Probing the Hydrophobic Binding Pocket of G-Protein-Coupled Lysophosphatidylserine Receptor GPR34/LPS1 by Docking-Aided Structure-Activity Analysis

J Med Chem. 2017 Jul 27;60(14):6384-6399. doi: 10.1021/acs.jmedchem.7b00693. Epub 2017 Jul 17.

Abstract

The ligands of certain G-protein-coupled receptors (GPCRs) have been identified as endogenous lipids, such as lysophosphatidylserine (LysoPS). Here, we analyzed the molecular basis of the structure-activity relationship of ligands of GPR34, one of the LysoPS receptor subtypes, focusing on recognition of the long-chain fatty acid moiety by the hydrophobic pocket. By introducing benzene ring(s) into the fatty acid moiety of 2-deoxy-LysoPS, we explored the binding site's preference for the hydrophobic shape. A tribenzene-containing fatty acid surrogate with modifications of the terminal aromatic moiety showed potent agonistic activity toward GPR34. Computational docking of these derivatives with a homology modeling/molecular dynamics-based virtual binding site of GPR34 indicated that a kink in the benzene-based lipid surrogates matches the L-shaped hydrophobic pocket of GPR34. A tetrabenzene-based lipid analogue bearing a bulky tert-butyl group at the 4-position of the terminal benzene ring exhibited potent GPR34 agonistic activity, validating the present hydrophobic binding pocket model.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Benzene Derivatives / chemical synthesis
  • Benzene Derivatives / chemistry*
  • Benzene Derivatives / pharmacology
  • Binding Sites
  • Fatty Acids / chemical synthesis
  • Fatty Acids / chemistry*
  • Fatty Acids / pharmacology
  • HEK293 Cells
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Mice
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Phosphoserine / analogs & derivatives*
  • Phosphoserine / chemical synthesis
  • Phosphoserine / chemistry
  • Phosphoserine / pharmacology
  • Receptors, Lysophospholipid / agonists
  • Receptors, Lysophospholipid / chemistry*
  • Structure-Activity Relationship

Substances

  • Benzene Derivatives
  • Fatty Acids
  • G-protein-coupled receptor 34
  • Receptors, Lysophospholipid
  • Phosphoserine