Jun12682 for COVID-19

Drug-escape, where a target evolves to escape inhibition from a drug, has the potential to lead to cross-resistance where drugs that are structurally related or share similar binding mechanisms all become less effective. PLpro inhibitors are currently under development and many emerging PLpro inhibitors are derived from GRL0617, a repurposed SARS-CoV PLpro inhibitor with moderate activity against SARS-CoV-2. Two leading derivatives, PF-07957472 and Jun12682, demonstrate low nanomolar activity and display activity in mice. WEHI-P8 is structurally distinct but binds to a similar pocket adjacent to the active site as GRL0617-like compounds. Using deep mutational scanning, we assessed the potential for PLpro to develop resistance to PF-07957472, Jun12682, and WEHI-P8. PF-07957472 and Jun12682 exhibited largely overlapping escape mutations due to their shared scaffold and binding modes, whereas WEHI-P8 resistance mutations were distinct. These findings underscore the importance of developing structurally diverse inhibitors to minimize resistance risks and ensure that viral mutations against one compound do not compromise the efficacy of others.

AbstractThe emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. In this study, we designed and synthesized 85 noncovalent PLproinhibitors that bind to the newly discovered Val70Ubsite and the known BL2 groove pocket. Potent compounds inhibited PLprowith inhibitory constant Kivalues from 13.2 to 88.2 nM. The co-crystal structures of PLprowith eight leads revealed their interaction modes. Thein vivoleadJun12682inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50from 0.44 to 2.02 µM. Oral treatment withJun12682significantly improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting PLproinhibitors are promising oral SARS-CoV-2 antiviral candidates.One-Sentence SummaryStructure-guided design of SARS-CoV-2 PLproinhibitors within vivoantiviral efficacy in a mouse model.