Assessment of native mass spectrometry as a screening method to identify and characterize RNA-targeting small molecules

The intentional targeting of RNA with small molecules is recognized as a viable pathway to new therapeutics with potential to vastly expand the proportion of the human genome considered druggable. The practical considerations to deliberately target RNA are largely under development, including optimal screening methods to identify small molecules for binding to RNA. Native mass spectrometry (nMS) is established as a valuable biophysical method for identifying small molecule hits against diverse biomolecular targets, most frequently proteins and protein-protein interactions. Herein we assess nMS for studying the binding of small molecules with RNA aptamers as a model for nMS screening of RNA as a drug target. We first develop workflows for characterizing the binding of cognate RNA aptamer ligands and then establish a nMS method to screen a small molecule library against the RNA aptamers. nMS analysis permitted identification of binders, quantitation of binding strength and generation of structure-activity relationships with some dependence on the aptamer class. This work demonstrates the utility of nMS as a complementary and efficient target-based biophysical screening method that can characterize RNA-small molecule interactions and the potential of nMS becoming a powerful enabling tool in RNA-targeting drug discovery.