8FEG image
Entry Detail
PDB ID:
8FEG
EMDB ID:
Title:
CryoEM structure of Kappa Opioid Receptor bound to a semi-peptide and Gi1
Biological Source:
PDB Version:
Deposition Date:
2022-12-06
Release Date:
2023-12-06
Method Details:
Experimental Method:
Resolution:
2.54 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:ACE-TYR-ALA-DTY-THR-THR-CYS-THR-DPN-XT9
Chain IDs:F (auth: A)
Chain Length:10
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Description:Kappa-type opioid receptor
Chain IDs:E (auth: B)
Chain Length:308
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Guanine nucleotide-binding protein G(i) subunit alpha-1
Mutations:S47N,G203A,E245A,A326S
Chain IDs:A (auth: C)
Chain Length:354
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Chain IDs:B (auth: D)
Chain Length:358
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Chain IDs:C (auth: E)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:scFv16 antibody fragment
Chain IDs:D (auth: F)
Chain Length:251
Number of Molecules:1
Biological Source:Mus musculus
Primary Citation

Abstact

Despite the increasing number of GPCR structures and recent advances in peptide design, the development of efficient technologies allowing rational design of high-affinity peptide ligands for single GPCRs remains an unmet challenge. Here, we develop a computational approach for designing conjugates of lariat-shaped macrocyclized peptides and a small molecule opioid ligand. We demonstrate its feasibility by discovering chemical scaffolds for the kappa-opioid receptor (KOR) with desired pharmacological activities. The designed De Novo Cyclic Peptide (DNCP)-β-naloxamine (NalA) exhibit in vitro potent mixed KOR agonism/mu-opioid receptor (MOR) antagonism, nanomolar binding affinity, selectivity, and efficacy bias at KOR. Proof-of-concept in vivo efficacy studies demonstrate that DNCP-β-NalA(1) induces a potent KOR-mediated antinociception in male mice. The high-resolution cryo-EM structure (2.6 Å) of the DNCP-β-NalA-KOR-Gi1 complex and molecular dynamics simulations are harnessed to validate the computational design model. This reveals a network of residues in ECL2/3 and TM6/7 controlling the intrinsic efficacy of KOR. In general, our computational de novo platform overcomes extensive lead optimization encountered in ultra-large library docking and virtual small molecule screening campaigns and offers innovation for GPCR ligand discovery. This may drive the development of next-generation therapeutics for medical applications such as pain conditions.

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