Lee Kuo Hao, Shi Lei
Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
bioRxiv. 2023 Nov 14:2023.11.11.566699. doi: 10.1101/2023.11.11.566699.
Effective rational drug discovery targeting a specific protein hinges on understanding their functional states and distinguishing it from homologs. However, for the G protein coupled receptors, both the activation-related conformational changes (ACCs) and the intrinsic divergence among receptors can be misled or obscured by ligand-induced conformational changes (LCCs). Here, we unraveled ACCs and intrinsic divergence from LCCs of the dopamine D3 and D2 receptors (D3R and D2R), by analyzing their experimentally determined structures and the molecular dynamics simulation results of the receptors bound with different ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors including TM5e and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found pronounced outward tilting of TM6e in the D2R compared to the D3R in both experimental structures and simulations with ligands in different scaffolds. This tilting was drastically reduced in the simulations of the receptors bound with nonselective full agonist quinpirole, suggesting a misleading impact of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may obscure intrinsic divergence. In addition, our analysis showed that the impact of the nonconserved TM1 propagated to conserved Trp and Glu, both are ligand binding residues. We also found that the D2R exhibited heightened flexibility compared to the D3R in the extracellular portions of TMs 5, 6, and 7, potentially associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting D2R or D3R with more precise pharmacological profiles.
针对特定蛋白质的有效合理药物发现取决于对其功能状态的理解以及将其与同源物区分开来。然而，对于G蛋白偶联受体，激活相关的构象变化（ACCs）和受体之间的内在差异都可能被配体诱导的构象变化（LCCs）误导或掩盖。在这里，我们通过分析多巴胺D3和D2受体（D3R和D2R）的实验测定结构以及与不同配体结合的受体的分子动力学模拟结果，揭示了它们的ACCs以及与LCCs的内在差异。除了其他胺能受体共有的ACCs外，我们还揭示了这两种受体独特的ACCs，包括TM5e和TM6e远离TM2e和TM3e移动，同时TM5e有轻微旋转。在识别内在差异时，我们发现在实验结构以及与不同支架配体的模拟中，与D3R相比，D2R中的TM6e有明显的向外倾斜。在与非选择性完全激动剂喹吡罗结合的受体模拟中，这种倾斜显著减少，表明LCCs有误导性影响。此外，在与喹吡罗结合的模拟中，TM1在这些受体之间表现出更大的差异，表明LCCs可能掩盖内在差异。此外，我们的分析表明，非保守TM1的影响传播到了保守的色氨酸和谷氨酸，这两个都是配体结合残基。我们还发现，与D3R相比，D2R在TMs 5、6和7的细胞外部分表现出更高的灵活性，这可能与其更大的配体结合位点可塑性有关。我们的结果为设计具有更精确药理学特征的特异性靶向D2R或D3R的配体奠定了基础。
