Department of Regulatory Bioorganic Chemistry, SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Nucleic Acids Res. 2022 Sep 23;50(17):9621-9631. doi: 10.1093/nar/gkac740.
Trinucleotide repeat (TNR) diseases are caused by the aberrant expansion of CXG (X = C, A, G and T) sequences in genomes. We have reported two small molecules binding to TNR, NCD, and NA, which strongly bind to CGG repeat (responsible sequence of fragile X syndrome) and CAG repeat (Huntington's disease). The NMR structure of NA binding to the CAG/CAG triad has been clarified, but the structure of NCD bound to the CGG/CGG triad remained to be addressed. We here report the structural determination of the NCD-CGG/CGG complex by NMR spectroscopy and the comparison with the NA-CAG/CAG complex. While the NCD-CGG/CGG structure shares the binding characteristics with that of the NA-CAG/CAG complex, a significant difference was found in the overall structure caused by the structural fluctuation at the ligand-bound site. The NCD-CGG/CGG complex was suggested in the equilibrium between stacked and kinked structures, although NA-CAG/CAG complex has only the stacked structures. The dynamic fluctuation of the NCD-CGG/CGG structure at the NCD-binding site suggested room for optimization in the linker structure of NCD to gain improved affinity to the CGG/CGG triad.
三核苷酸重复（TNR）疾病是由基因组中 CXG（X=C、A、G 和 T）序列的异常扩增引起的。我们已经报道了两种与 TNR、NCD 和 NA 结合的小分子，它们与 CGG 重复（脆性 X 综合征的责任序列）和 CAG 重复（亨廷顿病）强烈结合。NA 与 CAG/CAG 三联体结合的 NMR 结构已经阐明，但 NCD 与 CGG/CGG 三联体结合的结构仍有待解决。我们在这里通过 NMR 光谱法报告了 NCD-CGG/CGG 复合物的结构测定，并与 NA-CAG/CAG 复合物进行了比较。虽然 NCD-CGG/CGG 结构与 NA-CAG/CAG 复合物具有相同的结合特征，但由于配体结合部位的结构波动，整体结构存在显著差异。NCD-CGG/CGG 复合物被认为处于堆叠和扭曲结构之间的平衡状态，而 NA-CAG/CAG 复合物只有堆叠结构。NCD-CGG/CGG 结构在 NCD 结合部位的动态波动表明，在 NCD 的连接体结构中还有优化的空间，以提高对 CGG/CGG 三联体的亲和力。
