Evaluation of SARS-CoV-2 Main Protease Inhibitors Using a Novel Cell-Based Assay

As an essential enzyme of SARS-CoV-2, main protease (M^Pro) triggers acute toxicity to its human cell host, an effect that can be alleviated by an M^Pro inhibitor. Using this toxicity alleviation, we developed an effective method that allows a bulk analysis of the cellular potency of M^Pro inhibitors. This novel assay is advantageous over an antiviral assay in providing precise cellular M^Pro inhibition information to assess an M^Pro inhibitor. We used this assay to analyze 30 known M^Pro inhibitors. Contrary to their strong antiviral effects and up to 10 μM, 11a, calpain inhibitor II, calpain XII, ebselen, bepridil, chloroquine, and hydroxychloroquine showed relatively weak to undetectable cellular M^Pro inhibition potency implicating their roles in interfering with key steps other than just the M^Pro catalysis in the SARS-CoV-2 life cycle. Our results also revealed that MPI5, MPI6, MPI7, and MPI8 have high cellular and antiviral potency. As the one with the highest cellular and antiviral potency among all tested compounds, MPI8 has a remarkable cellular M^Pro inhibition IC₅₀ value of 31 nM that matches closely to its strong antiviral effect with an EC₅₀ value of 30 nM. Therefore, we cautiously suggest exploring MPI8 further for COVID-19 preclinical tests.