Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul, Republic of Korea.
Elife. 2023 Sep 1;12:RP90773. doi: 10.7554/eLife.90773.
G-protein coupled receptors (GPCRs) present specific activation pathways and signaling among receptor subtypes. Hence, an extensive knowledge of the structural dynamics of the receptor is critical for the development of therapeutics. Here, we target the adenosine A receptor (AR), for which a negligible number of drugs have been approved. We combine molecular dynamics simulations, enhanced sampling techniques, network theory and pocket detection to decipher the activation pathway of AR, decode the allosteric networks and identify transient pockets. The AR activation pathway reveal hidden intermediate and pre-active states together with the inactive and fully-active states observed experimentally. The protein energy networks computed throughout these conformational states successfully unravel the extra and intracellular allosteric centers and the communication pathways that couples them. We observe that the allosteric networks are dynamic, being increased along activation and fine-tuned in presence of the trimeric G-proteins. Overlap of transient pockets and energy networks uncover how the allosteric coupling between pockets and distinct functional regions of the receptor is altered along activation. By an in-depth analysis of the bridge between activation pathway, energy networks and transient pockets, we provide a further understanding of AR. This information can be useful to ease the design of allosteric modulators for AR.
G 蛋白偶联受体(GPCRs)在受体亚型之间呈现出特定的激活途径和信号转导。因此,对受体结构动力学的广泛了解对于治疗药物的开发至关重要。在这里,我们以腺苷 A 受体(AR)为目标,尽管已经批准了极少数药物,但针对该受体的药物却寥寥无几。我们结合分子动力学模拟、增强采样技术、网络理论和口袋检测来破译 AR 的激活途径,解码别构网络并识别瞬时口袋。AR 的激活途径揭示了隐藏的中间和预激活状态,以及实验中观察到的非活性和完全激活状态。在这些构象状态下计算出的蛋白质能量网络成功地揭示了细胞内外的别构中心以及将它们连接起来的通讯途径。我们观察到,别构网络是动态的,随着激活而增加,并在存在三聚体 G 蛋白的情况下进行微调。瞬时口袋和能量网络的重叠揭示了沿着激活,别构偶联如何在口袋和受体不同功能区域之间发生变化。通过对激活途径、能量网络和瞬时口袋之间的桥梁进行深入分析,我们进一步了解了 AR。这些信息可用于减轻 AR 的变构调节剂的设计。