1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Bioinformatic screening of Lamiaceae family compounds as potential inhibitors of spike-mediated receptor-binding of SARS-CoV-2
Paper ID : 1304-ICB10
Authors:
Abbas Alibakhshi *, Shima Gharibi1, Shahrzad Ahangarzadeh1, fatemeh yarian2
1Isfahan University of Medical Sciences
2Department of medical biotechnology, schol of advanced technology in medicine, fasa unoversity of medical sciences
Abstract:
COVID-19 (coronavirus disease 2019) still remains a major challenge worldwide. The coronavirus causes the disease by binding to ACE2 receptors on lung cells, infecting the cells and triggering the onset of symptoms. The prevention of such binding in which the virus is eventually unable to enter the cell could be a promising therapeutic approach. In this in silico study, 306 compounds of Lamiaceae family native in Iran were retrieved from ChEBI, PubChem, Chemspider and ZINC15 serevers as 3D structures in SDF files. Crystal structure of SARS-CoV-2 spike RBD was obtained as bound with ACE2 from Protein Data Bank (PDB) database (PDB ID: 6M0J). Then, the compounds with inhibitory potential were selected by molecular docking and virtual screening using Autodock vina tools embedded in PyRx software, in terms of free energy binding against the spike protein of the virus. The pharmacokinetic profile of selected compounds was evaluated using SwissADME website. Afterwards, by molecular dynamic simulation using GROMACS package and RMSD and RMSF analysis as well as MM/PBSA method, four compounds were further assessed for binding affinities against the receptor-binding domain of spike. The results showed that two compounds, Catechin gallate and Perovskone B derived from Stachys and Salvia genus generated stronger binding affinity against the target and thus could act as potential inhibitory compounds of RBD of the SARS-CoV-2 spike protein.
Keywords:
Lamiaceae family; SARS-CoV-2; RBD; Molecular docking; Molecular dynamic
Status : Paper Accepted (Poster Presentation)