Atomistic Computational Models To Evaluate Protein-Ligand Off-Target Interactions

为了具有生物活性，小分子、蛋白质和其他细胞成分必须物理上适合于它们在靶标内的结合部位(S)。一个世纪前，费舍尔将这一事件描述为一种锁和钥匙的契合。然而，在达到其准确的结合位置时，配体(与另一种分子结合的分子)与各种结构和功能的各种细胞成分相互作用。所有这些事件都增加了配体，特别是外源性细胞来源的小分子(如合成药物)与不希望看到的脱靶物质(S)结合的可能性，从而改变了它们的细胞功能。正如2013年诺贝尔化学奖所承认的那样，计算机模拟目前非常适合于解决这些问题。我们研究的长期目标是评估小分子与关键的细胞外靶点的相互作用。然而，这项拨款申请将集中在小分子与控制正常心律的一类关键蛋白质的潜在相互作用上。我们将关注小分子对心脏离子通道的潜在阻断，这是一种可能导致获得性长QT综合征(LQTS)和致命性心律失常的关键事件。虽然LQTS通常被认为是人类Ether-à-Go-Go相关基因(HERG)通道的阻塞，但最近的研究表明，实际上需要多个离子通道的相互作用来预测QT间期的变化。我们最近对HERG离子通道的主要研究的证明为这项拨款申请提供了基础。在这里，我们建议扩大我们的努力，为所有心脏离子通道建立详细的分子模型，并在原子水平上研究它们与小分子的相互作用。具体来说，我们将重点研究人的NaV1.5钠通道、Cav1.2钙通道以及KCNQ1和Kir2.1钾通道。关于这些离子通道的现有功能和结构信息，以及它们与各种配体的巨大相互作用，以及我们建立的电生理分析，使它们成为开发和验证敏感模型的合适平台，以预测它们潜在的非靶标作用。*我们的方法包括三个主要步骤：*1.建立心脏离子通道的结构原子动力学模型。*2.评估离子通道与小分子的相互作用。*3.使用实验膜片钳分析和突变分析来验证AIMS 1和2的结果。*我们的建议的结果将对加拿大的生物科学产生重大的积极影响，由此产生的计算框架最终可能被放大并自动化，用于工业和学术界。*

To be biologically active, small molecules, proteins and other cellular components must physically fit into their binding site(s) within their targets. A century ago, Fischer described this event as a lock-and-key fit. However, in reaching its precise binding location, a ligand (a molecule that binds to another) interacts with a variety of cellular components of various structures and functions. All these events increase the probability for a ligand, particularly a small molecule of exogenous cellular origin (e.g. synthetic drugs) to bind to an undesired off-target(s), altering their cellular functions. Computer simulations are currently well suited to address these problems as recognized with the 2013 Nobel Prize in Chemistry. The long-term goal of our research is to evaluate the interaction of small molecules with critical cellular off-targets. This grant application, however, will be centered on the potential interactions of small molecules with a critical class of proteins that controls the normal heart rhythm. We will focus on the potential blockade of cardiac ion channels by small molecules, a critical event that can lead to acquired cardiac long QT syndrome (LQTS) and fatal cardiac arrhythmias. Although LQTS has been often attributed to human Ether-à-go-go-Related Gene (hERG) channel blockage, recent studies show that multiple ion channel interactions are in fact required to predict changes in QT intervals. Our recent proof of principal study on the hERG ion channel provides the foundation for this grant application. Here, we propose to expand our efforts and build detailed molecular models for all cardiac ion channels and investigate their interactions with small molecules at the atomic level. Specifically, we will focus on the human Nav1.5 sodium channel, the Cav1.2 calcium channel and the KCNQ1 and Kir2.1 potassium channels. The available functional and structural information on these ion channels along with their immense reported interactions with various ligands as well as our established electrophysiology assays make them suitable platforms to develop and validate sensitive models to predict their potential off-target roles. ***Our methodology involves three main steps:***1. Build structural atomistic dynamical models for the cardiac ion channels.***2. Evaluate the interactions of the ion channels with small molecules.***3. Validate the outcomes of Aims 1 and 2 using experimental patch clamp assay and mutational analyses.*******The outcomes of our proposal will have a significant positive impact on Canadian biological sciences and the resulting computational framework may ultimately be scaled up and automated for use in industry and academia.*****