Fast NMR-Based Determination of the 3D Structure of the Binding Site of Protein–Ligand Complexes with Weak Affinity Binders

In early drug discovery approaches, screening hits are often weak affinity binders that are difficult to characterize in structural detail, particularly towards obtaining the 3D structure of protein–ligand complexes at atomic resolution. NMR is the outstanding technique to tackle such problems, yet suffers from a tedious structure calculation process. NMR² was recently developed to alleviate the laborious element of routine NMR structure calculation procedures and provides the structural information at protein–ligand interaction sites orders of magnitude faster than standard procedures. The NMR² method was extended to weak binders and applied to the oncoproteins HDM2 and MDMX. The structure of the MDMX-SJ212 complex is reported with a K_d of approximately 0.7 μm; the complex structure of HDM2 with the mm affinity ligand #845 exhibits a new scaffold.