Recent advances in understanding the relevance of noncoding RNA (ncRNA) to disease have increased interest in drugging ncRNA with small molecules. The recent discovery of ribocil, a structurally distinct synthetic mimic of the natural ligand of the flavin mononucleotide (FMN) riboswitch, has revealed the potential chemical diversity of small molecules that target ncRNA. Affinity-selection mass spectrometry (AS-MS) is theoretically applicable to high-throughput screening (HTS) of small molecules binding to ncRNA. Here, we report the first application of the Automated Ligand Detection System (ALIS), an indirect AS-MS technique, for the selective detection of small molecule–ncRNA interactions, high-throughput screening against large unbiased small-molecule libraries, and identification and characterization of novel compounds (structurally distinct from both FMN and ribocil) that target the FMN riboswitch. Crystal structures reveal that different compounds induce various conformations of the FMN riboswitch, leading to different activity profiles. Our findings validate the ALIS platform for HTS screening for RNA-binding small molecules and further demonstrate that ncRNA can be broadly targeted by chemically diverse yet selective small molecules as therapeutics.

中文翻译：

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通过亲和选择质谱发现选择性结合RNA的小分子

在理解非编码RNA（ncRNA）与疾病的相关性方面的最新进展增加了对使用小分子进行ncRNA药物治疗的兴趣。核黄素的最新发现，是黄素单核苷酸（FMN）核糖开关天然配体的结构独特的合成模拟物，它揭示了靶向ncRNA的小分子的潜在化学多样性。亲和选择质谱（AS-MS）理论上适用于与ncRNA结合的小分子的高通量筛选（HTS）。在这里，我们报告了自动配体检测系统（ALIS）的首次应用，这是一种间接AS-MS技术，用于小分子与ncRNA相互作用的选择性检测，针对大型无偏小分子文库的高通量筛选，靶向FMN核糖开关的新型化合物（结构上不同于FMN和核糖体）的鉴定和表征。晶体结构表明，不同的化合物会诱导FMN核糖开关的各种构象，从而导致不同的活性谱。我们的发现验证了ALIS平台用于HTS筛选结合RNA的小分子的能力，并进一步证明了ncRNA可以被化学上多样化但选择性的小分子作为治疗剂广泛靶向。