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: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=744188
• 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）通道在肌肉和神经的生理学中起关键作用。它们是各种药物和毒素（配体）的靶标。低温电子显微镜（cryo-EM）结构的几个钠和钙通道配体是可用的，但大多数配体的原子机制仍然不清楚。此外，深冻蛋白质样品和活细胞中的配体-通道相互作用可能不同。基于计算机的建模采用了几十年的实验研究数据，可以用来了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。 钙通道与心血管药物。令人惊讶的是，在冷冻EM结构中，二氢吡啶（DHP）远离Ca渗透途径和几个DHP敏感残基，其突变影响DHP作用。此外，具有促进或阻断Ca电流的DHP的通道几何形状是相同的。我们将探索一个有趣的可能性，DHP和DHP敏感残基影响钙电流扰动钙水合壳，是看不见的冷冻EM。 特别地，一些阳离子和电中性配体靶向离子通道中的相同位点。早先我们提出，阳离子配体取代Na、Ca或K并结合在它们的位点，而Na、Ca或K吸引配体的电负性原子。现在，K通道显示了这种机制，但对于Na或Ca通道，它仍然是一种假设。在我们的模型中，维拉帕米在通道选择性过滤器中与Ca离子结合，但在冷冻EM结构中，这种接触受到活细胞中不存在的去污剂分子的阻碍。我们将维拉帕米和电中性配体对接到Ca通道，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。钙通道与芋螺毒素。海洋芋螺产生的芋螺毒素肽选择性阻断特异性钙通道。有趣的是，阳离子和阴离子芋螺毒素都靶向相同的Ca通道亚型。我们将这些芋螺毒素对接在通道中，以测试一个假设，即阴离子毒素结合到孔中的Ca离子，而阳离子芋螺毒素取代Ca离子并结合到它们的网站。 带配体的钠通道。Na通道的孔被具有有趣的不同结构的配体靶向。我们将模拟钠通道复合物与一些药物和毒素。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预测配体-蛋白质复合物的成功率不低于更好的程序。我们不断在内部调整ZMM，以解决日益复杂的计算问题。 我们的研究将推进有关配体调节神经元和肌肉细胞的知识，并协助基于结构的药物设计。