Bioinformatic screening of Lamiaceae family compounds as potential inhibitors of spikemediated receptor-binding of SARS-CoV-۲

COVID-۱۹ (coronavirus disease ۲۰۱۹) still remains a major challenge worldwide. The coronavirus causesthe disease by binding to ACE۲ receptors on lung cells, infecting the cells and triggering the onset ofsymptoms. The prevention of such binding in which the virus is eventually unable to enter the cell could bea promising therapeutic approach. In this in silico study, ۳۰۶ compounds of Lamiaceae family native in Iranwere retrieved from ChEBI, PubChem, Chemspider and ZINC۱۵ serevers as ۳D structures in SDF files.Crystal structure of SARS-CoV-۲ spike RBD was obtained as bound with ACE۲ from Protein Data Bank(PDB) database (PDB ID: ۶M۰J). Then, the compounds with inhibitory potential were selected by moleculardocking and virtual screening using Autodock vina tools embedded in PyRx software, in terms of free energybinding against the spike protein of the virus. The pharmacokinetic profile of selected compounds wasevaluated using SwissADME website. Afterwards, by molecular dynamic simulation using GROMACSpackage and RMSD and RMSF analysis as well as MM/PBSA method, four compounds were furtherassessed for binding affinities against the receptor-binding domain of spike. The results showed that twocompounds, Catechin gallate and Perovskone B derived from Stachys and Salvia genus generated strongerbinding affinity against the target and thus could act as potential inhibitory compounds of RBD of the SARSCoV-۲ spike protein.

Keywords:

Lamiaceae family , SARS-CoV-۲ , RBD , Molecular docking , Molecular dynamic