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

• Published in: Nature communications 2023-12, Vol.14 (1), p.8064-8064, Article 8064
• Main Authors: Muratspahić, Edin, Deibler, Kristine, Han, Jianming, Tomašević, Nataša, Jadhav, Kirtikumar B., Olivé-Marti, Aina-Leonor, Hochrainer, Nadine, Hellinger, Roland, Koehbach, Johannes, Fay, Jonathan F., Rahman, Mohammad Homaidur, Hegazy, Lamees, Craven, Timothy W., Varga, Balazs R., Bhardwaj, Gaurav, Appourchaux, Kevin, Majumdar, Susruta, Muttenthaler, Markus, Hosseinzadeh, Parisa, Craik, David J., Spetea, Mariana, Che, Tao, Baker, David, Gruber, Christian W.
• Format: Article
• Language: English
• Subjects: 101/28; 119/118; 49/75; 631/114/469; 631/154/436/2387; 631/92/611; 64/60; 96/95; Affinity; Analgesics, Opioid - chemistry; Animals; Computer applications; Conjugates; Design; Drug development; Effectiveness; G protein-coupled receptors; Humanities and Social Sciences; In vivo methods and tests; Ligands; Male; Mice; Molecular dynamics; multidisciplinary; Narcotics; Opioid receptors (type kappa); Opioid receptors (type mu); Pain perception; Peptides; Peptides, Cyclic - chemistry; Receptors; Receptors, Opioid, kappa - metabolism; Receptors, Opioid, mu - metabolism; Science; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-43718-w

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. Despite advances in GPCR structures and peptide design, creating high-affinity ligands remains a challenge. Here the authors develop a computational method, successfully identifying peptide-based molecules for KOR: their platform shows promise for streamlined GPCR ligand discovery.