Structure-Guided Design of Potent and Selective Covalent Inhibitors Targeting the SARS-CoV‑2 Papain-like Protease

The
COVID-19 pandemic led to numerous initiatives to create antiviral
medications and vaccines for the treatment and prevention of infections.
However, the need remains for new therapies with distinct mechanisms
of action from current treatment of COVID-19 infections as well as
for future pandemic preparedness. SARS-CoV-2 papain-like protease
(PLpro) is a cysteine protease that cleaves the viral polyprotein
and possesses deubiquitylase (DUB) and deISGylase activity that can
act on host proteins. Here, we report the structure-guided development
of covalent inhibitors of SARS-CoV-2 PLpro that possess low nanomolar
to subnanomolar antiviral activity in cell assays and inhibit viral
replication in a mouse model of SARS-CoV-2 infection. The most potent
inhibitors contain N-propargylamide electrophiles,
a relatively inert warhead not typically featured in covalent protease
inhibitors. These findings provide a foundation for further discovery
and optimization of covalent PLpro inhibitors that could lead to future
antiviral therapeutics.