The P2Y12R structure was prepared using the Protein Preparation Wizard36 (link) tool implemented in the Schrödinger suite, adding all the hydrogen atoms and the missing side chains of residues whose backbone coordinates were observed in the structure. The orientation of polar hydrogens was optimized, the protein protonation states were adjusted and the overall structure was minimized with harmonic restraints on the heavy atoms, to remove strain. Then, all the hetero groups and water molecules were deleted.
The SiteMap tool of the Schrödinger suite was used to identify potential binding sites in the structure. A bifurcated cavity was identified on the extracellular side of the receptor and was selected as the docking site. Molecular docking of selected compounds (ADP, 2MeSADP, AZD1283, Ap4A and the active metabolites of clopidogrel and prasugrel) at the P2Y12R structure was performed by means of the Glide package from the Schrödinger suite. In particular, a Glide Grid was centred on the centroid of residues located within 6 Å from the previously identified cavity (considering both pocket 1 and pocket 2). The Glide Grid was built using an inner box (ligand diameter midpoint box) of 14 Å × 14 Å × 14 Å (so that both pockets could be explored) and an outer box that extended 10 Å in each direction from the inner one (so that ligands up to 20 Å could be docked). Docking of ligands was performed in the rigid binding site using the standard precision procedure. The top scoring docking conformations for each ligand were subjected to visual inspection and analysis of protein–ligand interactions to select the final binding conformations in agreement with the experimental data.
The SiteMap tool of the Schrödinger suite was used to identify potential binding sites in the structure. A bifurcated cavity was identified on the extracellular side of the receptor and was selected as the docking site. Molecular docking of selected compounds (ADP, 2MeSADP, AZD1283, Ap4A and the active metabolites of clopidogrel and prasugrel) at the P2Y12R structure was performed by means of the Glide package from the Schrödinger suite. In particular, a Glide Grid was centred on the centroid of residues located within 6 Å from the previously identified cavity (considering both pocket 1 and pocket 2). The Glide Grid was built using an inner box (ligand diameter midpoint box) of 14 Å × 14 Å × 14 Å (so that both pockets could be explored) and an outer box that extended 10 Å in each direction from the inner one (so that ligands up to 20 Å could be docked). Docking of ligands was performed in the rigid binding site using the standard precision procedure. The top scoring docking conformations for each ligand were subjected to visual inspection and analysis of protein–ligand interactions to select the final binding conformations in agreement with the experimental data.
