Currently the entire human population is in the midst of a global
pandemic caused by SARS-CoV-2 (
S
evere
A
cute
R
espiratory
S
yndrome
Co
rona
V
irus
2). This highly pathogenic virus has to date caused >71
million infections and >1.6 million deaths in >180
countries. Several vaccines and drugs are being studied as
possible treatments or prophylactics of this viral infection.
M3CLpro (coronavirus main cysteine protease) is a promising drug
target as it has a significant role in viral replication. Here
we use the X-ray crystal structure of M3CLpro in complex with
boceprevir to study the dynamic changes of the protease upon
ligand binding. The binding free energy was calculated for water
molecules at different locations of the binding site, and
molecular dynamics (MD) simulations were carried out for the
M3CLpro/boceprevir complex, to thoroughly understand the
chemical environment of the binding site. Several HCV NS3/4a
protease inhibitors were tested
in vitro
against M3CLpro. Specifically, asunaprevir, narlaprevir,
paritaprevir, simeprevir, and telaprevir all showed inhibitory
effects on M3CLpro. Molecular docking and MD simulations were
then performed to investigate the effects of these ligands on
M3CLpro and to provide insights into the chemical environment of
the ligand binding site. Our findings and observations are
offered to help guide the design of possible potent protease
inhibitors and aid in coping with the COVID-19 pandemic.