei, Y., Wu, W., Xie, X., Yin, W., Li, H., Liu, M., … Cao, B. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet, 395(10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
   PubMed Web of Science ®Google Scholar
• 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. (Springer Nature. https://doi.org/10.1038/s41401-020-0485-4
   PubMed Web of Science ®Google Scholar
• Hui, X., Yue, Q., Zhang, D. D., Li, H., Yang, S. Q., & Gao, W. Y. (2016). Antimicrobial mechanism of theaflavins: They target 1-deoxy-D-xylulose 5-phosphate reductoisomerase, the key enzyme of the MEP terpenoid biosynthetic pathway. Scientific Reports, 6(1), 38945–38948. https://doi.org/10.1038/srep38945
   PubMedGoogle Scholar
• Imran, A., Butt, M. S., Xiao, H., Imran, M., Rauf, A., Mubarak, M. S., & Ramadan, M. F. (2019). Inhibitory effect of black tea (Camellia sinensis) theaflavins and thearubigins against HCT 116 colon cancer cells and HT 460 lung cancer cells. Journal of Food Biochemistry, 43(5), e12822. https://doi.org/10.1111/jfbc.12822
   PubMed Web of Science ®Google Scholar
• Joshi, R. S., Jagdale, S. S., Bansode, S. B., Shiva Shankar, S., Tellis, M. B., Pandya, K., Chugh, A., Giri, A. P., Kulkarni, M. J., & Joshi, S. (2020). Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/10.1080/07391102.2020.1760137
   Google Scholar
• Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., & Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. https://doi.org/10.1021/ar000033j
   PubMed Web of Science ®Google Scholar
• Kong, R., Yang, G., Xue, R., Liu, M., Wang, F., Hu, J., Guo, X., Chang, S. (2020). COVID-19 Docking Server: An interactive server for docking small molecules, peptides and antibodies against potential targets of COVID-19. J ArXiv Preprint. https://arxiv.org/abs/2003.00163
   Google Scholar
• Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A., & Vriend, G. (2004). Making optimal use of empirical energy functions: Force-field parameterization in crystal space. Proteins, 57(4), 678–683. https://doi.org/10.1002/prot.20251
   PubMed Web of Science ®Google Scholar
• Krieger, E., & Vriend, G. (2015). New ways to boost molecular dynamics simulations. Journal of Computational Chemistry, 36(13), 996–1007. https://doi.org/10.1002/jcc.23899
   PubMed Web of Science ®Google Scholar
• Kumar, A., Mehta, V., Raj, U., Varadwaj, P. K., Udayabanu, M., Yennamalli, R. M., & Singh, T. R. (2019). Computational and In-Vitro Validation of Natural Molecules as Potential Acetylcholinesterase Inhibitors and Neuroprotective Agents. Current Alzheimer Research, 16(2), 116–127. https://doi.org/10.2174/1567205016666181212155147
   PubMed Web of Science ®Google Scholar
• Kumar, S. P., Patel, C. N., Jha, P. C., & Pandya, H. A. (2017). Molecular dynamics-assisted pharmacophore modeling of caspase-3-isatin sulfonamide complex: Recognizing essential intermolecular contacts and features of sulfonamide inhibitor class for caspase-3 binding. Computational Biology and Chemistry, 71, 117–128. https://doi.org/10.1016/j.compbiolchem.2017.08.006
   PubMed Web of Science ®Google Scholar
• Kumar, S. P., Patel, C. N., Rawal, R. M., & Pandya, H. A. (2020). Energetic contributions of amino acid residues and its cross-talk to delineate ligand-binding mechanism . Proteins: Structure, Function, and Bioinformatics, 88(9), 1207–1225. https://doi.org/10.1002/prot.25894
   PubMed Web of Science ®Google Scholar
• Lani, R., Hassandarvish, P., Chiam, C. W., Moghaddam, E., Chu, J. J. H., Rausalu, K., Merits, A., Higgs, S., Vanlandingham, D., Abu Bakar, S., & Zandi, K. (2015). Antiviral activity of silymarin against chikungunya virus. Scientific Reports, 5(1), 11421–11410. https://doi.org/10.1038/srep11421
   PubMedGoogle Scholar
• Li, D., Hu, J., Wang, T., Zhang, X., Liu, L., Wang, H., Wu, Y., Xu, D., & Wen, F. (2016). Silymarin attenuates cigarette smoke extract-induced inflammation via simultaneous inhibition of autophagy and ERK/p38 MAPK pathway in human bronchial epithelial cells. Scientific Reports, 6(1), 37751–37710. https://doi.org/10.1038/srep37751
   PubMedGoogle Scholar
• Mangal, M., Sagar, P., Singh, H., Raghava, G. P. S., & Agarwal, S. M. (2013). NPACT: Naturally occurring plant-based anti-cancer compound-activity-target database. Nucleic Acids Research, 41(Database issue), D1124–D1129. https://academic.oup.com/nar/article-abstract/41/D1/D1124/1052661 https://doi.org/10.1093/nar/gks1047
   PubMedGoogle Scholar
• Massova, I., & Kollman, P. A. (2000). Combined molecular mechanical and continuum solvent approach (MM- PBSA/GBSA) to predict ligand binding. Perspectives in Drug Discovery and Design, 18(1), 113–135. In https://doi.org/10.1023/A:1008763014207
   Google Scholar
• Mukherjee, S., Dasgupta, S., Adhikary, T., Adhikari, U., & Panja, S. S. (2020). 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 and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1804458
   Google Scholar
• Ou, X., Liu, Y., Lei, X., Li, P., Mi, D., Ren, L., Guo, L., Guo, R., Chen, T., Hu, J., Xiang, Z., Mu, Z., Chen, X., Chen, J., Hu, K., Jin, Q., Wang, J., & Qian, Z. (2020). Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nature Communications, 11(1), 1–13. https://doi.org/10.1038/s41467-020-15562-9
   Google Scholar
• Pandey, P., Rane, J. S., Chatterjee, A., Kumar, A., Khan, R., Prakash, A., & Ray, S. (2020). Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: An in silico study for drug development. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/10.1080/07391102.2020.1796811
   Google Scholar
• Parmar, P., Shukla, A., Rao, P., Saraf, M., Patel, B., & Goswami, D. (2020). The Rise of Gingerol as Anti-QS Molecule: Darkest Episode in the LuxR-Mediated Bioluminescence Saga. Bioorganic Chemistry, 99, 103823. https://doi.org/10.1016/j.bioorg.2020.103823
   PubMed Web of Science ®Google Scholar
• Patel, C. N., Georrge, J. J., Modi, K. M., Narechania, M. B., Patel, D. P., Gonzalez, F. J., & Pandya, H. A. (2018). Pharmacophore-based virtual screening of catechol-o-methyltransferase (COMT) inhibitors to combat Alzheimer's disease. Journal of Biomolecular Structure & Dynamics, 36(15), 3938–3957. https://doi.org/10.1080/07391102.2017.1404931
   PubMed Web of Science ®Google Scholar
• Patel, C. N., Kumar, S. P., Modi, K. M., Soni, M. N., Modi, N. R., & Pandya, H. A. (2019). Cardiotonic steroids as potential Na+/K+-ATPase inhibitors - a computational study. Journal of Receptor and Signal Transduction Research, 39(3), 226–234. https://doi.org/10.1080/10799893.2019.1660893
   PubMed Web of Science ®Google Scholar
• Patel, C. N., & Narechania, M. B. (2018). Targeting epidermal growth factor receptors inhibition in non-small-cell lung cancer: A computational approach. Molecular Simulation, 44(17), 1478–1488. https://doi.org/10.1080/08927022.2018.1515484
   Web of Science ®Google Scholar
• 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. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Rao, P., Shukla, A., Parmar, P., Rawal, R. M., Patel, B., Saraf, M., & Goswami, D. (2020a). Reckoning a fungal metabolite, Pyranonigrin A as a potential Main protease (Mpro) inhibitor of novel SARS-CoV-2 virus identified using docking and molecular dynamics simulation. Biophysical Chemistry, 264, 106425. https://doi.org/10.1016/j.bpc.2020.106425
   PubMed Web of Science ®Google Scholar
• Rao, P., Shukla, A., Parmar, P., Rawal, R., Patel, B., Saraf, M., & Goswami, D. (2020b). Proposing a fungal metabolite-Flaviolin as a potential inhibitor of 3CLpro of novel coronavirus SARS-CoV-2 identified using Docking and Molecular Dynamics. Journal of Biomolecular Structure and Dynamics, https://doi.org/10.1080/07391102.2020.1813202
   Google Scholar
• Ren, Z., Yan, L., Zhang, N., Guo, Y., Yang, C., Lou, Z., & Rao, Z. (2013). The newly emerged SARS-Like coronavirus HCoV-EMC also has an “ "Achilles' heel": current effective inhibitor targeting a 3C-like protease. Protein & Cell, 4(4), 248–250. https://doi.org/10.1007/s13238-013-2841-3
   PubMed Web of Science ®Google Scholar
• Schwartz, D. A., & Graham, A. L. (2020). Potential maternal and infant outcomes from coronavirus 2019-NCOV (SARS-CoV-2) infecting pregnant women: Lessons from SARS, MERS, and other human coronavirus infections. Viruses, 12(2), 194. https://doi.org/10.3390/v12020194
   PubMed Web of Science ®Google Scholar
• Shang, J., Wan, Y., Luo, C., Ye, G., Geng, Q., Auerbach, A., & Li, F. (2020). Cell entry mechanisms of SARS-CoV-2. Proceedings of the National Academy of Sciences, 117(21), 11727–11734. https://doi.org/10.1073/pnas.2003138117
   PubMed Web of Science ®Google Scholar
• Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 581(7807), 221–224. https://doi.org/10.1038/s41586-020-2179-y
   PubMed Web of Science ®Google Scholar
• Shukla, A., Parmar, P., Rao, P., Goswami, D., & Saraf, M. (2020). Twin Peaks: Presenting the Antagonistic Molecular Interplay of Curcumin with LasR and LuxR Quorum Sensing Pathways. Current Microbiology, 77(8), 1800–1810. https://doi.org/10.1007/s00284-020-01997-2
   PubMed Web of Science ®Google Scholar
• Sinha, S. K., Prasad, S. K., Islam, M. A., Gurav, S. S., Patil, R. B., AlFaris, N. A., Aldayel, T. S., AlKehayez, N. M., Wabaidur, S. M., & Shakya, A. (2020). Identification of bioactive compounds from Glycyrrhiza glabra as possible inhibitor of SARS-CoV-2 spike glycoprotein and non-structural protein-15: A pharmacoinformatics study. Journal of Biomolecular Structure and Dynamics, 1–15. https://doi.org/10.1080/07391102.2020.1779132
   Google Scholar
• Song, Z., Xu, Y., Bao, L., Zhang, L., Yu, P., Qu, Y., Zhu, H., Zhao, W., Han, Y., & Qin, C. (2019). From SARS to MERS, thrusting coronaviruses into the spotlight. Viruses, 11(1), 59. https://doi.org/10.3390/v11010059
   PubMed Web of Science ®Google Scholar
• Trezza, A., Iovinelli, D., Santucci, A., Prischi, F., & Spiga, O. (2020). An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors. Scientific Reports, 10(1), 1–8. https://doi.org/10.1038/s41598-020-70863-9
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Wang, W., Donini, O., Reyes, C. M., & Kollman, P. A. (2001). Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. In Annual Review of Biophysics and Biomolecular Structure, ( 30, 211–243. https://doi.org/10.1146/annurev.biophys.30.1.211
   PubMedGoogle Scholar
• Wang, J., Hou, T., & Xu, X. (2006). Recent Advances in Free Energy Calculations with a Combination of Molecular Mechanics and Continuum Models. Current Computer Aided-Drug Design, 2(3), 287–306. https://doi.org/10.2174/157340906778226454
   Web of Science ®Google Scholar
• Wu, F., Zhao, S., Yu, B., Chen, Y. M., Wang, W., Song, Z. G., Hu, Y., Tao, Z. W., Tian, J. H., Pei, Y. Y., Yuan, M. L., Zhang, Y. Z. Y. Z. L., Dai, F. H., Liu, Y., Wang, Q. M., Zheng, J. J., Xu, L., Holmes, E. C., & Zhang, Y. Z. Y. Z. L. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265–269. https://doi.org/10.1038/s41586-020-2008-3
   PubMed Web of Science ®Google Scholar
• Xia, S., Liu, M., Wang, C., Xu, W., Lan, Q., Feng, S., Qi, F., Bao, L., Du, L., Liu, S., Qin, C., Sun, F., Shi, Z., Zhu, Y., Jiang, S., & Lu, L. (2020). Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion . Cell Research, 30(4), 343–355. https://doi.org/10.1038/s41422-020-0305-x
   PubMed Web of Science ®Google Scholar
• Xia, S., Yan, L., Xu, W., Agrawal, A. S., Algaissi, A., Tseng, C. T. K., Wang, Q., Du, L., Tan, W., Wilson, I. A., Jiang, S., Yang, B., & Lu, L. (2019). A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike. Science Advances, 5(4), eaav4580. https://doi.org/10.1126/sciadv.aav4580
   PubMed Web of Science ®Google Scholar
• Xia, S., Zhu, Y., Liu, M., Lan, Q., Xu, W., Wu, Y., Ying, T., Liu, S., Shi, Z., Jiang, S., & Lu, L. (2020). Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein. Cellular & Molecular Immunology, 17(7), 765–767. https://doi.org/10.1038/s41423-020-0374-2
   PubMed Web of Science ®Google Scholar
• Yang, H., Bartlam, M., & Rao, Z. (2006). Drug Design Targeting the Main Protease, the Achilles' heel of coronaviruses. Current Pharmaceutical Design, 12(35), 4573–4590. https://doi.org/10.2174/138161206779010369
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., Chen, H.-D., Chen, J., Luo, Y., Guo, H., Jiang, R.-D., Liu, M.-Q., Chen, Y., Shen, X.-R., Wang, X., … Shi, Z.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/10.1038/s41586-020-2012-7
   PubMed Web of Science ®Google Scholar