Investigation of D2 Receptor–Agonist Interactions Using a Combination of Pharmacophore and Receptor Homology Modeling

A combined modeling approach was used to identify structural factors that underlie the structure-activity relationships (SARs) of full dopamine D₂ receptor agonists and structurally similar inactive compounds. A 3D structural model of the dopamine D₂ receptor was constructed, with the agonist (-)-(R)-2-OH-NPA present in the binding site during the modeling procedure. The 3D model was evaluated and compared with our previously published D₂ agonist pharmacophore model. The comparison revealed an inconsistency between the projected hydrogen bonding feature (Ser-TM5) in the pharmacophore model and the TM5 region in the structure model. A new refined pharmacophore model was developed, guided by the shape of the binding site in the receptor model and with less emphasis on TM5 interactions. The combination of receptor and pharmacophore modeling also identified the importance of His393⁶·⁵⁵ for agonist binding. This convergent 3D pharmacophore and protein structure modeling strategy is considered to be general and can be highly useful in less well-characterized systems to explore ligand-receptor interactions. The strategy has the potential to identify weaknesses in the individual models and thereby provides an opportunity to improve the discriminating predictivity of both pharmacophore searches and structure-based virtual screens.