Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan.
Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana SI-1000, Slovenia.
Nucleic Acids Res. 2021 Sep 7;49(15):8449-8461. doi: 10.1093/nar/gkab189.
Non-coding RNAs are regarded as promising targets for the discovery of innovative drugs due to their abundance in the genome and their involvement in many biological processes. Phytochemicals (PCs) are the primary source of ligand-based drugs due to their broad spectrum of biological activities. Since many PCs are heterocyclic and have chemical groups potentially involved in the interaction with nucleic acids, detailed interaction analysis between PCs and RNA is crucial to explore the effect of PCs on RNA functions. In this study, an integrated approach for investigating interactions between PCs and RNAs were demonstrated to verify the RNA-mediated PCs functions by using berberine (BRB) as a model PC. RNA screening of a transcriptome library followed by sequence refinement found minimal RNA motif consisting of a cytosine bulge with U-A and G-U neighbouring base pairs for interaction with BRB. NMR-based structure determination and physicochemical analyses using chemical analogues of BRB demonstrated the importance of electrostatic and stacking interactions for sequence selective interaction and RNA stabilization. The selective interaction with a relatively small RNA motif based on a chemical structure of a planer heterocyclic highlights the biological activities of various PCs mediated by the interactions with particular functional RNAs. In addition, the systematic and quantitative investigations demonstrated in this study could be useful for the development of therapeutic chemicals targeting functional RNAs, based on the PCs, in the future.
非编码 RNA 因其在基因组中的丰富性和在许多生物过程中的参与而被视为发现创新药物的有前途的靶点。植物化学物质（PCs）是配体药物的主要来源，因为它们具有广泛的生物活性。由于许多 PCs 是杂环的，并且具有可能与核酸相互作用的化学基团，因此详细的 PC 与 RNA 之间的相互作用分析对于探索 PCs 对 RNA 功能的影响至关重要。在这项研究中，采用小檗碱（BRB）作为模型 PC，展示了一种综合方法来研究 PCs 与 RNA 之间的相互作用，以验证 RNA 介导的 PCs 功能。通过对转录组文库进行 RNA 筛选，然后对序列进行精修，发现了由胞嘧啶凸起与 U-A 和 G-U 相邻碱基对组成的最小 RNA 基序，与 BRB 相互作用。基于 BRB 的化学类似物的 NMR 结构测定和物理化学分析表明，静电和堆积相互作用对于序列选择性相互作用和 RNA 稳定化非常重要。基于平面杂环的化学结构，与相对较小的 RNA 基序的选择性相互作用突出了各种 PCs 通过与特定功能 RNA 的相互作用介导的生物活性。此外，本研究中进行的系统和定量研究将来可能有助于基于 PCs 开发针对功能 RNA 的治疗性化学物质。
