Modeling ligand recognition at the P2Y₁₂ receptor in light of X-ray structural information

The G protein-coupled P2Y₁₂ receptor (P2Y₁₂R) is an important antithrombotic target and of great interest for pharmaceutical discovery. Its recently solved, highly divergent crystallographic structures in complex either with nucleotides (full or partial agonist) or with a nonnucleotide antagonist raise the question of which structure is more useful to understand ligand recognition. Therefore, we performed extensive molecular modeling studies based on these structures and mutagenesis, to predict the binding modes of major classes of P2Y₁₂R ligands previously reported. Various nucleotide derivatives docked readily to the agonist-bound P2Y₁₂R, but uncharged nucleotide-like antagonist ticagrelor required a hybrid receptor resembling the agonist-bound P2Y₁₂R except for the top portion of TM6. Supervised molecular dynamics (SuMD) of ticagrelor binding indicated interactions with the extracellular regions of P2Y₁₂R, defining possible meta-binding sites. Ureas, sulfonylureas, sulfonamides, anthraquinones and glutamic acid piperazines docked readily to the antagonist-bound P2Y₁₂R. Docking dinucleotides at both agonist- and antagonist-bound structures suggested interactions with two P2Y₁₂R pockets. Thus, our structure-based approach consistently rationalized the main structure-activity relationships within each ligand class, giving useful information for designing improved ligands. Graphical Abstract: [Figure not available: see fulltext.]