Discovery of Drug-like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3

The Mac1 domain of the multifunctional SARS-CoV-2 non-structural protein 3 (nsp3) is a potential COVID-19 drug target because it is suspected to enhance the ability of the virus to evade the human immune system The SARS-CoV-2 Mac1 domain binds ADP-ribose and proteins harboring this important post-translational modification Small molecules that bind the Mac1 domain in place of ADP-ribose might therefore be useful as molecular probes or scaffolds for antiviral drug discovery Two high throughput screens were used here to identify such ligands in small libraries of drugs and drug-like compounds The first screen used differential scanning fluorimetry (DSF, aka the thermal shift or ThermoFluor assay) to examine the melting temperature of SARS-CoV-2 Mac1 domain in the presence of various compounds In the second screen, various high-resolution SARS-CoV-2 Mac1 structures were used with Autodock VINA to identify potential ligands Numerous hit compounds were either steroids (estradiol valerate & flunisolide), beta-lactams (cefaclor & cefatrizine), or benzimidazoles (telmisartan, rabeprazole, omeprazole, & esomeprazole) Isothermal titration calorimetry was used to confirm that rabeprazole, omeprazole, and compounds in other chemical classes, such as irinotecan, nifedipine, trifluoperazine, bind SARS-CoV-2 Mac1 with an affinity similar to ADP-ribose