References
- 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. Chemrxiv, 1–8. https://doi.org/https://doi.org/10.26434/chemrxiv.11860011.v2
- Bekker, H., Berendsen, H. J. C., & Dijkstra, E. W. (1993).Gromacs: A parallel computer for molecular dynamics simulations(Vol. 92, pp.252-256).
- Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. In Pullman B. (Eds.), Intermolecular forces. The Jerusalem Symposia on Quantum Chemistry and Biochemistry, vol 14. Springer, Dordrecht. https://doi.org/https://doi.org/10.1007/978-94-015-7658-1_21
- 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. https://doi.org/https://doi.org/10.1080/07391102.2020.1772109
- Bhardwaj, V. K., Singh, R., & Sharma, J. (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/https://doi.org/10.1080/07391102.2020.1766572
- Borkotoky, S., & Banerjee, M. (2020). A computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem). Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/https://doi.org/10.1080/07391102.2020.1774419
- Cui, W., Cui, S., Chen, C., Chen, X., Wang, Z., Yang, H., & Zhang, L. (2019). The crystal structure of main protease from mouse hepatitis virus A59 in complex with an inhibitor. J Biochemical Research Communications, 511(4), 794–799.
- Dai, W., Zhang, B., Jiang, X.-M., Su, H., Li, J., Zhao, Y., Xie, X., Jin, Z., Peng, J., Liu, F., Li, C., Li, Y., Bai, F., Wang, H., Cheng, X., Cen, X., Hu, S., Yang, X., Wang, J., … Liu, H. (2020). Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science (New York, N.Y.).), 368(6497), 1331–1335. https://doi.org/https://doi.org/10.1126/science.abb4489
- Das, S., Sarmah, S., Lyndem, S., & Singha, R. A. (2020). An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/https://doi.org/10.1080/07391102.2020.1763201
- Gasteiger, J., & Jochum, C. (1979). An algorithm for the perception of synthetically important rings. Journal of Chemical Information and Modeling, 19(1), 43–48. https://doi.org/https://doi.org/10.1021/ci60017a011
- Ghosh, R., Chakraborty, A., Biswas, A., & Chowdhuri, S. (2020). Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors–an in silico docking and molecular dynamics simulation study. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/https://doi.org/10.1080/07391102.2020.1779818
- Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
- 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. Lancet (London, England), 395(10223), 497–506. https://doi.org/https://doi.org/10.1016/S0140-6736(20)30183-5
- Huynh, T., Wang, H., & Luan, B. (2020). In silico exploration of the molecular mechanism of clinically oriented drugs for possibly inhibiting SARS-CoV-2’s main protease. Journal of Physical Chemistry Letters, 11(11), 4413–4420. https://doi.org/https://doi.org/10.1021/acs.jpclett.0c00994
- 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
- Joshi, R. S., Jagdale, S. S., & Bansode, S. B. (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/https://doi.org/10.1080/07391102.2020.1760137
- Kong, R., Yang, G., Xue, R., Liu, M., Wang, F., Hu, J., Guo, X., & Chang, S. (2020). COVID-19 Docking Server: A meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19, Bioinformatics. https://doi.org/https://doi.org/10.1093/bioinformatics/btaa645
- Krivov, G. G., Shapovalov, M. V., & Dunbrack, R. L. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 77(4), 778–795. https://doi.org/https://doi.org/10.1002/prot.22488 19603484
- 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/https://doi.org/10.2174/1567205016666181212155147
- Linnakoski, R., Reshamwala, D., Veteli, P., Cortina-Escribano, M., Vanhanen, H., & Marjomäki, V. (2018). Antiviral agents from fungi: Diversity, mechanisms and potential applications. Frontiers in Microbiology, 9, 2325. https://doi.org/https://doi.org/10.3389/fmicb.2018.02325
- Macchiagodena, M., & Pagliai, M. (2020). Inhibition of the main protease 3CL-pro of the coronavirus disease 19 via structure-based ligand design and molecular modeling. arXiv Prepr arXiv:.09937.
- 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/https://doi.org/10.1016/j.bioorg.2020.103823
- Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/https://doi.org/10.1002/jcc.20084
- 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/https://doi.org/10.1021/acs.jmedchem.5b00104
- Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B., & Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England)), 29(7), 845–854. https://doi.org/https://doi.org/10.1093/bioinformatics/btt055
- Rao, P., Shukla, A., Parmar, P., Rawal, R. M., Patel, B., Saraf, M., & Goswami, D. (2020). 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/https://doi.org/10.1016/j.bpc.2020.106425
- 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/https://doi.org/10.1007/s13238-013-2841-3
- 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/https://doi.org/10.1007/s00284-020-01997-2
- St. John, S. E., Tomar, S., Stauffer, S. R., & Mesecar, A. D. (2015). Targeting zoonotic viruses: Structure-based inhibition of the 3C-like protease from bat coronavirus HKU4 - The likely reservoir host to the human coronavirus that causes Middle East Respiratory Syndrome (MERS). Bioorganic and Medicinal Chemistry, 23(17), 6036–6048. https://doi.org/https://doi.org/10.1016/j.bmc.2015.06.039
- 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
- Turner, P. J. (2005). XMGRACE, version 5.1. 19. Center for Coastal and Land-Margin Research, Oregon Graduate Institute of Science and Technology.
- Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/https://doi.org/10.1002/jcc.20291
- Wang, F., Chen, C., Tan, W., Yang, K., & Yang, H. (2016). Structure of Main Protease from Human Coronavirus NL63: Insights for Wide Spectrum Anti-Coronavirus Drug Design. Scientific Reports, 6, 22677. https://doi.org/https://doi.org/10.1038/srep22677
- Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2001). Antechamber: An accessory software package for molecular mechanical calculations. Journal of the American Chemical Society, 222, U403.
- 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.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E. C., & Zhang, Y.-Z. (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579(7798), 265–269. https://doi.org/https://doi.org/10.1038/s41586-020-2008-3
- Xue, X., Yang, H., Shen, W., Zhao, Q., Li, J., Yang, K., Chen, C., Jin, Y., Bartlam, M., & Rao, Z. (2007). Production of Authentic SARS-CoV M(pro) with enhanced activity: Application as a novel tag-cleavage endopeptidase for protein overproduction . Journal of Molecular Biology, 366(3), 965–975. https://doi.org/https://doi.org/10.1016/j.jmb.2006.11.073
- Yang, H., Yang, M., Ding, Y., Liu, Y., Lou, Z., Zhou, Z., Sun, L., Mo, L., Ye, S., Pang, H., Gao, G. F., Anand, K., Bartlam, M., Hilgenfeld, R., – Rao, Z. (2003). The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc Natl Acad Sci USA, 100(23), 13190–13195. https://doi.org/https://doi.org/10.1073/pnas.1835675100
- 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/https://doi.org/10.2174/138161206779010369
- Yang, H., Xie, W., Xue, X., Yang, K., Ma, J., Liang, W., Zhao, Q., Zhou, Z., Pei, D., Ziebuhr, J., Hilgenfeld, R., Yuen, K. Y., Wong, L., Gao, G., Chen, S., Chen, Z., Ma, D., Bartlam, M., & Rao, Z. (2005). Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biology, 3(10), e324. https://doi.org/https://doi.org/10.1371/journal.pbio.0030324
- 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/https://doi.org/10.1038/s41586-020-2012-7
- Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G. F., & Tan, W. (2020). A Novel Coronavirus from Patients with Pneumonia in China, 2019. New England Journal of Medicine, 382(8), 727–733. https://doi.org/https://doi.org/10.1056/NEJMoa2001017
- Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368. https://doi.org/https://doi.org/10.1002/jcc.21816