3.7. Molecular Modeling

To clarify the binding mode of compounds to the human P2Y12 receptor, we carried out a flexible docking analysis using the Schrödinger Glide v.6.6 program with standard precision settings (Schrödinger LLC, New York, NY, USA). The two X-ray co-crystal structures of hP2Y12 were obtained from the Protein Data Bank (PDB; codes 4NTJ and 4PXZ, respectively) (http://www.rcsb.org). Ligands were minimized using a Merck Molecular Force Field (MMFF) with a dielectric constant of 80.0 using the MacroModel v.10.7 program. We selected a binding model based on the best docking score and visual inspection. All molecular graphics figures were generated using the visualizer in Discovery Studio v.4.5 (Biovia, San Diego, CA, USA).