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Agonist-bound structure of the human P2Y12 receptor.

Zhang J, Zhang K, Gao ZG, Paoletta S, Zhang D, Han GW, Li T, Ma L, Zhang W, Müller CE, Yang H, Jiang H, Cherezov V, Katritch V, Jacobson KA, Stevens RC, Wu B, Zhao Q - Nature (2014)

Bottom Line: Agonist and non-nucleotide antagonist adopt different orientations in the P2Y12R, with only partially overlapped binding pockets.The agonist-bound P2Y12R structure answers long-standing questions surrounding P2Y12R-agonist recognition, and reveals interactions with several residues that had not been reported to be involved in agonist binding.As a first example, to our knowledge, of a GPCR in which agonist access to the binding pocket requires large-scale rearrangements in the highly malleable extracellular region, the structural and docking studies will therefore provide invaluable insight into the pharmacology and mechanisms of action of agonists and different classes of antagonists for the P2Y12R and potentially for other closely related P2YRs.

View Article: PubMed Central - PubMed

Affiliation: 1] CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China [2].

ABSTRACT
The P2Y12 receptor (P2Y12R), one of eight members of the P2YR family expressed in humans, is one of the most prominent clinical drug targets for inhibition of platelet aggregation. Although mutagenesis and modelling studies of the P2Y12R provided useful insights into ligand binding, the agonist and antagonist recognition and function at the P2Y12R remain poorly understood at the molecular level. Here we report the structures of the human P2Y12R in complex with the full agonist 2-methylthio-adenosine-5'-diphosphate (2MeSADP, a close analogue of endogenous agonist ADP) at 2.5 Å resolution, and the corresponding ATP derivative 2-methylthio-adenosine-5'-triphosphate (2MeSATP) at 3.1 Å resolution. These structures, together with the structure of the P2Y12R with antagonist ethyl 6-(4-((benzylsulfonyl)carbamoyl)piperidin-1-yl)-5-cyano-2-methylnicotinate (AZD1283), reveal striking conformational changes between nucleotide and non-nucleotide ligand complexes in the extracellular regions. Further analysis of these changes provides insight into a distinct ligand binding landscape in the δ-group of class A G-protein-coupled receptors (GPCRs). Agonist and non-nucleotide antagonist adopt different orientations in the P2Y12R, with only partially overlapped binding pockets. The agonist-bound P2Y12R structure answers long-standing questions surrounding P2Y12R-agonist recognition, and reveals interactions with several residues that had not been reported to be involved in agonist binding. As a first example, to our knowledge, of a GPCR in which agonist access to the binding pocket requires large-scale rearrangements in the highly malleable extracellular region, the structural and docking studies will therefore provide invaluable insight into the pharmacology and mechanisms of action of agonists and different classes of antagonists for the P2Y12R and potentially for other closely related P2YRs.

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Ligands used in the docking studies. The chemical structures of parts of ligands that are discussed and used in the docking studies are shown. Ticagrelor and AR-C78511 could not be docked in a conformation similar to 2MeSADP because the presence of their bulky N6 substituents would cause a steric clash with helices V and VI. AR-C78511 was previously shown to lack partial agonist properties.
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Figure 12: Ligands used in the docking studies. The chemical structures of parts of ligands that are discussed and used in the docking studies are shown. Ticagrelor and AR-C78511 could not be docked in a conformation similar to 2MeSADP because the presence of their bulky N6 substituents would cause a steric clash with helices V and VI. AR-C78511 was previously shown to lack partial agonist properties.

Mentions: The 2MeSADP binding cavity appears to accommodate a number of other nucleotide ligands that mimic a triphosphate chain, including AR-C67085 and Cangrelor27 (Extended Data Fig. 7 and 8). However, the nucleoside antagonist Ticagrelor does not dock with a similar conformation to 2MeSADP in the P2Y12R due to the bulky N6 substituent, unless a helical rearrangement occurs, particularly in helix VI. This docking observation suggests that reduction of agonist efficacy of these ligands is likely facilitated by N6 substitutions in the nucleoside scaffold27. Consistently, we have shown that non-nucleotides AZD1283 and Ticagrelor behave as competitive P2Y12R antagonists. Thus, we predict that the ligand-bound receptor conformations and consequently pharmacology of nucleotide-mimetic and non-nucleotide antagonists will be divergent.


Agonist-bound structure of the human P2Y12 receptor.

Zhang J, Zhang K, Gao ZG, Paoletta S, Zhang D, Han GW, Li T, Ma L, Zhang W, Müller CE, Yang H, Jiang H, Cherezov V, Katritch V, Jacobson KA, Stevens RC, Wu B, Zhao Q - Nature (2014)

Ligands used in the docking studies. The chemical structures of parts of ligands that are discussed and used in the docking studies are shown. Ticagrelor and AR-C78511 could not be docked in a conformation similar to 2MeSADP because the presence of their bulky N6 substituents would cause a steric clash with helices V and VI. AR-C78511 was previously shown to lack partial agonist properties.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4128917&req=5

Figure 12: Ligands used in the docking studies. The chemical structures of parts of ligands that are discussed and used in the docking studies are shown. Ticagrelor and AR-C78511 could not be docked in a conformation similar to 2MeSADP because the presence of their bulky N6 substituents would cause a steric clash with helices V and VI. AR-C78511 was previously shown to lack partial agonist properties.
Mentions: The 2MeSADP binding cavity appears to accommodate a number of other nucleotide ligands that mimic a triphosphate chain, including AR-C67085 and Cangrelor27 (Extended Data Fig. 7 and 8). However, the nucleoside antagonist Ticagrelor does not dock with a similar conformation to 2MeSADP in the P2Y12R due to the bulky N6 substituent, unless a helical rearrangement occurs, particularly in helix VI. This docking observation suggests that reduction of agonist efficacy of these ligands is likely facilitated by N6 substitutions in the nucleoside scaffold27. Consistently, we have shown that non-nucleotides AZD1283 and Ticagrelor behave as competitive P2Y12R antagonists. Thus, we predict that the ligand-bound receptor conformations and consequently pharmacology of nucleotide-mimetic and non-nucleotide antagonists will be divergent.

Bottom Line: Agonist and non-nucleotide antagonist adopt different orientations in the P2Y12R, with only partially overlapped binding pockets.The agonist-bound P2Y12R structure answers long-standing questions surrounding P2Y12R-agonist recognition, and reveals interactions with several residues that had not been reported to be involved in agonist binding.As a first example, to our knowledge, of a GPCR in which agonist access to the binding pocket requires large-scale rearrangements in the highly malleable extracellular region, the structural and docking studies will therefore provide invaluable insight into the pharmacology and mechanisms of action of agonists and different classes of antagonists for the P2Y12R and potentially for other closely related P2YRs.

View Article: PubMed Central - PubMed

Affiliation: 1] CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China [2].

ABSTRACT
The P2Y12 receptor (P2Y12R), one of eight members of the P2YR family expressed in humans, is one of the most prominent clinical drug targets for inhibition of platelet aggregation. Although mutagenesis and modelling studies of the P2Y12R provided useful insights into ligand binding, the agonist and antagonist recognition and function at the P2Y12R remain poorly understood at the molecular level. Here we report the structures of the human P2Y12R in complex with the full agonist 2-methylthio-adenosine-5'-diphosphate (2MeSADP, a close analogue of endogenous agonist ADP) at 2.5 Å resolution, and the corresponding ATP derivative 2-methylthio-adenosine-5'-triphosphate (2MeSATP) at 3.1 Å resolution. These structures, together with the structure of the P2Y12R with antagonist ethyl 6-(4-((benzylsulfonyl)carbamoyl)piperidin-1-yl)-5-cyano-2-methylnicotinate (AZD1283), reveal striking conformational changes between nucleotide and non-nucleotide ligand complexes in the extracellular regions. Further analysis of these changes provides insight into a distinct ligand binding landscape in the δ-group of class A G-protein-coupled receptors (GPCRs). Agonist and non-nucleotide antagonist adopt different orientations in the P2Y12R, with only partially overlapped binding pockets. The agonist-bound P2Y12R structure answers long-standing questions surrounding P2Y12R-agonist recognition, and reveals interactions with several residues that had not been reported to be involved in agonist binding. As a first example, to our knowledge, of a GPCR in which agonist access to the binding pocket requires large-scale rearrangements in the highly malleable extracellular region, the structural and docking studies will therefore provide invaluable insight into the pharmacology and mechanisms of action of agonists and different classes of antagonists for the P2Y12R and potentially for other closely related P2YRs.

Show MeSH
Related in: MedlinePlus