Molecular insights into the mechanism of 4-hydroxyphenylpyruvate dioxygenase inhibition: enzyme kinetics, X-ray crystallography and computational simulations

Hong Yan Lin, Jing Fang Yang, Da Wei Wang, Ge Fei Hao, Jiang Qing Dong, Yu Xia Wang, Wen Chao Yang, Jia Wei Wu, Chang Guo Zhan, Guang Fu Yang

Research output: Contribution to journalArticlepeer-review

50 Scopus citations

Abstract

Slow-binding inhibitors with long residence time on the target often display superior efficacy in vivo. Rationally designing inhibitors with low off-target rates is restricted by a limited understanding of the structural basis of slow-binding inhibition kinetics in enzyme–drug interactions. 4-Hydroxyphenylpyruvate dioxygenase (HPPD) is an important target for drug and herbicide development. Although the time-dependent behavior of HPPD inhibitors has been studied for decades, its structural basis and mechanism remain unclear. Herein, we report a detailed experimental and computational study that explores structures for illustrating the slow-binding inhibition kinetics of HPPD. We observed the conformational change of Phe428 at the C-terminal α-helix in the inhibitor-bound structures and further identified that the inhibition kinetics of drugs are related to steric hindrance of Phe428. These detailed structural and mechanistic insights illustrate that steric hindrance is highly associated with the time-dependent behavior of HPPD inhibitors. These findings may enable rational design of new potent HPPD-targeted drugs or herbicides with longer target residence time and improved properties. Database: Structure data are available in the PDB under the accession numbers 5CTO (released), 5DHW (released), and 5YWG (released).

Original languageEnglish
Pages (from-to)975-990
Number of pages16
JournalFEBS Journal
Volume286
Issue number5
DOIs
StatePublished - Mar 2019

Bibliographical note

Funding Information:
We thank the Shanghai Synchrotron Radiation Facility (BL17U beam line) for providing the facility support. This work was supported by the National Key Research and Development Program of China (2017YFD0200507) and the National Natural Science Foundation of China (No. 21837001, 21332004 and 21672079), and the self-determined research funds of Central China Normal University (CCNU18ZDPY01 and CCNU18TS007) from the colleges' basic research and operation of Ministry of Education.

Funding Information:
We thank the Shanghai Synchrotron Radiation Facility (BL17U beam line) for providing the facility support. This work was supported by the National Key Research and Development Program of China (2017YFD0200507) and the National Natural Science Foundation of China (No. 21837001, 21332004 and 21672079), and the self-determined research funds of Central China Normal University (CCNU18ZDPY01 and CCNU18TS007) from the colleges’ basic research and operation of Ministry of Education.

Publisher Copyright:
© 2019 Federation of European Biochemical Societies

Keywords

  • 4-hydroxyphenylpyruvate dioxygenase
  • X-ray crystallography
  • computational simulations
  • herbicide
  • inhibition kinetics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

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