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

钠（Na）和钙（Ca）通道在肌肉和神经生理中起着关键作用。它们是各种药物和毒素（配体）的靶标。低温电子显微镜（cryo-EM）研究了几种具有配体的Na和Ca通道的结构，但大多数配体的原子机制尚不清楚。此外，深度冷冻的蛋白质样品和活细胞中的配体通道相互作用可能不同。利用几十年实验研究数据的计算机建模可以用来理解生理条件下配体的原子机制。为实现这一目标，我提出以下方案。钙通道与心血管药物。令人惊讶的是，在低温电镜结构中，二氢吡啶（DHPs）远离钙渗透途径和一些DHP敏感残基，这些残基的突变会影响DHP的作用。此外，具有促进或阻止Ca电流的dhp的通道几何形状是相同的。我们将探索一种有趣的可能性，即DHPs和dhp传感残基通过干扰在低温电镜中不可见的Ca水化壳来影响Ca电流。矛盾的是，一些阳离子配体和电中性配体在离子通道中靶向相同的位点。之前我们提出阳离子配体取代Na， Ca或K并在其位置结合，而Na， Ca或K吸引配体的电负性原子。这种机制现在在K通道中得到了证明，但对于Na或Ca通道，它仍然是一个假设。在我们的模型中，维拉帕米在通道选择性过滤器中与钙离子结合，但在低温电镜结构中，这种接触被活细胞中不存在的洗涤剂分子所阻碍。我们将把维拉帕米和电中性配体停靠在Ca通道上，以探索配体-离子的相互作用，并解释配体结构-活性关系中有趣的悖论。有concontoxins的Ca通道。海螺产生的螺毒素肽选择性阻断特定的钙通道。有趣的是，阳离子型和阴离子型conotoxin都针对相同的Ca通道亚型。我们将把这些concontoxins停靠在通道中，以验证一个假设，即阴离子毒素与孔中的钙离子结合，而阳离子concontoxins取代钙离子并结合到它们的位置。带有配体的Na通道。钠离子通道的孔被不同结构的配体靶向。我们将用一些药物和毒素模拟钠通道复合物。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-蛋白复合物的成功率并不低于已知的程序。我们不断调整ZMM内部，以解决日益复杂的计算问题。我们的研究将促进对配体调控神经元和肌肉细胞的认识，并有助于基于结构的药物设计。

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.