Proteomic discovery and characterization of chemical tools that degrade the NuRD chromatin regulatory complex

降解 NuRD 染色质调控复合物的化学工具的蛋白质组学发现和表征

基本信息

批准号：
10324559
负责人：
David Ian Remillard
金额：
$ 5.05万
依托单位：
SCRIPPS RESEARCH INSTITUTE, THE
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-01-01 至 2022-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10324559
关键词：
Ablation Alkynes Architecture Behavior Biochemical CHD4 gene Case Study Cells Cellular biology Chemicals Chromatin Clustered Regularly Interspaced Short Palindromic Repeats Co-Immunoprecipitations Complex Cysteine DNA Binding Deacetylase Dependence Development Disease Drug Design Drug Targeting Face Gene Expression Genes Genetic Genetic Transcription Goals HDAC1 gene Homeostasis Human Human Cell Line Individual Knock-out Laboratories Libraries Maps Mediating Medicine Modality Modification Mutagenesis NuRD complex Nucleosomes Pathway interactions Pharmacology Phenotype Process Proteins Proteomics Regulator Genes Research Role Site Specificity Suppressor-Effector T-Lymphocytes System T-Cell Activation T-Lymphocyte Transcription Process Transcription Regulatory Protein Transcriptional Regulation Triage Validation analog biological systems cell behavior cell type chemical group comparative design empowered gain of function gene therapy genetic regulatory protein improved insight loss of function member multicatalytic endopeptidase complex novel pleiotropism programs protein complex protein degradation response small molecule tool ubiquitin ligase virtual

项目摘要

Project Summary As virtually all aspects of cell behavior and identity converge upon programmed responses in gene expression, transcriptional control features centrally in both normal homeostasis and progression to disease. Accordingly, pharmacologic perturbation of gene regulatory machinery is an attractive approach for understanding and modulating complex cellular disease states. Transcriptionally targeted drugs must overcome key hurdles, however, including the limited accessibility of DNA binding factors and multi-component complexes to traditional drug design approaches, as well as the indiscriminate activity caused by disruption of transcriptional processes shared across distinct cell types and states. In this proposal, we present and build on a novel discovery of an immunosuppressive electrophilic chemical probe termed "L4" that avoids these pitfalls through its remarkable ability to cause selective degradation of multiple NuRD (Nucleosome Remodeling Deacetylase) complex subunits in a T-cell-restricted manner. Empowered by our laboratory’s recent development of chemical proteomic strategies to globally map small molecule-protein interactions in native biological systems, we propose a research strategy to study the mechanism of the unprecedented pharmacological features of L4 and their implications for broader drug design approaches to target transcriptional complexes. In addition, we will investigate the relationship between L4-mediated degradation of the NuRD complex and the compound’s blockade of T-cell activation. In Specific Aim 1, we will apply our group’s chemical proteomic expertise to characterize NuRD degradation by L4 and map relevant protein targets in human T-cells using a suite of L4- related compounds and NuRD complex-directed enrichment approaches. In Specific Aim 2, we will evaluate the role of candidate L4 targets underpinning NuRD degradation using genetic and biochemical approaches and examine how the identified mechanisms result in the striking features of multi-subunit degradation and state- dependent (cell type-restricted) activity. In Specific Aim 3, we extend to examine the relationship of L4’s action on NuRD to its ability to block T-cell activation, and assess and apply this compound as a tool for further study of T-cell biology. By providing in-depth understanding of the unique pharmacological activity of L4, the proposed research will contribute to the overarching goals of exploring both novel mechanisms in targeted protein degradation and state-dependent control of gene regulatory proteins. Together, these broader ambitions represent promising avenues to overcome challenges in the development of transcriptionally targeted chemical probes and medicines.

项目摘要由于细胞行为和身份的几乎所有方面都在基因表达中的编程响应上融合，所以转录控制特征以正常的体内平衡和发展为疾病。因此，基因调节机械的药理扰动是一种有吸引力的理解和调节复杂的细胞疾病状态。具有转录靶向药物必须克服关键障碍，但是，包括DNA结合因子的有限可访问性和对传统的多组分复合物药物设计方法以及因转录过程中断而引起的不加区分区别的活性分享不同的细胞类型和状态。在此提案中，我们介绍并建立在一个新发现的基础上被称为“ L4”的免疫抑制电力化学探针，通过其显着能够导致多个NURD（核小体重塑脱乙酰基酶）复合物选择性降解的能力以T细胞限制的方式亚基。我们实验室最近开发化学蛋白质组学的能力在本地生物系统中，全球绘制小分子 - 蛋白质相互作用的策略，我们提出了一个研究L4及其前所未有的药物特征的机制的研究策略对靶向转录复合物的更广泛的药物设计方法的影响。此外，我们将调查L4介导的NURD综合体降解与该化合物之间的关系 T细胞激活的块。在特定目标1中，我们将应用小组的化学蛋白质组学专业知识用L4的L4降解NURD降解，并使用一套L4-- 相关化合物和NURD复杂导向的富集方法。在特定目标2中，我们将评估候选L4目标使用遗传和生化方法和检查确定的机制如何导致多支亚基降解和状态的罢工特征依赖性（细胞类型限制）活性。在特定目标3中，我们扩展以检查L4行动的关系在NURD上可以阻止T细胞激活，评估和应用该化合物作为进一步研究的工具 T细胞生物学。通过对L4的独特药物活动提供深入的理解，提出了研究将有助于探索靶向蛋白质中这两种新机制的总体目标基因调节蛋白的降解和状态依赖性控制。在一起，这些更广泛的野心代表承诺在转录靶向化学的发展方面克服挑战的途径探针和药物。