Potential SARS-CoV-2 Nonstructural Protein 15 (NSP15) Inhibitors: Repurposing FDA-Approved Drugs

Purpose: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths worldwide, pushing the urgent need for an efficient treatment. Nonstructural protein 15 (NSP15) is a promising target due to its importance for SARS-CoV-2’s evasion of the host’s innate immune response. Methods: Using the crystal structure of SARS-CoV-2 NSP15 endoribonuclease, we developed a pharmacophore model of the functional centers in the NSP15 inhibitor’s binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. The conformations of these compounds underwent 3D fingerprint similarity clustering, and possible conformers were docked to the NSP15 binding pocket. We also simulated docking of random compounds to the NSP15 binding pocket for comparison. Results: This search identified 170 compounds as potential inhibitors of SARS-CoV-2 NSP15. The mean free energy of docking for the group of potential inhibitors were significantly lower than for the group of random compounds. Twenty-one of the compounds identified as potential NSP15 inhibitors were antiviral compounds used in the inhibition of a range of viruses, including MERS, SARS-CoV, and even SARS-CoV-2. Eight of the selected antiviral compounds in cluster A are pyrimidine analogues, six of which are currently used in a clinical setting. Four tyrosine kinase inhibitors were identified with potential SARS-CoV-2 inhibition, which is consistent with previous studies showing some kinase inhibitors acting as antiviral drugs. Conclusions: We recommended testing of these 21 selected antiviral compounds for the treatment of COVID-19.