Crystal structure of the µ-opioid receptor bound to a morphinan antagonist

Abstract

Opium is one of the world's oldest drugs, and its derivatives morphine and codeine are among the most used clinical drugs to relieve severe pain. These prototypical opioids produce analgesia as well as many undesirable side effects (sedation, apnoea and dependence) by binding to and activating the G-protein-coupled µ-opioid receptor (µ-OR) in the central nervous system. Here we describe the 2.8 Å crystal structure of the mouse µ-OR in complex with an irreversible morphinan antagonist. Compared to the buried binding pocket observed in most G-protein-coupled receptors published so far, the morphinan ligand binds deeply within a large solvent-exposed pocket. Of particular interest, the µ-OR crystallizes as a two-fold symmetrical dimer through a four-helix bundle motif formed by transmembrane segments 5 and 6. These high-resolution insights into opioid receptor structure will enable the application of structure-based approaches to develop better drugs for the management of pain and addiction.

Figure 1. Overall view of μOR receptor structure

a, Views from within the membrane plane (left), extracellular side (top, center panel) and intracellular side (bottom, center panel) show the typical seven-pass transmembrane GPCR architecture of the μOR. The ligand, β-FNA, is shown in green spheres. b, The chemical structure of morphine. c, The chemical structure of β-FNA and the chemical reaction with the side chain of K233^5.39 in the receptor are shown. β-FNA is a semisynthetic opioid antagonist derived from morphine, shown at right.

Figure 2. Comparison of ligand binding pockets

a, The binding pocket for μOR is wide and open above the ligand, in stark contrast to the deeply buried binding pocket of the muscarinic receptors, as exemplified by the M₃R shown in b. c, The small molecule antagonist IT1t (magenta) occupies a binding pocket closer to the extracellular surface of CXCR4 than β-FNA in μOR. β-FNA is positioned more similarly to the distantly related aminergic receptors as shown in c (bottom panel) for the binding site of carazolol (yellow) in the β₂-adrenergic receptor (β₂AR).

Figure 3. Structural basis for morphinan ligand binding to the μOR

a, Side view of the ligand binding pocket with polar interactions shown. TM6 is excluded from this view. The electron density used to position interacting side chains is shown in light blue colored mesh depicting the 2Fo-Fc electron density contoured at 1.3 σ. Green mesh depicts an omit map of β-FNA and K233^5.39 side chain atoms contoured at 3.0 σ. b, Binding pocket viewed from the extracellular surface. Water molecules are shown as red spheres, with the accompanying electron density shown in light blue mesh. c, The binding site is diagrammed, showing the chemical structure of β-FNA (green) covalently bound to the receptor through K233^5.39 (bold). Hydrophobic interactions are shown in orange and polar contacts with red dotted lines. V300^6.55 and I296^6.51 form extensive hydrophobic contacts with the back face of the ligand (not shown). Two water molecules are positioned between H297^6.52 and the phenolic group of β-FNA d, The δOR selective ligand naltrindole includes an indole group that would clash with W318^7.35 in μOR, but not with the leucine found in the equivalent position in δOR. The indole has been described as an "address" to target the ligand to δOR, while its efficacy ("message") is determined by the morphinan group on the left .

Figure 4. μOR oligomeric arrangement

a, b μOR crystallized as intimately associated pairs, with two different interfaces as defined in the text. The interface defined by TMs 5 and 6 (c) is much more extensive than for the one defined by TM1-TM2-H8 (d).

Figure 5. The four-helix bundle interface

a, Schematic showing the four-helix bundle architecture of the TM5-TM6 interface b, Viewed from the extracellular surface, the binding pocket shows tight association between the ligand (green sticks) and residues that are involved directly or indirectly in forming the dimeric interface (blue spheres). c, The four-helix bundle is expanded and shown in detail with interacting residues within 4.2 Å shown as sticks. d, Tomographic representation along the dimer interface viewed from the extracellular side (as indicated in panel c) showing the high surface complementarity within the four-helix bundle interface.