Miniaturized weak affinity chromatography for ligand identification of nanodiscs-embedded G-protein coupled receptors

Biophysical techniques that enable the screening and identification of weak affinity fragments against a target protein are at the heart of Fragment Based Drug Design approaches. In the case of membrane proteins, the crucial criteria for fragment screening are low protein consumption, unbiased conformational states and rapidity because of the difficulties in obtaining sufficient amounts of stable and functionally folded proteins. Here we show for the first time that lipid-nanodisc systems (membrane-mimicking environment) and miniaturized affinity chromatography can be combined to identify specific small molecule ligands that bind to an integral membrane protein. The approach was exemplified using the AA2AR GPCR. Home-made affinity nano-columns modified with nanodiscs-embedded AA2AR (only about 1 μg of protein per column) were fully characterized by frontal chromatographic experiments. This method allows (i) to distinguish specific and unspecific ligand/receptor interactions, (ii) to assess dissociation constants, (iii) to identify the binding pocket of uncharacterized ligands using a reference compound (whose binding site is known) with competition experiments. Weak affinity ligands with Kd in the low to high micromolar range can be detected. At last, the applicability of this method was demonstrated with 6 fragments recently identified as ligands or non-ligands of AA2AR. [Display omitted] •Nanodiscs-embedded AA2AR were immobilized onto monolithic nano-columns.•Streptavidin-biotin immobilization ensures low protein consumption (∼1 μg/column).•Frontal affinity chromatography was used to identify ligand/receptor interaction.•Weak affinity interactions (low to high μM range) can be detected/quantified.•6 fragments (low affinity ligands) were identified.