Neutron encoded activity based probes

基于中子编码活动的探针

• 批准号: 10624458
• 负责人: Damian Winston Young
• 金额: $ 42.95万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10624458
• 关键词: Acceleration; Amino Acids; Area; Bar Codes; Basic Science; Binding; Biochemical Pathway; Biological; Catalogs; Cell Line; Cells; Chemicals; Chromatin; Clinical; Collection; Data Analyses; Defect; Detection; Development; Disease; Drug Design; Drug Targeting; Elements; Enzymes; Frustration; Generations; Histone Acetylation; Histone Deacetylase; Histone Deacetylase Inhibitor; Isotopes; Libraries; Life; Ligation; Malignant Neoplasms; Mass Spectrum Analysis; Measures; Metabolic; Methodology; Methods; Molecular Mechanisms of Action; Neutrons; Nuclear; Pattern; Pharmaceutical Preparations; Pharmacology; Photoaffinity Labels; Physiological; Piperazines; Process; Proteins; Proteome; Reaction; Reagent; Regulation; Resistance; Resolution; Sampling; Site; Specificity; Statistical Data Interpretation; Structure; Support Groups; System; Systems Analysis; Technology; Testing; Toxic effect; Treatment Efficacy; Work; blind; candidate selection; clinical application; combinatorial; design; drug candidate; drug development; drug discovery; drug-like compound; enantiomer; high throughput screening; in vivo; inhibitor; innovation; novel; novel drug class; pharmacologic; scaffold; side effect; small molecule; small molecule inhibitor; success

Drugs are designed to modulate the function of a critical protein involved in a disease; however, almost all small molecules have off-targets which can mitigate or altogether terminate their therapeutic efficacy. Unfortunately, there are no general methods that can identify all the protein targets that a drug binds to in an unbiased manner. For example, Histone Deacetylase Inhibitors (HDACIs) show promising clinical activity in many diseases; however, they are generally of low to moderate specificity and may act in part through, or be hindered by, uncharacterized off-target interactions. We propose a strategy that will allow for rapid and deep pharmacological profiling of early drug candidates that 1) identifies protein targets with extraordinary confidence, 2) localizes the precise site of interaction often with amino acid residue specificity, 3) is robust against metabolic alterations, 4) distinguishes the pharmacology of metabolites, 5) quantitates differences in pharmacological activity between cellular contexts. With this approach we will quantitate all interactions that each inhibitor has with proteins in a living cell. An neutron-encoded ‘bar code’ is added to activity-based probes during a click capture and release that allows us to blindly trace the drug in a nominal mass independent manner and simultaneously introduce quantitation channels. The barcodes are revealed in the isotopic fine structure by high resolution mass spectrometry yet do not compromise sensitivity at lower resolution fragmentation spectra. The neutron bar code is implemented by moving neutrons between elements and results in a prescribed pattern of relativistic nuclear mass defects embedded in the framework of a small molecule. With this method we can confidently retrieve drug-protein reaction products from in vivo systems regardless of metabolic alterations to the HDAC inhibitors, measure a pharmacological profile and determine molecular mechanism of action. Our central hypothesis is that neutron encoded activity based probe pharmacological profiling combined with innovative fragment-based discovery to generate selective HDACIs will enable the generation of a library of highly characterized and diversely selective HDACI probes. This will be realized through three specific aims: in aim 1 we will employ a novel and systematically diverse group of sp3-enriched fragments to generate HDACIs that sample the rim region of HDACs leading to highly selective interactions. In aim 2 we will measure the pharmacological profile of our novel HDACi’s and their effect on histone acetylation. In aim 3, we will develop a multiplexed barcoding system which to enable higher detection and resolution of drug targets over the entire proteome. This overcomes many challenges universal to early stage drug development efforts that have frustrated the development of specific HDAC inhibitors in particular. Although HDACIs will be the general focus of this proposal our method is general for drug development in any area.

药物被设计用于调节与疾病有关的关键蛋白质的功能;然而，几乎所有的小分子药物都是通过调节蛋白质的功能来实现的。 分子具有脱靶，这可以减轻或完全终止它们的治疗功效。不幸的是， 没有通用的方法可以以无偏的方式鉴定药物结合的所有蛋白质靶。 例如，组蛋白去乙酰化酶抑制剂（HDACIs）在许多疾病中显示出有希望的临床活性; 然而，它们通常具有低至中等特异性， 未表征的脱靶相互作用。我们提出了一个战略，将允许快速和深入的 早期候选药物的药理学特征分析，1）鉴定具有显著 置信度，2）定位相互作用的精确位点，通常具有氨基酸残基特异性，3）对 代谢改变，4）区分代谢物的药理学，5）定量 细胞环境之间的药理活性。通过这种方法，我们将量化所有的相互作用， 每种抑制剂都与活细胞中的蛋白质发生作用。一个中子编码的“条形码”被添加到基于活动的 探针在点击捕获和释放，使我们能够盲目地跟踪药物在一个标称质量独立 方式，同时引入定量通道。条形码显示在同位素微粒中 但在较低分辨率下不损害灵敏度 碎裂谱中子条形码是通过在元素和结果之间移动中子来实现的 在小分子框架中嵌入相对论性核质量缺陷的规定模式中。与 这种方法我们可以自信地从体内系统中回收药物-蛋白质反应产物， HDAC抑制剂的代谢改变，测量药理学特征并确定分子水平。 作用机制。我们的中心假设是基于中子编码活性的探针药理学 分析与创新的基于片段的发现相结合，以生成选择性HDACI， 产生高度表征的和双特异性选择性HDACI探针文库。这将通过以下方式实现 三个具体目标：在目标1中，我们将采用一组新的和系统多样的富含sp3的片段 以产生HDACIs，所述HDACIs对HDACs的边缘区域进行采样，从而导致高度选择性的相互作用。在目标2中， 将测量我们的新型HDACi的药理学特征及其对组蛋白乙酰化的影响。在目标3中， 我们将开发一种多重条形码系统，以实现更高的药物靶点检测和分辨率， 覆盖整个蛋白质组。这克服了早期药物开发普遍存在的许多挑战 这些努力尤其阻碍了特定HDAC抑制剂的开发。虽然HDACIs 将是本提案的总体重点，我们的方法适用于任何领域的药物开发。

项目成果

Expeditious Extraction of Histones from Limited Cells or Tissue Samples and Quantitative Top-Down Proteomic Analysis.

• DOI: 10.1002/cpz1.26
• 发表时间: 2021-03
• 期刊: Current protocols
• 作者: Holt MV;Wang T;Young NL
• 通讯作者: Young NL

Mechanistic insights into KDM4A driven genomic instability.

• DOI: 10.1042/bst20191219
• 发表时间: 2021-02-26
• 期刊: Biochemical Society transactions
• 影响因子: 3.9
• 作者: Young NL;Dere R
• 通讯作者: Dere R

Gene therapy using Aβ variants for amyloid reduction.

使用 Aβ 变体进行淀粉样蛋白减少的基因治疗。

• DOI: 10.1016/j.ymthe.2021.02.026
• 发表时间: 2021
• 期刊: Molecular therapy : the journal of the American Society of Gene Therapy
• 作者: Park,Kyung-Won;Wood,CalebA;Li,Jun;Taylor,BethanyC;Oh,SaeWoong;Young,NicolasL;Jankowsky,JoannaL
• 通讯作者: Jankowsky,JoannaL

A Concise Synthetic Method for Constructing 3-Substituted Piperazine-2-Acetic Acid Esters from 1,2-Diamines.

• DOI: 10.3390/molecules27113419
• 发表时间: 2022-05-25
• 期刊: Molecules (Basel, Switzerland)

Chemical Catalysis Guides Structural Identification for the Major In Vivo Metabolite of the BET Inhibitor JQ1.

• DOI: 10.1021/acsmedchemlett.3c00464
• 发表时间: 2024-01-11
• 期刊: ACS MEDICINAL CHEMISTRY LETTERS
• 影响因子: 4.2
• 作者: Holmes, Secondra;Jain, Prashi;Rodriguez, Kenneth Guzman;Williams, Jade;Yu, Zhifeng;Cerda-Smith, Christian;Samuel, Errol L. G.;Campbell, James;Hakenjos, John Michael;Monsivais, Diana;Li, Feng;Chamakuri, Srinivas;Matzuk, Martin M.;Santini, Conrad;Mackenzie, Kevin R.;Young, Damian W.
• 通讯作者: Young, Damian W.