The 3D structures of Ca2+‐S100B bound to small molecules within the target cleft of S100B as determined by x‐ray crystallography

Abstract

Structural studies are part of a rational drug design program underway to inhibit the S100B‐p53 interaction and restore p53 function in malignant melanoma. Three small molecules were found to bind S100B and structures of these compounnds SBi132, SBi1279 and SBi523 were determined by X‐ray crystallography at 2.10Å, 1.98Å and 1.90 Åresolution, respectively. These small molecules were seen to bind in separate locations in the hydrophobic pocket of Ca2+‐S100B and were compared. SBi523 interacts with residues in loop2 that is found below the hydrophobic cleft. SBi132 binds in the hydrophobic pocket of Ca2+‐S100B and is nearby residues in loop2 and helix 4. SBi279 overlaps both sites of SBi132 and SBi523 and makes contacts with both with loop2 and helix 4. There are very minor changes in S100B when comparing the structures of S100B in complex with each SBi molecule. The orientations of SBi compounds 132, 279 and 523, in their respective binding sites, were consistent with NMR data including saturation transfer difference and 15N backbone and 13C sidechain chemical shift perturbations. These small molecules in close proximity to each other will be useful for developing novel inhibitors of protein‐protein interactions of S100B. This work was supported by grants from the National Institutes of Health [GM58888 and CA107331], the American Cancer Society [CDD107745], and the University of Maryland Drug Design Center.