Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22

Kangshuai Li, Xuben Hou, Ruirui Li, Wenxiang Bi, Fan Yang, Xu Chen, Peng Xiao, Tiantian Liu, Tiange Lu, Yuan Zhou, Zhaomei Tian, Yuemao Shen, Yingkai Zhang, Jiangyun Wang, Hao Fang, Jinpeng Sun, Xiao Yu

Research output: Contribution to journalArticlepeer-review

Abstract

Protein-tyrosine phosphatase nonreceptor type 22 (PTPN22) is a lymphoid-specific tyrosine phosphatase (LYP), and mutations in the PTPN22 gene are highly correlated with a spectrum of autoimmune diseases. However, compounds and mechanisms that specifically inhibit LYP enzymes to address therapeutic needs to manage these diseases remain to be discovered. Here, we conducted a similarity search of a commercial database for PTPN22 inhibitors and identified several LYP inhibitor scaffolds, which helped identify one highly active inhibitor, NC1. Using noncompetitive inhibition curve and phosphatase assays, we determined NC1's inhibition mode toward PTPN22 and its selectivity toward a panel of phosphatases.Wefound thatNC1is a noncompetitive LYP inhibitor and observed that it exhibits selectivity against other protein phosphatases and effectively inhibits LYP activity in lymphoid T cells and modulates T-cell receptor signaling. Results from site-directed mutagenesis, fragment- centric topographic mapping, and molecular dynamics simulation experiments suggested that NC1, unlike other known LYP inhibitors, concurrently binds to a "WPD" pocket and a second pocket surrounded by an LYP-specific insert, which contributes to its selectivity against other phosphatases. Moreover, using a newly developed method to incorporate the unnatural amino acid 2-fluorine-tyrosine and 19F NMR spectroscopy, we provide direct evidence that NC1 allosterically regulates LYP activity by restricting WPD-loop movement. In conclusion, our approach has identified a new allosteric binding site in LYP useful for selective LYP inhibitor development; we propose that the 19F NMR probe developed here may also be useful for characterizing allosteric inhibitors of other tyrosine phosphatases.

Original languageEnglish (US)
Pages (from-to)8653-8663
Number of pages11
JournalJournal of Biological Chemistry
Volume294
Issue number21
DOIs
StatePublished - May 24 2019

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

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