Receptor-bound conformation of cilengitide better represented by its solution-state structure than the solid-state structure

The X-ray crystal and NMR spectroscopic structures of the peptide drug candidate Cilengitide (cyclo-(RGDf(N Me)Val)) in various solvents are obtained and compared in addition to the integrin receptor bound conformation. The NMR-based solution structures exhibit conformations closely resembling the X-ray structure of Cilengitide bound to the head group of integrin avb3. In contrast, the structure of pure Cilengitide recrystallized from methanol reveals a different conformation controlled by the lattice forces of the crystal packing. Molecular modeling studies of the various ligand structures docked to the avb3 integrin revealed that utilization of the solidstate conformation of Cilengitide leads-unlike the solu-tion-based structures-to a mismatch of the ligand-receptor interactions compared with the experimentally determined structure of the protein-ligand complex. Such discrepancies between solution and crystal conformations of ligands can be misleading during the structure-based lead optimization process and should thus be taken carefully into account in ligand orientated drug design.