2. Academic Validation
  3. Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22

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

  • J Biol Chem. 2019 May 24;294(21):8653-8663. doi: 10.1074/jbc.RA118.007129.
Kangshuai Li 1,  Xuben Hou 2,  Ruirui Li 1,  Wenxiang Bi 1,  Fan Yang 3,  Xu Chen 3,  Peng Xiao 1,  Tiantian Liu 1,  Tiange Lu 1,  Yuan Zhou 4,  Zhaomei Tian 1,  Yuemao Shen 4,  Yingkai Zhang 5,  Jiangyun Wang 6,  Hao Fang 7,  Jinpeng Sun 8,  Xiao Yu 9
Affiliations

Affiliations

  • 1 Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China.
  • 2 Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China; Department of Chemistry, New York University, New York, New York 10003.
  • 3 Department of Physiology, School of Medicine, Shandong University, Jinan, Shandong 250012, China.
  • 4 Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China.
  • 5 Department of Chemistry, New York University, New York, New York 10003; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
  • 6 Laboratory of Quantum Biophysics and Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, 100101, China.
  • 7 Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China.
  • 8 Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong 250012, China. Electronic address: sunjinpeng@sdu.edu.cn.
  • 9 Department of Physiology, School of Medicine, Shandong University, Jinan, Shandong 250012, China. Electronic address: yuxiao@sdu.edu.cn.
PMID: 30979725 DOI: 10.1074/jbc.RA118.007129
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. We found that NC1 is 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.

Keywords

WPD-loop; allosteric regulation; autoimmunity; enzyme; enzyme inhibitor; inhibitor; lymphoid-specific tyrosine phosphatase (LYP); nuclear magnetic resonance (NMR); protein-tyrosine phosphatase nonreceptor type 22 (PTPN22); tyrosine phosphatase inhibitor.

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