Kaustav Khatua, Yugendar R. Alugubelli , Kai S. Yang, Veerabhadra R. Vulupala, Lauren R. Blankenship , Demonta Coleman, Sandeep Atla , Sankar P. Chaki, Zhi Zachary Geng , Xinyu R. Ma , Jing Xiao , Peng-Hsun Chen , Chia-Chuan D. Cho, Shivangi Sharma, Erol C. Vatansever, Yuying Ma, Ge Yu, Benjamin W. Neuman, Shiqing Xu , Wenshe Ray Liu
Antiviral Research, 225, 2024, 105874
https://doi.org/10.1016/j.antiviral.2024.105874
The main protease (MPro) of SARS-CoV-2, the causative agent of COVID-19, is a pivotal nonstructural protein critical for viral replication and pathogenesis. Its protease function relies on three active site pockets for substrate recognition and a catalytic cysteine for enzymatic activity. To develop potential SARS-CoV-2 antivirals, we successfully synthesized a diverse range of azapeptide inhibitors with various covalent warheads to target MPro's catalytic cysteine. Our characterization identified potent MPro inhibitors, including MPI89 that features an aza-2,2-dichloroacetyl warhead with a remarkable EC50 value of 10 nM against SARS-CoV-2 infection in ACE2+ A549 cells and a selective index of 875. MPI89 is also remarkably selective and shows no potency against SARS-CoV-2 papain-like protease and several human proteases. Crystallography analyses demonstrated that these inhibitors covalently engaged the catalytic cysteine and used the aza-amide carbonyl oxygen to bind to the oxyanion hole. MPI89 stands as one of the most potent MPro inhibitors, suggesting the potential for further exploration of azapeptides and the aza-2,2-dichloroacetyl warhead for developing effective therapeutics against COVID-19.
