Sequence-based Design of Small Molecules Targeting RNA

 描述(由申请人提供)：基因组测序工作的一个主要目标是实现针对患者的治疗。我们的实验室致力于开发仅从基因组序列设计选择性先导疗法的一般方法。虽然寡核苷酸已被用于靶向和研究RNA，但它们受到细胞和组织渗透性差、可用于优化的修饰/衍生物有限、对结构RNA的靶向无效等性质的限制。我们正在利用我们开发的几种新的和变革性的技术，通过瞄准具有小分子的基因的RNA产物来解决这个难题。这些方法发现了RNA(4)的新的生物学作用，并提供了允许受疾病影响的细胞合成自己的药物的变革性方法。(9)此外，我们还表明，基因组序列可以用来提供高度选择性的针对患者的治疗和功能的化学探针--事实上，具有更高的选择性。 或与通过寡核苷酸识别RNA的选择性相同。(1，24)设计调节RNA功能的小分子是困难的，这在很大程度上是由于对RNA-小分子识别事件的不完全理解。也就是说，适合与RNA结合的化学空间和形成小分子结合位点的RNA支架是未知的。我们正在以创新和新颖的方式填补这些知识空白，从而能够以前所未有的准确性设计针对RNA的化学探针。我们提议的工作旨在扩展我们的自下而上的方法，名为Inforna：特定目标1：识别结合RNA的类药物支架。为了推进Inforna，需要填补两个知识空白：(I)鉴定细胞RNA中高度普遍的基序类型；(Ii)鉴定类药物小分子中赋予RNA亲和力的特征。我们将通过探索一个类似药物的小分子文库来填补这些知识空白，该文库可以与重要的RNA基序结合，而Inforna中对这些基序的数据有限。特定目标2：使用特定目标1中确定的铅小分子靶向疾病相关的miRNAs。Inforna提供了许多针对疾病相关RNAs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)它使目标不可知性方法能够发现针对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、有效地靶向miRNA前体。这一亚目标的中心假设是，尽管在转录组中存在可靶向的RNA基序，但具有多个可靶向基序的RNA要少得多。具体目标3b：开发以单个小分子靶向两个miRNAs的小分子，并通过设计多药研究疾病途径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.