9BQJ

RO76 bound muOR-Gi1-scFv16 complex structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Signaling Modulation Mediated by Ligand Water Interactions with the Sodium Site at mu OR.

Ople, R.S.Ramos-Gonzalez, N.Li, Q.Sobecks, B.L.Aydin, D.Powers, A.S.Faouzi, A.Polacco, B.J.Bernhard, S.M.Appourchaux, K.Sribhashyam, S.Eans, S.O.Tsai, B.A.Dror, R.O.Varga, B.R.Wang, H.Huttenhain, R.McLaughlin, J.P.Majumdar, S.

(2024) ACS Cent Sci 10: 1490-1503

  • DOI: https://doi.org/10.1021/acscentsci.4c00525
  • Primary Citation of Related Structures:  
    9BQJ

  • PubMed Abstract: 

    The mu opioid receptor (μOR) is a target for clinically used analgesics. However, adverse effects, such as respiratory depression and physical dependence, necessitate the development of alternative treatments. Recently we reported a novel strategy to design functionally selective opioids by targeting the sodium binding allosteric site in μOR with a supraspinally active analgesic named C6guano . Presently, to improve systemic activity of this ligand, we used structure-based design, identifying a new ligand named RO76 where the flexible alkyl linker and polar guanidine guano group is swapped with a benzyl alcohol, and the sodium site is targeted indirectly through waters. A cryoEM structure of RO76 bound to the μOR-G i complex confirmed that RO76 interacts with the sodium site residues through a water molecule, unlike C6guano which engages the sodium site directly. Signaling assays coupled with APEX based proximity labeling show binding in the sodium pocket modulates receptor efficacy and trafficking. In mice, RO76 was systemically active in tail withdrawal assays and showed reduced liabilities compared to those of morphine. In summary, we show that targeting water molecules in the sodium binding pocket may be an avenue to modulate signaling properties of opioids, and which may potentially be extended to other G-protein coupled receptors where this site is conserved.


  • Organizational Affiliation

    Center for Clinical Pharmacology, University of Health Sciences & Pharmacy at St. Louis and Washington University School of Medicine, St. Louis, Missouri 63110, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1A [auth B]344Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2B [auth C]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mu-type opioid receptorC [auth D]356Mus musculusMutation(s): 0 
Gene Names: Oprm1MorOprm
UniProt
Find proteins for P42866 (Mus musculus)
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UniProt GroupP42866
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1D [auth A]354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
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Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16259Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AQ2 (Subject of Investigation/LOI)
Query on A1AQ2

Download Ideal Coordinates CCD File 
F [auth D]N-{[3-(hydroxymethyl)phenyl]methyl}-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide
C24 H32 N2 O2
BOKVRDQXYXXJGL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA057790

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Structure summary