Improving Fragment Based Drug Discovery and the Development of Tools for Chemical Biology through Nanoscale Encapsulation and NMR Spectroscopy

通过纳米级封装和核磁共振波谱改善基于片段的药物发现和化学生物学工具的开发

• 批准号: 10419416
• 负责人: A. JOSHUA WAND
• 金额: $ 29.87万
• 依托单位: TEXAS A&M AGRILIFE RESEARCH
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-20 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10419416
• 关键词: Address; Affinity; Automation; Binding; Binding Sites; Biological Assay; Biology; Catalogs; Characteristics; Chemicals; Companions; Complex; Crystallography; Data; Detection; Development; Dissociation; Elements; Eligibility Determination; Encapsulated; Entropy; Equilibrium; Ethane; Foundations; Goals; Individual; Interleukin-1 beta; Lead; Libraries; Ligand Binding; Ligands; Link; Liquid substance; Membrane Proteins; Methods; Micelles; Molecular Structure; NMR Spectroscopy; Natural Products; Pharmaceutical Chemistry; Pharmaceutical Preparations; Phase; Preparation; Process; Propane; Protein NMR Spectroscopy; Proteins; Resources; Sampling; Site; Standardization; Surface; Technology; Testing; Uncertainty; Validation; Water; Work; automated analysis; base; cost; cost effective; design; detection limit; detection method; drug development; drug discovery; experimental study; flexibility; high throughput screening; improved; innovation; insight; nanoscale; screening; small molecule; small molecule libraries; small molecule therapeutics; surfactant; tool; tool development

Despite tremendous technical advances in drug discovery, de novo development of small molecule drugs is still challenging. High-throughput screening (HTS) with libraries of natural products and other complex molecules remains the bedrock approach. However, HTS is unsatisfactory in many ways: extraordinary cost, poor efficiency, rampant false positives and a complexity of “hits” that hinders hit-to-lead development. Fragment based drug discovery (FBDD) was brilliantly conceived to overcome these limitations, but has arguably not performed as hoped. The limited impact of FBDD is because most fragment “hit” molecules are very weak binders and are undetectable by current assay methods. The enormous potential of FBDD is therefore lost. Here, an approach is to be developed that can reliably detect weak but specific binding with the goal of helping to reinvigorate and enhance early phase small molecule drug discovery. Faithful detection of binding requires that the ligand and protein concentrations be at least on the order of the dissociation constant, which is practically and financially unrealistic for weak binders. The strategy to remove this basic barrier is simple. The water core of the reverse micelle (RM) is used to confine a single protein molecule and fragments at high enough concentrations to overcome the unfavorable binding entropy. NMR spectroscopy then permits site-resolved detection and quantification of binding affinity at reasonable cost. The first application of RM NMR FBDD highlights its potential to greatly expand small drug discovery. A rule- of-three (Ro3) fragment screen of interleukin-1β (IL-1β) shows that 1) weak yet specific binding can be efficiently detected in a structural context; 2) achieving the required high protein and ligand concentrations is economically feasible; 3) a high hit rate is observed; 4) surface coverage is extraordinary and gives unprecedented connectivity potential; 5) highly desired more polar binders are illuminated. The door is now open to more fully realize the tremendous promise of FBDD but critical questions remain: Is the IL-1β surface coverage typical? What is the distribution of fragment hit affinities of Ro3 and rule-of-five (Ro5) libraries more generally? What are the chemical characteristics of useful fragments to choose for an optimal RM NMR screening library? How useful are the very weakly binding hits for lead development? Does the Ro5 library offer a better compromise of hit affinity and surface coverage? What is the most efficient way to carry out RM NMR screening? Is RM NMR screening quantitatively reliable? This project will address these and other technical challenges that stand in the way of creating a strategy that more fully enables the brilliant insights of the FBDD paradigm and unleashes its originally anticipated potential.

尽管药物发现方面取得了巨大的技术进步，但小分子药物的从头开发仍然困难重重。 利用天然产物和其他复杂分子库进行高通量筛选 (HTS) 具有挑战性。 然而，HTS 在很多方面都不尽如人意：成本高昂、效果不佳。 效率、猖獗的误报和“命中”的复杂性阻碍了从命中到领先的开发。 基于药物发现（FBDD）的设想非常出色，可以克服这些限制，但有争议的是，它并没有 FBDD 的影响有限是因为大多数片段“命中”分子都是非常弱的结合物。 因此，目前的分析方法无法检测到 FBDD 的巨大潜力。 将开发一种能够可靠地检测弱但特异性结合的方法，目的是帮助 重振和加强早期小分子药物发现。 结合的忠实检测要求配体和蛋白质浓度至少约为 解离常数，这对于弱结合剂来说在实践和经济上都是不现实的。 这个基本屏障很简单，反胶束 (RM) 的水核用于限制单个蛋白质分子。 和碎片的浓度足够高，以克服 NMR 光谱的不利结合熵。 然后允许以合理的成本进行位点解析检测和结合亲和力的定量。 RM NMR FBDD 的首次应用凸显了其极大扩展小药物发现的潜力。 白细胞介素 1β (IL-1β) 的三 (Ro3) 片段筛选表明 1) 弱但特异性的结合可以有效地 在结构背景下检测；2) 达到所需的高蛋白质和配体浓度是经济的 可能；3) 观察到高命中率；4) 表面覆盖范围非常大，并提供前所未有的连接性 潜力；5) 非常需要的更多极性粘合剂被照亮。 现在，更充分地实现 FBDD 的巨大前景的大门已经敞开，但关键问题仍然存在： IL-1β 表面覆盖率典型情况是什么？ Ro3 和五规则 (Ro5) 的片段命中亲和力分布如何？ 更一般地，为最佳 RM 选择的有用片段的化学特征是什么？ NMR 筛选库？ Ro5 库对于先导化合物开发有多大用处？ 提供更好的命中亲和力和表面覆盖率的折衷方案进行 RM 的最有效方法是什么？ NMR 筛选？ RM NMR 筛选在定量上可靠吗？ 阻碍制定战略的技术挑战，以更充分地实现 FBDD 范式并释放其最初预期的潜力。