Affinity Selection Mass Spectrometry (AS-MS) as a Tool for Prospecting Target Ligands

Affinity selection mass spectrometry (AS-MS) has been shown to be a powerful tool for identifying bioactive molecules in synthetic and/or natural libraries. The selection provided by the formation of the target-ligand complex allows the identification of hits irrespective of their functional effect. Moreover, it precludes the use of label, since the binders are identified by their exact mass.1 The binders are determined by an affinity or index ratio calculated through control assays. The target protein can be used in solution or immobilized in a solid support (Figure 1). Both approaches have pros and cons. Unlike most conventional high-throughput screening assays, AS-MS has fewer or no limitations when it comes to target selection. It is important, however, to understand the implications of choosing membrane proteins as targets. Membrane proteins correspond to 42% of all drug targets listed in DrugBank. Moreover, they are likely to be selected as protein targets due to their participation in many disease pathways, acting as ion channels, molecular transporters, solute carriers, receptors, and anchors. One of the bottlenecks in working with membrane proteins comes from the need to use a detergent for solubilization, folding, and structure maintenance. Detergents are usually used above the critical micelle concentration, which can lead to empty micelles and thus to false positive results, caused by nonspecific interactions with the detergent micelles.8 Interference in the ionization of the binders also needs to be examined.