Abstract
Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has assumed importance especially in the context of emerging new viral variants. In this paper, we describe the discovery of a novel noncovalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the SARS-Cov-2 main protease (M pro ) by employing a scalable high-throughput virtual screening (HTVS) framework and a targeted compound library of over 6.5 million molecules that could be readily ordered and purchased. Our HTVS framework leverages the U.S. supercomputing infrastructure achieving nearly 91% resource utilization and nearly 126 million docking calculations per hour. Downstream biochemical assays validate this M pro inhibitor with an inhibition constant ( K i ) of 2.9 μM (95% CI 2.2, 4.0). Furthermore, using room-temperature X-ray crystallography, we show that MCULE-5948770040 binds to a cleft in the primary binding site of M pro forming stable hydrogen bond and hydrophobic interactions. We then used multiple μs-time scale molecular dynamics (MD) simulations and machine learning (ML) techniques to elucidate how the bound ligand alters the conformational states accessed by M pro , involving motions both proximal and distal to the binding site. Together, our results demonstrate how MCULE-5948770040 inhibits M pro and offers a springboard for further therapeutic design.
【초록키워드】 SARS-CoV-2, Vaccine, coronavirus, Virtual screening, X-ray crystallography, docking, molecular dynamics, protease, SARS-CoV-2 main protease, binding site, therapeutic, Viral variants, therapeutic agent, molecular, inhibitor, resource, Hydrogen bond, Ligand, hydrogen, acute respiratory syndrome, 95% CI, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, hour, M pro, hydrophobic, hydrophobic interactions, offer, inhibitory, conformational states, Alter, biochemical assay, cleft, springboard, bind, inhibit, proximal, assumed, conformational state, distal, 【제목키워드】 SARS-CoV-2, Screening, validation,