8FEG

CryoEM structure of Kappa Opioid Receptor bound to a semi-peptide and Gi1

Summary for 8FEG

• Entry DOI: 10.2210/pdb8feg/pdb
• EMDB information: 29026 42601
• Descriptor: Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, ... (7 entities in total)
• Functional Keywords: gpcr, kappa opioid receptor, rosetta, membrane protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 6
• Total formula weight: 150625.13

Authors

Fay, J.F.,Che, T. (deposition date: 2022-12-06, release date: 2023-12-06, Last modification date: 2025-06-04)

Primary citation

Muratspahic, E.,Deibler, K.,Han, J.,Tomasevic, N.,Jadhav, K.B.,Olive-Marti, A.L.,Hochrainer, N.,Hellinger, R.,Koehbach, J.,Fay, J.F.,Rahman, M.H.,Hegazy, L.,Craven, T.W.,Varga, B.R.,Bhardwaj, G.,Appourchaux, K.,Majumdar, S.,Muttenthaler, M.,Hosseinzadeh, P.,Craik, D.J.,Spetea, M.,Che, T.,Baker, D.,Gruber, C.W.
Design and structural validation of peptide-drug conjugate ligands of the kappa-opioid receptor.
Nat Commun, 14:8064-, 2023

PubMed Abstract: 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.

PubMed: 38052802
DOI: 10.1016/0006-2952(73)90196-2

Experimental method

ELECTRON MICROSCOPY (2.54 Å)