Shape RNA Structure Analysis for Drug Discovery and Translational Research

用于药物发现和转化研究的形状 RNA 结构分析

• 批准号: 8979660
• 负责人: Katherine Deigan Warner
• 金额: $ 22.47万
• 依托单位: RIBOMETRIX, LLC
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-05-01 至 2017-10-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8979660
• 关键词: Adoption; Affect; Affinity; Antibiotics; Area; Benchmarking; Biological; Biological Process; Biology; Cell physiology; Chemicals; Chemistry; Communities; Complex; Computer Analysis; Computing Methodologies; Consult; Data; Development; Diagnosis; Diagnostic; Escherichia coli; Eukaryotic Cell; Evaluation; Formulation; Genome; Gold; HIV; Higher Order Chromatin Structure; Human Genome; In Situ; Influenza; Laboratories; Massive Parallel Sequencing; Medical; Messenger RNA; Methods; Molecular Biology; Nucleic Acids; Nucleotides; Pharmaceutical Preparations; Pharmacologic Substance; Phase; Proteins; RNA; RNA Sequences; RNA Viruses; RNA analysis; Reading; Reagent; Reporting; Research; Research Personnel; Resolution; Ribosomal RNA; Role; Science; Shapes; Single Nucleotide Polymorphism; Site; Small Business Technology Transfer Research; Small Interfering RNA; Structure; Technology; Testing; Therapeutic; Therapeutic Agents; Transcript; Translating; Translational Research; Untranslated RNA; Validation; Viral Pathogenesis; Virus Replication; Vision; Work; base; design; drug discovery; high throughput technology; human disease; interest; novel; prototype; public health relevance; research study; small molecule; targeted treatment; therapeutic development; therapeutic target; tool; user-friendly

 DESCRIPTION (provided by applicant): Roughly 70% of the human genome is transcribed into RNA and, in most of these RNAs, complex higher-order structures underlie or fundamentally affect critical biological processes. RNA structures are the targets of many antibiotics, and RNA structure should be further exploited in small-molecule drug discovery efforts. For example, structures in the genomes of RNA viruses like HIV and influenza are essential for viral replication and pathogenesis. Half of the single nucleotide polymorphisms that are most strongly associated with human diseases occur in non-coding regions and are likely associated with abnormal RNA structures. Many nucleic acid-based therapeutics - including clinically important antisense and siRNA approaches - only work when exceedingly rare, high affinity, and structurally accessible sites are targeted. The Weeks laboratory has developed a chemical probing strategy, called SHAPE-MaP, that accurately reports on RNA structure in physiologically relevant contexts. This technology enables nucleotide-resolution RNA structure analysis information to be read out by massively parallel sequencing. Although independent groups describe SHAPE as the "gold standard" of RNA structure analysis, in its current form, SHAPE-MaP represents a cutting-edge but research-grade technology. The long-term vision of Ribometrix is to make SHAPE-MaP a platform technology with applications in drug discovery, translational research, and basic biological discovery. In this work, we will conduct proof-of-concept studies to solve impediments to adoption of SHAPE-MaP by non-expert laboratories via two aims: (1) to create and experimentally validate diagnostic controls to enable efficient evaluation and troubleshooting of a prototype SHAPE-MaP RNA structure analysis pipeline by non-expert users and (2) to examine and optimize formulation of SHAPE reagents for consistent handling. Progress to Phase 2 will be justified by data showing that novice users are able to implement and diagnose RNA structure probing experiments using easily handled, long-lifetime reagents, consistent with quantitative benchmarks. In Phase 2, Ribometrix will automate the downstream computational steps required to fully interpret SHAPE-MaP experiments and will create complete industrialized reagent platforms for use by pharmaceutical and academic customers and collaborators. Successful development of a user-friendly SHAPE technology platform will enable researchers in all areas of biomedical science to perform robust, quantitative experiments that explore the fundamental role of RNA in biology and that facilitate creation of RNA-based and RNA-directed therapeutics.

 描述（由申请人提供）：大约70%的人类基因组被转录为RNA，并且在大多数这些RNA中，复杂的高阶结构是关键生物过程的基础或从根本上影响关键生物过程。RNA结构是许多抗生素的靶标，并且RNA结构应该在小分子药物发现工作中进一步利用。例如，RNA病毒（如HIV和流感病毒）基因组中的结构对于病毒复制和发病机制至关重要。与人类疾病最密切相关的单核苷酸多态性中有一半发生在非编码区，并且可能与异常RNA结构相关。许多基于核酸的疗法-包括临床上重要的反义和siRNA方法-仅在靶向非常罕见、高亲和力和结构上可接近的位点时才起作用。Weeks实验室开发了一种化学探测策略，称为SHAPE-MaP，可以准确地报告生理相关背景下的RNA结构。该技术能够通过大规模并行测序读取核苷酸分辨率RNA结构分析信息。尽管独立团体将SHAPE描述为RNA结构分析的“黄金标准”，但以目前的形式，SHAPE-MaP代表了一种尖端但研究级的技术。Ribomestrium的长期愿景是使SHAPE-MaP成为一种平台技术，应用于药物发现，转化研究和基础生物学发现。在这项工作中，我们将通过两个目标进行概念验证研究，以解决非专家实验室采用SHAPE-MaP的障碍：（1）创建和实验验证诊断控制，以使非专家用户能够对原型SHAPE-MaP RNA结构分析管道进行有效评估和故障排除，以及（2）检查和优化SHAPE试剂的配方，以实现一致的处理。第2阶段的进展将通过数据证明，新手用户能够使用易于处理的长寿命试剂实施和诊断RNA结构探测实验，与定量基准一致。在第二阶段，RibomeTM将自动化下游计算步骤，以充分解释SHAPE-MaP实验，并将创建完整的工业化试剂平台，供制药和学术客户和合作者使用。用户友好的SHAPE技术平台的成功开发将使生物医学科学各个领域的研究人员能够进行强大的定量实验，探索RNA在生物学中的基本作用，并促进基于RNA和RNA导向疗法的创建。