Variant-specific pharmacophoric shifts in glucagon-like peptide-1 receptor-orforglipron complexes revealed by Boltz-2 co-folding and membrane molecular dynamics.
The study reveals that GLP-1R variants can enhance orforglipron binding, but this does not guarantee effective pharmacological action, highlighting the need for further validation.
Where it sits
this study against the rest of the orforglipron (ly-3502970) corpusSummary and findings
The study investigates how single-nucleotide polymorphisms in the glucagon-like peptide-1 receptor (GLP-1R) affect the binding of orforglipron (ORF), an orally bioavailable GLP-1R agonist. It employs computational methods to analyze binding affinities and conformational changes in various receptor variants. The findings suggest that all variants showed enhanced binding compared to wild-type GLP-1R, with specific alterations in hydrogen-bond networks.
Abstract
Background Orforglipron (ORF), the first orally bioavailable non-peptide glucagon-like peptide-1 receptor (GLP-1R) agonist to complete Phase 3 clinical trials, binds a distinct extracellular vestibule pocket not engaged by peptide GLP-1RAs. How commonly GLP-1R single-nucleotide polymorphisms alter this unique binding mode at the molecular level remains uncharacterized. Methods We employed an integrative computational framework that combines Boltz-2 deep learning co-folding for variant complex generation, 500 ns all-atom molecular dynamics simulations in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer, MM/GBSA binding free-energy decomposition, and protein ligand hydrogen-bond occupancy analysis. Wild-type (WT) GLP-1R and four clinically annotated variants L260F3.53b (TM3), G168S (stalk), R131Q (ECD), and A316T5.46 (TM5) were characterized. Results All variants exhibited enhanced MM/GBSA binding (24-35% vs WT) despite conformational destabilization, as evidenced by elevated RMSD, altered free energy landscapes, and reorganized H-bond networks. H-bond occupancy trajectory analysis identified Lys1972.67 as the canonical pharmacophoric anchor in WT (79.8%), preserved in L260F (57.1%) and A316T (63.9%). However, Lys1972.67 was absent in G168S and R131Q, which substitute Tyr2052.75/Gln221 and Tyr202, respectively. G168S exhibited the strongest binding (-117.18 kcal/mol) through compensatory contacts, while displaying a diffuse free-energy landscape and conformational disorder. A316T exhibited bistable dynamics related to Y2423.45-T3165.46H-bond-mediated constitutive activation, while preserving canonical engagement. Conclusions Binding energies and contact analysis describe variant-dependent ORF engagement. Binding enhancement alone is insufficient to characterize pharmacophoric quality. Lys1972.67 occupancy differentiates variants with canonical binding from those substituting it, offering a structure-based framework for pharmacogenomic associations. The loss of Lys1972.67 in G168S offers a testable structural hypothesis for the diminished glycemic response observed in carriers, which requires functional validation.
Background
This paper addresses the interaction of orforglipron (ORF) with glucagon-like peptide-1 receptor (GLP-1R) variants, particularly how genetic variations may influence binding. Prior knowledge indicates that ORF is the first orally bioavailable non-peptide GLP-1R agonist, but the effects of single-nucleotide polymorphisms on its binding characteristics were not well understood. Understanding these interactions is critical for potential pharmacogenomic implications.
Methods
The study employed an integrative computational framework, including Boltz-2 deep learning for complex generation and 500 ns molecular dynamics simulations in a POPC lipid bilayer. It characterized wild-type GLP-1R and four variants: L260F, G168S, R131Q, and A316T. Primary outcome measures included MM/GBSA binding free-energy decomposition and hydrogen-bond occupancy analysis.
Results
All variants exhibited enhanced MM/GBSA binding (24-35% vs WT). G168S exhibited the strongest binding (-117.18 kcal/mol) with a diffuse free-energy landscape. Lys197<sup>2.67</sup> occupancy was 79.8% in WT, reduced in L260F and A316T, and absent in G168S and R131Q. The study noted conformational destabilization in variants, evidenced by elevated RMSD and altered free energy landscapes.
Interpretation
The findings suggest that while binding affinities are enhanced in GLP-1R variants, this does not necessarily correlate with pharmacophoric quality. The absence of Lys197<sup>2.67</sup> in certain variants indicates a potential mechanism for reduced efficacy in carriers, which requires further functional validation. The effect sizes observed may not be clinically meaningful without in vivo confirmation.
Key findings
- All variants exhibited enhanced MM/GBSA binding (24-35% vs WT).
- G168S exhibited the strongest binding (-117.18 kcal/mol).
- Lys1972.67 occupancy was preserved in L260F (57.1%) and A316T (63.9%).
- Lys1972.67 was absent in G168S and R131Q.
- G168S displayed a diffuse free-energy landscape and conformational disorder.
Limitations
- Computational modeling may not fully replicate in vivo conditions.
- Single-site analysis limits generalizability.
- No functional validation provided for binding hypotheses.