Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors

While vaccines and antivirals are now being deployed for the current SARS-CoV-2 pandemic, we require additional antiviral therapeutics to not only effectively combat SARS-CoV-2 and its variants, but also future coronaviruses. All coronaviruses have relatively similar genomes that provide a potential exploitable opening to develop antiviral therapies that will be effective against all coronaviruses. Among the various genes and proteins encoded by all coronaviruses, one particularly druggable or relatively easy-to-drug target is the coronavirus Main Protease (3CL(pro) or Mpro), an enzyme that is involved in cleaving a long peptide translated by the viral genome into its individual protein components that are then assembled into the virus to enable viral replication in the cell. Inhibiting Mpro with a small-molecule antiviral would effectively stop the ability of the virus to replicate, providing therapeutic benefit. In this study, we have utilized activity-based protein profiling (ABPP)-based chemoproteomic approaches to discover and further optimize cysteine-reactive pyrazoline-based covalent inhibitors for the SARS-CoV-2 Mpro. Structure-guided medicinal chemistry and modular synthesis of di- and tri-substituted pyrazolines bearing either chloroacetamide or vinyl sulfonamide cysteine-reactive warheads enabled the expedient exploration of structure-activity relationships (SAR), yielding nanomolar potency inhibitors against Mpro from not only SARS-CoV-2, but across many other coronaviruses. Our studies highlight promising chemical scaffolds that may contribute to future pancoronavirus inhibitors.

Automated summary

While vaccines and antivirals are available to combat the SARS-CoV-2 pandemic, additional antiviral therapeutics are needed for future coronaviruses. The coronavirus Main Protease (Mpro) is a promising target for antiviral therapies. This study discovered and optimized cysteine-reactive pyrazoline-based covalent inhibitors for SARS-CoV-2 Mpro, which showed nanomolar potency against not only SARS-CoV-2, but also other coronaviruses. These findings provide potential chemical scaffolds for future pancoronavirus inhibitors.