Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
J Comput Aided Mol Des. 2011 Apr;25(4):329-38. doi: 10.1007/s10822-011-9423-3. Epub 2011 Apr 3.
The P2Y(12) receptor (P2Y(12)R) is an ADP-activated G protein-coupled receptor (GPCR) that is an important target for antithrombotic drugs. Three homology models of P2Y(12)R were compared, based on different GPCR structural templates: bovine rhodopsin (bRHO), human A(2A) adenosine receptor (A(2A)AR), and human C-X-C chemokine receptor type 4 (CXCR4). By criteria of sequence analysis (25.6% identity in transmembrane region), deviation from helicity in the second transmembrane helix (TM2), docked poses of ligands highlighting the role of key residues, accessibility of a conserved disulfide bridge that is reactive toward irreversibly-binding antagonists, and the presence of a shared disulfide bridge between the third extracellular loop (EL3) and the N-terminus, the CXCR4-based model appeared to be the most consistent with known characteristics of P2Y(12)R. The docked poses of agonist 2MeSADP and charged anthraquinone antagonist PSB-0739 in the binding pocket of P2Y(12)R-CXC agree with previously published site-directed mutagenesis studies of Arg256 and Lys280. A sulfonate at position 2 of the anthraquinone core created a strong interaction with the Lys174(EL2) side chain. The docking poses of the irreversibly-binding, active metabolite (existing as two diastereoisomers in vivo) of the clinically utilized antagonist Clopidogrel were compared. The free thiol group of the 4S diastereoisomer, but not the 4R isomer, was found in close proximity (~4.7 Å) to the sulfur atom of a disulfide bridge involving Cys175, suggesting greater activity in covalent binding. Therefore, ligand docking to the CXCR4-based model of the P2Y(12)R predicted poses of both reversibly and irreversibly-binding small molecules, consistent with observed pharmacology and mutagenesis studies.
P2Y(12) 受体（P2Y(12)R）是一种 ADP 激活的 G 蛋白偶联受体（GPCR），是抗血栓药物的重要靶点。基于不同的 GPCR 结构模板，比较了 P2Y(12)R 的三个同源模型：牛视紫红质（bRHO）、人 A(2A) 腺苷受体（A(2A)AR）和人 C-X-C 趋化因子受体 4（CXCR4）。根据序列分析（跨膜区 25.6%的同一性）、第二个跨膜螺旋（TM2）中螺旋偏离、配体对接构象突出关键残基的作用、可及性保守二硫键对不可逆结合拮抗剂的反应性以及第三细胞外环（EL3）和 N 端之间共享二硫键的存在，基于 CXCR4 的模型似乎与已知的 P2Y(12)R 特征最一致。激动剂 2MeSADP 和带电荷的蒽醌拮抗剂 PSB-0739 在 P2Y(12)R-CXC 结合口袋中的对接构象与先前发表的 Arg256 和 Lys280 的定点突变研究一致。蒽醌核心 2 位上的磺酸基与 Lys174(EL2)侧链形成强烈相互作用。比较了临床上使用的拮抗剂氯吡格雷的不可逆结合、活性代谢物（在体内存在两种非对映异构体）的对接构象。发现 4S 非对映异构体的游离巯基而非 4R 异构体与涉及 Cys175 的二硫键的硫原子非常接近（~4.7 Å），表明在共价结合中具有更高的活性。因此，配体对接到基于 CXCR4 的 P2Y(12)R 模型预测了可逆和不可逆结合小分子的构象，与观察到的药理学和突变研究一致。
