TOP-100 DOCKING POSES OF FDA APPROVED DRUGS AND DRUGS IN CLINICAL INVESTIGATION AT SARS-CoV2 MAIN PROTEASE

7922 compounds were downloaded from NPC database (https://tripod.nih.gov/npc/). In order
to eliminate the non-specific binders, some criteria including molecular weight, between 100 to
1000 g/mol; number of rotatable bonds, <100; number of atoms, between 10 and 100; number
of aliphatic and aromatic rings, <10; number of hydrogen-bond acceptor and donors, <10 were
set and as a result the total number of compounds was decreased to 6654. These ligands were
prepared using LigPrep module of Maestro at neutral pH (LigPrep, Schrodinger v.2017). In
molecular docking, we used following protein structure: SARS-CoV2 Main Protease, (PDB, 6LU7). The protein
was prepared using Protein Preparation module of Maestro. PROPKA was used for
determination of protonation states of amino acid residues. Restrained minimization was
performed with OPLS3 force field for the protein using 0.3 Å heavy atom convergence.
Docking was performed with Glide/SP using default settings. Top-100 docking poses were provided.