Uncovering Allosteric Signaling Pathways of GLP-1R via Molecular Dynamics and Network Theory

The glucagon-like peptide-1 receptor (GLP-1R) is a class B1 G protein-coupled receptor (GPCR) and an important therapeutic target for type 2 diabetes and obesity. While structural studies have identified binding sites on GLP-1R for agonists and allosteric modulators, the residue-level communication pathways underlying receptor activation and inhibition, as well as allosteric regulation, are not completely understood. Here, we performed 3-μs molecular dynamics simulations of GLP-1R in its apo state and when independently bound to a positive allosteric modulator (PAM), a negative allosteric modulator (NAM), and to agonists such as glucagon-like peptide-1 (GLP-1) and the stimulatory G protein (Gs). The resulting trajectories were analyzed using root-mean square deviation (RMSD) analysis and protein structure network (PSN) theory. Comparison of the dynamic structural changes in GLP-1R, such as in its conserved HETx motif and polar networks in the transmembrane domain (TMD) in particular, revealed distinct communication pathways associated with receptor activation and inhibition. Negative effectors, such as NAM NNC0640, reinforced interactions within the central polar network, whereas positive effectors, like PAM C-1 or GLP-1 with Gs, favored signaling through TM3/TM5 or TM6/TM7 pathways, respectively. Across all systems, R190^2.60b emerged as a highly recurrent communication hub. These results identify residue-level pathways that may contribute to receptor activation and inhibition and suggest that positive and negative modulators reshape the allosteric communication network of GLP-1R in distinct ways.