Small molecule receptor protein tyrosine phosphatase γ (RPTPγ) ligands that inhibit phosphatase activity via perturbation of the tryptophan-proline-aspartate (WPD) loop

J Med Chem. 2011 Oct 13;54(19):6548-62. doi: 10.1021/jm2003766. Epub 2011 Sep 20.

Abstract

Protein tyrosine phosphatases (PTPs) catalyze the dephosphorylation of tyrosine residues, a process that involves a conserved tryptophan-proline-aspartate (WPD) loop in catalysis. In previously determined structures of PTPs, the WPD-loop has been observed in either an "open" conformation or a "closed" conformation. In the current work, X-ray structures of the catalytic domain of receptor-like protein tyrosine phosphatase γ (RPTPγ) revealed a ligand-induced "superopen" conformation not previously reported for PTPs. In the superopen conformation, the ligand acts as an apparent competitive inhibitor and binds in a small hydrophobic pocket adjacent to, but distinct from, the active site. In the open and closed WPD-loop conformations of RPTPγ, the side chain of Trp1026 partially occupies this pocket. In the superopen conformation, Trp1026 is displaced allowing a 3,4-dichlorobenzyl substituent to occupy this site. The bound ligand prevents closure of the WPD-loop over the active site and disrupts the catalytic cycle of the enzyme.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Catalytic Domain
  • Crystallography, X-Ray
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Ligands
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Binding
  • Protein Conformation
  • Receptor-Like Protein Tyrosine Phosphatases, Class 5 / antagonists & inhibitors*
  • Receptor-Like Protein Tyrosine Phosphatases, Class 5 / chemistry
  • Structure-Activity Relationship
  • Thiophenes / chemical synthesis
  • Thiophenes / chemistry*

Substances

  • Ligands
  • Thiophenes
  • Receptor-Like Protein Tyrosine Phosphatases, Class 5

Associated data

  • PDB/3QCB
  • PDB/3QCC
  • PDB/3QCD
  • PDB/3QCE
  • PDB/3QCF
  • PDB/3QCG
  • PDB/3QCH
  • PDB/3QCI
  • PDB/3QCJ
  • PDB/3QCK
  • PDB/3QCL
  • PDB/3QCM
  • PDB/3QCN