Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.
Cell Chem Biol. 2019 Jul 18;26(7):950-959.e8. doi: 10.1016/j.chembiol.2019.03.013. Epub 2019 Apr 25.
Naturally occurring pradimicins (PRMs) show specific recognition of d-mannose (d-Man) in aqueous media, which has never been achieved by artificial small molecules. Although the Ca-mediated dimerization of PRMs is essential for their d-Man binding, the dimeric structure has yet to be elucidated, leaving the question open as to how PRMs recognize d-Man. Thus, we herein report the structural elucidation of the dimer by a combination of X-ray crystallography and solid-state NMR spectroscopy. Coupled with our previous knowledge regarding the d-Man binding geometry of PRMs, elucidation of the dimer allowed reliable estimation of the mode of d-Man binding. Based on the binding model, we further developed an azide-functionalized PRM derivative (PRM-Azide) with d-Man binding specificity. Notably, PRM-Azide stained Candida rugosa cells having mannans on their cell surface through conjugation with the tetramethylrhodamine fluorophore. The present study provides the practical demonstration that PRMs can serve as lectin mimics for use in glycobiological studies.
天然产生的普瑞美菌素（PRMs）在水相介质中显示出对 d-甘露糖（d-Man）的特异性识别，这是人工小分子从未实现的。尽管 PRMs 的 Ca 介导二聚对于它们与 d-Man 的结合是必不可少的，但二聚体结构尚未阐明，这使得 PRMs 如何识别 d-Man 的问题悬而未决。因此，我们通过 X 射线晶体学和固态 NMR 光谱学的组合报告了二聚体的结构阐明。结合我们以前关于 PRMs 与 d-Man 结合几何形状的知识，阐明二聚体可以可靠地估计 d-Man 的结合方式。基于该结合模型，我们进一步开发了一种带有叠氮化物官能团的 PRM 衍生物（PRM-Azide），其具有 d-Man 结合特异性。值得注意的是，PRM-Azide 通过与四甲基罗丹明荧光团缀合，可对细胞表面具有甘露聚糖的粗糙假丝酵母（Candida rugosa）细胞进行染色。本研究提供了实际的证明，即 PRMs 可以用作糖生物学研究中的凝集素模拟物。
