Excitatory signaling mediated by N-methyl-d-aspartate receptor (NMDAR) is critical for brain development and function, as well as for neurological diseases and disorders. Channel blockers of NMDARs are of medical interest owing to their potential for treating depression, Alzheimer’s disease, and epilepsy. However, precise mechanisms underlying binding and channel blockade have remained limited owing to challenges in obtaining high-resolution structures at the binding site within the transmembrane domains. Here, we monitor the binding of three clinically important channel blockers: phencyclidine, ketamine, and memantine in GluN1-2B NMDARs at local resolutions of 2.5–3.5 Å around the binding site using single-particle electron cryo-microscopy, molecular dynamics simulations, and electrophysiology. The channel blockers form different extents of interactions with the pore-lining residues, which control mostly off-speeds but not on-speeds. Our comparative analyses of the three unique NMDAR channel blockers provide a blueprint for developing therapeutic compounds with minimal side effects.

由N -甲基 - d介导的兴奋性信号- 天冬氨酸受体 (NMDAR) 对大脑发育和功能以及神经系统疾病和失调至关重要。NMDARs 的通道阻滞剂因其治疗抑郁症、阿尔茨海默病和癫痫症的潜力而具有医学意义。然而，由于在跨膜域内的结合位点获得高分辨率结构的挑战，结合和通道阻断的精确机制仍然有限。在这里，我们使用单粒子电子冷冻显微镜、分子动力学模拟和在结合位点周围以 2.5-3.5 Å 的局部分辨率监测 GluN1-2B NMDAR 中三种临床上重要的通道阻滞剂：苯环利定、氯胺酮和美金刚胺的结合，以及电生理学。通道阻滞剂与孔隙衬里残基形成不同程度的相互作用，它主要控制关闭速度但不控制开启速度。我们对三种独特的 NMDAR 通道阻滞剂的比较分析为开发副作用最小的治疗化合物提供了蓝图。