Multi-frequency Saturation Transfer Difference NMR to Characterize Weak Protein–Ligand Complexes

Abstract

Weak protein–ligand interactions have been demonstrated to play key roles in biological processes, particularly in those involving quick cellular responses after certain stimuli (e.g. signal transduction). Although powerful biophysical techniques are available to gain high-resolution structural information of protein–ligand complexes of high affinity, NMR spectroscopy has been demonstrated to stand out among them for protein–ligand studies within the limit of weak affinity. In particular, ligand-based NMR techniques allow the detection and quantification of weak biomolecular binding processes, where saturation transfer difference (STD) NMR techniques have demonstrated through the years their strong ability to not only detect binding processes but also to provide structural information about the ligand mode of binding in the receptor-binding pocket, a highly valuable piece of information for the further development of enhanced binders along the process of drug discovery. This is particularly useful in fragment-based drug-discovery approaches, where the binding of the identified initial small fragments tends to fall within the low affinity range of the spectrum. In this chapter we briefly introduce the different classical STD NMR approaches, and later focus in detail on novel developments based on multi-frequency STD NMR experiments, which expand further the analytical capabilities of STD NMR, exemplified by the DEEP-STD NMR protocol, by providing also some key information on the nature of the protein residues in contact with the ligands in the bond state.