SARS-CoV-2 main protease inhibition through dimerization promotion by peptidomimetic inhibitors and disruption by ebselen.

Peptidomimetic inhibitors (PF-07321332, PF-00835231, GC376, boceprevir) significantly shift SARS-CoV-2 main protease toward the active dimer state, suppressing subunit exchange and rigidifying the dimer interface.

• Why it matters: The M pro monomer–dimer equilibrium is a therapeutic vulnerability, but inhibitor-specific mechanisms for stabilizing or disrupting dimerization and interface dynamics remain unclear.
• What they did: Using 13C labeling with native mass spectrometry and HDX-MS, the study compared peptidomimetic versus non-peptidomimetic inhibitors on dimerization and subunit exchange, and used tandem MS plus MD and mutational analyses for ebselen.
• The result: Ebselen impaired dimer formation, increased interface flexibility, and covalently bound at C300, where the modification allosterically alters the dimer-interface hydrogen-bond network, contributing to dimer disruption and enzymatic inhibition.