INPHARMA based determination of ligand binding modes at α1-adrenergic receptors explains the molecular basis of subtype selectivity

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, alpha 1A -AR and alpha 1B -AR which belong to the G-protein coupled receptor (GPCR) superfamily by employing the solution-based ligand-observed NMR method INPHARMA (Interligand Noes for PHARmacophore Mapping). 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 weak binding alpha 1A -AR selective agonist, A-61603, relative to an endogenous agonist, epinephrine, at both alpha 1A -AR and alpha 1B -AR. The NMR experimental data were quantitatively compared, 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 alpha 1A -AR, demonstrating an approach for targeting subtype selectivity in ARs.