Theoretical studies of ligand-receptor interactions in sodium and calcium channels

钠和钙通道配体-受体相互作用的理论研究

• 批准号: RGPIN-2020-07100
• 负责人: Zhorov, Boris
• 金额: $ 2.33万
• 依托单位: McMaster University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2021
• 资助国家: 加拿大
• 起止时间: 2021-01-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=741595
• 关键词: Theoretical; studies; ligand; receptor; interactions

Sodium (Na) and calcium (Ca) channels play key roles in physiology of muscle and nerves. They are targets for various drugs and toxins (ligands). Cryo-electron microscopy (cryo-EM) structures of several Na and Ca channels with ligands are available, but for most of ligands atomic mechanisms remain unclear. Besides, ligand-channel interactions in deeply frozen protein samples and in living cells may differ. Computer-based modeling employing data from decades of experimental studies can be used to understand ligands' atomic mechanisms at physiological conditions. Towards this goal I propose the following program. Ca channel with cardiovascular drugs. Surprisingly, in cryo-EM structures dihydropyridines (DHPs) are far from the Ca permeation pathway and from several DHP-sensing residues whose mutations affect DHP action. Furthermore, the channel geometry with DHPs that either facilitate or block Ca current is the same. We will explore an intriguing possibility that DHPs and DHP-sensing residues affect Ca current by perturbing Ca hydration shell that is invisible in cryo-EM. Paradoxically, some cationic and electroneutral ligands target the same sites in ion channels. Earlier we proposed that cationic ligands displace Na, Ca or K and bind at their sites, while Na, Ca or K attract ligands' electronegative atoms. This mechanism is now shown for K channels, but for Na or Ca channels it is still a hypothesis. In our models verapamil binds to a Ca ion in the channel selectivity filter, but in a cryo-EM structure such contact is obstructed by a detergent molecule, which is absent in the living cell. We will dock verapamil and electroneutral ligands to the Ca channel to explore ligand-ion interactions and explain intriguing paradoxes in the ligands' structure-activity relations. Ca channel with conotoxins. Conotoxin peptides produced by marine cone snails selectivity block specific Ca channels. Intriguingly, both cationic and anionic conotoxins target the same Ca channel subtype. We will dock these conotoxins in the channel to test a hypothesis that anionic toxins bind to Ca ions in the pore, whereas cationic conotoxins displace Ca ions and bind to their sites. Na channels with ligands. The pore of Na channels is targeted by ligands of intriguingly different structure. We will model Na channel complexes with some drugs and toxins. We collaborate with Dr. Ke Dong (USA) to study action of insecticides on insect Na channels and understand how insects adapt to insecticides. We will continue this productive collaboration. We use the ZMM program, which I have created, as a principal (but not the only) computational tool. ZMM success rate in predicting ligand-protein complexes is not lower than that of better known programs. We keep adapting ZMM in-house to address computational problems of ever increasing complexity. Our studies will advance the knowledge on neuron and muscle cells regulation by ligands and assist in structure-based drug design.

钠(Na)和钙(Ca)通道在肌肉和神经生理学中起着关键作用。它们是各种药物和毒素(配体)的靶子。几种含配体的钠和钙通道的冷冻电子显微镜(Cryo-EM)结构是可用的，但对于大多数配体，其原子机制尚不清楚。此外，在冷冻蛋白质样品和活细胞中，配体-通道相互作用可能不同。基于计算机的建模使用了数十年的实验研究数据，可以用来理解配体在生理条件下的原子机制。为了实现这一目标，我提出以下方案。心血管药物的CA通道。令人惊讶的是，在低温EM结构中，二氢吡啶(DHP)远离钙渗透途径，也远离几个DHP敏感残基，这些残基的突变会影响DHP的作用。此外，具有促进或阻断钙电流的DHP的通道几何结构是相同的。我们将探索一种有趣的可能性，即DHP和DHP敏感残基通过扰乱低温EM中看不见的钙水合壳来影响钙电流。矛盾的是，一些阳离子和电子中和配体针对离子通道中的相同位置。早期我们提出了阳离子配体取代Na、Ca或K并结合在它们的位置上，而Na、Ca或K吸引配体的电负性原子。这一机制现已被证明适用于钾通道，但对于钠或钙通道，这仍是一个假设。在我们的模型中，维拉帕米与通道选择性过滤器中的钙离子结合，但在冷冻-EM结构中，这种接触被洗涤剂分子阻挡，这在活细胞中是不存在的。我们将把维拉帕米和电子中和配体对接到钙通道上，以探索配体-离子相互作用，并解释配体结构-活性关系中有趣的悖论。在CA通道中加入芋螺毒素。海洋锥螺产生的芋螺毒素多肽选择性地阻断特异性钙通道。有趣的是，阳离子和阴离子芋螺毒素都针对相同的钙通道亚型。我们将这些芋螺毒素停靠在通道中，以测试一个假说，即阴离子毒素与毛孔中的钙离子结合，而阳离子芋螺毒素取代钙离子并结合到它们的位置。有配基的NA通道。钠通道的孔被有趣的不同结构的配体作为靶标。我们将用一些药物和毒素来模拟钠离子通道复合体。我们与柯东博士(美国)合作，研究杀虫剂对昆虫钠通道的作用，了解昆虫如何适应杀虫剂。我们将继续这种富有成效的合作。我们使用我创建的ZMM程序作为主要的(但不是唯一的)计算工具。ZMM预测配基-蛋白质复合体的成功率不低于更知名的程序。我们一直在内部采用ZMM来解决日益复杂的计算问题。我们的研究将促进对神经元和肌肉细胞通过配体调节的知识，并有助于基于结构的药物设计。