Development of the Novel Nsp16 Inhibitors as Potential Anti-SARS-CoV-2 Agents

Computer aided structural based approach was used to find inhibitors of SARS-CoV-2 nsp16 (2'-O-methyltransferase). Docking based virtual screening of three libraries, Enamine Coronavirus Library, Enamine Nucleoside Mimetics Library, and Chemdiv Nucleoside Analogue Library, was performed. In total, 39350 3D-structures of low molecular weight ligands were docked into a model of nsp16 prepared using the structure of 6WKQ complex from the Protein Data Bank. Docking was performed by the SOL docking program. For the best SOL scored ligands, the protein-ligand binding enthalpy was calculated using the PM7 semiempirical quantum-chemical method with the COSMO implicit solvent model. The most promising eleven compounds were purchased and their inhibitory activity against the recombinant viral nsp16 protein was measured using MST assay with Monolith NT.115. As a result, two compounds, Z195979162 and Z1333277068, from Enamine Coronavirus Library demonstrated dissociation constants Kd for nsp16/nsp10 complex equal to 2.0 and 5.0 μM. The relative stability of these ligands in their docked positions in the nsp16 S-adenosylmethionine (SAM) binding site was confirmed in the molecular dynamics simulations along 70 ns trajectories. Z195979162 and Z1333277068 compounds belong to two chemical classes: 1,4-disubstituted tetrahydropyridines and derivatives of pyrazole-5-carboxamide, respectively, and can be good starting points for further hit optimization in the field of nsp16 inhibitors design.