Structure-Based Design of Potent Peptidomimetic Inhibitors Covalently Targeting SARS-CoV-2 Papain-like Protease

The papain-like protease (PL ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a critical role in the proteolytic processing of viral polyproteins and the dysregulation of the host immune response, providing a promising therapeutic target. Here, we report the structure-guide design of novel peptidomimetic inhibitors covalently targeting SARS-CoV-2 PL . The resulting inhibitors demonstrate submicromolar potency in the enzymatic assay (IC = 0.23 μM) and significant inhibition of SARS-CoV-2 PL in the HEK293T cells using a cell-based protease assay (EC = 3.61 μM). Moreover, an X-ray crystal structure of SARS-CoV-2 PL in complex with compound confirms the covalent binding of the inhibitor to the catalytic residue cysteine 111 (C111) and emphasizes the importance of interactions with tyrosine 268 (Y268). Together, our findings reveal a new scaffold of SARS-CoV-2 PL inhibitors and provide an attractive starting point for further optimization.