Structural Biophysics-Guided Computational Design of Semaglutide Analogues to Enhance GLP-1R Activation

CagriSema is a fixed-dose combination of cagrilintide (an amylin analogue) and semaglutide (a GLP-1 receptor agonist), and is currently an experimental obesity drug developed by Novo Nordisk. In March 2025, CagriSema underperformed expectations in a Phase III trial, achieving 15.7% weight loss instead of the anticipated 25%, raising concerns about its efficacy and clinical value. Given its chemical composition, the weight-loss efficacy of CagriSema is inextricably linked to the activations of GLP-1R and amylin receptors (AMYRs). With GLP-1R as an example target here, this study employs a structural biophysics-guided computational approach for the design of semaglutide analogues to enhance the activation of its receptor GLP-1R. To fully harness the therapeutic potential of GLP-1R activation, an experimental structural basis (PDB entry 4ZGM) of the GLP-1-GLP-1R interaction is essential for the design of semaglutide analogues, where site-specific missense mutations are engineered into its peptide backbone to establish additional stabilizing interactions with the extracellular domain (ECD) of GLP-1R. Specifically, this study puts forward an automated systemic natural amino acid scanning of the peptide backbone of semaglutide, where PDB entry 4ZGM was used as the structural template for high-throughput structural modeling by Modeller and ligand-receptor binding affinity (Kd) calculations by Prodigy. To sum up, this article reports a total of 564 computationally designed semaglutide analogues with improved GLP-1R ECD binding affinity. Moreover, this study proposes a concept of an interfacial electrostatic scaffold comprising four salt bridges at the binding interface of GLP-1R ECD and semaglutide analogues. Drawing parallels with the continued optimization in the past century of the history of insulin, this article argues that the interfacial electrostatic scaffold here constitutes a robust framework for the continued development of next-generation GLP-1R agonists, enabling more effective therapies for patients with diabetes and/or obesity.