Exploiting Enzyme Plasticity in Drug Discovery: application to glutamate racemase

在药物发现中利用酶可塑性：在谷氨酸消旋酶中的应用

基本信息

批准号：
8534789
负责人：
Michael Ashley Spies
金额：
$ 27.02万
依托单位：
UNIVERSITY OF IOWA
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-09-01 至 2017-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8534789
关键词：
Adopted Affinity Bacillus anthracis Back Behavior Binding Biological Assay Charge Chemicals Chemistry Complex Computer Assisted Computer Simulation Data Development Diagnosis Dissociation Diversity Library Docking Drug Design Drug Targeting Electrostatics Enzymes Equilibrium Equipment and supply inventories Evaluation Failure Family Future Glutamate racemase Glutamates Goals Heptanes Hybrids Isotopes Kinetics Knowledge Lead Libraries Ligands Mammalian Cell Methods Mining Modeling Molecular Conformation Motion Pharmaceutical Preparations Phase Physics Property Protein Isoforms Proteins Publishing Race Reaction Research Resources Screening Result Shapes Solutions Solvents Structure Testing Therapeutic Toxic effect analog antimicrobial antimicrobial drug base carbanion computational chemistry design drug development drug discovery enzyme mechanism falls feeding flexibility in vitro Assay inhibitor/antagonist meetings mimicry novel pharmacophore programs racemization receptor scaffold screening small molecule stem virtual

项目摘要

DESCRIPTION (provided by applicant): We propose to develop a new class of antimicrobial drugs based on the fundamental principles of transition state analysis. Rather than "structure-based" drug design, which is based largely on substrate mimicry, transition-state analysis is "reaction-based" drug design, stemming from a rigorous chemical evaluation of the relevant catalytic chemistry to reveal the enzyme mechanism and the structural changes that stabilize a transition state. Transition state analysis will yield small molecule transition state analogs that closely mimic the transition state structure. For the proposed studies we selected Glutamate Racemase (GR), an increasingly important antimicrobial drug target. GR has been widely validated to be an attractive drug target in numerous pathogenic species. GR-catalyzed racemization is primarily achieved through extensive flexibility, which is information that is largely absent from GR crystal structures. Recent studies by our research group have strongly suggested that a more chemically diverse inhibitor space can be discovered against GR by considering its transition state structure in virtual screening campaigns. These studies have produced a potentially powerful approach for the discovery of diverse inhibitory scaffolds with high ligand efficiency, which provides a solution to the problems of meeting the relatively narrow requirements of antimicrobial drug space. However, the enormous potential of virtual screening methods are significantly hindered by the pronounced failures to relatively rapidly make quality predictions about protein-ligand affinities. This proposal directly fills two significant and related knowledge gaps that hinder discovery of true transition state inhibitors for GR: 1) determination of an experimentally validated transition state structure for GR, and the transition state pharmacophore that leads to the ultra tight binding along the reaction trajectory and 2) how to accurately rank-order hits from virtual screening against a highly flexible protein receptor. The successful completion of the proposed studies will enable the discovery and design of novel high efficiency inhibitory scaffolds for flexible enzyme drug targets, and thus yield transformative results in the field of drug discovery. The specific aims for this proposal are as follows: Aim 1: An integrated computational approach to solve the rank-order problem for a flexible enzyme drug target: the Flexible Enzyme Receptor Method (FERM) for Steered MD (SMD)-Docking. Aim 2: A FERM Challenge: a conformational inventory of GR using a library of conformationally restricted glutamate analogs (the spiro[3.3]heptane family) Aim 3: Elucidation of the Transition State Pharmacophore for GR (B. subtilis RacE and B. anthracis RacE1 and RacE2) via Kinetic Isotope Effects. Aim 4: Bringing it all together: the application of FERM-SMD Docking against the GR transition state pharmacophore and ground state ensembles.

描述（由申请人提供）：我们建议根据过渡状态分析的基本原理开发一类新的抗菌药物。过渡状态分析不是基于底物模仿的“基于结构”的药物设计，而是基于反应的药物设计，这是源于对相关催化化学的严格化学评估，以揭示酶机制和结构性变化，从而稳定过渡状态。过渡态分析将产生小分子过渡态类似物，这些类似物非常模仿过渡态结构。对于拟议的研究，我们选择了谷氨酸种族酶（GR），这是一个越来越重要的抗菌药物靶标。 GR已被广泛证实是许多致病物种中有吸引力的药物靶标。 GR催化的种族化主要是通过广泛的灵活性来实现的，该信息在很大程度上没有GR晶体结构。我们的研究小组的最新研究强烈建议，可以通过在虚拟筛选运动中考虑其过渡状态结构来发现更多样化的抑制剂空间。这些研究为发现具有高配体效率的不同抑制性支架的抑制作用提供了一种潜在的强大方法，这为满足抗菌药物空间的相对狭窄需求的问题提供了解决方案。但是，虚拟筛选方法的巨大潜力受到明显的失败的明显阻碍，从而相对迅速地对蛋白质配体亲和力做出了质量预测。该提案直接填补了两个显着且相关的知识差距，这些差距阻碍了GR的真正过渡状态抑制剂：1）确定GR的实验验证的过渡状态结构，以及过渡状态的药学团，从而导致沿着反应轨迹沿反应轨迹的超紧密结合和2）如何从虚拟筛选中进行虚拟筛选抗固定的蛋白质受体，从而如何准确地筛选。拟议的研究的成功完成将使新型高效抑制支架的发现和设计用于柔性酶药物靶标，从而在药物发现领域产生变革性的结果。该提案的具体目的如下：目标1：一种综合计算方法来解决柔性酶药物靶标的等级问题：用于转导的MD（SMD）dock的柔性酶受体法（FERM）。 AIM 2：FERM挑战：使用构型受限的谷氨酸类似物（Spiro [3.3] Heptane家族）的GR构象清单AIM 3：通过动力学同位素效应阐明GR（B. untilis Race和Anthracis Race1和Race2）的GR（B. untilis Race1和b。AnthracisRace1和Race2）的过渡状态药物实现。 AIM 4：将所有内容结合在一起：FERM-SMD对接对GR过渡状态药理和基态合奏的应用。