Discovery of novel SARS-CoV-2 inhibitors targeting the main protease Mpro by virtual screenings and hit optimization

Two years after its emergence, SARS-CoV-2 still represents a serious and global threat to human health. Antiviral drug development usually takes a long time and, to increase the chances of success, chemical variability of hit compounds represents a valuable source for the discovery of new antivirals. In this work, we applied a platform of variably oriented virtual screening campaigns to seek for novel chemical scaffolds for SARS-CoV-2 main protease (M-pro) inhibitors. The study on the resulting 30 best hits led to the identification of a series of struc-turally unrelated M-pro inhibitors. Some of them exhibited antiviral activity in the low micromolar range against SARS-CoV-2 and other human coronaviruses (HCoVs) in different cell lines. Time-of-addition experiments demonstrated an antiviral effect during the viral replication cycle at a time frame consistent with the inhibition of SARS-CoV-2 M-pro activity. As a proof-of-concept, to validate the pharmaceutical potential of the selected hits against SARS-CoV-2, we rationally optimized one of the hit compounds and obtained two potent SARS-CoV-2 inhibitors with increased activity against M-pro both in vitro and in a cellular context, as well as against SARS- CoV-2 replication in infected cells. This study significantly contributes to the expansion of the chemical vari-ability of SARS-CoV-2 M-pro inhibitors and provides new scaffolds to be exploited for pan-coronavirus antiviral drug development.

Automated summary

Two years after its emergence, SARS-CoV-2 still poses a serious global threat to human health. In this study, researchers used a virtual screening platform to identify new chemical scaffolds with potential as inhibitors of the SARS-CoV-2 main protease (M-pro). Several of these compounds exhibited antiviral activity against SARS-CoV-2 and other human coronaviruses in different cell lines. Time-of-addition experiments showed that these compounds had an antiviral effect during the viral replication cycle. By optimizing one of the hit compounds, the researchers obtained two potent SARS-CoV-2 inhibitors with increased activity against M-pro in vitro and in infected cells. This study significantly expands the chemical diversity of SARS-CoV-2 M-pro inhibitors and provides new scaffolds for pan-coronavirus antiviral drug development.