Divalent metal ion complexes of S100B in the absence and presence of pentamidine

As part of an effort to inhibit S100B, structures of pentamidine (Pnt) bound to Ca2+-loaded and Zn2+, Ca2+-loaded S100B were determined by X-ray crystallography at 2.15 angstrom (R-free = 0.266) and 1.85 angstrom (R-free = 0.243) resolution, respectively. These data were compared to X-ray structures solved in the absence of Pnt, including Ca2+-loaded S100B and Zn2+ Ca2+-loaded S100B determined here (1.88 angstrom; R-free = 0.267). In the presence and absence of Zn2+ electron density corresponding to two Pnt molecules per S100B subunit was mapped for both drug-bound structures. One Pnt binding site (site 1) was adjacent to a p53 peptide binding site on S100B (+/- Zn2+), and the second Pnt molecule was mapped to the dimer interface (site 2; Zn2+) and in a pocket near residues that define the Zn2+ binding site on S100B. In addition, a conformational change in S100B was observed upon the addition of Zn2+ to Ca2+-S100B, which changed the conformation and orientation of Pnt bound to sites 1 and 2 of Pnt-Zn2+, Ca2+-S100B when compared to Pnt-Ca2+-S100B. That Pnt can adapt to this Zn2+-dependent conformational change was unexpected and provides a new mode for S100B inhibition by this drug. These data will be useful for developing novel inhibitors of both Ca2+- and Ca2+, Zn2+-bound S100B. (C) 2008 Elsevier Ltd. All rights reserved.