Enthalpy–Entropy Trade-Off Underlies Geometric Isomer Selectivity in Histamine H1Receptor–Doxepin Interaction

Abstract

Understanding the thermodynamic basis of ligand recognition by G-protein-coupled receptors (GPCRs) is crucial for rational drug design. Here, we directly characterized the binding thermodynamics of the histamine H1 receptor (H1R) interacting with the geometric isomers of doxepin using isothermal titration calorimetry combined with molecular dynamics (MD) simulations. The Z-isomer binding to H1R_WT exhibited a larger enthalpic gain but a greater entropic loss than the E-isomer, whereas these differences were diminished in the T1123.37V mutant. Cluster analysis of MD trajectories revealed that Z-doxepin adopts a more restricted conformation upon binding, consistent with its enthalpy-driven interaction and reduced conformational entropy. These findings indicate that H1R distinguishes between E- and Z-isomers not only by affinity but also through distinct thermodynamic fingerprints. This study provides mechanistic insight into the enthalpy–entropy trade-off in GPCR–ligand interactions, highlighting the importance of conformational restriction and flexibility in designing ligands with optimized thermodynamic and functional properties.