Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany.
Department of Computational Biology and Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA.
Int J Mol Sci. 2020 Sep 12;21(18):6693. doi: 10.3390/ijms21186693.
The histamine H2 receptor (HR) plays an important role in the regulation of gastric acid secretion. Therefore, it is a main drug target for the treatment of gastroesophageal reflux or peptic ulcer disease. However, there is as of yet no 3D-structural information available hampering a mechanistic understanding of HR. Therefore, we created a model of the histamine-HR-G complex based on the structure of the ternary complex of the β2-adrenoceptor and investigated the conformational stability of this active GPCR conformation. Since the physiologically relevant motions with respect to ligand binding and conformational changes of GPCRs can only partly be assessed on the timescale of conventional MD (cMD) simulations, we also applied metadynamics and Gaussian accelerated molecular dynamics (GaMD) simulations. A multiple walker metadynamics simulation in combination with cMD was applied for the determination of the histamine binding mode. The preferential binding pose detected is in good agreement with previous data from site directed mutagenesis and provides a basis for rational ligand design. Inspection of the HR-G interface reveals a network of polar interactions that may contribute to HR coupling selectivity. The cMD and GaMD simulations demonstrate that the active conformation is retained on a μs-timescale in the ternary histamine-HR-G complex and in a truncated complex that contains only G helix α5 instead of the entire G protein. In contrast, histamine alone is unable to stabilize the active conformation, which is in line with previous studies of other GPCRs.
组胺 H2 受体 (HR) 在胃酸分泌的调节中起着重要作用。因此，它是治疗胃食管反流或消化性溃疡病的主要药物靶点。然而，目前还没有可用的 3D 结构信息，这阻碍了对 HR 的机制理解。因此，我们基于β2-肾上腺素能受体的三元复合物的结构创建了组胺-HR-G 复合物的模型，并研究了这种活性 GPCR 构象的构象稳定性。由于配体结合和 GPCR 构象变化的生理相关运动只能在传统 MD (cMD) 模拟的时间尺度的部分进行评估，因此我们还应用了元动力学和高斯加速分子动力学 (GaMD) 模拟。应用多步元动力学模拟与 cMD 结合，用于确定组胺的结合模式。检测到的优先结合构象与来自定向诱变的先前数据非常吻合，为合理的配体设计提供了基础。对 HR-G 界面的检查揭示了一个可能有助于 HR 偶联选择性的极性相互作用网络。cMD 和 GaMD 模拟表明，在三元组胺-HR-G 复合物和仅包含 G 螺旋 α5 而不是整个 G 蛋白的截短复合物中，活性构象在 μs 时间尺度上得以保留。相比之下，组胺本身无法稳定活性构象，这与其他 GPCR 的先前研究一致。
