Molecular Basis of Mannose Recognition by Pradimicins and their Application to Microbial Cell Surface Imaging

  • Cell Chem Biol. 2019 Jul 18;26(7):950-959.e8. doi: 10.1016/j.chembiol.2019.03.013.
Yu Nakagawa  1 ,  Takashi Doi  2 ,  K Takegoshi  2 ,  Takahiro Sugahara  3 ,  Dai Akase  3 ,  Misako Aida  3 ,  Kazue Tsuzuki  4 ,  Yasunori Watanabe  4 ,  Tomohiko Tomura  4 ,  Makoto Ojika  4 ,  Yasuhiro Igarashi  5 ,  Daisuke Hashizume  6 ,  Yukishige Ito  7
Affiliations
  • 1. 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. Electronic address: [email protected].
  • 2. Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.
  • 3. Center for Quantum Life Sciences, and Department of Chemistry, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
  • 4. Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
  • 5. Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
  • 6. RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
  • 7. Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
PMID: 31031141 DOI: 10.1016/j.chembiol.2019.03.013
Abstract

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 CA2+-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.

Keywords
analog design; carbohydrates; glycan detection; lectin; molecular recognition; natural products; structural elucidation.
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