The predicted ensemble of low-energy conformations of human somatostatin receptor subtype 5 and the binding of antagonists

Sijia S. Dong, Ravinder Abrol, William A. Goddard

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Human somatostatin receptor subtype 5 (hSSTR5) regulates cell proliferation and hormone secretion. However, the identification of effective therapeutic small-molecule ligands is impeded because experimental structures are not available for any SSTR subtypes. Here, we predict the ensemble of low-energy 3D structures of hSSTR5 using a modified GPCR Ensemble of Structures in Membrane BiLayer Environment (GEnSeMBLE) complete sampling computational method. We find that this conformational ensemble displays most interhelical interactions conserved in class A G protein-coupled receptors (GPCRs) plus seven additional interactions (e.g., Y2.43-D3.49, T3.38-S4.53, K5.64-Y3.51) likely conserved among SSTRs. We then predicted the binding sites for a series of five known antagonists, leading to predicted binding energies consistent with experimental results reported in the literature. Molecular dynamics (MD) simulation of 50 ns in explicit water and lipid retained the predicted ligand-bound structure and formed new interaction patterns (e.g. R3.50-T6.34) consistent with the inactive μ-opioid receptor X-ray structure. We suggest more than six mutations for experimental validation of our prediction. The final predicted receptor conformations and antagonist binding sites provide valuable insights for designing new small-molecule drugs targeting SSTRs.

Original languageEnglish (US)
Pages (from-to)650-661
Number of pages12
JournalChemMedChem
Volume10
Issue number4
DOIs
StatePublished - Apr 1 2015

Bibliographical note

Publisher Copyright:
© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Keywords

  • G protein-coupled receptors (GPCRs)
  • computational chemistry
  • docking
  • molecular dynamics
  • protein structures
  • somatostatin receptor subtype 5 (SSTR5)

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