Predicting Antiviral Resistance Mutations in SARS-CoV‑2 Main Protease with Computational and Experimental Screening

The
main protease (Mpro) of SARS-CoV-2 is essential
for viral replication and has been the focus of many drug discovery
efforts since the start of the COVID-19 pandemic. Nirmatrelvir (NTV)
is an inhibitor of SARS-CoV-2 Mpro that is used in the
combination drug Paxlovid for the treatment of mild to moderate COVID-19.
However, with increased use of NTV across the globe, there is a possibility
that future SARS-CoV-2 lineages will evolve resistance to NTV. Early
prediction and monitoring of resistance mutations could allow for
measures to slow the spread of resistance and for the development
of new compounds with activity against resistant strains. In this
work, we have used in silico mutational scanning
and inhibitor docking of Mpro to identify potential resistance
mutations. Subsequent in vitro experiments revealed
five mutations (N142L, E166M, Q189E, Q189I, and Q192T) that reduce
the potency of NTV and of a previously identified non-covalent cyclic
peptide inhibitor of Mpro. The E166M mutation reduced the
half-maximal inhibitory concentration (IC50) of NTV 24-fold
and 118-fold for the non-covalent peptide inhibitor. Our findings
inform the ongoing genomic surveillance of emerging SARS-CoV-2 lineages.