Estimating Protein-Ligand Binding Affinity by NMR

Deep knowledge of how the binding processes occur, such as drugreceptor, signal transduction and cellular recognition, is indispensable for a greater understanding of biological functions. Medicinal chemistry in the path of drug discovery has focused on studies of the molecular interactions which are involved in the development of severe disease state. Thereby, an accurate knowledge about the underlying protein receptor-ligand recognition events at atomic level is fundamental in the process to comprehension, identification and optimization of more potent drug candidates. In this sense, several novel NMR spectroscopic techniques can yield insight into protein-protein interactions in solutions at the molecular level. Resonance signal of the protein or the ligand can be used to identify binding events from a broad range of experiments. For this purpose, changes in NMR spectroscopy parameters such as chemical shifts, relaxation times, diffusion constants, NOEs or exchange of saturation can serve as a measure of binding. In this chapter, the main NMR experimental approaches applied to characterize protein-ligand binding affinity will be discussed. Thus, we hope to provide the reader with a broader and better understanding of how NMR spectroscopy techniques can be applied to a drug discovery process.

Keywords: 13C-labeled protein, 15N-labeled protein, binding affinity, diffusion constant, diffusion ordered spectroscopy (dosy), drug discovery, hsqc (heteronuclear single quantum coherence), intermolecular interaction, nmr screening methods, nuclear magnetic resonance (nmr), nuclear overhauser effects (noe), protein-ligand interaction, relaxation time, std (saturation transfer difference), trosy (transverse relaxation optimized spectroscopy), waterlogsy (water-ligand observed via Gradient Spectroscopy).