Blind Docking Analysis of Potential Drugs against SARS-COV-1 and SARS-COV-2 Proteins
Keywords:
Autodock Vina, PyRxAbstract
In this short communication, more than 300 drugs were investigated by Blind Docking approach, by Autodock Vina Scoring Function with Pyrx Software. From Blind Docking Results, Deslanoside, Dactinomycin, Teicoplanin aglycone, Conivaptan, Paritaprevir, Acetyldigitoxin, Nafarelin, Lanatoside_C, Dydroergocristine, Dydroergotamine, Tirilazad, and Ubrogepant are potential candidates against SARS-COV-1 and SARS-COV-2 proteins. Particular attention, Acetyldigitoxin, Dactinomycin, and Deslanoside with Binding Energy about -12 .00 kcal mol -1 are higher binding Energies values against SARS-COV-2 Mpro. Regarding SARS-COV-2 RBD, Teicoplanin aglycone and Dactinomycin have a potentially significant role with a binding energy value of -12.50 kcal mol -1.
References
Dallakyan, S., and Olson, A. J. “Small-molecule library screening by docking with PyRx”, Methods in molecular biology (Clifton, N.J.), Vol. 1263, pp. 243–250, 2015.https://doi.org/10.1007/978-1-4939-2269-7_19.
Llabrés, M., and Valiente, G. “ Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2”, PloS one, Vol.15, Issue. 12, pp.e0236304, 2020.https://doi.org/10.1371/journal.pone.0236304.
Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., and Olson, A. J. “Computational protein-ligand docking and virtual drug screening with the AutoDock suite”, Nature protocols, Vol.11, Issue.5, pp.905–919,2016. https://doi.org/10.1038/nprot.2016.051.
Trott, O., and Olson, A. J. “AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading”, Journal of computational chemistry, Vol.31, Issue.2, pp. 455–461, 2010. https://doi.org/10.1002/jcc.21334
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., and Olson, A. J.” AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility”, Journal of computational chemistry, Vol.30, Isssue.16, pp.2785–2791, 2009. https://doi.org/10.1002/jcc.21256.
Kaplan, W., & Littlejohn, T. G.” Swiss-PDB Viewer (Deep View)”Briefings in bioinformatics, Vol.2, Issue. 2, pp.195–197, 2001. https://doi.org/10.1093/bib/2.2.195.
Sulimov, A. V., Kutov, D. K., Ilin, I. S., & Sulimov, V. B. “Doking s kombinirovannym primeneniem silovogo polia i kvantovo-khimicheskogo metoda [Docking with combined use of a force field and a quantum-chemical method]”, Biomeditsinskaia khimiia, Vol.65, Issue.2, pp.80–85, 2019.
Downloads
Published
How to Cite
Issue
Section
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors contributing to this journal agree to publish their articles under the Creative Commons Attribution 4.0 International License, allowing third parties to share their work (copy, distribute, transmit) and to adapt it, under the condition that the authors are given credit and that in the event of reuse or distribution, the terms of this license are made clear.
