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

Abstract

Summary 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.

Inverse agonism at the P2Y12 receptor and ENT1 transporter blockade contribute to platelet inhibition by ticagrelor

“…51 Ticagrelor's bulky side chains on N6 have been suggested to cause a steric clash, with docking likely requiring P2Y 12 R helical rearrangements. 5 A study assessing P2Y 12 R function in CHO cells indicated that ticagrelor acted in a competitive manner based on functional readouts although only low concentrations of ticagrelor (,30 nM) were included in the analysis. 28 In conflicting studies, ticagrelor has been shown to display characteristics of a noncompetitive antagonist, decreasing the maximum response (E max ) as well as right-shifting the ADP concentration-response curve.…”

“…2,3 Unlike the thienopyridine P2Y 12 R antagonists (ticlopidine, clopidogrel, and prasugrel), ticagrelor binds to the P2Y 12 R in a reversible manner. 4,5 Also unlike the thienopyridines, which are all prodrugs requiring metabolic activation to exert an antiplatelet effect, ticagrelor is direct acting. In addition, its main circulating metabolite, AR-C124910XX (present in plasma at 30% to 40% of parent 6 ), has similar potency at the P2Y 12 R as ticagrelor.…”

Medicinal chemistry of adenosine, P2Y and P2X receptors

“…While, in general, 5′-diphosphates are more potent and efficacious, ATP 4 acts as a partial agonist or agonist, respectively, at the P2Y 1 R and P2Y 12 R (Waldo and Harden, 2004; Paoletta et al, 2015). ATP-γ-S 67 is also an agonist at various P2YRs, including the P2Y 1 R (Waldo and Harden, 2004).…”

“…A huge number of nucleotide and nonnucleotide antagonists of the P2Y 12 R have been reported (Paoletta et al, 2015). The reason for this focus on P2Y 12 R antagonists is their value as antithrombotic agents.…”

“…Also, both forms of X-ray structures of the P2Y 12 R have been helpful in characterizing the specific protein-ligand interactions for a wide variety of P2Y 12 R agonists and antagonists (Paoletta et al, 2015). This suggested that the new P2YR X-ray structures are suitable templates for structure-based design of new ligands.…”