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Phyto-compounds from a rather poisonous plant, Strychnos nux-vomica, show high potency against SARS-CoV-2 RNA-dependent RNA polymerase

Author(s):

Acharya Balkrishna, Subarna Pokhrel* and Anurag Varshney*  

Abstract:


Background: Strategy to inhibit the virus replication is an attractive means in combating SARS-CoV-2 infection.

Objective: We studied phyto-compounds from Strychnos nux-vomica (a poisonous plant) against SARS-CoV-2 RNA-dependent RNA polymerase by computational methods.

Method: Molecular docking, molecular dynamics (MD) simulation and energetics calculations were employed to elucidate the role of the phyto-compounds.

Results: Ergotamine with a binding free energy of -14.39 kcal/mol showed a promising capability in terms of both the binding affinity and interacting to conserved motifs, especially the SDD signature sequence. The calculated dissociation constants for ATP, ergotamine, isosungucine and sungucine were 12 ┬ÁM, 0.072 nM, 0.011 nM and 0.152 nM, respectively. The exhibited kd by these phyto-compounds reflected a tens of thousands fold potency as compared to ATP. The binding free energies of sungucine and isosungucine were much lower (-13.93 and -15.55 kcal/mol, respectively) compared to that of ATP (-6.98 kcal/mol).

Conclusion: Sharing the same binding location as that of ATP and having high binding affinities, Ergotamine, Isosungucine, Sungucine and Strychnine N-oxide could be effective in controlling the SARS-CoV-2 virus replication by blocking the ATP and inhibiting the enzyme function.

Keywords:

SARS-CoV-2, RNA-dependent RNA polymerase, inhibition, Strychnos nux-vomica, phyto-compounds, computational methods

Affiliation:

Drug Discovery and Development Division, Patanjali Research Institute, Patanjali Research Foundation Trust, Roorkee-Haridwar Road, Haridwar-249405, Uttarakhand, Drug Discovery and Development Division, Patanjali Research Institute, Patanjali Research Foundation Trust, Roorkee-Haridwar Road, Haridwar-249405, Uttarakhand, Drug Discovery and Development Division, Patanjali Research Institute, Patanjali Research Foundation Trust, Roorkee-Haridwar Road, Haridwar-249405, Uttarakhand



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