Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22
© 2019 Li et al..
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.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2019 |
|---|---|
| Erschienen: |
2019 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:294 |
|---|---|
| Enthalten in: |
The Journal of biological chemistry - 294(2019), 21 vom: 24. Mai, Seite 8653-8663 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Li, Kangshuai [VerfasserIn] |
|---|
| Links: |
|---|
| Anmerkungen: |
Date Completed 09.12.2019 Date Revised 14.03.2021 published: Print-Electronic PDB: 2QCJ, 3H2X, 1J4X, 2HNP, 2CJT, 2OC3, 2GJT, 2P6X, 2QCT, 3BRH, 3OLR, 3OMH, 4J51, 2PQR, 3HX2 Citation Status MEDLINE |
|---|
| doi: |
10.1074/jbc.RA118.007129 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM296006807 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM296006807 | ||
| 003 | DE-627 | ||
| 005 | 20231225084911.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231225s2019 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1074/jbc.RA118.007129 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n0986.xml |
| 035 | |a (DE-627)NLM296006807 | ||
| 035 | |a (NLM)30979725 | ||
| 035 | |a (PII)S0021-9258(20)36351-1 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Li, Kangshuai |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22 |
| 264 | 1 | |c 2019 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 09.12.2019 | ||
| 500 | |a Date Revised 14.03.2021 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a PDB: 2QCJ, 3H2X, 1J4X, 2HNP, 2CJT, 2OC3, 2GJT, 2P6X, 2QCT, 3BRH, 3OLR, 3OMH, 4J51, 2PQR, 3HX2 | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2019 Li et al. | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, N.I.H., Extramural | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a WPD-loop | |
| 650 | 4 | |a allosteric regulation | |
| 650 | 4 | |a autoimmunity | |
| 650 | 4 | |a enzyme | |
| 650 | 4 | |a enzyme inhibitor | |
| 650 | 4 | |a inhibitor | |
| 650 | 4 | |a lymphoid-specific tyrosine phosphatase (LYP) | |
| 650 | 4 | |a nuclear magnetic resonance (NMR) | |
| 650 | 4 | |a protein-tyrosine phosphatase nonreceptor type 22 (PTPN22) | |
| 650 | 4 | |a tyrosine phosphatase inhibitor | |
| 650 | 7 | |a Enzyme Inhibitors |2 NLM | |
| 650 | 7 | |a Receptors, Antigen, T-Cell |2 NLM | |
| 650 | 7 | |a PTPN22 protein, human |2 NLM | |
| 650 | 7 | |a EC 3.1.3.48 |2 NLM | |
| 650 | 7 | |a Protein Tyrosine Phosphatase, Non-Receptor Type 22 |2 NLM | |
| 650 | 7 | |a EC 3.1.3.48 |2 NLM | |
| 700 | 1 | |a Hou, Xuben |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Ruirui |e verfasserin |4 aut | |
| 700 | 1 | |a Bi, Wenxiang |e verfasserin |4 aut | |
| 700 | 1 | |a Yang, Fan |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Xu |e verfasserin |4 aut | |
| 700 | 1 | |a Xiao, Peng |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Tiantian |e verfasserin |4 aut | |
| 700 | 1 | |a Lu, Tiange |e verfasserin |4 aut | |
| 700 | 1 | |a Zhou, Yuan |e verfasserin |4 aut | |
| 700 | 1 | |a Tian, Zhaomei |e verfasserin |4 aut | |
| 700 | 1 | |a Shen, Yuemao |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Yingkai |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Jiangyun |e verfasserin |4 aut | |
| 700 | 1 | |a Fang, Hao |e verfasserin |4 aut | |
| 700 | 1 | |a Sun, Jinpeng |e verfasserin |4 aut | |
| 700 | 1 | |a Yu, Xiao |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t The Journal of biological chemistry |d 1945 |g 294(2019), 21 vom: 24. Mai, Seite 8653-8663 |w (DE-627)NLM000004995 |x 1083-351X |7 nnns |
| 773 | 1 | 8 | |g volume:294 |g year:2019 |g number:21 |g day:24 |g month:05 |g pages:8653-8663 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1074/jbc.RA118.007129 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 294 |j 2019 |e 21 |b 24 |c 05 |h 8653-8663 | ||