SOS-NMR:  A Saturation Transfer NMR-Based Method for Determining the Structures of Protein−Ligand Complexes

An NMR-based alternative to traditional X-ray crystallography and NMR methods for structure-based drug design is described that enables the structure determination of ligands complexed to virtually any biomolecular target regardless of size, composition, or oligomeric state. The method utilizes saturation transfer difference (STD) NMR spectroscopy performed on a ligand complexed to a series of target samples that have been deuterated everywhere except for specific amino acid types. In this way, the amino acid composition of the ligand-binding site can be defined, and, given the three-dimensional structure of the protein target, the three-dimensional structure of the protein−ligand complex can be determined. Unlike earlier NMR methods for solving the structures of protein−ligand complexes, no protein resonance assignments are necessary. Thus, the approach has broad potential applications − especially in cases where X-ray crystallography and traditional NMR methods have failed to produce structural data. The method is called SOS-NMR for structural information using Overhauser effects and selective labeling and is validated on two protein−ligand complexes:  FKBP complexed to 2-(3‘-pyridyl)-benzimidazole and MurA complexed to uridine diphosphate N-acetylglucosamine.