Almena Rodriguez Laura, Kallert Elisabeth, Husmann Jan-Åke, Schaubruch Kirsten, Meisel Katherina I S, Schwickert Marvin, Hoba Sabrina N, Heermann Ralf, Kersten Christian
Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany.
Institute of Molecular Physiology, Microbiology and Biotechnology, Johannes Gutenberg-University, Hanns-DieterHüsch-Weg 17, 55128 Mainz, Germany.
J Med Chem. 2025 Apr 24;68(8):8659-8678. doi: 10.1021/acs.jmedchem.5c00339. Epub 2025 Apr 7.
Targeting RNA with small molecules is an emerging field in medicinal chemistry. However, highly potent ligands are often challenging to achieve. One intuitive strategy to enhance ligand's potency is the implementation of positively charged moieties to interact with the negatively charged RNA phosphate backbone. We investigated the effect of such "electrostatic anchors" on binding affinity, kinetics, thermodynamics, and selectivity by MST, SPR, and ITC experiments, respectively, with the SAM-VI riboswitch and the preQ riboswitch aptamer model systems. RNA-ligand interactions were dominated by enthalpy, and electrostatic anchors had moderate effects on binding affinity driven by faster association rates for higher charged ligands. Despite the observations of loose binding interactions in SPR experiments with multibasic ligands, selectivity over structurally unrelated RNA off-targets was maintained. Therefore, the addition of positively charged moieties is no universal RNA-ligand design principle, but a purposefully implemented ionic RNA-ligand interaction can enhance potency without impairing selectivity.
利用小分子靶向RNA是药物化学中一个新兴的领域。然而，要获得高效能的配体往往具有挑战性。一种直观的提高配体效能的策略是引入带正电荷的基团，使其与带负电荷的RNA磷酸骨架相互作用。我们分别通过微量热泳动（MST）、表面等离子体共振（SPR）和等温滴定量热法（ITC）实验，研究了这种“静电锚”对结合亲和力、动力学、热力学和选择性的影响，所使用的模型系统为SAM-VI核糖开关和preQ核糖开关适配体。RNA-配体相互作用主要由焓主导，并且对于带电量更高的配体，由于其更快的缔合速率，静电锚对结合亲和力有适度的影响。尽管在与多碱性配体的SPR实验中观察到了较弱的结合相互作用，但对结构不相关的RNA脱靶的选择性得以保持。因此，添加带正电荷的基团并非通用的RNA-配体设计原则，但有目的地实现离子型RNA-配体相互作用可以在不损害选择性的情况下提高效能。
