References
- Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020). The proximal origin of SARS-CoV-2. Nature Medicine, 26(4), 450–452. https://doi.org/https://doi.org/10.1038/s41591-020-0820-9
- Beigel, J. H., Tomashek, K. M., Dodd, L. E., Mehta, A. K., Zingman, B. S., Kalil, A. C., Hohmann, E., Chu, H. Y., Luetkemeyer, A., Kline, S., Lopez de Castilla, D., Finberg, R. W., Dierberg, K., Tapson, V., Hsieh, L., Patterson, T. F., Paredes, R., Sweeney, D. A., Short, W. R., … Lane, H. C. (2020). Remdesivir for the treatment of Covid-19 — Preliminary report. New England Journal of Medicine, NEJMoa2007. PMID: 32445440. https://doi.org/https://doi.org/10.1056/nejmoa2007764
- 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. https://doi.org/https://doi.org/10.1080/07391102.2020.1766572
- Bonow, R. O., Fonarow, G. C., O'Gara, P. T., & Yancy, C. W. (2020). Association of coronavirus disease 2019 (COVID-19) with myocardial injury and mortality. JAMA Cardiology, 5(7), 751–753. https://doi.org/https://doi.org/10.1001/jamacardio.2020.1105
- Cai, Z., Zhang, G., Tang, B., Liu, Y., Fu, X., & Zhang, X. (2015). Promising anti-influenza properties of active constituent of Withania somnifera Ayurvedic herb in targeting neuraminidase of H1N1 influenza: Computational study. Cell Biochemistry and Biophysics, 72(3), 727–739. https://doi.org/https://doi.org/10.1007/s12013-015-0524-9
- Case, D. A., Belfon, K., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham, III, T. E., Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Giambasu, G., Gilson, M. K., Gohlke, H., Goetz, A. W., Harris, R., Izadi, S., Izmailov, S. A., Kasavajhala, K., Kovalenko, A., Krasny, R., … Kollman, P. A. (2020). AMBER 2020. University of California.
- Chen, J. L., Blanc, P., Stoddart, C. A., Bogan, M., Rozhon, E. J., Parkinson, N., Ye, Z., Cooper, R., Balick, M., Nanakorn, W., & Kernan, M. R. (1998). New iridoids from the medicinal plant Barleria prionitis with potent activity against respiratory syncytial virus. Journal of Natural Products, 61(10), 1295–1297. https://doi.org/https://doi.org/10.1021/np980086y
- Cornélio Favarin, D., Robison De Oliveira, J., Jose Freire De Oliveira, C., & De Paula Rogerio, A. (2013). Potential effects of medicinal plants and secondary metabolites on acute lung injury. BioMed Research International, 2013, 576479. https://doi.org/https://doi.org/10.1155/2013/576479
- 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, 42717. https://doi.org/https://doi.org/10.1038/srep42717
- Dong, J., Wang, N. N., Yao, Z. J., Zhang, L., Cheng, Y., Ouyang, D., Lu, A. P., & Cao, D. S. (2018). Admetlab: A platform for systematic ADMET evaluation based on a comprehensively collected ADMET database. Journal of Cheminformatics, 10(1), 29. https://doi.org/https://doi.org/10.1186/s13321-018-0283-x
- Drwal, M. N., Banerjee, P., Dunkel, M., Wettig, M. R., & Preissner, R. (2014). ProTox: A web server for the in silico prediction of rodent oral toxicity. Nucleic Acids Research, 42(Web Server issue), W53–W58. https://doi.org/https://doi.org/10.1093/nar/gku401
- Ertl, P., & Schuffenhauer, A. (2009). Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. Journal of Cheminformatics, 1(1), 8. https://doi.org/https://doi.org/10.1186/1758-2946-1-8
- Estari, M., Venkanna, L., Sripriya, D., & Lalitha, R. (2012). Human immunodeficiency virus (HIV-1) reverse transcriptase inhibitory activity of phyllanthus emblica plant extract. Biology and Medicine, 4(4), 178. https://doi.org/https://doi.org/10.4172/0974-8369.1000175
- Filimonov, D. A., Lagunin, A. A., Gloriozova, T. A., Rudik, A. V., Druzhilovskii, D. S., Pogodin, P. V., & Poroikov, V. V. (2014). Prediction of the biological activity spectra of organic compounds using the pass online web resource. Chemistry of Heterocyclic Compounds, 50(3), 444–457. https://doi.org/https://doi.org/10.1007/s10593-014-1496-1
- Fiore, C., Eisenhut, M., Krausse, R., Ragazzi, E., Pellati, D., Armanini, D., & Bielenberg, J. (2008). Antiviral effects of Glycyrrhiza species. Phytotherapy Research, 22(2), 141–148. https://doi.org/https://doi.org/10.1002/ptr.2295
- Ganjhu, R. K., Mudgal, P. P., Maity, H., Dowarha, D., Devadiga, S., Nag, S., & Arunkumar, G. (2015). Herbal plants and plant preparations as remedial approach for viral diseases. Virusdisease, 26(4), 225–236. https://doi.org/https://doi.org/10.1007/s13337-015-0276-6
- Glue, P., & Clement, R. P. (1999). Cytochrome P450 enzymes and drug metabolism - Basic concepts and methods of assessment. Cellular and Molecular Neurobiology, 19(3), 309–323. https://doi.org/https://doi.org/10.1023/a:1006993631057
- Goyal, B., & Goyal, D. (2020). Targeting the dimerization of the main protease of coronaviruses: A potential broad-spectrum therapeutic strategy. ACS Combinatorial Science, 22(6), 297–305. https://doi.org/https://doi.org/10.1021/acscombsci.0c00058
- Hepcy Kalarani, D., Dinakar, A., & Senthilkumar, N. (2012). Antidiabetic, analgesic and anti-inflammatory activity of aqueous extracts of stem and leaves of Alangium salvifolium and Pavonia zeylanica. International Journal of Drug Development and Research, 4, 298–306.
- Hong, J. F., Song, Y. F., Liu, Z., Zheng, Z. C., Chen, H. J., & Wang, S. S. (2016). Anticancer activity of taraxerol acetate in human glioblastoma cells and a mouse xenograft model via induction of autophagy and apoptotic cell death, cell cycle arrest and inhibition of cell migration. Molecular Medicine Reports, 13(6), 4541–4548. https://doi.org/https://doi.org/10.3892/mmr.2016.5105
- Huo, J., Zhao, Y., Ren, J., Zhou, D., Duyvesteyn, H. M. E., Ginn, H. M., Carrique, L., Malinauskas, T., Ruza, R. R., Shah, P. N. M., Tan, T. K., Rijal, P., Coombes, N., Bewley, K. R., Tree, J. A., Radecke, J., Paterson, N. G., Supasa, P., Mongkolsapaya, J., … Stuart, D. I. (2020). Neutralization of SARS-CoV-2 by destruction of the prefusion spike. Cell Host & Microbe, 28(3), 445–454.e6. https://doi.org/https://doi.org/10.1016/j.chom.2020.06.010
- Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293. https://doi.org/https://doi.org/10.1038/s41586-020-2223-y
- Kamath, P. R., Sunil, D., & Ajees, A. A. (2016). Synthesis of indole–quinoline–oxadiazoles: Their anticancer potential and computational tubulin binding studies. Research on Chemical Intermediates, 42(6), 5899–5914. https://doi.org/https://doi.org/10.1007/s11164-015-2412-8
- Kamath, P. R., Sunil, D., Ajees, A. A., Pai, K. S. R., & Das, S. (2015). Some new indole-coumarin hybrids; Synthesis, anticancer and Bcl-2 docking studies. Bioorganic Chemistry, 63, 101–109. https://doi.org/https://doi.org/10.1016/j.bioorg.2015.10.001
- Kesharwani, A., Polachira, S. K., Nair, R., Agarwal, A., Mishra, N. N., & Gupta, S. K. (2017). Anti-HSV-2 activity of Terminalia chebula Retz extract and its constituents, chebulagic and chebulinic acids. BMC Complementary and Alternative Medicine, 17(1), 110. https://doi.org/https://doi.org/10.1186/s12906-017-1620-8
- Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2019). PubChem 2019 update: Improved access to chemical data. Nucleic Acids Research, 47(D1), D1102–D1109. https://doi.org/https://doi.org/10.1093/nar/gky1033
- Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., & Wang, X. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581(7807), 215–220. https://doi.org/https://doi.org/10.1038/s41586-020-2180-5
- 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/https://doi.org/10.1021/ci200227u
- Limban, C., Nuţă, D. C., Chiriţă, C., Negreș, S., Arsene, A. L., Goumenou, M., Karakitsios, S. P., Tsatsakis, A. M., & Sarigiannis, D. A. (2018). The use of structural alerts to avoid the toxicity of pharmaceuticals. Toxicology Reports, 5, 943–953. https://doi.org/https://doi.org/10.1016/j.toxrep.2018.08.017
- Liperoti, R., Vetrano, D. L., Bernabei, R., & Onder, G. (2017). Herbal medications in cardiovascular medicine. Journal of the American College of Cardiology, 69(9), 1188–1199. https://doi.org/https://doi.org/10.1016/j.jacc.2016.11.078
- Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today: Technologies, 1(4), 337–341. https://doi.org/https://doi.org/10.1016/j.ddtec.2004.11.007
- MarvinSketch. (n.d.). MarvinSketch was used to convert chemical structures from 2D to 3D. ChemAxon. https://www.chemaxon.com.
- Merad, M., & Martin, J. C. (2020). Pathological inflammation in patients with COVID-19: A key role for monocytes and macrophages. Nature Reviews: Immunology, 20(6), 355–362. https://doi.org/https://doi.org/10.1038/s41577-020-0331-4
- Mishra, A., Dixit, S., Ratan, V., Srivastava, M., Trivedi, S., & Srivastava, Y. K. (2018). Identification and in silico screening of biologically active secondary metabolites isolated from Trichoderma harzianum. Annals of Phytomedicine: An International Journal, 7(1), 78–86. https://doi.org/https://doi.org/10.21276/ap.2018.7.1.9
- Morris, G. M., Huey, R., Lindstrom, W., Scanner, M. F., Belew, R. S., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/https://doi.org/10.1002/jcc.21256
- Mukhtar, M., Arshad, M., Ahmad, M., Pomerantz, R. J., Wigdahl, B., & Parveen, Z. (2008). Antiviral potentials of medicinal plants. Virus Research, 131(2), 111–120. https://doi.org/https://doi.org/10.1016/j.virusres.2007.09.008
- Nagarkar, B., Nirmal, P., Narkhede, A., Kuvalekar, A., Kulkarni, O., Harsulkar, A., & Jagtap, S. (2013). Comparative evaluation of anti-inflammatory potential of medicinally important plants. International Journal of Pharmacy and Pharmaceutical Sciences, 5, 239–243.
- Naidoo, D., Roy, A., Kar, P., Mutanda, T., & Anandraj, A. (2020). Cyanobacterial metabolites as promising drug leads against the Mpro and PLpro of SARS-CoV-2: An in silico analysis. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/https://doi.org/10.1080/07391102.2020.1794972
- O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/https://doi.org/10.1186/1758-2946-3-33
- Onawole, A. T., Kolapo, T. U., Sulaiman, K. O., & Adegoke, R. O. (2018). Structure based virtual screening of the Ebola virus trimeric glycoprotein using consensus scoring. Computational Biology and Chemistry, 72, 170–180. https://doi.org/https://doi.org/10.1016/j.compbiolchem.2017.11.006
- Pruthvish, R., & Gopinatha, R. P. (2018). Antiviral prospective of Tinospora cordifolia on HSV-1. International Journal of Current Microbiology and Applied Sciences, 7(1), 3617–3624. https://doi.org/https://doi.org/10.20546/ijcmas.2018.701.425
- Radchenko, E. V., Dyabina, A. S., Palyulin, V. A., & Zefirov, N. S. (2016). Prediction of human intestinal absorption of drug compounds. Russian Chemical Bulletin, 65(2), 576–580. https://doi.org/https://doi.org/10.1007/s11172-016-1340-0
- Rodríguez-Morales, A. J., MacGregor, K., Kanagarajah, S., Patel, D., & Schlagenhauf, P. (2020). Going global - Travel and the 2019 novel coronavirus. Travel Medicine and Infectious Disease, 33, 101578. https://doi.org/https://doi.org/10.1016/j.tmaid.2020.101578
- Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/https://doi.org/10.1021/ct400341p
- Roy, S., Mukherjee, S., Pawar, S., & Chowdhary, A. (2016). Evaluation of in vitro antiviral activity of Datura metel Linn. against rabies virus. Pharmacognosy Research, 8(4), 265–269. https://doi.org/https://doi.org/10.4103/0974-8490.188874
- Salam, A. A. A., Nayek, U., & Sunil, D. (2018). Homology modeling and docking studies of Bcl-2 and Bcl-xL with small molecule inhibitors: Identification and functional studies. Current Topics in Medicinal Chemistry, 18(31), 2633–2663. https://doi.org/https://doi.org/10.2174/1568026619666190119144819
- Sève, P., & Dumontet, C. (2005). Chemoresistance in non-small cell lung cancer. Current Medicinal Chemistry. Anti-Cancer Agents, 5(1), 73–88. https://doi.org/https://doi.org/10.2174/1568011053352604
- Shahidul Alam, M., Quader, M. A., & Rashid, M. A. (2000). HIV-inhibitory diterpenoid from Anisomeles indica. Fitoterapia, 71(5), 574–576. https://doi.org/https://doi.org/10.1016/S0367-326X(00)00197-0
- 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/https://doi.org/10.1038/s41586-020-2179-y
- Sharma, K., & Zafar, R. (2015). Occurrence of taraxerol and taraxasterol in medicinal plants. Pharmacognosy Reviews, 9(17), 19. https://doi.org/https://doi.org/10.4103/0973-7847.156317
- Towler, P., Staker, B., Prasad, S. G., Menon, S., Tang, J., Parsons, T., Ryan, D., Fisher, M., Williams, D., Dales, N. A., Patane, M. A., & Pantoliano, M. W. (2004). ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis. The Journal of Biological Chemistry, 279(17), 17996–18007. https://doi.org/https://doi.org/10.1074/jbc.M311191200
- 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/https://doi.org/10.1002/jcc.21334
- Veeramachaneni, G. K., Thunuguntla, V. B. S. C., Bobbillapati, J., & Bondili, J. S. (2020). Structural and simulation analysis of hotspot residues interactions of SARS-CoV 2 with human ACE2 receptor. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/https://doi.org/10.1080/07391102.2020.1773318
- Vellingiri, B., Jayaramayya, K., Iyer, M., Narayanasamy, A., Govindasamy, V., Giridharan, B., Ganesan, S., Venugopal, A., Venkatesan, D., Ganesan, H., Rajagopalan, K., Rahman, P. K. S. M., Cho, S. G., Kumar, N. S., & Subramaniam, M. D. (2020). COVID-19: A promising cure for the global panic. The Science of the Total Environment, 725, 138277. https://doi.org/https://doi.org/10.1016/j.scitotenv.2020.138277
- Verma, H. N., & Baranwal, V. K. (1983). Antiviral activity and the physical properties of the leaf extract of Chenopodium ambrosoides L. Proceedings: Plant Sciences, 92(6), 461–465. https://doi.org/https://doi.org/10.1007/BF03053019
- Verma, H. N., Chowdhury, B., & Rastogi, P. (1984). Antiviral activity in leaf extracts of different Clerodendrum species. Journal of Plant Diseases and Protection, 91 (1), 34–41. https://doi.org/https://doi.org/10.2307/43382724
- 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/https://doi.org/10.1126/science.abb2762
- Yao, X., Li, G., Bai, Q., Xu, H., & Lü, C. (2013). Taraxerol inhibits LPS-induced inflammatory responses through suppression of TAK1 and Akt activation. International Immunopharmacology, 15(2), 316–324. https://doi.org/https://doi.org/10.1016/j.intimp.2012.12.032
- Yi, C., Sun, X., Ye, J., Ding, L., Liu, M., Yang, Z., Lu, X., Zhang, Y., Ma, L., Gu, W., Qu, A., Xu, J., Shi, Z., Ling, Z., & Sun, B. (2020). Key residues of the receptor binding motif in the spike protein of SARS-CoV-2 that interact with ACE2 and neutralizing antibodies. Cellular and Molecular Immunology, 17(6), 621–630. https://doi.org/https://doi.org/10.1038/s41423-020-0458-z
- Yuan, M., Wu, N. C., Zhu, X., Lee, C. C. D., So, R. T. Y., Lv, H., Mok, C. K. P., & Wilson, I. A. (2020). A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Science (New York, N.Y.), 368(6491), 630–633. https://doi.org/https://doi.org/10.1126/science.abb7269