A molecular toolbox to accelerate drug development for histone lysine methylation regulators

加速组蛋白赖氨酸甲基化调节剂药物开发的分子工具箱

基本信息

批准号：
10481092
负责人：
JONATHAN MICHAEL BURG
金额：
$ 102.51万
依托单位：
EPICYPHER, INC.
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-05-01 至 2024-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10481092
关键词：
ASH1L gene Address Affinity Antibodies Area Automobile Driving Binding Biological Assay Biomedical Research Caymans Chemicals Chromatin Chromatin Structure Custom Development Disease Drug Design Engineering Enzymes Epigenetic Process G-Protein-Coupled Receptors Gene Expression High Pressure Liquid Chromatography Histone-Lysine N-Methyltransferase Histones KDM5B gene Length Letters Libraries Lysine MLL gene Mass Spectrum Analysis Methylation Molecular Noise Nucleosomes Parents Peptides Pharmaceutical Chemistry Pharmacologic Substance Phase Phosphotransferases Physiological Play Positioning Attribute Post-Translational Protein Processing Process Protocols documentation Reagent Research Resolution Role Series Services Signal Transduction Specificity Structure System Technology Tertiary Protein Structure Validation Work assay development base commercialization cost design drug development drug discovery enzyme activity high throughput screening improved inhibitor innovation liquid chromatography mass spectrometry novel open source preference screening small molecule libraries targeted cancer therapy therapeutic development therapeutic enzyme therapeutic target tool user-friendly

项目摘要

PROJECT SUMMARY Nucleosomes (Nucs) are the repeating unit of chromatin structure and are decorated with diverse post- translational modifications (PTMs) to regulate gene expression. The enzymes that add and remove lysine methylation (KMTs & KDMs) on Nucs play driving roles in many diseases and are important targets for cancer therapy. However, the complexity of chromatin structure has greatly challenged the accurate characterization of these enzymes for drug development. Indeed, many KMTs & KDMs contain multiple domains that engage distinct Nuc features in a multivalent manner, underscoring the need to use full-length enzymes and Nucs to define their activity. Notably, these reagents are difficult / costly to produce, require extensive / customized assay optimization, and are not widely supported by existing high-throughput screening (HTS) platforms, driving the use of protein domains and non-physiological histone peptide-based assays. Further, the field has been stalled by the lack of target-focused chemical compound sets, which are crucial to KMT & KDM inhibitor development, mechanistic analysis, and drug design. Better tools are needed to support this key area of biomedical research. Here, EpiCypher® is directly addressing these problems with the development of EpiVance™, a comprehensive toolbox comprising dNuc substrates, full-length enzymes, validated assays, user-friendly protocols, and a KMT & KDM focused chemical library to advance chromatin research. This innovative, integrated system will enable reliable and sensitive characterization of diverse KMTs & KDMs, which will improve our understanding of these enzymes for therapeutic development. For Phase I proof-of-concept, we developed HTS-compatible enzyme assays for nine KMTs & KDMs using dNuc (or peptide) substrates. We then worked with expert medicinal chemists Drs. Jian Jin and H. Ümit Kaniskan to apply an innovative structure-based optimization strategy, expanding existing KMT & KDM inhibitors into a 200-compound set for HTS. We discovered several compounds with novel target selectivity and found that a defined G9a inhibitor also displayed potent activity towards KDM7A, illustrating the importance of rigorous counter-screening to related enzymes and demonstrating strong feasibility for our approach. In Phase II, we are partnering with Cayman Chemical to exclusively develop and commercialize the EpiVance toolbox and services for drug discovery research. In Aim 1, we will develop a series of HTS assays using full-length KMT & KDM enzymes, dNuc substrates, and highly specific antibodies. In Aim 2, we will work with Drs. Jin / Kaniskan and Cayman Chemical to expand open-source KMT & KDM inhibitors, generating an ~500 compound set. In Aim 3, we will complete end-to-end validation of this system, performing HTS using select enzyme assays from Aim 1 and the chemical set from Aim 2. This project will demonstrate the power of EpiVance for accurate enzyme characterization and inhibitor development, thereby fulfilling a major need in the chromatin field. Our team’s expertise in assay development and medicinal chemistry uniquely positions us to deliver this system, which is expected to have significant market impact.

项目概要核小体（Nucs）是染色质结构的重复单元，并被多种后修饰修饰。调节基因表达的翻译修饰 (PTM) 酶。 Nucs 上的甲基化（KMT 和 KDM）在许多疾病中发挥驱动作用，并且是癌症的重要靶标然而，染色质结构的复杂性极大地挑战了其准确表征。事实上，许多 KMT 和 KDM 包含多个参与药物开发的域。以多价方式呈现独特的 Nuc 特征，强调需要使用全长酶和 Nucs 值得注意的是，这些试剂生产起来很困难/成本很高，需要大量/定制的测定。优化，并且没有得到现有高通量筛选（HTS）平台的广泛支持，从而推动了此外，基于蛋白质结构域和非生理组蛋白肽的分析领域已陷入停滞。由于缺乏针对 KMT 和 KDM 抑制剂开发至关重要的目标化合物组，需要更好的工具来支持生物医学研究的这一关键领域。 EpiCypher® 正在通过开发 EpiVance™ 来直接解决这些问题，EpiVance™ 是一种综合工具箱，包括 dNuc 底物、全长酶、经过验证的测定、用户友好的协议，以及以 KMT 和 KDM 为重点的化学库，以推进这一创新的、集成系统将能够可靠、灵敏地表征不同的 KMT 和 KDM，这将改善为了了解我们对这些酶用于治疗开发的理解，我们开发了第一阶段概念验证。然后我们使用 dNuc（或肽）底物对九种 KMT 和 KDM 进行 HTS 兼容酶测定。与药物化学家Jian Jin 博士和H. Ümit Kaniskan 博士一起应用基于创新结构的药物优化策略，将现有的 KMT 和 KDM 抑制剂扩展为 200 种 HTS 化合物。发现了几种具有新靶点选择性的化合物，并发现一种确定的 G9a 抑制剂也表现出对 KDM7A 的有效活性，说明了对相关酶进行严格反筛选的重要性在第二阶段，我们与开曼化学公司合作，证明了我们的方法的强大可行性。 In Aim 专门为药物发现研究开发并商业化 EpiVance 工具箱和服务。 1，我们将使用全长 KMT 和 KDM 酶、dNuc 底物和高度在目标 2 中，我们将与 Jin / Kaniskan 博士和 Cayman Chemical 合作扩大开源。 KMT 和 KDM 抑制剂，生成约 500 种化合物集在目标 3 中，我们将完成端到端验证。该系统，使用目标 1 中的选定酶测定和目标 2 中的化学品组执行 HTS。该项目将展示 EpiVance 在准确酶表征和抑制剂开发方面的强大功能，满足染色质领域的主要需求，从而满足我们团队在检测开发和药物方面的专业知识。化学使我们能够提供该系统，预计将产生重大的市场影响。