Chemical Probe Development for Epigenetic Complexes Enabled by Protein-Observed 19F NMR

通过蛋白质观察的 19F NMR 开发表观遗传复合物的化学探针

• 批准号: 10375536
• 负责人: William Charles Krause Pomerantz
• 金额: $ 38.24万
• 依托单位: UNIVERSITY OF MINNESOTA
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-04-01 至 2026-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10375536
• 关键词: Address; Affinity; Autophagocytosis; Biology; Bromodomain; Cells; Chemicals; Chromatin; Complex; DNA; Development; Disease; Drug Targeting; Epigenetic Process; Fluorine; Gene Expression Regulation; Genetic Transcription; Goals; Health; Human; Inflammation; Lead; Ligand Binding; Malignant Neoplasms; Mediating; Methodology; Methods; Molecular; Nature; Nucleosomes; Nylons; Pharmaceutical Preparations; Protein Isoforms; Proteins; Rapid screening; Reader; Regulation; Research; Role; Tertiary Protein Structure; Transcriptional Regulation; base; biophysical techniques; chemical genetics; drug discovery; epigenetic therapy; epigenome; improved; inhibitor; innovation; millisecond; molecular assembly/self assembly; next generation; novel; programs; protein protein interaction; public health relevance; small molecule; structural biology; tool; transcription factor; tumor progression

PROJECT SUMMARY Our long-term goal is to develop new chemical probes to dissect the molecular mechanisms associated with epigenetic-complexes and transcriptional regulation. Establishing detailed mechanisms for the dynamic regulation of gene expression remains a significant challenge for the field of epigenetics. Our research program is addressing these challenges by developing selective chemical probes, discovery of new protein- protein interactions, and improving structural biology and biophysical approaches to quantify these dynamic multivalent interactions. These approaches are helping to create a detailed picture of diverse molecular assemblies of epigenetic complexes and facilitating development of new epigenetic therapies. Bromodomain-containing proteins are a subset of epigenetic reader protein, and are an emerging protein- drug class for epigenome therapy. My research program is developing chemical biology approaches to study two specific bromodomain-containing proteins, BPTF and BRD4. One innovation behind our approach uses a 19F NMR protein-based methodology for the discovery of isoform selective bromodomain inhibitors. Due to the hyper-responsive nature of fluorine to ligand binding and simplified spectra, this structural biology tool is ideally suited to rapidly screen small molecules, characterize the transient interactions associated with native transcription factor-protein interactions, and to quantify the dynamics of the interactions from micro to millisecond timescales. Over the next five years, we will further develop this approach for enabling small molecule discovery, characterizing large (> 50 kDa) proteins, and quantifying the affinity and dynamics of multidomain proteins associated with synthetic nucleosomes. With their discovery enabled by 19F NMR, our new chemical probes for BPTF reader domains have potential for high impact as chemical tools for inhibiting cancer progression and regulating autophagy, while more specific BRD4 chemical probes will help uncover new biology in cancer and inflammation obscured by less specific tool compounds. We will use these tools to dissect the functional roles of these bromodomains on transcription, including gene regulation, chromatin engagement, and novel-protein-protein interactions. Next generation chemical probes will be further developed including bifunctional molecules as inhibitors of multi-domain proteins, PROTACs with improved selectivity profiles, and synthetic transcription factors through conjugation to DNA-targeting polyamides. This proposal has broad biomedical significance for early lead discovery and studies of epigenetic reader domains important in human health and disease. Given that epigenetic proteins represent a major class of potential drug targets, our new 19F NMR small molecule discovery method and cell-based approaches for epigenetic reader domains described here could significantly increase the repertoire of targets and thereby open up new avenues for drug discovery.

项目摘要 我们的长期目标是开发新的化学探针，以剖析与 表观遗传复合体和转录调节。建立详细的机制， 基因表达的调节仍然是表观遗传学领域的一个重大挑战。我们的研究 该计划通过开发选择性化学探针，发现新的蛋白质， 蛋白质相互作用，并改善结构生物学和生物物理方法，以量化这些动态 多价相互作用这些方法有助于创建不同分子的详细图片 表观遗传复合物的组装和促进新的表观遗传疗法的开发。 含溴结构域蛋白是表观遗传阅读蛋白的一个子集，是一种新兴的蛋白质， 表观基因治疗的药物类别。我的研究项目是开发化学生物学方法来研究 两种特定的含溴结构域蛋白，BPTF和BRD 4。我们的方法背后的一个创新是使用 用于发现同种型选择性溴结构域抑制剂的基于19 F NMR蛋白质的方法。由于 由于氟对配体结合的高响应性和简化的光谱，这种结构生物学工具是理想的 适用于快速筛选小分子，表征与天然药物相关的瞬时相互作用， 转录因子-蛋白质相互作用，并量化从微观到微观的相互作用动力学， 毫秒时间尺度。在未来五年，我们将进一步发展这种方法， 分子发现，表征大（> 50 kDa）蛋白质，并量化的亲和力和动力学 与合成核小体相关的多结构域蛋白质。通过19 F NMR的发现， 用于BPTF阅读器结构域的新化学探针具有作为抑制BPTF阅读器结构域的化学工具的高影响力的潜力。 癌症进展和调节自噬，而更具体的BRD 4化学探针将有助于揭示 癌症和炎症的新生物学被不太具体的工具化合物所掩盖。我们将使用这些工具， 剖析这些布罗莫结构域对转录的功能作用，包括基因调控、染色质 接合和新型蛋白质-蛋白质相互作用。下一代化学探针将更进一步 开发了包括双功能分子作为多结构域蛋白质的抑制剂，具有改善的PROTAC 选择性谱和通过缀合至DNA靶向聚酰胺的合成转录因子。 这一建议对于早期发现先导化合物和表观遗传阅读器的研究具有广泛的生物医学意义 对人类健康和疾病至关重要的领域。鉴于表观遗传蛋白代表了一个主要类别， 潜在的药物靶点，我们新的19 F NMR小分子发现方法和基于细胞的方法， 这里描述的表观遗传阅读器结构域可以显著增加靶的库， 为药物研发开辟了新的途径