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

Misa Sayama, Asuka Inoue, Sho Nakamura, Sejin Jung, Masaya Ikubo, Yuko Otani, Akiharu Uwamizu, Takayuki Kishi, Kumiko Makide, Junken Aoki, Takatsugu Hirokawa, Tomohiko Ohwada

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)6384-6399
Number of pages16
JournalJournal of Medicinal Chemistry
Issue number14
Publication statusPublished - 2017 Jul 27

ASJC Scopus subject areas

  • Molecular Medicine
  • Drug Discovery

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