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 non-covalent
small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the
SARS-Cov-2 main protease (Mpro) 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
Mpro inhibitor with an inhibition constant
(Ki)
of 2.9 µM [95% CI 2.2, 4.0]. Further, using
room-temperature X-ray crystallography, we show that MCULE-5948770040 binds to a
cleft in the primary binding site of Mpro forming stable
hydrogen bond and hydrophobic interactions. We then used multiple
µs-timescale molecular dynamics (MD) simulations,
and machine learning (ML) techniques to elucidate how the bound ligand alters
the conformational states accessed by Mpro, involving
motions both proximal and distal to the binding site. Together, our results
demonstrate how MCULE-5948770040 inhibits Mpro and offers a
springboard for further therapeutic design.
Significance Statement
The ongoing novel coronavirus pandemic (COVID-19) has prompted a
global race towards finding effective therapeutics that can target
the various viral proteins. Despite many virtual screening campaigns
in development, the discovery of validated inhibitors for SARS-CoV-2
protein targets has been limited. We discover a novel inhibitor
against the SARS-CoV-2 main protease. Our integrated platform
applies downstream biochemical assays, X-ray crystallography, and
atomistic simulations to obtain a comprehensive characterization of
its inhibitory mechanism. Inhibiting Mpro can
lead to significant biomedical advances in targeting SARS-CoV-2
treatment, as it plays a crucial role in viral replication.
High Throughput Virtual Screening and Validation of a SARS-CoV-2 Main
Protease Non-Covalent Inhibitor