Finding potential inhibitors for Main protease (Mpro) of SARS-CoV-2 through virtual screening and MD simulation studies.

Publication date: Dec 01, 2023

SARS-CoV-2 is a highly hazardous species that can infect people with Covid-19 disease, dramatically increasing mortality rates worldwide. Plenty of researches have been done to find drugs or inhibitors, with this study aiming to identify an inhibitor within the ChEMBL database using computational approaches. From the ChEMBL library, 19,43,048 compounds which are known type of small compounds and proteins were downloaded and docked with the Main protease (M). After performing compound screening using Lipinski’s rule, Qikprop analysis following with virtual Screening, Induced Fit Docking (IFD) and MM-GBSA analysis with the Glide and Prime modules of SchrcF6dinger, the best complex was subjected to MD simulation with Desmond. According to the docking results, small protein 2,371,668 and compound 1,090,395 were docked with Main protease with -12. 6, -12. 0 kcal/mol dock score and interacted with the functional site residues His 41 and Cys 145, as well as the binding site residues Thr 26, Phe 140, Asn 142, Gly 143, Glu 166, and Gln 189. Complex structures were shown to be steadier by the MD simulation study because both the ligands heavy atoms and the protein Cα atoms’ RMSD values fell within acceptable ranges. As a result, this research suggests that the molecule CHEMBL2371668 and the compound CHEMBL1090395 may inhibit the activity of Main protease, and the usefulness of these molecules will be examined further through experimental research.

Concepts Keywords
Chembl1090395 Covid-19
Disease Main protease (Mpro)
Library MD simulation
Performing SARS-CoV-2
Saudi Virtual screening


Type Source Name
disease MESH Covid-19
disease IDO site
drug DRUGBANK L-Cysteine
drug DRUGBANK L-Threonine
drug DRUGBANK L-Phenylalanine
drug DRUGBANK L-Asparagine
drug DRUGBANK Glycine
drug DRUGBANK Glutamic Acid
drug DRUGBANK Protein C

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