The isolated S-protein model 6MOJ was obtained from the protein data bank and the ligands were obtained from the ZINC15 database. The S-protein was converted to from PDB to PDBQT format using AutoDock tools. The ligands were first converted from SDF to PDB using the ” Online SMILES Translator and Structure File Generator” supplied by the NIH and then converted from PDB to PDBQT using AutoDock tools.
In all ligands, all water was removed from the space. Polar hydrogens were added and non-polar hydrogens were merged. Kollman charges were assigned for the amino acids in the protein, and Gasteiger charges were computed for each of the ligands.
The gridbox corresponding to the S-protein’s receptor binding domain was then built around amino acids 331-5241. We created a configuration file to run Vina on with the coordinates from the gridbox and set the exhaustiveness to 20 (Figure 1).
All top scoring modes were then further analyzed with molecular visualization software PyMOL. The amino acids that bound with the ligands were selected and sequenced to see if they resided within our RBD of amino acids 331-524.