Despite its widespread use, X-ray crystallography has some shortcomings in SBDD. In such cases, solution NMR spectroscopy can serve as an alternative to X-ray crystallography for obtaining structural information at the level of individual amino acids on ligand-binding sites, binding affinities, and ligand orientations during optimization of lead compounds. See a recent paper on the advantages of NMR spectroscopy in structure-based drug design. With NMR spectroscopy, ligand complexes with affinities in the µM to mM range can be analyzed, making the method suitable for studying the binding of small-molecule ligands, peptides, and proteins. The ligand binding site can be thoroughly analyzed using one-dimensional (1D) or two-dimensional (2D) NMR spectroscopy. The choice between the two methods depends on the availability of isotope-labeled protein and peak assignments. For 1D experiments, ligand-detection NMR experiments, combined with competition experiments using a known binder, can effectively identify a compound’s binding site. For 2D experiments, the binding site of a compound can be precisely identified at an atomic resolution if an assignment is available. However, even without an assignment, it is entirely feasible to identify the binding site if a known binder is available. Contact us for a detailed discussion of the method and its potential application to your project.
