Chelator Fragment Libraries for Optimizing Metal-Ligand Interactions in Metallopr

用于优化 Metallopr 中金属-配体相互作用的螯合剂片段库

• 批准号: 8154112
• 负责人: SETH M COHEN
• 金额: $ 28.21万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-01 至 2015-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8154112
• 关键词: AIDS/HIV problem; Achievement; Active Sites; Address; Affinity; Area; Arthritis; Bacterial Infections; Binding; Bioinorganic Chemistry; Calorimetry; Chelating Agents; Chemicals; Collaborations; Communities; Complex; Computer Simulation; Crystallography; Data; Development; Disease; Docking; Enzymes; Evaluation; Goals; Heart Diseases; Ions; Knowledge; Laboratories; Lead; Length; Letters; Libraries; Ligands; Malignant Neoplasms; Matrix Metalloproteinases; Metalloproteins; Metals; Methods; Modeling; Molecular; Molecular Conformation; Pathology; Pharmaceutical Chemistry; Proteins; Research; Screening procedure; Stromelysin 1; Structural Models; Structure; System; Testing; Therapeutic; Thermodynamics; Time; Titrations; Work; base; carbonate dehydratase; design; drug development; experience; improved; inhibitor/antagonist; insight; interest; metal chelator; metalloenzyme; novel; novel strategies; preference; programs; restraint; scaffold; therapeutic target

DESCRIPTION (provided by applicant): This proposal is focused on developing new approaches and strategies to the discovery of metalloprotein inhibitors. Metalloproteins are an important class of medicinal targets that are relevant to treating numerous diseases including cancer, arthritis, bacterial infections, and many others. Most therapeutics that inhibit metalloproteins use a metal-binding group (MBG) to bind to the active site metal ion. Despite the importance of these MBGs, very few studies have developed methods to identify, optimize, and understand what MBGs are best for a given metalloprotein of interest. This proposal seeks to answer the 'what, why, and how' about the MBGs used in metalloprotein inhibitors, namely: a) WHAT MBGs best inhibit a given metalloprotein? b) WHY some MBGs give the best inhibition against a certain metalloprotein? c) HOW can the discovery, evaluation, and development of MBGs be accelerated from hit-to-lead? Answering these questions will address a fundamental problem at the intersection of medicinal and bioinorganic chemistry. Our research group is experienced in the field of metalloprotein inhibitors, and we have made substantial progress toward answering the aforementioned questions. Fundamentally, our laboratory is pursuing a fragment-based lead discovery (FBLD) approach to inhibitor development, where for the first time, metal chelators are being used as fragments that will explore chemical space targeted to binding metalloprotein active sites. In implementing this approach we have developed a chelator-fragment library (CFL) that can be readily screened against metalloproteins to identify what MBGs bind best to a given target. We have also determined the structure of an MBG in the active site of a metalloprotein to understand why the MBG binds with high affinity to the active site. Next, we have used and combination of bioinorganic model complexes and computational docking approaches to develop improved methods to determine how the discovery of MBG fragments can be developed into lead inhibitors. Finally, we have combined all of the aforementioned studies to prepare chelator sublibraries that provide more advanced fragment hits that probe beyond the metal ion active site. In our ongoing studies we will screen our libraries against a large number of metalloproteins (Aim 1, Aim 4), but will focus our more detailed studies on two specific Zn2+dependent systems (Aim 2, Aim 3), the matrix metalloproteinases (MMPs) and carbonic anhydrases (CAs). These metalloproteins, which share a common metal active site motif, but different MBG preferences, will serve as excellent systems against which to test our ideas and compare and contrast the details of MBG binding. We propose to: 1. Develop and screen chelator fragment libraries (CFLs) against a wide range of metalloprotein targets. Using existing and new CFLs, screens against more than ten different metalloenzymes will be performed to reveal what MBGs bind best to various targets. 2. Perform structural and thermodynamic studies with proteins to obtain a molecular understanding of why a given MBG binds tightly to a given metalloprotein active site. Hits from CFLs will be examined with MMP-3 and hCAI, where: a) crystallographic structure determinations with co-crystallized MBGs will reveal key features of MBG-metalloprotein binding, and b) thermodynamic studies via isothermal titration calorimetry will provide binding constants and relevant energetic parameters. 3. Model MBG fragments in the MMP and CA active site to compare with structural data obtained from protein crystallography. Synthetic bioinorganic model compounds will be crystallized providing structural data on the unrestrained mode of MBG binding, while computational docking studies will be used to predict the overall conformation and second coordination sphere interactions between the MBG and the metalloprotein. By combining bioinorganic modeling and computational docking we will try to accurately recapitulate the crystallographic data. 4. Sublibraries containing MBG derivatives will be prepared to advance these scaffolds from hit- to-lead. Elaboration of MBG scaffolds will produce sublibraries containing compounds that can be screened against metalloproteins to provide more advanced lead structures. These will be developed for the MMPs and CAs, as well as a variety of other metalloproteins of medicinal interest. PUBLIC HEALTH RELEVANCE: The inhibition of metalloproteins is important for the treatment of pathologies ranging from cardiac disease to cancer. This project seeks to discover novel compounds and new approaches to the identification of metalloprotein inhibitors. Improved understanding and optimization of the interactions between the inhibitor and the metal ions in the enzyme active site will be realized.

描述(由申请人提供)：这项提案的重点是开发发现金属蛋白抑制剂的新方法和战略。金属蛋白是一类重要的药物靶点，与治疗癌症、关节炎、细菌感染等多种疾病有关。大多数抑制金属蛋白的治疗药物使用金属结合基团(MBG)与活性部位的金属离子结合。尽管这些MBGS很重要，但很少有研究开发出方法来识别、优化和了解哪些MBGS对特定的感兴趣金属蛋白是最好的。这项建议试图回答关于金属蛋白抑制剂中使用的MBGS是什么、为什么和如何的问题，即：a)什么MBGS最能抑制给定的金属蛋白？B)为什么某些MBG对某种金属蛋白具有最好的抑制作用？C)如何加快MBGS的发现、评估和发展？回答这些问题将解决药物化学和生物无机化学交叉的一个基本问题。我们的研究小组在金属蛋白抑制剂领域经验丰富，在回答上述问题方面取得了实质性进展。从根本上说，我们的实验室正在寻求一种基于片段的铅发现(FBLD)方法来开发抑制剂，其中金属螯合剂首次被用作片段，将探索以结合金属蛋白活性位点为目标的化学空间。在实施这一方法时，我们开发了一个螯合剂-片段文库(CFL)，它可以很容易地与金属蛋白进行筛选，以确定什么MBGS与给定的靶点结合得最好。我们还测定了金属蛋白活性部位的MBG的结构，以了解为什么MBG与活性部位有高亲和力。接下来，我们使用生物无机模型络合物和计算对接方法相结合的方法来开发改进的方法，以确定如何将MBG片段的发现开发为铅抑制剂。最后，我们结合上述所有研究制备了螯合剂亚库，提供了更先进的片段命中，探测到了金属离子活性部位以外的地方。在我们正在进行的研究中，我们将针对大量的金属蛋白(目标1，目标4)筛选我们的文库，但将重点放在两个特定的锌依赖系统(目标2，目标3)上，即基质金属蛋白酶(MMPs)和碳酸氢酶(CAS)。这些金属蛋白具有共同的金属活性位点基序，但不同的MBG偏好，将成为检验我们的想法以及比较和对比MBG结合细节的优秀系统。我们建议：1.开发和筛选针对多种金属蛋白靶点的螯合剂片段文库(CFL)。利用现有的和新的CFL，将对十多种不同的金属酶进行筛选，以揭示哪些MBGS与不同的靶标结合得最好。2.对蛋白质进行结构和热力学研究，以获得对为什么给定的MBG与给定的金属蛋白活性部位紧密结合的分子理解。来自CFL的HITS将用MMP-3和HCAI进行检测，其中：a)共结晶MBGS的晶体结构测定将揭示MBG-金属蛋白结合的关键特征，以及b)通过等温滴定量热法进行热力学研究将提供结合常数和相关的能量参数。3.对基质金属蛋白酶和CA活性部位的MBG片段进行模型化，并与蛋白质结晶学的结构数据进行比较。合成的生物无机模型化合物将被结晶，提供关于MBG结合无限制模式的结构数据，而计算对接研究将用于预测MBG和金属蛋白之间的整体构象和第二配位球相互作用。通过将生物无机建模和计算对接相结合，我们将尝试准确地概括晶体数据。4.将准备包含MBG衍生品的子库，以推动这些支架从点击到领先。MBG支架的精加工将产生包含化合物的子库，这些化合物可以针对金属蛋白进行筛选，以提供更先进的铅结构。这些将被开发用于MMPs和CA，以及各种其他具有药用价值的金属蛋白。 公共卫生相关性：金属蛋白的抑制对于从心脏疾病到癌症的各种病理疾病的治疗都很重要。该项目寻求发现新的化合物和新的方法来鉴定金属蛋白抑制剂。更好地理解和优化抑制剂与酶活性部位金属离子之间的相互作用。