Photoaffinity labeling probes for development of novel isoform selective HDAC inh

用于开发新型亚型选择性 HDAC inh 的光亲和标记探针

基本信息

批准号：
8067976
负责人：
Pavel A Petukhov
金额：
$ 30.83万
依托单位：
UNIVERSITY OF ILLINOIS AT CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2008
资助国家：
美国
起止时间：
2008-07-01 至 2013-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8067976
关键词：
Abbreviations Address Affect Azides Binding Biological Testing Biology Biotin Cell Death Chemicals Clinical Trials Complex Computer Assisted Development Disease Docking Drug Design Enzymes FDA approved Fingerprint Gene Expression Regulation Goals HDAC1 gene HDAC7 histone deacetylase Health Hela Cells Histone Deacetylase Histone Deacetylase Inhibitor Homology Modeling Image Individual Label Life Ligand Binding Ligands Malignant Neoplasms Maps Mass Spectrum Analysis Methods Modification Nature Pharmaceutical Chemistry Photoaffinity Labels Problem Solving Protein Isoforms Proteins Proteomics Recombinants Research Resolution Series Site Structure Study models Surface Testing Therapeutic Toxic effect Transcription factor genes Treatment Efficacy Zinc anti-cancer therapeutic base cancer therapy cell growth cytotoxicity design drug discovery histone acetyltransferase human HDAC1 protein human HDAC11 protein improved inhibitor/antagonist innovation knowledge of results molecular dynamics multidisciplinary neoplastic cell novel novel strategies research study small molecule success three dimensional structure

项目摘要

DESCRIPTION (provided by applicant): This proposal is intended to charter new directions for design of more selective and more active histone deacetylase (HDAC) inhibitors by mapping the binding "fingerprints" of the HDAC ligands in the different HDAC isoforms using small molecule photoaffinity probes. Since many cancers are associated with aberrant transcriptional activity, and the HDACs can affect transcription factors and gene regulation, these enzymes have been identified as attractive targets for cancer therapy. Indeed, chemical inhibitors of HDACs have been shown to inhibit tumor cell growth and induce differentiation and cell death. At least one non-selective HDAC inhibitor was approved by FDA for cancer and several non-selective HDAC inhibitors are in clinical trials. Multiple studies have shown that therapeutics selective for one or a limited number of specific HDAC isoforms may improve overall efficacy and lower toxicity of these compounds. While some rather limited degree of isoform selectivity has been shown by a few compounds, the problem of identifying selective inhibitors is far from solved. Recent success in the elucidation of the crystal structure of HDAC7, 8 and homologous HDAC proteins has opened a possibility for structure-based drug design. Despite the progress, both ligand-based and structure-based approaches are limited in their applicability to design of isoform selective HDAC inhibitors either because only few isoform selective inhibitors are available as a starting point for ligand based drug design or because high resolution three-dimensional structures are available only for 2 out of 11 class I and II HDAC isoforms. It is also poorly understood how the binding modes of those portions of the HDAC ligands that bind on the surface of the HDAC protein affect the activity of HDAC inhibitors. Clearly, a new approach to this problem is needed. We hypothesize that it will be possible to map the binding modes available to the ligands in different HDAC isoforms by small molecule photoaffinity probes (PAP) and use the resulting knowledge to design isoform selective HDAC inhibitors as potential therapeutics for cancer. Our specific aims in this proposal are as follow: Aim 1: Design and synthesize at least three series of photoaffinity probes (PAPs) consisting of (1) an HDAC ligand, (2) an aromatic azide group for photoaffinity labeling (PAL) of the protein residues directly involved in the binding of the ligand, and (3) an aliphatic azide (a imaging tag attachment group - imTAG) for attaching a fluorescent or a biotin tag. Aim 2: Evaluate the ligands containing either PAL or PAL+imTAG or both groups in photoaffinity labeling experiments with available recombinant purified class I and class II HDACs and determine the modification sites on the proteins using mass-spectrometry proteomics methods. Match the proteomics results with the modeling studies and refine later to better reproduce the experimental findings. Aim 3. Evaluate the cytotoxicity, selectivity, and binding "fingerprints" of the most potent photoaffinity probes in live Hela cells. Aim 4. Incorporate the findings of Aims 1-3 in the structure-based drug design and perform several rounds of CADD, medicinal chemistry, and biological tests to improve the activity and selectivity of the HDAC ligands. PUBLIC HEALTH RELEVANCE: This proposal is intended to charter new directions for design of more selective and more active histone deacetylase (HDAC) inhibitors by mapping the binding "fingerprints" of the HDAC ligands in the different HDAC isoforms using small molecule photoaffinity probes. The ultimate goal of this proposal is to design HDAC inhibitors suitable as HDAC based therapeutics for cancer and other HDAC relevant diseases and conditions.

描述（由申请人提供）：该提案旨在通过使用小分子光亲和探针绘制不同 HDAC 异构体中 HDAC 配体的结合“指纹”，为设计更具选择性和活性的组蛋白脱乙酰酶 (HDAC) 抑制剂制定新方向。由于许多癌症与异常转录活性有关，并且 HDAC 可以影响转录因子和基因调控，因此这些酶已被确定为癌症治疗的有吸引力的靶标。事实上，HDAC 的化学抑制剂已被证明可以抑制肿瘤细胞生长并诱导分化和细胞死亡。至少一种非选择性 HDAC 抑制剂已被 FDA 批准用于癌症治疗，并且几种非选择性 HDAC 抑制剂正在进行临床试验。多项研究表明，针对一种或有限数量的特定 HDAC 亚型的选择性治疗可以提高这些化合物的总体疗效并降低毒性。虽然一些化合物显示出相当有限程度的异构体选择性，但识别选择性抑制剂的问题还远未解决。最近成功阐明了 HDAC7、8 和同源 HDAC 蛋白的晶体结构，为基于结构的药物设计提供了可能性。尽管取得了进展，但基于配体和基于结构的方法在设计异构体选择性 HDAC 抑制剂方面的适用性受到限制，要么是因为只有很少的异构体选择性抑制剂可用作基于配体的药物设计的起点，要么是因为高分辨率三维结构仅适用于 11 种 I 类和 II 类 HDAC 同工型中的 2 种。人们还很少了解 HDAC 配体中与 HDAC 蛋白表面结合的那些部分的结合模式如何影响 HDAC 抑制剂的活性。显然，需要一种新的方法来解决这个问题。我们假设可以通过小分子光亲和探针 (PAP) 绘制不同 HDAC 异构体中配体可用的结合模式，并利用所得知识设计异构体选择性 HDAC 抑制剂作为潜在的癌症治疗方法。我们在此提案中的具体目标如下：目标 1：设计并合成至少三个系列的光亲和探针 (PAP)，其中包括 (1) HDAC 配体、(2) 用于光亲和标记 (PAL) 的芳香族叠氮基团。直接参与配体结合的蛋白质残基，以及 (3) 用于附着荧光或生物素标签的脂肪族叠氮化物（成像标签附着基团 - imTAG）。目标 2：使用可用的重组纯化 I 类和 II 类 HDAC 在光亲和标记实验中评估包含 PAL 或 PAL+imTAG 或两个基团的配体，并使用质谱蛋白质组学方法确定蛋白质上的修饰位点。将蛋白质组学结果与建模研究相匹配，并在以后进行改进，以更好地重现实验结果。目标 3. 评估活 Hela 细胞中最有效的光亲和探针的细胞毒性、选择性和结合“指纹”。目标 4. 将目标 1-3 的发现纳入基于结构的药物设计中，并进行多轮 CADD、药物化学和生物测试，以提高 HDAC 配体的活性和选择性。公共健康相关性：该提案旨在通过使用小分子光亲和探针绘制不同 HDAC 亚型中 HDAC 配体的结合“指纹”，为设计更具选择性和活性的组蛋白脱乙酰酶 (HDAC) 抑制剂制定新方向。该提案的最终目标是设计适合作为基于 HDAC 的癌症和其他 HDAC 相关疾病和病症的疗法的 HDAC 抑制剂。

项目成果

期刊论文数量（9）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Scaffold dependent histone deacetylase (HDAC) inhibitor induced re-equilibration of the subcellular localization and post-translational modification state of class I HDACs.

支架依赖性组蛋白脱乙酰酶 (HDAC) 抑制剂诱导 I 类 HDAC 的亚细胞定位和翻译后修饰状态的重新平衡。

DOI：
10.1371/journal.pone.0186620
发表时间：
2017
期刊：
PloS one
影响因子：
3.7
作者：
Hanigan,ThomasW;Taha,TahaY;Aboukhatwa,ShaimaaM;Frasor,Jonna;Petukhov,PavelA
通讯作者：
Petukhov,PavelA

Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies.

DOI：
10.1007/s00894-009-0488-z
发表时间：
2009-11
期刊：
JOURNAL OF MOLECULAR MODELING
影响因子：
2.2
作者：
Pieffet, Gilles;Petukhov, Pavel A.
通讯作者：
Petukhov, Pavel A.

Design, synthesis, modeling, biological evaluation and photoaffinity labeling studies of novel series of photoreactive benzamide probes for histone deacetylase 2.

用于组蛋白脱乙酰酶 2 的新型光反应性苯甲酰胺探针系列的设计、合成、建模、生物学评估和光亲和标记研究。

DOI：
10.1016/j.bmcl.2012.06.017
发表时间：
2012
期刊：
Bioorganic & medicinal chemistry letters
影响因子：
2.7
作者：
Vaidya,AdityaSudheer;Karumudi,Bhargava;Mendonca,Emma;Madriaga,Antonett;Abdelkarim,Hazem;vanBreemen,RichardB;Petukhov,PavelA
通讯作者：
Petukhov,PavelA

Design, Synthesis, and Biological Evaluation of Tetrahydroisoquinoline-Based Histone Deacetylase 8 Selective Inhibitors.

DOI：
10.1021/acsmedchemlett.7b00126
发表时间：
2017-08
期刊：
ACS medicinal chemistry letters
影响因子：
4.2
作者：
T. Y. Taha;Shaimaa M. Aboukhatwa;Rachel C Knopp;N. Ikegaki;Hazem Abdelkarim;Jayaprakash Neerasa;Yunlong Lu;Raghupathi Neelarapu;T. Hanigan;G. Thatcher;P. Petukhov
通讯作者：
T. Y. Taha;Shaimaa M. Aboukhatwa;Rachel C Knopp;N. Ikegaki;Hazem Abdelkarim;Jayaprakash Neerasa;Yunlong Lu;Raghupathi Neelarapu;T. Hanigan;G. Thatcher;P. Petukhov

A One-Pot Selective Synthesis of N-Boc Protected Secondary Amines: Tandem Direct Reductive Amination/N-Boc Protection.

N-Boc 保护仲胺的一锅选择性合成：串联直接还原胺化/N-Boc 保护。