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: 10001564
• 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/10001564
• 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的、RNA靶向的小分子配体，以探测靶向RNA的分子。 动态结构，基础生物学和治疗潜力的长链非编码RNA（lncRNA）。选择 已发现lncRNA在癌症进展中起关键作用，包括lncRNA HOTAIR，其 与转移性乳腺癌有关，lncRNA MALAT-1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，但足够小的 分子靶向策略还有待实现。这种缓慢的进展部分是由于RNA的性质， 具有有限的化学功能的动态结构，但也存在关于指导的知识空白 小分子：RNA相互作用的原理和方法。我们的中心假设是， 小分子化学空间和RNA拓扑空间的发现将产生 对小分子的基本见解：RNA识别，可应用于快速发展， 这些配体对广泛的RNA靶标具有高亲和力和特异性。在之前的工作中，PI已确定 生物活性RNA配体的常见化学性质，用于改善的RNA结合支架 识别小RNA靶点，揭示了RNA二级结构，可以通过 小分子和计算鉴定的靶向lncRNA HOTAIR的"热点"。拟议 工作，我们将同时追求两个独立但互补的基本调查路线 并将开发的指导原则和技术应用于两个关键的lncRNA靶点。在第1区，我们将 利用化学信息学分析、有机合成和快速筛选方法鉴定小分子 偏向于特定RNA识别的特性。在区域2中，我们将使用模式识别协议， 识别容易被小分子区分的RNA结构。在第三区，我们将联合收割机 偏见库和优化的筛选试验来鉴定lncRNA三级结构的第一个抑制剂， 特别是MALAT1的3 ′-三螺旋。在区域4中，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HOTAIR及其 蛋白结合伴侣PRC2。这项研究的基本原理是，我们的新型RNA特异性文库和 技术将使新的研究RNA的结构和功能，并作为一个丰富的平台， RNA靶向治疗的未来发展。总之，我们的工作将（i）产生第一个广泛的 可利用的RNA偏向分子文库，其对RNA靶点具有已证明的亲和力和特异性;（ii）开发 一系列的计算，合成和筛选工具，以提高RNA配体识别;和（iii）产量第一- 开发lncRNA小分子配体的一流技术。这些不同但互补的 这种方法不仅可以确保这项研究的成功，而且可以在小分子领域取得进展：RNA 它不仅可以用于靶向，而且还将为人类健康中一系列至关重要的目标提供先导小分子。