Small Molecule Protease Inhibitors against MERS-CoV and Coronaviruses of Pandemic Potential

PROJECT SUMMARY Middle East respiratory syndrome coronavirus (MERS-CoV) emerged suddenly in 2012 as the cause of severe respiratory illness in humans. Despite the high mortality rate (~ 40%) and the significant potential for a public health emergency, there are no FDA-approved vaccines or antiviral drugs for MERS. Consequently, there is an urgent and unmet need for the development of small-molecule drugs to control MERS-CoV infection. Furthermore, members of the Merbecovirus and Sarbecovirus subgenera within the Betacoronavirus genus pose a high risk of future spillover into humans. However, efforts to develop general strategies to mitigate the impact of future pandemics have been limited. Coronavirus 3C-like protease (3CLpro) is a well-characterized therapeutic target as it processes most cleavage sites on virus polyproteins and is essential for virus replication. Multiple series of 3CLpro inhibitors with potent activity against MERS-CoV and in vivo efficacy in mouse models were reported by our group. However, these compound series are parenterally administrable with limited oral bioavailability. Hypothesize of this project is that inhibitors exploiting the exquisite stereochemical control and multiple diversity sites afforded by the 1,3,2-oxazaphospholidin-3-one scaffold (series I and II) and decorated with a novel transition state analog endowed with favorable oral bioavailability can serve as a launching pad for the development of orally bioavailable MERS-CoV-specific antivirals. As these inhibitors can engage in binding interactions with the Sn and Sn' pockets of various coronavirus 3CLpros, the scaffold provides a versatile platform for merbecoviruses and sarbecoviruses. Aims of this project are 1) Conduct iterative structure-guided design, synthesis, and multiparameter optimization of inhibitors for MERS-CoV; 2) Conduct biochemical, structural, and virological studies to characterize and prioritize analogs for MERS-CoV 3CLpro and conduct structure-activity relationship studies with the generated series for merbecovirus/sarbecovirus 3CLpros; and 3) Demonstrate in vivo efficacy of optimized leads in a mouse model of MERS-CoV infection. The overarching goal of this project is the identification of an orally bioavailable preclinical candidate and 1-2 backup compounds based on inhibitor series (I and II) for MERS-CoV infection, and the exploration and utilization of the generated inhibitors against the 3CLpros of merbecoviruses and sarbecoviruses.