Discovery of a new SARS-CoV-2 Mpro inhibitor from a natural product and natural product-like compound database using in silico and in vitro studies.

This current study employs structure-guided virtual screening to identify potential inhibitors from 69,075 natural product or natural product-like compounds in the InterBioscreen (IBS) database against the SARS-CoV-2 Main protease (Mpro), a well-validated target. From high-throughput structure-guided virtual screening, subsequently followed by more rigorous re-docking, top seven compounds were chosen as hits based on their high binding affinity and specific H-bond interactions with the active-site residues of Mpro. All these compounds were new for this target as well as the virus. The stability of the seven protein-ligand complexes was further assessed using molecular dynamics (MD) simulations and the MM-GBSA method. The ADME/Tox profile of these seven compounds was also predicted theoretically. After MD simulation, only three compounds, viz. STOCK1N-86169, STOCK1N-88750, and STOCK1N-65657 were identified as high-potential candidates for Mpro inhibition. To confirm the in silico analysis results, an in vitro FRET-based Mpro inhibition assay and an ELISA-based SARS-CoV-2 inhibition assay were performed. From these in vitro investigations, STOCK1N-86169 was identified as the only potent Mpro inhibitor, exhibiting an IC