Discovery of Quinoxaline-Based P1–P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity against Drug-Resistant Hepatitis C Virus Variants

The
three pan-genotypic HCV NS3/4A protease inhibitors (PIs) currently
in clinical usegrazoprevir, glecaprevir, and voxilaprevirare
quinoxaline-based P2–P4 macrocycles and thus exhibit similar
resistance profiles. Using our quinoxaline-based P1–P3 macrocyclic
lead compounds as an alternative chemical scaffold, we explored structure–activity
relationships (SARs) at the P2 and P4 positions to develop pan-genotypic
PIs that avoid drug resistance. A structure-guided strategy was used
to design and synthesize two series of compounds with different P2
quinoxalines in combination with diverse P4 groups of varying sizes
and shapes, with and without fluorine substitutions. Our SAR data
and cocrystal structures revealed the interplay between the P2 and
P4 groups, which influenced inhibitor binding and the overall resistance
profile. Optimizing inhibitor interactions in the S4 pocket led to
PIs with excellent antiviral activity against clinically relevant
PI-resistant HCV variants and genotype 3, providing potential pan-genotypic
inhibitors with improved resistance profiles.