Current Science

Open Access Open Access  Restricted Access Subscription Access

Molecular Docking Analysis of Selected Natural Products from Plants for Inhibition of SARS-CoV-2 Main Protease


Affiliations
1 School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bengaluru 560 065, India
2 Indian Institute of Integrative Medicine, Council of Scientific and Industrial Research, Jammu 180 001, India
3 Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru 560 065, India
 

In this article, we report results of a molecular docking analysis of commonly occurring natural product compounds against COVID-19 6LU7 and 6Y2E proteases. Our results show that several of these compounds have binding affinity against both the COVID-19 proteases, and compare well with a known anti-HIV drug, Saquinavir. Many of the compounds form an integral component of many cuisines, both Indian as well as others. We propose that some of these compounds could be easily and quickly positioned to hold fort against the COVID-19 virus, until of course newer therapies are discovered and detailed studies are taken to empirically validate some of the compounds for their ability to inhibit the virus.

Keywords

Affinity/Binding Energy, COVID-19 Protease, Drug Discovery, Ligands, Natural Products.
User
Notifications
Font Size

  • Khaerunnisa, S., Kurniawan, H., Awaluddin, R., Suhartati, S. and Soetjipto, S., Potential inhibitor of COVID-19 main protease (Mpro) from several medicinal plant compounds by molecular docking study. 2020. Preprints 2020, 2020030226 (doi:10.20944/preprints202003.0226.v1).

  • Wu, C. et al., Analysis of therapeutic targets for SARS -CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceut. Sin. B, 2020.

  • Zhang, L. et al., Crystal structure of SARS -CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science, 2020, eabb3405.

  • Noble, S. and Faulds, D., Saquinavir. Drugs, 1996, 52, 93–112.

  • Liu, X., Zhang, B., Jin, Z., Yang, H. and Rao, Z., The crystal structure of 2019 -NCoV main protease in complex with an inhibitor N3. RCSB Protein Data Bank, 2020.

  • Tian, W., Chen, C., Lei, X., Zhao, J. and Liang, J., CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Res., 2018, 46, W363–W367.

  • Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., and Hutchison, G. R., Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J. Cheminform., 2012, 4, 17.

  • Morris, G. M., Goodsell, D. S., Huey, R. and Olson, A. J., Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J. Comp.-Aided Mol. Design, 1996, 10, 293–304.

  • Trott, O. and Olson, A. J., AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput, Chem,, 2010, 31, 455–461.

  • DeLano, W. L., PyMOL: An open-source molecular graphics tool. CCP4 Newslett. Protein Crystallogr., 2002, 40(1), 82–92.

  • Shityakov, S. and Förster, C., In silico predictive model to determine vector-mediated transport properties for the blood –brain barrier choline transporter. Adv. Appl. Bioinform. Chem., 2014, 7, 23.

  • Ceska, O., Chaudhary, S. K., Warrington, P., Ashwood-Smith, M. J., Bushnell, G. W. and Poultont, G. A., Coriandrin, a novel hig hly photoactive compound isolated from Coriandrum sativum. Phyto-chemistry, 1988, 27, 2083–2087.

  • Tian, M., Yan, H. and Row, K. H., Simultaneous extraction and separation of liquiritin, glycyrrhizic acid, and glabridin from licorice ischolar_main with analytical and preparative chromatograp hy. Biotechnol. Bioproc. Eng., 2008, 13, 671–676.

  • Ishtiyaq, A., Alam, A., Siddiqui, J. I. and Kazmi, M. H., Therapeutic potential of widely used unani drug Asl-Us-Soos (Glycyr-rhiza glabra Linn.): a systematic review. J. Drug Deliv. Therap., 2019, 9, 765–773.

  • Kumari, A. and Kumar, J., Phyto-chemical screening of ischolar_main extracts of Glycyrrhiza glabra by spectroscopic methods (UV-VIS spectrophotometer, FTIR and HPLC). Int. J. Pharmaceut. Sci. Drug Res., 2019, 11, 376–381.

  • Lin, J.-H., Chen, S.-Y., Lu, C.-C., Lin, J.-A. and Yen, G.-C., Ur-solic acid promotes apoptosis, autophagy, and chemosensitivity in gemcitabine-resistant human pancreatic cancer cells. Phytother. Res., 2020, 1–14, doi:10.1002/ptr.6669.

  • Khwaza, V., Oyedeji, O. O. and Aderibigbe, B. A., Antiviral activities of oleanolic acid and its analogues. Molecules, 2018, 23, 2300.

  • Wu, A.-G. et al., Hederagenin and α-hederin promote degradation of proteins in neurodegenerative diseases and improve motor deficits in MPTP-mice. Pharmacol. Res., 2017, 115, 25–44.

  • Zeng, J. et al., Current knowledge and development of hederagenin as a promising medicinal agent: a comprehensive review. RSC Adv., 2018, 8, 24188–24202.

  • Redeploying plant defences. Nature Plants, 2020, 6, 177.


Abstract Views: 389

PDF Views: 161




  • Molecular Docking Analysis of Selected Natural Products from Plants for Inhibition of SARS-CoV-2 Main Protease

Abstract Views: 389  |  PDF Views: 161

Authors

Megha Hastantram Sampangi-Ramaiah
School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bengaluru 560 065, India
Ram Vishwakarma
Indian Institute of Integrative Medicine, Council of Scientific and Industrial Research, Jammu 180 001, India
R. Uma Shaanker
Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru 560 065, India

Abstract


In this article, we report results of a molecular docking analysis of commonly occurring natural product compounds against COVID-19 6LU7 and 6Y2E proteases. Our results show that several of these compounds have binding affinity against both the COVID-19 proteases, and compare well with a known anti-HIV drug, Saquinavir. Many of the compounds form an integral component of many cuisines, both Indian as well as others. We propose that some of these compounds could be easily and quickly positioned to hold fort against the COVID-19 virus, until of course newer therapies are discovered and detailed studies are taken to empirically validate some of the compounds for their ability to inhibit the virus.

Keywords


Affinity/Binding Energy, COVID-19 Protease, Drug Discovery, Ligands, Natural Products.

References





DOI: https://doi.org/10.18520/cs%2Fv118%2Fi7%2F1087-1092