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

基本信息

批准号：
8325053
负责人：
SETH M COHEN
金额：
$ 28.28万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
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/8325053
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

项目摘要

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.

描述（由申请人提供）：该提案的重点是开发新的方法和策略来发现金属蛋白抑制剂。金属蛋白是一类重要的医学靶点，与治疗多种疾病相关，包括癌症、关节炎、细菌感染等。大多数抑制金属蛋白的疗法都使用金属结合基团 (MBG) 与活性位点金属离子结合。尽管这些 MBG 很重要，但很少有研究开发出方法来识别、优化和了解什么 MBG 最适合给定的目标金属蛋白。该提案旨在回答金属蛋白抑制剂中使用 MBG 的“内容、原因和方式”，即： a) 哪种 MBG 最能抑制特定的金属蛋白？ b) 为什么某些 MBG 对某种金属蛋白具有最佳抑制作用？ c) 如何加速 MBG 的发现、评估和开发？回答这些问题将解决药物化学和生物无机化学交叉领域的一个基本问题。我们的研究小组在金属蛋白抑制剂领域经验丰富，并且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先导物发现（FBLD）方法来开发抑制剂，其中金属螯合剂首次被用作片段，以探索针对结合金属蛋白活性位点的化学空间。在实施这种方法时，我们开发了一个螯合剂片段库 (CFL)，可以轻松地针对金属蛋白进行筛选，以确定哪些 MBG 与给定靶点的结合效果最好。我们还确定了金属蛋白活性位点中 MBG 的结构，以了解为什么 MBG 以高亲和力与活性位点结合。接下来，我们使用生物无机模型复合物和计算对接方法的组合来开发改进的方法，以确定如何将MBG片段的发现开发成先导抑制剂。最后，我们结合了所有上述研究来制备螯合剂子库，这些子库提供了更先进的片段命中，可探测金属离子活性位点之外的区域。在我们正在进行的研究中，我们将针对大量金属蛋白筛选我们的文库（目标 1、目标 4），但将更详细的研究重点放在两个特定的 Zn2+ 依赖性系统（目标 2、目标 3），即基质金属蛋白酶 (MMP) ）和碳酸酐酶（CA）。这些金属蛋白具有共同的金属活性位点基序，但具有不同的 MBG 偏好，将作为优秀的系统来测试我们的想法并比较和对比 MBG 结合的细节。我们建议： 1. 针对多种金属蛋白靶标开发和筛选螯合剂片段库 (CFL)。使用现有的和新的 CFL，将针对十多种不同的金属酶进行筛选，以揭示哪些 MBG 与各种靶标结合得最好。 2. 对蛋白质进行结构和热力学研究，从分子角度理解为什么给定的 MBG 与给定的金属蛋白活性位点紧密结合。 CFL 的命中将使用 MMP-3 和 hCAI 进行检查，其中：a) 共结晶 MBG 的晶体结构测定将揭示 MBG-金属蛋白结合的关键特征，b) 通过等温滴定量热法的热力学研究将提供结合常数和相关能量参数。 3. 对 MMP 和 CA 活性位点中的 MBG 片段进行建模，以与从蛋白质晶体学中获得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，提供有关 MBG 结合的无限制模式的结构数据，同时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。通过结合生物无机建模和计算对接，我们将尝试准确地概括晶体学数据。 4. 将准备包含 MBG 衍生物的子文库，以将这些支架从命中到先导推进。 MBG 支架的精加工将产生含有化合物的子文库，这些化合物可以针对金属蛋白进行筛选，以提供更先进的先导结构。这些将针对 MMP 和 CA 以及各种其他具有药用价值的金属蛋白进行开发。