Harnessing Small Molecules to Probe the Structure and Function of Long Noncoding RNAs

利用小分子探测长非编码 RNA 的结构和功能

• 批准号: 9754206
• 负责人: Amanda E Hargrove
• 金额: $ 38.06万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-15 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9754206
• 关键词: Affinity; Area; Bacterial Infections; Binding Proteins; Biological; Biological Assay; Biological Process; Biology; Chemicals; Development; Disease; Disseminated Malignant Neoplasm; Ensure; Future; Goals; HIV; Health; Hot Spot; Human; Investigation; Knowledge; Lead; Libraries; Ligands; MALAT1 gene; Malignant Neoplasms; Metastatic breast cancer; Methods; Molecular Bank; Nature; Neuromuscular Diseases; Non-Small-Cell Lung Carcinoma; Organic Synthesis; Pattern Recognition; Play; Property; Protocols documentation; RNA; RNA Binding; RNA-Protein Interaction; Research; Role; Screening procedure; Small RNA; Specificity; Structure; Technology; Therapeutic; Untranslated RNA; Virus Diseases; Work; bacterial resistance; chemical function; chemical property; cheminformatics; human disease; improved; inhibitor/antagonist; insight; novel; overexpression; scaffold; screening; small molecule; small molecule libraries; success; targeted treatment; tool; triple helix; tumor progression

Project Summary The long-term goal of the PI is to develop highly specific, RNA-targeted, small molecule ligands to probe the dynamic structure, fundamental biology, and therapeutic potential of long noncoding RNAs (lncRNAs). Select lncRNAs have been found to play critical roles in cancer progression, including lncRNA HOTAIR, which is implicated in metastatic breast cancer, and lncRNA MALAT-1, which is over-expressed in several cancers, including non-small cell lung cancer. Despite the proposed therapeutic potential of lncRNAs, adequate small molecule targeting strategies have yet to be realized. This slow progress is due in part to the nature of RNA as a dynamic structure with limited chemical functionality but also to a gap in knowledge with respect to guiding principles and methods for small molecule:RNA interactions. Our central hypothesis is that the parallel discovery of small molecule chemical space and RNA topological space privileged for differentiation will yield fundamental insights into small molecule:RNA recognition that can be applied to the rapid development of ligands with high affinity and specificity for a wide range of RNA targets. In prior work, the PI has identified common chemical properties of biologically active RNA ligands, elaborated RNA binding scaffolds for improved recognition of small RNA targets, revealed RNA secondary structures that can be differentially recognized by small molecules, and computationally identified “hot spots” for targeting lncRNA HOTAIR. In the proposed work, we will simultaneously pursue two independent but complementary lines of fundamental investigation and apply the developed guiding principles and technologies to two critical lncRNA targets. In Area 1, we will use cheminformatic analysis, organic synthesis, and rapid screening methods to identify small molecule properties biased toward specific RNA recognition. In Area 2, we will use pattern recognition protocols to identify RNA structures that are readily differentiated by small molecules. In Area 3, we will combine our RNA- biased libraries and optimized screening assays to identify the first inhibitors of lncRNA tertiary structure, particularly the 3'-triple helix of MALAT1. In Area 4, we will use a wide range of computational and experimental tools to identify small molecules that inhibit lncRNA:protein interactions, viz. HOTAIR and its protein binding partner, PRC2. The rationale for this research is that our novel RNA-specific libraries and technologies will enable new investigations of RNA structure and function and serve as a rich platform for future development of RNA targeted therapeutics. In summary, our work will (i) produce the first widely available RNA-biased molecular library with demonstrated affinity and specificity for RNA targets; (ii) develop a range of computational, synthetic, and screening tools to enhance RNA ligand identification; and (iii) yield first- in-class technologies to develop small molecule ligands for lncRNAs. These distinct but complementary approaches will not only ensure success of this research and progress in the field of small molecule:RNA targeting, but will also provide lead small molecules for a range of critically important targets in human health.

项目摘要 PI的长期目标是开发高度特异性，靶向RNA的小分子配体以探测 长期非编码RNA（LNCRNA）的动态结构，基本生物学和治疗潜力。选择 已经发现lncrnas在癌症进展中起关键作用，包括lncrna hotair， 在转移性乳腺癌和lncrna malat-1中实施，在几种癌症中过表达， 包括非小细胞肺癌。尽管提出了LNCRNA的治疗潜力，但很小 分子靶向策略尚未实现。这种缓慢的进展部分是由于RNA的性质 具有有限化学功能的动态结构，但在指导方面的知识差距也有差距 小分子的原理和方法：RNA相互作用。我们的中心假设是平行 发现小分子化学空间和具有分化特权的RNA拓扑空间将产生 对小分子的基本见解：可用于快速发展的RNA识别 具有高亲和力和特异性的配体，适用于广泛的RNA靶标。在先前的工作中，PI已确定 生物活性RNA配体的常见化学特性，详细的RNA结合支架可改善 识别小的RNA靶标，揭示了RNA二级结构，可以通过 小分子和用于靶向lncrna热水的计算“热点”。在提议中 工作，我们只需追求两种独立但完整的基本投资行 并将开发的指导原理和技术应用于两个关键的LNCRNA目标。在区域1中，我们将 使用化学形式分析，有机合成和快速筛选方法鉴定小分子 特性偏向于特定的RNA识别。在区域2中，我们将使用模式识别协议 识别很容易通过小分子区分的RNA结构。在区域3中，我们将结合我们的RNA- 有偏见的文库和优化的筛选测定法，以识别lncRNA三级结构的第一个抑制剂， 特别是malat1的3'-Triple螺旋。在第4区，我们将使用广泛的计算和 鉴定抑制lncRNA的小分子的实验工具：蛋白质相互作用，即。热带及其 蛋白质结合伴侣PRC2。这项研究的理由是我们新颖的RNA特定图书馆和 Technologies将实现RNA结构和功能的新投资，并成为丰富的平台 RNA靶向疗法的未来发展。总而言之，我们的工作将（i）产生第一个宽度 可用的RNA偏置分子文库具有与RNA靶标具有亲和力和特异性的可见； （ii）开发 计算，合成和筛选工具的范围，以增强RNA配体识别； （iii）首先产生 在类型的lncRNA中开发小分子配体的课堂技术。这些独特但完整的 方法不仅可以确保这项研究的成功和小分子领域的进展：RNA 靶向，但还将为人类健康中一系列至关重要的目标提供铅小分子。