Exploring Phytochemicals of Traditional Medicinal Plants Exhibiting Inhibitory Activity Against Main Protease, Spike Glycoprotein, RNA-dependent RNA Polymerase and Non-Structural Proteins of SARS-CoV-2 Through Virtual Screening

Abstract

Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) being a causative agent for global pandemic disease nCOVID'19, has acquired much scientific attention for the development of effective vaccines and drugs. Several attempts have been made to explore repurposing existing drugs known for their anti-viral activities, and test the traditional herbal medicines known for their health benefiting and immune-boosting activity against SARS-CoV-2. In this study, efforts were made to examine the potential of 605 phytochemicals from 37 plant species (of which 14 plants were endemic to India) and 139 antiviral molecules (Pubchem and Drug bank) in inhibiting SARS-CoV-2 multiple protein targets through a virtual screening approach. Results of our experiments revealed that SARS-CoV-2 M^Pro shared significant disimilarities against SARS-CoV M^Pro and MERS-CoV M^Pro indicating the need for discovering novel drugs. This study has screened the phytochemical cyanin (Zingiber officinale) which may exhibit broad-spectrum inhibitory activity against main proteases of SARS-CoV-2, SARS-CoV and MERS-CoV with binding energies of (-) 8.3 kcal/mol (-) 8.2 kcal/mol and (-) 7.7 kcal/mol respectively. Amentoflavone, agathisflavone, catechin-7-o-gallate and chlorogenin were shown to exhibit multi-target inhibitory activity. Further, Mangifera indica, Anacardium occidentale, Vitex negundo, Solanum nigrum, Pedalium murex, Terminalia chebula, Azadirachta indica, Cissus quadrangularis, Clerodendrum serratum and Ocimum basilicumaree reported as potential sources of phytochemicals for combating nCOVID'19. More interestingly, this study has highlighted the anti-viral properties of the traditional herbal formulation "Kabasura kudineer" recommended by AYUSH, a unit of Government of India. Short listed phytochemicals could be used as leads for future drug design and development. Genomic analysis of identified herbal plants will help in unraveling molecular complexity of therapeutic and anti-viral properties which proffer lot of chance in the pharmaceutical field for researchers to scout new drugs in drug discovery.

Keywords: SARS-CoV-2; agathisflavone; amentoflavone; cyanin; molecular docking; nCOVID-19.

FIGURE 1

Multiple sequence alignment of SARS-CoV-2 (PDB ID: 5R81), SARS-CoV (PDB ID: 2GZ9) and MERS-CoV (PDB ID: 5C3N) main proteases. Binding site residues are marked with blue box. Red marked residues indicate the change observed between SARS-CoV-2 and SARS CoV. * denotes the conserved regions with identical residues. Serine to Alanine change at the 45th position observed in the binding site is marked with circle.

FIGURE 2

Phylogenetic analysis of SARS-CoV-2M^PRO with other CoV M^PRO proteins.

FIGURE 3

Complex structure of Cyanin with (A) SARS-CoV-2 M^Pro (PDB ID: 5R81) (B) SARS-CoV M^Pro (PDB ID: 2GZ9) (C) MERS-CoVM^Pro (PDB ID: 5C3N).

FIGURE 4

Docked complex structures of spike protein with (A) ivermectin, (B) agasthisflavone, (C) amentoflavone, and RdRp with (D) ivermectin (E) agasthisflavone (F) amentoflavone.

FIGURE 5

Docked complex structures of NSP3 protein with (A) ivermectin (B) agasthisflavone (C) amentoflavone, and NSP9 with (D) ivermectin (E) agasthisflavone (F) amentoflavone.

FIGURE 6

(A) PDB ID: 6M0J - Residue interaction between ACE-2 (chain A) and spike glycoprotein (chain E). (B) PDB ID: 6W4H - Interface of NSP10-NSP16 complex.

FIGURE 7

Spike protein (PDB ID: 6M0J) complex with 1,8-Dichloro-9,10-diphenylanthracene-9,10-diol (binding affinity: 8.2 kcal/mol).

FIGURE 8

Network diagram showing the interaction of plant phytochemcials with SARS-CoV-2 protein targets. Degree of connectivity represents number of SARS-CoV-2 that may be inhibited by each plant. In this network, NSP 15 stands first in the order where many plants connected (degree of connectivity) which indicates that metabolites from the connected plants has shown highest binding affinity (top ten screened compounds). Likewise, Vitex negundo was predicted to inhibit highest number of SARS-CoV-2 targets in the virtual screening. Plants name with * indicates their presence in Kabasura kudineer.