CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica , Chinese Academy of Sciences (CAS) , Shanghai 201203 , China.
School of Pharmacy , University of Chinese Academy of Sciences , Beijing 100049 , China.
J Chem Theory Comput. 2018 May 8;14(5):2761-2770. doi: 10.1021/acs.jctc.8b00046. Epub 2018 Apr 27.
The crystal structure of P2Y receptor (P2YR), a class A GPCR, revealed a special extra-helical site for its antagonist, BPTU, which locates in-between the membrane and the protein. However, due to the limitation of crystallization experiments, the membrane was mimicked by use of detergents, and the information related to the binding of BPTU to the receptor in the membrane environment is rather limited. In the present work, we conducted a total of ∼7.5 μs all-atom simulations in explicit solvent using conventional molecular dynamics and multiple enhanced sampling methods, with models of BPTU and a POPC bilayer, both in the absence and presence of P2YR. Our simulations revealed that BPTU prefers partitioning into the interface of polar/lipophilic region of the lipid bilayer before associating with the receptor. Then, it interacts with the second extracellular loop of the receptor and reaches the binding site through the lipid-receptor interface. In addition, by use of funnel-metadynamics simulations which efficiently enhance the sampling of bound and unbound states, we provide a statistically accurate description of the underlying binding free energy landscape. The calculated absolute ligand-receptor binding affinity is in excellent agreement with the experimental data (Δ G = -11.5 kcal mol, Δ G= -11.7 kcal mol). Our study broadens the view of the current experimental/theoretical models and our understanding of the protein-ligand recognition mechanism in the lipid environment. The strategy used in this work is potentially applicable to investigate ligands association/dissociation with other membrane-embedded sites, allowing identification of compounds targeting membrane receptors of pharmacological interest.
P2Y 受体（P2YR）是一种 A 类 G 蛋白偶联受体，其晶体结构揭示了其拮抗剂 BPTU 的一个特殊的额外螺旋位，该位位于膜和蛋白质之间。然而，由于结晶实验的限制，膜是用去污剂模拟的，因此关于 BPTU 在膜环境中与受体结合的信息相当有限。在本工作中，我们使用传统的分子动力学和多种增强采样方法，在含有和不含有 P2YR 的情况下，分别对 BPTU 和 POPC 双层模型进行了总共约 7.5 μs 的全原子模拟。我们的模拟结果表明，BPTU 优先分配到脂质双层的极性/疏水区界面，然后与受体相互作用。然后，它与受体的第二细胞外环相互作用，并通过脂质-受体界面到达结合位点。此外，通过使用漏斗型元动力学模拟有效地增强了结合态和非结合态的采样，我们提供了一个对潜在结合自由能景观的统计上准确的描述。计算得到的绝对配体-受体结合亲和力与实验数据非常吻合（Δ G = -11.5 kcal mol，Δ G = -11.7 kcal mol）。我们的研究拓宽了当前实验/理论模型的视野，加深了我们对脂质环境中蛋白质-配体识别机制的理解。本工作中使用的策略可能适用于研究其他膜嵌入位点的配体缔合/解离，从而鉴定针对药理学感兴趣的膜受体的化合物。
