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 表观遗传复合物和转录调节。建立动态的详细机制 基因表达的调节仍然是表观遗传学领域的重大挑战。我们的研究 计划通过开发选择性化学探针，发现新蛋白质来解决这些挑战。 蛋白质相互作用，并改善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各种分子的详细图片 表观遗传复合物的组装，并促进新的表观遗传疗法的发展。 含溴构域的蛋白是表观遗传读取子蛋白的子集，是一种新兴的蛋白质 - 表观基因组治疗的药物类。我的研究计划正在开发化学生物学方法来研究 两种含溴脱域的特定蛋白BPTF和BRD4。我们方法背后的一种创新使用 基于19F NMR蛋白的方法，用于发现同工型选择性溴结构域抑制剂。由于 氟与配体结合和简化光谱的高反应性，该结构生物学工具是理想情况下的 适用于快速筛选小分子的特征，表征与天然相关的瞬态相互作用 转录因子 - 蛋白质相互作用，并量化从微观到的相互作用的动力学 毫秒时标。在接下来的五年中，我们将进一步开发这种方法，以实现小型 分子发现，表征大型（> 50 kDa）蛋白，并量化的亲和力和动力学 与合成核小体相关的多域蛋白。通过19F NMR启用了他们的发现 BPTF读取器领域的新化学探针具有抑制化学工具的高影响力 癌症的进展和调节自噬，而更具体的BRD4化学探针将有助于发现 癌症和炎症中的新生物学被较不具体的工具化合物遮盖了。我们将使用这些工具来 剖析这些溴结构域在转录中的功能作用，包括基因调节，染色质 参与和新颖的蛋白质 - 蛋白质相互作用。下一代化学探针将进一步 开发的包括双功能分子作为多域蛋白的抑制剂，具有改善的Protac 选择性曲线和合成转录因子通过结合与DNA靶向聚酰胺。 该提议对于早期发现和对表观遗传学读者的研究具有广泛的生物医学意义 在人类健康和疾病中重要的领域。鉴于表观遗传蛋白代表了主要类 潜在的药物靶标，我们的新型19F NMR小分子发现方法和基于细胞的方法 此处描述的表观遗传读取器领域可能会显着增加目标的曲目，从而 打开新的毒品发现途径。

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.