Structural basis for bifunctional peptide recognition at human δ-opioid receptor

Abstract

Bifunctional μ- and δ-opioid receptor (OR) ligands are potential therapeutic alternatives, with diminished side effects, to alkaloid opiate analgesics. We solved the structure of human δ-OR bound to the bifunctional δ-OR antagonist and μ-OR agonist tetrapeptide H-Dmt-Tic-Phe-Phe-NH2 (DIPP-NH2) by serial femtosecond crystallography, revealing a cis-peptide bond between H-Dmt and Tic. The observed receptor-peptide interactions are critical for understanding of the pharmacological profiles of opioid peptides and for development of improved analgesics.

Figure 1. Structure of the BRILΔ₃₆δ-OR–DIPP-NH2 complex

a, Overall view of δ-OR (purple cartoon, red ECL2) in complex with DIPP-NH₂ (orange sticks and transparent spheres); residues lining the binding pocket are shown as light blue sticks, hydrogen bonds as black dotted lines, and water molecules as red spheres. b, Chemical structures of DIPP-NH₂, endomorphin-1 and endomorphin-2 showing the structural similarities between the peptide analogue DIPP-NH₂ and endogenous OR peptides. c, Close-up view of the DIPP-NH₂ binding site; residues forming the DIPP-NH₂ pocket are shown as light blue sticks. d, Sliced surface representation of the peptide binding pocket. The omit Fo-Fc electron density around the peptide DIPP-NH₂ is contoured at 3σ and shown as a blue mesh.

Figure 2. Structural basis for the recognition of DIPP-NH₂ by δ-OR

a, Superposition of the δ-OR structure (purple cartoon with red ECL2) bound to the bifunctional peptide DIPP-NH₂ (orange sticks), and the μ-OR structure (beige cartoon) bound to β-FNA (yellow sticks). b, Superposition indicates that the Tic(2) group on DIPP-NH₂ would clash with Trp318 (transparent beige sphere) on μ-OR. c, Superposition of BRILΔ₃₆δ-OR–DIPP-NH₂ (purple) and naltrindole-bound δ-OR (light blue) showing helix movements (indicated by arrows) observed upon DIPPNH₂ binding. d, Close-up view of conformational changes occurring upon DIPP-NH₂ binding compared to naltrindole bound receptor, including the shift of the Val281^6.55 side chain. The change in orientation of the Trp274^6.58 side chain in the naltrindole bound δ-OR structure is caused by the positioning of the cyclopentene group of naltrindole deeper into the receptor core.