A cyclic peptide inhibitor of the SARS-CoV-2 main protease

This paper presents the design and study of a first-in-class cyclic peptide inhibitor against the SARS-CoV-2 main protease (M(pro)). The cyclic peptide inhibitor is designed to mimic the conformation of a substrate at a C-terminal autolytic cleavage site of M(pro). The cyclic peptide contains a [4-(2-aminoethyl)phenyl]-acetic acid (AEPA) linker that is designed to enforce a conformation that mimics a peptide substrate of M(pro). In vitro evaluation of the cyclic peptide inhibitor reveals that the inhibitor exhibits modest activity against M(pro) and does not appear to be cleaved by the enzyme. Conformational searching predicts that the cyclic peptide inhibitor is fairly rigid, adopting a favorable conformation for binding to the active site of M(pro). Computational docking to the SARS-CoV-2 M(pro) suggests that the cyclic peptide inhibitor can bind the active site of M(pro) in the predicted manner. Molecular dynamics simulations provide further insights into how the cyclic peptide inhibitor may bind the active site of M(pro). Although the activity of the cyclic peptide inhibitor is modest, its design and study lays the groundwork for the development of additional cyclic peptide inhibitors against M(pro) with improved activities.