Inhibition of RNA-dependent RNA polymerase from SARSCoV-2 by compounds in Vangag herbal preparation: an in silico evaluation

Abstract

Coronavirus disease (COVID-19) has presented unprecedented challenges to healthcare systems worldwide. There are no proven effective therapeutic agents or vaccines. Some antiviral agents and micronutrients have been repurposed for the management. There are claims of herbal preparations with therapeutic effects. Vangag herbal formulation for the management of COVID-19 is a combination of six plants. Molecular docking and virtual screening were used for the study. Ligands and protein target for molecular docking were prepared in Autodock Tools using PyRx 0.8 package. 3D structures of 24 phytochemicals in Vangag were downloaded from PubChem and optimized in Discovery Studio 4.5 visualizer. Nine agents currently used for management of COVID-19 were also downloaded and included in the ligand library to serve as control. Results of the binding affinities of phytochemicals in constituentplants of Vangag to SARS-CoV-2 molecular target (7BV2.pdb) were ranked from 1 to 21. Kolaviron (binding affinity -8.1 Kcal/mol) ranked 1, Ritonavir 5, Remdesivir 6, Quinine 7, Hydroxychloroquine 9, Chloroquine 18 and the least Allicin 21 (binding affinity -3.7 Kcal/mol). Phytochemicals in Vangag have good binding affinity to COVID-19 viral target proteins. Vangag also contains high concentration of zinc and other micronutrients, making it a promising formula for management of COVID-19. Keywords: COVID-19; SARS-CoV-2; Molecular docking; Herbal formulation