Biological and Medicinal Chemistry

Structural Basis for the Friedel-Crafts Alkylation in Cylindrocyclophane Biosynthesis

Authors

  • Hua-Qi Wang Peking University Shenzhen Graduate School ,
  • Shu-Bin Mou Peking University Shenzhen Graduate School ,
  • Wen Xiao Peking University Shenzhen Graduate School ,
  • Huan Zhou Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China ,
  • Xu-Dong Hou Peking University Shenzhen Graduate School ,
  • Su-Jing Wang Peking University Shenzhen Graduate School ,
  • Qian Wang Peking University Shenzhen Graduate School ,
  • Jiali Gao Peking University Shenzhen Graduate School, Shenzhen Bay Laboratory ,
  • Zhiyi Wei Southern University of Science and Technology ,
  • Lijun Liu Peking University Shenzhen Graduate School, DLX Scientific ,
  • Zheng Xiang State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China

Abstract

The Lewis acid-catalyzed Friedel-Crafts alkylation of an aromatic ring with an alkyl halide is extensively used in organic synthesis. However, its biological counterpart was not reported until the elucidation of the cylindrocyclophane biosynthetic pathway in Cylindrospermum licheniforme ATCC 29412 by Balskus and co-workers. CylK is the key enzyme to catalyze the formation of the cylindrocyclophane scaffold through the Friedel-Crafts alkylation reactions with regioselectivity and stereospecificity. Further research demonstrates that CylK can accept other resorcinol rings and secondary alkyl halides as substrates. To date, the crystal structure of CylK has not been disclosed and the catalytic mechanism remains obscure. Herein we report the crystal structures of CylK in its apo form and its complexes with the analogues of its substrate and reaction intermediate. Combining the crystal structures, free energy simulations and the mutagenesis experiments, we proposed a concerted double-activation mechanism, which could explain the regioselectivity and stereospecificity. This work provides a foundation for engineering CylK as a biocatalyst to expand its substrate scope and applications in organic synthesis.

Version notes

PDB codes have been provided in the new version.

Content

Thumbnail image of Structural Basis for the Friedel-Crafts Alkylation in Cylindrocyclophane Biosynthesis.pdf

Supplementary material

Thumbnail image of Supporting Information.pdf
CylK structure supporting information
Experimental details, computational details, and supplementary tables and figures