Inhibitors of Coronavirus 3CL Proteases Protect Cells from Protease-Mediated Cytotoxicity
Samuel J. Resnick, Sho Iketani, Seo Jung Hong, Arie Zask, Hengrui Liu, Sung Soo Kim, Schuyler Melore, Fang-Yu Lin, Manoj S. Nair, Yaoxing Huang, Sumin Lee, Nicholas E. S. Tay, Tomislav Rovis, Hee Won Yang, Xing Li, Brent R. Stockwell, David D. Ho, Alejandro Chavez
Abstract
Multiple coronavirus pandemics have occurred over the last 2 decades. This has highlighted a need to be proactive in the development of therapeutics that can be readily deployed in the case of future coronavirus pandemics. We developed and validated a simplified cell-based assay for the identification of chemical inhibitors of 3CL proteases encoded by a wide range of coronaviruses. This assay is reporter free, does not require specialized biocontainment, and is optimized for performance in high-throughput screening. By testing reported 3CL protease inhibitors against a large collection of 3CL proteases with variable sequence similarity, we identified compounds with broad activity against 3CL proteases and uncovered structural insights into features that contribute to their broad activity. Furthermore, we demonstrated that this assay is suitable for identifying chemical inhibitors of proteases from families other than 3CL proteases.