Sequence-based Design of Small Molecules Targeting RNA

 描述（由申请人提供）：基因组测序工作的主要目标是实现患者特异性治疗。我们的实验室专注于开发通用方法，仅从基因组序列设计选择性先导疗法。尽管寡核苷酸已被用于靶向和研究RNA，但它们受到次优性质的阻碍，例如差的细胞和组织渗透性、有限的可用于优化的修饰/衍生物、结构化RNA的无效靶向。我们正在通过使用我们开发的几种新颖的变革性技术，用小分子靶向基因的RNA产物来解决这个难题。这些方法揭示了RNA的新生物学作用，并提供了变革性方法，允许受疾病影响的细胞合成自己的药物。(9)此外，我们已经表明，基因组序列可以用于提供患者特异性治疗和高度选择性的功能化学探针-实际上具有更大的生物学活性。 或与通过寡核苷酸识别RNA的选择性相等。（1，24）设计调节RNA功能的小分子在很大程度上是困难的，这是由于对RNA-小分子识别事件的不完全理解。也就是说，对于结合RNA和形成小分子结合位点的RNA支架来说是特权的化学空间是未知的。我们正在以创新和新颖的方式填补这些知识空白，以使化学探针的设计能够以前所未有的准确性靶向RNA。我们提出的工作旨在扩展我们自下而上的方法，名为Inforna：特定目标1：识别结合RNA的药物样支架。为了推进Inforna，需要填补两个知识空白：（i）识别细胞RNA中高度流行的基序类型;（ii）识别赋予RNA亲和力的药物样小分子的特征。我们将通过探测药物样小分子文库来填补这些知识空白，以结合Inforna中数据有限的重要RNA基序。 特异性目标2：使用特异性目标1中鉴定的先导小分子靶向疾病相关的miRNA。Inforna提供了许多针对疾病相关RNA的生物活性化合物。在我们最近发表在《自然化学生物学》上的报告中，（1）它使一种目标不可知的方法能够发现针对miRNA前体的先导化合物，提供了44%的生物活性命中率。 具体目标3a：开发精确的多价二聚体，允许选择性地，有效地靶向miRNA前体。该子目标的中心假设是，尽管转录组中存在可靶向的RNA基序，但具有以相同距离分开的多个可靶向基序的RNA要少得多。 具体目标3b：开发用单个小分子靶向两个miRNA的小分子，并通过设计师多药疗法研究疾病通路的双重靶向的细胞后果。

 DESCRIPTION (provided by applicant): A major goal of genome sequencing efforts is to enable patient-specific therapies. Our laboratory is focused on developing general approaches to design selective lead therapeutics from only genome sequence. Although oligonucleotides have been used to target and study RNA, they are hampered by suboptimal properties such as poor cell and tissue permeability, limited available modifications/derivatives for optimization, an ineffective targeting of structured RNAs. We are tackling this difficult problem by targeting the RNA products of genes with small molecules, using several novel and transformative technologies we developed. These approaches uncovered new biological roles for RNA (4) and provided transformative approaches to allow for a disease-affected cell to synthesize its own drug.(9) Furthermore, we have shown that genome sequence can be utilized to afford patient-specific therapies and chemical probes of function that are highly selective - in fact with greater or equal selectivity as recognition of RNA via oligonucleotides.(1, 24) Designing small molecules that modulate RNA function is difficult in large part due to an incomplete understanding of RNA-small molecule recognition events. That is, the chemical space that is privileged for binding RNA and RNA scaffolds that form small molecule binding sites are unknown. We are filling these knowledge gaps in innovative and novel ways to enable design of chemical probes that target RNA with unprecedented accuracy. Our proposed work seeks to expand our bottom-up approach, named Inforna: Specific Aim 1: Identify drug-like scaffolds that bind RNA. To advance Inforna, two knowledge gaps need to be filled: (i) identification of highly prevalent motif types in cellular RNAs; and (ii) identification of features in drug-like small molecules that confer avidity for RNA. We will fill these knowledge gaps by probing a drug-like small molecule library for binding to important RNA motifs for which there are limited data in Inforna. Specific Aim 2: Target disease-associated miRNAs using lead small molecules identified in Specific Aim 1. Inforna has provided numerous bioactive compounds against disease-associated RNAs. In our recent report in Nature Chemical Biology,(1) it enabled a target agnostic approach to discover lead compounds against miRNA precursors, affording a 44% bioactive hit rate. Specific Aim 3a: Develop precision multivalent dimers that allow for selective, potent targeting of miRNA precursors. The central hypothesis in this sub-aim is that although there are targetable RNA motifs in the transcriptome, there are far fewer RNAs that have the multiple targetable motifs separated by the same distance. Specific Aim 3b: Develop small molecules that target two miRNAs with a single small molecule and study the cellular consequences of dual targeting of disease pathways via designer poly-pharmacy.