Li Yuting, Tan Peng, Liu Qianpan, Sun Huaixin, Wang Yue, Chen Siyi, Kong Weixin, Sun Xiaoyi, Shao Xiang
Department of Geriatrics, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China.
Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215028, China.
Biophys Chem. 2025 May-Jun;320-321:107417. doi: 10.1016/j.bpc.2025.107417. Epub 2025 Feb 18.
The RNA N-adenosine methylation, resulting in N-methyl adenosine (m6A), is one of the most important post-transcriptional modification events in the eukaryotic transcriptome, which is dynamically regulated by methyltransferases (writers), recognition proteins (readers) and demethylases (erasers). Human has five m6A readers namely YTHDC1, YTHDC2, YTHDF1, YTHDF2 and YTHDF3 that specifically recognize and bind to the methylated m6A residue of RNA through their YT521-B homology (YTH) domains, which have been involved in the pathogenesis of diabetes mellitus and its diverse complications such as diabetic nephropathy. Instead of the native N-methylation, we herein attempted to explore the molecular effect of various non-native N-substitutions on adenosine (A) binding behavior to YTH domains. A systematic interaction profile of 40 reported N-substituted adenosine (x6A) mononucleotides with 5 human reader YTH domains was created computationally. Heuristic clustering of the profile divided these YTH domains and these x6A mononucleotides into two subfamilies and three classes, respectively; they represent distinct intrinsic interaction modes between the domains and mononucleotides. Statistical survey unraveled that the volume (V) and hydrophobicity (H) of N-substituted chemical groups exhibit linear and nonlinear correlations with the binding energy (ΔG) of x6A mononucleotides to YTH domains, respectively; N-substitutions with moderate size and weak polarity are favorable for the x6A binding. From the profile the N-bromomethyl adenosine (brm6A) was identified as a potent binder of YTHDF2 YTH domain; its affinity was improved significantly by 77.2-fold from A and considerably by 19.5-fold from m6A. Structural modeling observed that the N-bromomethyl group of brm6A is tightly packed against an aromatic cage defined by the Trp432-Trp486-Trp491 triad of YTHDF2 YTH domain. Electron-correlation analysis revealed that the bromine atom can form geometrically and energetically satisfactory halogen-π interactions with the aromatic cage, thus conferring considerable affinity and specificity to the domain-brm6A interaction.
RNA的N-腺苷甲基化会产生N-甲基腺苷（m6A），这是真核转录组中最重要的转录后修饰事件之一，它由甲基转移酶（写入器）、识别蛋白（读取器）和去甲基化酶（擦除器）动态调控。人类有五种m6A读取器，即YTHDC1、YTHDC2、YTHDF1、YTHDF2和YTHDF3，它们通过其YT521-B同源（YTH）结构域特异性识别并结合RNA的甲基化m6A残基，这些结构域参与了糖尿病及其多种并发症（如糖尿病肾病）的发病机制。本文中，我们没有研究天然的N-甲基化，而是试图探索各种非天然N-取代对腺苷（A）与YTH结构域结合行为的分子效应。通过计算创建了40种已报道的N-取代腺苷（x6A）单核苷酸与5种人类读取器YTH结构域的系统相互作用图谱。对该图谱进行启发式聚类，分别将这些YTH结构域和这些x6A单核苷酸分为两个亚家族和三个类别；它们代表了结构域和单核苷酸之间不同的内在相互作用模式。统计调查表明，N-取代化学基团的体积（V）和疏水性（H）分别与x6A单核苷酸与YTH结构域的结合能（ΔG）呈线性和非线性相关；中等大小和弱极性的N-取代有利于x6A的结合。从图谱中，N-溴甲基腺苷（brm6A）被确定为YTHDF2 YTH结构域的有效结合剂；其亲和力相对于A显著提高了77.2倍，相对于m6A也大幅提高了19.5倍。结构建模观察到，brm6A的N-溴甲基基团紧密堆积在由YTHDF2 YTH结构域的Trp432-Trp486-Trp491三联体定义的芳香笼上。电子相关分析表明，溴原子可以与芳香笼形成几何和能量上令人满意的卤-π相互作用，从而赋予结构域与brm6A相互作用相当大的亲和力和特异性。
