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.

项目概要由于细胞行为和身份的几乎所有方面都集中在基因表达的程序化反应上，转录控制在正常稳态和疾病进展中发挥着重要作用。基因调控机制的药理学扰动是理解和理解的一种有吸引力的方法调节复杂的细胞疾病状态。转录靶向药物必须克服关键障碍，然而，包括 DNA 结合因子和多组分复合物对传统方法的可及性有限药物设计方法，以及转录过程破坏引起的不加区别的活性在这个提案中，我们提出并建立在一个新的发现的基础上。称为“L4”的免疫抑制亲电化学探针通过其显着的特性避免了这些陷阱能够选择性降解多个 NuRD（核小体重塑脱乙酰酶）复合物我们实验室最近开发的化学蛋白质组学使我们能够以 T 细胞限制的方式识别亚基。为了在本地生物系统中全局绘制小分子-蛋白质相互作用的策略，我们提出了一个研究L4前所未有的药理特征及其机制的研究策略此外，我们还将对针对转录复合物的更广泛的药物设计方法产生影响。研究 L4 介导的 NuRD 复合物降解与该化合物的在具体目标 1 中，我们将应用我们团队的化学蛋白质组学专业知识来阻断 T 细胞激活。通过 L4 表征 NuRD 降解，并使用一套 L4- 绘制人类 T 细胞中的相关蛋白质靶标在具体目标 2 中，我们将评估相关化合物和 NuRD 复合物定向富集方法。候选 L4 靶标在使用遗传和生化方法支持 NuRD 降解中的作用，以及研究已确定的机制如何导致多亚基降解和状态的显着特征在特定目标 3 中，我们扩展了检查 L4 作用的关系。评价 NuRD 阻断 T 细胞激活的能力，并评估和应用该化合物作为进一步研究的工具通过深入了解 L4 的独特药理活性，提出了 T 细胞生物学的研究。研究将有助于实现探索靶向蛋白质的两种新机制的总体目标基因调控蛋白的降解和状态依赖性控制共同实现了这些更广泛的目标。克服转录靶向化学品开发中的挑战的有希望的途径探针和药物。