Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States.
J Chem Inf Model. 2024 Mar 25;64(6):1778-1793. doi: 10.1021/acs.jcim.3c01956. Epub 2024 Mar 7.
Effective rational drug discovery hinges on understanding the functional states of the target protein and distinguishing it from homologues. However, for the G protein coupled receptors, both activation-related conformational changes (ACCs) and intrinsic divergence among receptors can be misled or obscured by ligand-specific 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 (MD) simulation results of the receptors bound with various ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors, including the extracellular portion of TM5 (TM5e) and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found more outward tilting of TM6e in the D2R compared to the D3R in both the experimental structures and simulations bound with ligands in different scaffolds. However, this difference was drastically reduced in the simulations bound with nonselective agonist quinpirole, suggesting a misleading effect of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may also obscure intrinsic divergence. Importantly, our MD simulations revealed divergence in the dynamics of these receptors. Specifically, the D2R exhibited heightened flexibility compared to the D3R in the extracellular loops and TMs 5e, 6e, and 7e, associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting the D2R and D3R with more precise pharmacological profiles.
有效的合理药物发现取决于对靶蛋白功能状态的理解，并将其与同源物区分开来。然而，对于 G 蛋白偶联受体，激活相关构象变化（ACCs）和受体之间的固有差异都可能被配体特异性构象变化（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）与其结合的各种配体的实验确定结构和分子动力学（MD）模拟结果，揭示了 LCC 中的 ACCs 和固有差异。除了与其他胺能受体共同的 ACCs 外，我们还揭示了这两种受体特有的 ACCs，包括 TM5 的细胞外部分（TM5e）和 TM6e 远离 TM2e 和 TM3e 的移动，以及 TM5e 的细微旋转。在识别固有差异时，我们发现与配体结合的不同支架相比，在实验结构和模拟中，D2R 中 TM6e 的向外倾斜度比 D3R 更大。然而，在与非选择性激动剂喹吡罗尔结合的模拟中，这种差异大大减小，表明 LCCs 具有误导作用。此外，在喹吡罗尔结合的模拟中，TM1 显示出这些受体之间更大的差异，表明 LCCs 也可能掩盖固有差异。重要的是，我们的 MD 模拟揭示了这些受体在动力学上的差异。具体来说，与 D3R 相比，D2R 在细胞外环和 TM5e、6e 和 7e 中表现出更高的灵活性，与其更大的配体结合位点可塑性有关。我们的结果为设计针对 D2R 和 D3R 的具有更精确药理学特性的配体奠定了基础。
