Crystal structure of pentamidine bound to Ca²⁺-S100B

1936

Calcium-bound S100B interacts with the wild-type p53 tumor suppressor and down-regulates its function in cancers such as malignant melanoma (MM) and renal cell carcinoma (RCC). Therefore, structural studies are underway as part of a rational drug design program to inhibit the S100B-p53 interaction. In this study, we co-crystalized Ca²⁺-S100B bound to the drug pentamidine in the space-group P4₁2₁2. We solved the 2.4Å structure of pentamidine bound to Ca²⁺-S100B by X-ray crystallography using molecular replacement techniques to give an atomic resolution 3D structure of the S100B-pentamidine complex with a free R value of 0.254. Pentamidine binds in a location adjacent to a well-characterized Zn²⁺ binding site at the dimer interface of S100B. The location of pentamidine in the crystal structure is consistent with NMR data including intermolecular NOE correlations, saturation transfer difference (STD), and chemical shift perturbations upon the addition of pentamidine to both the Ca²⁺-bound and Zn²⁺-Ca²⁺-bound forms of S100B. Binding studies show that the calcium-dependent interaction of pentamidine is not significantly affected in the presence of Zn²⁺ despite its proximity to this site. Nonetheless, the location of pentamidine nearby the Zn²⁺ site on S100B represents a new small molecule binding site, adjacent to the p53 binding site, which could be important in strategies to inhibit the S100B-p53 interaction.