Suresh Blessy M, Li Weichao, Zhang Peiyuan, Wang Kye Won, Yildirim Ilyas, Parker Christopher G, Disney Matthew D
Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458.
Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL 33458.
Proc Natl Acad Sci U S A. 2020 Dec 29;117(52):33197-33203. doi: 10.1073/pnas.2012217117. Epub 2020 Dec 14.
RNAs have important functions that are dictated by their structure. Indeed, small molecules that interact with RNA structures can perturb function, serving as chemical probes and lead medicines. Here we describe the development of a fragment-based approach to discover and optimize bioactive small molecules targeting RNA. We extended the target validation method chemical cross-linking and isolation by pull-down (Chem-CLIP) to identify and map the binding sites of low molecular weight fragments that engage RNA or Chem-CLIP fragment mapping (Chem-CLIP-Frag-Map). Using Chem-CLIP-Frag-Map, we identified several fragments that bind the precursor to oncogenic microRNA-21 (pre-miR-21). Assembly of these fragments provided a specific bioactive compound with improved potency that inhibits pre-miR-21 processing, reducing mature miR-21 levels. The compound exerted selective effects on the transcriptome and selectively mitigated a miR-21-associated invasive phenotype in triple-negative breast cancer cells. The Chem-CLIP-Frag-Map approach should prove general to expedite the identification and optimization of small molecules that bind RNA targets.
RNA具有由其结构所决定的重要功能。实际上，与RNA结构相互作用的小分子能够干扰其功能，可作为化学探针和先导药物。在此，我们描述了一种基于片段的方法，用于发现和优化靶向RNA的生物活性小分子。我们扩展了靶标验证方法——化学交联与下拉分离（Chem-CLIP），以识别和定位与RNA结合的低分子量片段的结合位点，即化学交联与下拉片段定位（Chem-CLIP-Frag-Map）。使用Chem-CLIP-Frag-Map，我们鉴定出了几个与致癌性微小RNA-21（pre-miR-21）的前体结合的片段。这些片段的组装产生了一种具有更高活性的特异性生物活性化合物，该化合物可抑制pre-miR-21的加工过程，降低成熟miR-21的水平。该化合物对转录组产生选择性影响，并选择性减轻三阴性乳腺癌细胞中与miR-相关的侵袭表型。Chem-CLIP-Frag-Map方法应能普遍加快对结合RNA靶标的小分子的鉴定和优化。
