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

评估蛋白质-配体脱靶相互作用的原子计算模型

• 批准号: RGPGP-2015-00055
• 负责人: Barakat, Khaled
• 金额: $ 2.19万
• 依托单位: University of Alberta
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Group
• 财政年份: 2016
• 资助国家: 加拿大
• 起止时间: 2016-01-01 至 2017-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=612459
• 关键词: Atomistic; Computational; Models; Evaluate; Protein

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.

为了具有生物活性，小分子、蛋白质和其他细胞组分必须在物理上适合其靶标内的结合位点。一个世纪前，费舍尔将这一事件描述为一个锁和钥匙的配合。然而，在到达其精确的结合位置时，配体（与另一个分子结合的分子）与各种结构和功能的各种细胞组分相互作用。所有这些事件增加了配体，特别是外源性细胞来源的小分子（例如合成药物）与不期望的脱靶结合的可能性，改变了它们的细胞功能。计算机模拟目前非常适合解决这些问题，这一点在2013年诺贝尔化学奖中得到了认可。我们研究的长期目标是评估小分子与关键细胞脱靶的相互作用。然而，这项拨款申请将集中在小分子与控制正常心律的关键蛋白质类的潜在相互作用上。我们将重点关注小分子对心脏离子通道的潜在阻断，这是一种可导致获得性心脏长QT综合征（LQTS）和致命性心律失常的关键事件。虽然LQTS通常归因于人类Ether-à-go-go-Related Gene（hERG）通道阻断，但最近的研究表明，实际上需要多个离子通道相互作用来预测QT间期的变化。我们最近对hERG离子通道的主要研究证明为该资助申请提供了基础。在这里，我们建议扩大我们的努力，并建立详细的分子模型，为所有的心脏离子通道，并研究它们与小分子在原子水平上的相互作用。具体而言，我们将重点关注人类Nav1.5钠通道，Cav1.2钙通道以及KCNQ 1和Kir2.1钾通道。关于这些离子通道的可用功能和结构信息沿着它们与各种配体的大量报道的相互作用以及我们建立的电生理学测定使它们成为开发和验证敏感模型以预测其潜在脱靶作用的合适平台。 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.评价离子通道与小分子的相互作用。 3.使用实验性膜片钳测定和突变分析验证目标1和2的结果。 我们提案的结果将对加拿大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会扩大规模并自动化，供工业界和学术界使用。