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; 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.

尽管药物发现方面的技术进步巨大，但小分子药物的从头开发仍在 具有挑战性的。具有天然产物和其他复杂分子库的高通量筛选（HTS） 仍然是基岩方法。但是，HTS在许多方面都不令人满意：非凡的成本，差 效率，猖ramp的假阳性以及阻碍命中率发展的“命中”的复杂性。分段 基于药物发现（FBDD）是为了克服这些限制而出色地构想的，但可以说不是 表演如希望的。 FBDD的影响有限是因为大多数片段“命中”分子是非常弱的粘合剂 并且无法通过当前的测定方法检测到。因此，FBDD的巨大潜力丢失了。在这里，一个 可以开发出可以可靠地检测到弱但特定的约束力的方法，以帮助 振兴并增强早期小分子药物发现。 忠实的结合检测要求配体和蛋白质浓度至少在 解离常数，实际上和财务上对弱粘合剂是不现实的。删除的策略 这个基本障碍很简单。反向胶束（RM）的水芯用于局限于单个蛋白质分子 和足够浓度的片段以克服不利的结合熵。 NMR光谱 然后允许以合理的成本对位置分辨的检测和结合亲和力进行定量。 RM NMR FBDD的首次应用突出了其大大扩展小型药物发现的潜力。规则 - 白介素-1β（IL-1β）的三个（RO3）片段表明1）弱但特定的结合可以有效地有效 在结构背景下检测到； 2）实现所需的高蛋白质和配体浓度在经济上是 可行的; 3）观察到高命中率； 4）表面覆盖范围非常非凡，并提供了前所未有的连接性 潜在的; 5）高度期望的更多极性粘合剂被照亮。 现在，门开放以更充分地意识到FBDD的巨大希望，但仍然存在关键问题：是 IL-1β表面覆盖范围典型？ RO3和五规则（RO5）的碎片命中亲和力的分布是多少 图书馆更普遍？最佳RM选择有用片段的化学特征是什么 NMR筛选库？较弱的命运对铅开发的有用程度有多有用？ RO5库吗 提供更好的损失亲和力和表面覆盖范围的妥协？执行RM的最有效方法是什么 NMR筛选？ RM NMR筛选是否可以定量可靠？该项目将解决这些问题和其他 技术挑战阻碍建立一种更充分地实现的策略的方式 FBDD范式并释放了其最初具有预期的潜力。