A Refined Search of SARS-CoV-2 Main Protease Inhibitors as COVID-19 Antivirals
Veerabhadra R. Vulupala, Yugendar R. Alugubelli, Kaustav Khatua, Kai S. Yang, Xuejiao Shirley Guo, Dorsa Rabie, Tahmina Pervin, Lauren R. Blankenship, Demonta Coleman, Sathish Kumar, Chia-Chuan D. Cho, Zhi Zachary Geng, Xinyu R. Ma, Erol Vatansever, Banumathi Sankaran, Benjamin W. Neuman, Shiqing Xu, Wenshe Ray LiuAbstract
MPI8 was among one of the first SARS-CoV-2 main protease (MPro) inhibitors with strong antiviral potency. Building on its peptidomimetic aldehyde scaffold, we retained the P2 3-cyclohexylalanine and P3 O-tert-butylthreonine elements, which support S2 binding, S-subsite engagement, and likely cellular permeability, and varied the S4/S1′ substituents and covalent warheads. SAR and co-crystal structures identified compact N-terminal carbamates or amides bearing cyclopropane, isopropyl, or trifluoromethyl groups as favorable S4 binders. Benzoxazole/benzothiazole-carbonyl groups and acyloxymethyl ketones were explored as S1′-engaging motifs, with one benzoxazole-containing structure confirming tight S1′ packing by crystal structure. Nitrile and 2-amino-2-oxyacetyl warheads provided viable alternatives to the parent aldehyde. Combining optimized S4 groups with alternative warheads or S1′ motifs yielded multiple inhibitors more potent than MPI8. Notably, MPI-131 showed an IC50 of 1.7 nM, strong antiviral potency, and CC50 of 60.2 μM, placing it among the most potent MPro inhibitors reported.