Modulating gene expression by RNA-targeting chimeras

项目摘要 RNA结合小分子具有调节基因表达的潜力，所述基因的蛋白质产物 以前被认为是“不可用的”靶向前体mRNA的Risdiplam最近被批准用于 脊髓性肌萎缩症（SMA）的治疗，并证明了这种治疗方法的特异性和安全性。 approach.尽管已经发现了多种小分子支架作为RNA结合配体，但它们的功能和作用机制尚不清楚。 由于（1）缺乏特异性和（2）不可预测的功能而妨碍了使用。我们提出了一个研究计划， 将提供避免这些缺点的RNA靶向化学探针。蛋白水解靶向蛋白水解Proteolysis Targeting 嵌合体（PROTAC）技术，我们正在设计嵌合分子，将靶向RNA特异性， 以高度可预测的方式携带（递送）诱导RNA降解或抑制RNA翻译的能力。 我们对RNA靶向嵌合体平台的初步努力使用新发现的RNA结合香豆素 衍生物作为模型，并通过化学修饰微调其优先结合特性。通过 结构优化，其中包括使用“双齿”RNA配体策略，我们期望实现RNA- 结合选择性等于或大于寡核苷酸。同时，我们建议发展 并优化了三种新型效应子，用于精确降解RNA靶标或抑制靶RNA翻译。 这些新的效应物在抑制寨卡病毒（一种RNA病毒）基因表达方面显示出有希望的结果。 最终，我们提出的工作将产生一个自上而下的方法来设计选择性基因表达 不依赖于基因蛋白产物的抑制剂。我们实验室的长期目标是建立一个 用于使用RNA结合小分子进行基因特异性和患者特异性治疗的药物化学平台 分子。在这个过程中，我们不仅会产生用于研究重要疾病的各种工具化合物- 修改基因，但也联合收割机计算和实验技术，以了解详细的 RNA-小分子识别机制。

Project Summary RNA-binding small molecules have the potential to modulate the expression of genes whose protein products were previously considered “undruggable.” Risdiplam, targeting a precursor mRNA, was recently approved for the treatment of spinal muscular atrophy (SMA) and demonstrates the specificity and safety attainable by this approach. Although a variety of small-molecule scaffolds have been uncovered as RNA-binding ligands, their use is hampered by (1) lack of specificity and (2) unpredictable function. We propose a research program that will provide RNA-targeting chemical probes that will avoid these drawbacks. Inspired by Proteolysis Targeting Chimera (PROTAC) technology, we are designing chimeric molecules that will target RNA specifically and carry (deliver) the ability to induce RNA degradation or inhibit RNA translation, in a highly predictable manner. Our initial efforts towards an RNA-targeting chimera platform use a newly discovered RNA-binding coumarin derivative as a model and fine-tune its preferential binding properties through chemical modification. Through structural optimization, which includes using a “bidentate” RNA ligand strategy, we expect to achieve RNA- binding selectivity equal to or greater than that of oligonucleotides. At the same time, we propose to develop and optimize three novel effectors to precisely degrade RNA targets or inhibit the target RNA translation. These new effectors have shown promising results in inhibiting Zika virus (an RNA virus) gene expression. Ultimately, our proposed work will generate a top-down method for designing selective gene expression inhibitors that are independent of the gene's protein product. The long-term goal of our lab is to build a medicinal chemistry platform for making gene-specific and patient-specific therapies using RNA-binding small molecules. In this process, we will not only generate various tool compounds for studying important disease- modifying genes, but also combine computational and experimental technologies to understand the detailed mechanism of RNA-small molecule recognition.