Design and structural validation of peptide-drug conjugate ligands of the kappa-opioid receptor

Nat Commun. 2023 Dec 6;14(1):8064. doi: 10.1038/s41467-023-43718-w.

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.

MeSH terms

  • Analgesics, Opioid* / chemistry
  • Animals
  • Ligands
  • Male
  • Mice
  • Peptides, Cyclic / chemistry
  • Receptors, Opioid, kappa* / metabolism
  • Receptors, Opioid, mu / metabolism

Substances

  • Receptors, Opioid, kappa
  • Ligands
  • Analgesics, Opioid
  • Receptors, Opioid, mu
  • Peptides, Cyclic