Design of SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model

Abstract The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PL pro ) is a promising but challenging drug target. In this study, we designed and synthesized 85 noncovalent PL pro inhibitors that bind to the newly discovered Val70 Ub site and the known BL2 groove pocket. Potent compounds inhibited PL pro with inhibitory constant K i values from 13.2 to 88.2 nM. The co-crystal structures of PL pro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC 50 from 0.44 to 2.02 µM. Oral treatment with Jun12682 significantly improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting PL pro inhibitors are promising oral SARS-CoV-2 antiviral candidates. One-Sentence Summary Structure-guided design of SARS-CoV-2 PL pro inhibitors with in vivo antiviral efficacy in a mouse model.