Small molecules bound to unique sites in the target protein binding cleft of calcium-bound S100B as characterized by nuclear magnetic resonance and X-ray crystallography.

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TitleSmall molecules bound to unique sites in the target protein binding cleft of calcium-bound S100B as characterized by nuclear magnetic resonance and X-ray crystallography.
Publication TypeJournal Article
Year of Publication2009
AuthorsCharpentier, TH, Wilder, PT, Liriano, MA, Varney, KM, Zhong, S, Coop, A, Pozharski, E, Mackerell, AD, Toth, EA, Weber, DJ
JournalBiochemistry
Volume48
Issue26
Pagination6202-12
Date Published2009 Jul 07
ISSN1520-4995
KeywordsAnimals, Binding Sites, Cattle, Crystallography, X-Ray, Drug Design, Humans, Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Models, Molecular, Molecular Structure, Nerve Growth Factors, Nuclear Magnetic Resonance, Biomolecular, Peptide Fragments, Protein Binding, Protein Conformation, Rats, Recombinant Proteins, S100 Calcium Binding Protein beta Subunit, S100 Proteins, Tumor Suppressor Protein p53
Abstract

Structural studies are part of a rational drug design program aimed at inhibiting the S100B-p53 interaction and restoring wild-type p53 function in malignant melanoma. To this end, structures of three compounds (SBi132, SBi1279, and SBi523) bound to Ca(2+)-S100B were determined by X-ray crystallography at 2.10 A (R(free) = 0.257), 1.98 A (R(free) = 0.281), and 1.90 A (R(free) = 0.228) resolution, respectively. Upon comparison, SBi132, SBi279, and SBi523 were found to bind in distinct locations and orientations within the hydrophobic target binding pocket of Ca(2+)-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, and 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 Ca(2+)-S100B overlaps the SBi132 and SBi523 sites and contacts residues in both loop 2 (Ser-41, His-42, Phe-43, Leu-44, and Glu-45) and helix 4 (Ile-80, Ala-83, Cys-84, Phe-87, and Phe-88). NMR data, including saturation transfer difference (STD) and (15)N backbone and (13)C side chain 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 Ca(2+)-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 yielding novel tight binding inhibitors specific for blocking protein-protein interactions involving S100B.

DOI10.1021/bi9005754
Alternate JournalBiochemistry
PubMed ID19469484
PubMed Central IDPMC2804263
Grant ListS10 RR023447 / RR / NCRR NIH HHS / United States
S10 RR023447-01 / RR / NCRR NIH HHS / United States
S10 RR016812 / RR / NCRR NIH HHS / United States
R01 CA107331-01A3 / CA / NCI NIH HHS / United States
R01 CA107331-03 / CA / NCI NIH HHS / United States
R01 GM058888-11S1 / GM / NIGMS NIH HHS / United States
R01 CA107331 / CA / NCI NIH HHS / United States
S10 RR016812-01 / RR / NCRR NIH HHS / United States
GM58888 / GM / NIGMS NIH HHS / United States
R01 GM058888-11 / GM / NIGMS NIH HHS / United States
R01 CA107331-04S1 / CA / NCI NIH HHS / United States
R01 CA107331-02 / CA / NCI NIH HHS / United States
CA107331 / CA / NCI NIH HHS / United States
S10 RR015741-01 / RR / NCRR NIH HHS / United States
R01 GM058888-10 / GM / NIGMS NIH HHS / United States
R01 CA107331-04 / CA / NCI NIH HHS / United States
S10 RR015741 / RR / NCRR NIH HHS / United States
R01 GM058888-09 / GM / NIGMS NIH HHS / United States
R01 GM058888 / GM / NIGMS NIH HHS / United States