INPHARMA-Based Determination of Ligand Binding Modes at α1-Adrenergic Receptors Explains the Molecular Basis of Subtype Selectivity

Abstract

The structural poses of ligands that bind weakly to protein receptors are challenging to define. In this work we have studied ligand interactions with the adrenoreceptor (AR) subtypes, α1A-AR and α1B-AR, which belong to the G protein-coupled receptor (GPCR) superfamily, by employing the solution-based ligand-observed NMR method interligand NOEs for pharmacophore mapping (INPHARMA). A lack of receptor crystal structures and of subtype-selective drugs has hindered the definition of the physiological roles of each subtype and limited drug development. We determined the binding pose of the weakly binding α1A-AR-selective agonist A-61603 relative to an endogenous agonist, epinephrine, at both α1A-AR and α1B-AR. The NMR experimental data were quantitatively compared, by using SpINPHARMA, to the back-calculated spectra based on ligand poses obtained from all-atom molecular dynamics simulations. The results helped mechanistically explain the selectivity of (R)-A-61603 towards α1A-AR, thus demonstrating an approach for targeting subtype selectivity in ARs.