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: 10796381
• 负责人: William Charles Krause Pomerantz
• 金额: $ 9.49万
• 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/10796381
• 关键词: Address; Affinity; Autophagocytosis; Biology; Bromodomain; Cells; Chemicals; Chromatin; Complex; DNA; Development; Disease; Drug Targeting; Epigenetic Process; Fluorine; Gene Expression Regulation; Genetic; 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; Research; Role; Tertiary Protein Structure; Transcriptional Regulation; biophysical techniques; disorder control; 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.

项目概要 我们的长期目标是开发新的化学探针来剖析与相关的分子机制 表观遗传复合物和转录调控。建立动态细化机制 基因表达的调控仍然是表观遗传学领域的重大挑战。我们的研究 该计划正在通过开发选择性化学探针、发现新的蛋白质来应对这些挑战 蛋白质相互作用，并改进结构生物学和生物物理方法来量化这些动态 多价相互作用。这些方法有助于创建不同分子的详细图像 表观遗传复合物的组装并促进新的表观遗传疗法的开发。 含溴结构域的蛋白质是表观遗传读取蛋白的一个子集，并且是一种新兴的蛋白质- 表观基因组治疗的药物类别。我的研究项目是开发化学生物学研究方法 两种特定的含溴结构域蛋白：BPTF 和 BRD4。我们的方法背后的一项创新是使用 基于 19F NMR 蛋白质的方法用于发现异构体选择性溴结构域抑制剂。由于 由于氟对配体结合的超响应性质和简化的光谱，这种结构生物学工具是理想的选择 适用于快速筛选小分子，表征与天然相关的瞬时相互作用 转录因子-蛋白质相互作用，并量化从微观到蛋白质相互作用的动态 毫秒时间尺度。在接下来的五年里，我们将进一步发展这种方法，以实现小型化 分子发现，表征大（> 50 kDa）蛋白质，并量化亲和力和动力学 与合成核小体相关的多结构域蛋白。凭借 19F NMR 的发现，我们 用于 BPTF 阅读器域的新化学探针作为抑制化学反应的化学工具具有巨大影响力的潜力 癌症进展和调节自噬，而更具体的 BRD4 化学探针将有助于揭示 癌症和炎症中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来 剖析这些溴结构域对转录的功能作用，包括基因调控、染色质 参与和新型蛋白质-蛋白质相互作用。下一代化学探针将进一步 开发了包括双功能分子作为多结构域蛋白抑制剂的 PROTAC，其具有改进的 选择性特征，以及通过与 DNA 靶向聚酰胺缀合而合成的转录因子。 该提议对于早期先导化合物发现和表观遗传读者的研究具有广泛的生物医学意义 对人类健康和疾病具有重要意义的领域。鉴于表观遗传蛋白代表了一类主要的 潜在的药物靶点，我们新的 19F 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读者域可以显着增加目标的库，从而 开辟药物发现的新途径。

项目成果

Fluorous Liquids for Magnetic Resonance-Based Thermometry with Enhanced Responsiveness and Environmental Degradation

• DOI: 10.1021/acs.analchem.3c00172
• 发表时间: 2023-03-31
• 期刊: ANALYTICAL CHEMISTRY
• 影响因子: 7.4
• 作者: Li，Jiaqian;Mundhenke，Thomas F.;Pomerantz，William C. K.
• 通讯作者: Pomerantz，William C. K.

Development of a single culture E. coli expression system for the enzymatic synthesis of fluorinated tyrosine and its incorporation into proteins

开发用于酶促合成氟化酪氨酸及其掺入蛋白质的单一培养物大肠杆菌表达系统

• DOI: 10.1016/j.jfluchem.2022.110014
• 发表时间: 2022
• 期刊: Journal of Fluorine Chemistry
• 影响因子: 1.9
• 作者: Olson, Noelle M.;Johnson, Jorden A.;Peterson, Kerstin E.;Heinsch, Stephen C.;Marshall, Andrew P.;Smanski, Michael J.;Carlson, Erin E.;Pomerantz, William C.K.
• 通讯作者: Pomerantz, William C.K.