Divergent resistance pathways amongst SARS-CoV-2 PLpro inhibitors highlight the need for scaffold diversity.

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.