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We have applied a computational strategy, based on the synergy of virtualscreening, docking and molecular dynamics techniques, aimed at identifyingpossible lead compounds for the non-covalent inhibition of the main protease3CL-pro of the SARS-Cov2 Coronavirus. Based on the recently resolved 6LU7 PDBstructure, ligands were generated using a multimodal structure-based design andthen optimally docked to the 6LU7 monomer. Docking calculations show thatligand-binding is strikingly similar in SARS-CoV and SARS-CoV2 main proteases,irrespectively of the protonation state of the catalytic CYS-HIS dyad. The mostpotent docked ligands are found to share a common binding pattern with aromaticmoieties connected by rotatable bonds in a pseudo-linear arrangement. Moleculardynamics calculations fully confirm the stability in the 3CL-pro binding pocketof the most potent binder identified by docking, namely achlorophenyl-pyridyl-carboxamide derivative.

Inhibition of the Main Protease 3CL-pro of the Coronavirus Disease 19 via Structure-Based Ligand Design and Molecular Modeling