PMID: 19469484
Charpentier TH, Wilder PT, Liriano MA, Varney KM, Zhong S, Coop A, Pozharski E, Mackerell AD, Toth EA, Weber DJ
Small molecules bound to unique sites in the target protein binding cleft of calcium-bound S100B as characterized by nuclear magnetic resonance (NMR) and X-ray crystallography.
Biochemistry. 2009 May 26.
Structural studies are part of a rational drug design program underway to inhibit the S100B-p53 interaction and restore wild-type p53 function in malignant melanoma. To this end, structures of three compounds (SBi132, SBi1279, and SBi523) bound to Ca2+-S100B were determined by X-ray crystallography at 2.10 A (Rfree = 0.257), 1.98 A (Rfree = 0.281) and 1.90 A (Rfree = 0.228) resolution, respectively. Upon comparison, SBi132, SBi279, and SBi523 were found to bind in distinct locations/orientations within the hydrophobic target binding pocket of Ca2+-S100B with minimal structural changes observed for the protein upon complex formation with each compound. Specifically, SBi132 binds nearby residues in loop 2 (His-42, Phe-43, Leu-44) and helix 4 (Phe-76, Met-79, Ile-80, Ala-83, Cys-84, Phe-87 and Phe-88); whereas, SBi523 interacts with a separate site defined by residues within loop 2 (Ser-41, His-42, Phe-43, Leu-44, Glu-45 and Glu-46) and one residue on helix 4 (Phe-87). The SBi279 binding site on Ca2+-S100B overlaps the SBi132 and SBi523 sites and contacts residues in both loop 2 (Ser-41, His-42, Phe-43, Leu-44, Glu-45) and helix 4 (Ile-80, Ala-83, Cys-84, Phe-87 and Phe-88). NMR data, including saturation transfer difference (STD) and 15N backbone and 13C sidechain chemical shift perturbations were consistent with the X-ray crystal structures and demonstrated the relevance of all three small molecule-S100B complexes in solution. The discovery that SBi132, SBi279, and SBi523 bind to proximal sites on Ca2+-S100B could be useful for the development of a new class of molecule(s) that interacts with one or more of these binding sites simultaneously, thereby by yielding novel tight binding inhibitors specific for blocking protein-protein interactions involving S100B.