Structural basis for GLP-1 receptor activation by LY3502970, an orally active nonpeptide agonist

Abstract

Glucagon-like peptide-1 receptor (GLP-1R) agonists are efficacious antidiabetic medications that work by enhancing glucose-dependent insulin secretion and improving energy balance. Currently approved GLP-1R agonists are peptide based, and it has proven difficult to obtain small-molecule activators possessing optimal pharmaceutical properties. We report the discovery and mechanism of action of LY3502970 (OWL833), a nonpeptide GLP-1R agonist. LY3502970 is a partial agonist, biased toward G protein activation over β-arrestin recruitment at the GLP-1R. The molecule is highly potent and selective against other class B G protein–coupled receptors (GPCRs) with a pharmacokinetic profile favorable for oral administration. A high-resolution structure of LY3502970 in complex with active-state GLP-1R revealed a unique binding pocket in the upper helical bundle where the compound is bound by the extracellular domain (ECD), extracellular loop 2, and transmembrane helices 1, 2, 3, and 7. This mechanism creates a distinct receptor conformation that may explain the partial agonism and biased signaling of the compound. Further, interaction between LY3502970 and the primate-specific Trp33 of the ECD informs species selective activity for the molecule. In efficacy studies, oral administration of LY3502970 resulted in glucose lowering in humanized GLP-1R transgenic mice and insulinotropic and hypophagic effects in nonhuman primates, demonstrating an effect size in both models comparable to injectable exenatide. Together, this work determined the molecular basis for the activity of an oral agent being developed for the treatment of type 2 diabetes mellitus, offering insights into the activation of class B GPCRs by nonpeptide ligands.

Ligand-Receptor Interactions and Machine Learning in GCGR and GLP-1R Drug Discovery

“…In our recent work [ 3 , 29 ], we hypothesized, based on results from receptor-based virtual screening, that small-molecule ligands could effectively bind also orthosteric sites of class B GPCRs in a similar way to class A GPCRs. Recent advances in cryo-EM of class B GPCRs have proved that orthosteric sites of glucagon receptor family members are indeed druggable for small-molecule ligands [ 14 , 16 , 17 ]. Small-molecule full agonists of class B GPCRs bind to the orthosteric site of the receptor—the binding site 2 (see Figure 1 ).…”

“…Spacious orthosteric binding sites in all known at that time structures of secretin-like GPCRs (named also class B GPCRs) seemed to be less druggable for small-molecules compounds comparing class A, except for the region deep inside of the receptor core like in, e.g., CRF 1 (PDB id: 4K5Y) [ 10 , 11 , 12 ]. Recent advances in cryo-EM have finally provided a detailed structural description of class B GPCR receptors bound to small-molecule agonists [ 13 , 14 , 15 , 16 , 17 ]. Namely, three additional small-molecule binding sites of GLP-1R, located in or close to the TMD orthosteric site, have been revealed, providing a complete picture of class B GPCRs activation [ 13 , 14 , 16 , 17 ].…”

Peptidyl and Non-Peptidyl Oral Glucagon-Like Peptide-1 Receptor Agonists

“…As an alternative approach, non-peptide, small molecule oral GLP-1 receptor agonists offer a promising option. Earlier ambitious but futile attempts to develop these non-peptide drugs have been reviewed in detail elsewhere [ 10 , 38 ]. For many years, this alluring perspective seemed inconceivable; a comprehensive exploration of the structure-activity relationship of GLP-1 receptor activation in response to natural GLP-1 (7–36) amide revealed an extensive interaction of the C-terminus of GLP-1 with the peptide-binding groove of the N-terminal extracellular domain (ECD) of the GLP-1 receptor.…”

“…Two of the few recently recognized small molecules that succeeded in entering clinical development, namely LY3502790 and PF-06882961, activate the canonical G protein signaling activity only in the GLP-1 receptor with Trp33 ECD [ 38 , 42 ]. This was a phenomenal discovery, since primate-specific Trp33 ECD served as a critical point in the binding of small molecules, whereas it is not a critical component for the activation of the GLP-1 receptor by native GLP-1.…”

Molecular insights into ago-allosteric modulation of the human glucagon-like peptide-1 receptor

“…In 2017, two inactive structures bound to negative allosteric modulators (NAMs) 9 , one intermediate structure bound to a truncated peptide agonist 10 and one active structure in complex with GLP-1 and heterotrimeric G s 11 were reported. This was followed by eight G protein-bound structures in complex with peptides (GLP-1 and exendin-P5) 12,13 , non-peptidic agonists (TT-OAD2, PF-06882961, CHU-128, RGT1383 and LY3502970) 13–16 and a positive allosteric modulator (PAM) LSN3160440 (ref. 17 ), as well as a peptide-free apo state 18 and three thermal-stabilized TMD 9 structures.…”