Crystal structure of the complex between VEGF and a receptor-blocking peptide

Vascular endothelial growth factor (VEGF) is a specific and potent angiogen ic factor and, therefore, a prime therapeutic target for the development of antagonists for the treatment of cancer. As a first stop toward this goal, phage display was used to generate peptides that bind to the receptor-bind ing domain (residues 8-109) of VEGF and compete with receptor [Fairbrother, W. J., Christinger, H. W., Cochran, A. G., Fuh, G., Keenan, C. J., Quan, C ., Shriver, S. K., Tom, J. Y. K., Wells, J. A., and Cunningham, B. C. (1999 ) Biochemistry 38, 17754-17764]. The crystal structure of VEGF in complex w ith one of these peptides was solved and refined to a resolution of 1.9 Ang strom. The 20-mer peptide is unstructured in solution and adopts a largely extended conformation when bound to VEGF, Residues 3-8 form a B-strand whic h pairs with strand beta 6 of VEGF via six hydrogen bonds. The C-terminal f our residues of the peptide point away from the growth factor, consistent w ith NMR data indicating that these residues are flexible in the complex in solution. In contrast, shortening the N-terminus of the peptide leads to de creased binding affinities. Truncation studies show that the peptide can be reduced to 14 residues with only moderate effect on binding affinity. Howe ver, because of the extended conformation and the scarcity of specific side -chain interactions with VEGF, the peptide is not a promising lead for smal l-molecule development. The interface between the peptide and VEGF contains a subset of the residues recognized by a neutralizing Fab fragment and ove rlaps partially with the binding site for the Flt-1 receptor. The location of the peptide-binding site and the hydrophilic character of the interactio ns with VEGF resemble more the binding mode of the Fab fragment than that o f the receptor.