Discovery of the SARS-CoV-2 Papain-Like Protease Inhibitor MR1–114: From Structure-Based Design to <i>In Vivo</i> Antiviral Efficacy

The SARS-CoV-2 papain-like protease (PLpro) is a critical target for antiviral intervention. Here, we report the discovery of MR1-114 (compound <b>15</b>), a potent, noncovalent PLpro inhibitor. Guided by structure-based design, we incorporated a strategic alkyne linker hypothesized to access the cryptic Val70^Ub pocket, a modification that proved critical for driving cellular potency. Multiparameter optimization yielded MR1-114, which displays a desirable ADME profile characterized by high solubility, permeability, and hepatocyte stability, translating to high oral bioavailability in mice and rats. Notably, the compound exhibits preferential lung enrichment in mice and rats while maintaining broad-spectrum activity against variants, including Delta and Omicron BA.5 with nanomolar potency <i>in vitro</i>. In the K18-hACE2 mouse model, oral administration of MR1-114 matched the therapeutic efficacy of nirmatrelvir, significantly suppressing pulmonary viral replication and preventing disease-associated weight loss.