Department of Physics, Université de Montréal, Montréal, Canada.
Department of Pharmacology and Physiology, Université de Montréal, Montréal, Canada.
Sci Rep. 2019 Jan 24;9(1):465. doi: 10.1038/s41598-018-37116-2.
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels mediate rhythmic electrical activity of cardiac pacemaker cells, and in neurons play important roles in setting resting membrane potentials, dendritic integration, neuronal pacemaking, and establishing action potential threshold. Block of HCN channels slows the heart rate and is currently used to treat angina. However, HCN block also provides a promising approach to the treatment of neuronal disorders including epilepsy and neuropathic pain. While several molecules that block HCN channels have been identified, including clonidine and its derivative alinidine, lidocaine, mepivacaine, bupivacaine, ZD7288, ivabradine, zatebradine, and cilobradine, their low affinity and lack of specificity prevents wide-spread use. Different studies suggest that the binding sites of these inhibitors are located in the inner vestibule of HCN channels, but the molecular details of their binding remain unknown. We used computational docking experiments to assess the binding sites and mode of binding of these inhibitors against the recently solved atomic structure of human HCN1 channels, and a homology model of the open pore derived from a closely related CNG channel. We identify a possible hydrophobic groove in the pore cavity that plays an important role in conformationally restricting the location and orientation of drugs bound to the inner vestibule. Our results also help explain the molecular basis of the low-affinity binding of these inhibitors, paving the way for the development of higher affinity molecules.
超极化激活环核苷酸门控 (HCN) 通道介导心脏起搏细胞的节律性电活动，在神经元中，在设定静息膜电位、树突整合、神经元起搏和建立动作电位阈值方面发挥着重要作用。HCN 通道阻断可减缓心率，目前用于治疗心绞痛。然而，HCN 阻断也为治疗包括癫痫和神经性疼痛在内的神经元疾病提供了一种很有前途的方法。虽然已经鉴定出几种阻断 HCN 通道的分子，包括可乐定及其衍生物阿林定、利多卡因、甲哌卡因、布比卡因、ZD7288、伊伐布雷定、扎泰布定和西洛布定，但它们的亲和力低且缺乏特异性，限制了其广泛应用。不同的研究表明，这些抑制剂的结合位点位于 HCN 通道的内前庭，但它们的结合分子细节仍不清楚。我们使用计算对接实验来评估这些抑制剂与最近解决的人源 HCN1 通道原子结构以及源自密切相关的 CNG 通道的开放孔的同源模型的结合位点和结合模式。我们确定了孔腔内的一个可能的疏水性凹槽，该凹槽在构象上限制了与内前庭结合的药物的位置和取向方面起着重要作用。我们的研究结果还帮助解释了这些抑制剂低亲和力结合的分子基础，为开发更高亲和力的分子铺平了道路。
