Discovery of a Novel Trifluoromethyl Diazirine Inhibitor of SARS-CoV-2 M pro

SARS-CoV-2 M pro is a chymotrypsin-like cysteine protease playing a relevant role during the replication and infectivity of SARS-CoV-2, the coronavirus responsible for COVID-19. The binding site of M pro is characterized by the presence of a catalytic Cys145 which carries out the hydrolytic activity of the enzyme. As a consequence, several M pro inhibitors have been proposed to date in order to fight the COVID-19 pandemic. In our work, we designed, synthesized and biologically evaluated MPD112 , a novel inhibitor of SARS-CoV-2 M pro bearing a trifluoromethyl diazirine moiety. MPD112 displayed in vitro inhibition activity against SARS-CoV-2 M pro at a low micromolar level (IC 50 = 4.1 μM) in a FRET-based assay. Moreover, an inhibition assay against PL pro revealed lack of inhibition, assuring the selectivity of the compound for the M pro . Furthermore, the target compound MPD112 was docked within the binding site of the enzyme to predict the established intermolecular interactions in silico. MPD112 was subsequently tested on the HCT-8 cell line to evaluate its effect on human cells’ viability, displaying good tolerability, demonstrating the promising biological compatibility and activity of a trifluoromethyl diazirine moiety in the design and development of SARS-CoV-2 M pro binders.