Deciphering the principles of selective recognition of complex RNAs by small molecules

破译小分子选择性识别复杂RNA的原理

• 批准号: 10231110
• 负责人: Megan L Ken
• 金额: $ 5.1万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10231110
• 关键词: AIDS/HIV problem; Address; Area; Bacteria; Binding; Binding Sites; Biological Assay; Biological Process; Characteristics; Chemicals; Clinic; Communicable Diseases; Complex; Crystallization; Data; Development; Docking; Drug Interactions; Drug Targeting; Elements; Evolution; Exonuclease; Flavin Mononucleotide; Flavivirus; Gene Expression; Glutamine; HIV; HIV-1; Human Genome; Human Herpesvirus 4; Human Pathology; Hydrophobicity; Knowledge; Lead; Libraries; Ligand Binding; Ligands; Measures; Mission; Multiple Bacterial Drug Resistance; National Institute of Allergy and Infectious Disease; Nature; Pharmaceutical Preparations; Property; Proteins; Public Health; RNA; RNA Binding; Recombinants; Regulatory Element; Reporter; Resistance; Response Elements; Small RNA; Solvents; Specificity; Structure; Surveys; Testing; Therapeutic; Transactivation; Untranslated RNA; Viral; Virulence; Virus Replication; Work; Zika Virus; antimicrobial; antimicrobial drug; antimicrobial resistant pathogen; aptamer; base; cost; density; drug discovery; drug resistant bacteria; flexibility; high throughput screening; human disease; human pathogen; inhibitor/antagonist; lead optimization; microbial; molecular dynamics; new therapeutic target; novel; pathogen; prevent; scaffold; screening; small molecule; stem; success; three dimensional structure; transcriptome; virtual; virtual screening

ABSTRACT Noncoding RNAs (ncRNAs) are a new and growing class of biomolecules that are increasingly being shown to be important drug targets in many human pathogens. New drug targets are needed for many of the most important pathogens in human disease as resistance, latency, and cost are still significant challenges in treatment. While considerable effort has been made to target these essential ncRNAs, the most prominent examples being stem loop hairpins in HIV, no compounds have successfully reached the market. These studies have focused on simple RNAs that may not be ideal drug targets. Simple RNAs tend to have “low-druggability” properties such high solvent exposure, limited unique binding sites, and increased flexibility. We hypothesize that the lack of success in creating RNA-targeted small molecule drugs is due in large part due to difficulties in targeting these hairpins with high selectivity, especially given that similar hairpin motifs occur in great abundance in the transcriptome. However, there are a growing number of microbial ncRNA drug targets that fold into more complex 3D structures. These RNAs are marked by unique secondary structural motifs, long-range tertiary contacts, and often deeper and larger hydrophobic pockets. The main hypothesis of this proposal is that complex RNA structures have attributes that make them better drug targets for small molecule inhibition as compared to simpler hairpins. Aim 1 will used a structure-based survey, NMR-based binding assays, and computational docking to test the hypothesis that complex RNAs have unique binding pockets and modes that allow highly selective binding to ligands that otherwise only weakly bind to common hairpin RNAs. The Aim will also test the hypothesis that the binding pockets of complex RNAs have variable attributes that result in varying levels of binding selectivity, which can be predicted using computational docking. Aim 2 will use an ensemble-based virtual screening approach, in combination with experimental high throughput screening, to test the hypothesis that novel chemotypes bind to the pockets of complex RNAs, some of which can alter or inhibit biological function. This project will provide a deeper understanding regarding the druggability of RNA, identify novel chemotypes that may be further optimized for novel antimicrobial drugs, and help address the challenge of selectivity, which is one of the biggest obstacles in targeting RNA with small molecules. As very little drug discovery work has been done with these targets, this screening effort will vastly expand the chemical space surveyed for RNA binding. Novel chemotypes that are discovered will lead to a deeper understanding of the structural determinants of highly selective interactions and will become the basis of lead compounds that can be further optimized for novel antimicrobial drugs.

摘要 非编码RNA（ncRNA）是一类新的和不断增长的生物分子，越来越多地被证明是 是许多人类病原体的重要药物靶点。需要新的药物靶点来治疗许多 人类疾病中的重要病原体，如耐药性、潜伏期和成本，仍然是重大挑战， 治疗虽然已经做出了相当大的努力来靶向这些必需的ncRNA，但最突出的是 例如HIV中的茎环发夹，没有化合物成功进入市场。这些研究 一直专注于可能不是理想药物靶点的简单RNA。简单的RNA往往具有“低药物性” 这些特性包括高溶剂暴露、有限的独特结合位点和增加的柔性。我们假设 在创造RNA靶向小分子药物方面缺乏成功，在很大程度上是由于难以 以高选择性靶向这些发夹，特别是考虑到类似的发夹基序大量存在 在转录组中。然而，有越来越多的微生物ncRNA药物靶点， 复杂的3D结构这些RNA以独特的二级结构基序、长距离三级结构基序和高分子结构基序为特征。 接触，以及通常更深和更大的疏水口袋。这一提议的主要假设是， RNA结构具有使它们与RNA结构相比更好地用于小分子抑制的药物靶标的属性。 简单的发夹目的1将使用基于结构的调查，基于NMR的结合测定，和计算 对接来检验复杂的RNA具有独特的结合口袋和模式的假设， 选择性结合配体，否则仅弱结合常见发夹RNA。Aim还将测试 假设复杂RNA的结合口袋具有可变的属性，导致不同水平的 结合选择性，这可以使用计算对接来预测。Aim 2将使用基于集成的 虚拟筛选方法，结合实验高通量筛选，以检验假设 新的化学型与复杂RNA的口袋结合，其中一些可以改变或抑制生物功能。 该项目将提供有关RNA可药物化性的更深入了解，识别新的化学型 可以进一步优化新型抗菌药物，并帮助解决选择性的挑战， 是用小分子靶向RNA的最大障碍之一。 由于很少有药物发现工作已经完成了这些目标，这种筛选工作将大大扩大 研究了RNA结合的化学空间。新的化学类型的发现将导致更深层次的 了解高度选择性相互作用的结构决定因素，并将成为铅的基础 这些化合物可以进一步优化用于新型抗微生物药物。