A fluorescence polarization assay for the experimental validation of an in silico model of the chemokine CXCL8 binding to receptor-derived peptides.

Peptide based inhibitors of protein-protein interactions are of great interest in proteomics, structural biology and medicinal chemistry. Optimized inhibitors can be designed by experimental approaches or by computational prediction. Ideally, computational models are adjusted to the peptide-protein complex of interest according to experimental data obtained in specific binding experiments. The chemokine CXCL8 (interleukin-8) is an interesting target for drug discovery due to its role in inflammatory diseases. Given the available structural data and information on its receptor interactions it constitutes a basis for the rational design of inhibitor peptides. Starting from the reported structure of CXCL8 in complex with a peptide derived from its receptor CXCR1 we developed a computational docking procedure to estimate the changes in binding energy as a function of individual amino acid exchanges. This indicates whether the respective amino acid residue must be preserved or can be substituted to maintain or improve affinity, respectively. To validate and improve the assumptions made in this docking simulation we established a fluorescence polarization assay for receptor-derived peptides binding to CXCL8. A peptide library was tested comprising selected mutants characterized by docking simulations. A number of predictions regarding electrostatic interactions were confirmed by these experiments and it was revealed that the model needed to be corrected for backbone flexibility. Therefore, the assay presented here is a promising tool to systematically improve the computational model by iterative cycles of modeling, experimental validation and refinement of the algorithm, leading to a more reliable model and peptides with improved affinity.

Leukocyte responses to immobilized patterns of CXCL8.

The attachment of neutrophils to the endothelial surface and their migration towards the site of inflammation following chemokine gradients play an essential role in the innate immune response. Chemokines adhere to glycosaminoglycans on the endothelial surface to be detected by leukocytes and trigger their movement along surface- bound gradients in a process called haptotaxis. In assays to systematically study the response of leukocytes to surface-bound compounds both the spatial arrangement of the compound as well as the mode of immobilization need to be controlled. In this study microcontact printing was employed to create patterns of hydrophobic or functionalized thiols on gold-coated glass slides and CXCL8 was immobilized on the thiol coated areas using three different strategies. Human neutrophils adhered to the CXCL8-coated lines but not to the PEG-coated background. We could show that more cells adhered to CXCL8 adsorbed to hydrophobic octadecanethiol than on CXCL8 covalently bound to amino undecanethiol or CXCL8 specifically bound to immobilized heparin on aminothiol. Likewise general cell activity such as lamellipodia formation and random migration were most pronounced for CXCL8 adsorbed on a hydrophobic surface which may be attributed to the larger amounts of protein immobilized on this type of surface.