The SARS-CoV-2 main
protease (Mpro) plays an essential
role in the coronavirus lifecycle by catalyzing hydrolysis of the
viral polyproteins at specific sites. Mprois the target
of drugs, such as nirmatrelvir, though resistant mutants have emerged
that threaten drug efficacy. Despite its importance, questions remain
on the mechanism of how Mprobinds its substrates. Here,
we apply dynamical nonequilibrium molecular dynamics (D-NEMD) simulations
to evaluate structural and dynamical responses of Mproto
the presence and absence of a substrate. The results highlight communication
between the Mprodimer subunits and identify networks,
including some far from the active site, that link the active site
with a known allosteric inhibition site, or which are associated with
nirmatrelvir resistance. They imply that some mutations enable resistance
by altering the allosteric behavior of Mpro. More generally,
the results show the utility of the D-NEMD technique for identifying
functionally relevant allosteric sites and networks including those
relevant to resistance.