Biological evaluation of psoralen derivatives as inhibitors of NF-κB/DNA interaction: molecular modeling, 3D-QSAR, EMSA assays and inhibition of IL-8 gene expression

Inhibition of the activity of NF-kB is critical for some biomedical appplications including treatment of the inflammatory phenotype associated with cystic fibrosis especially after infection of the lung by Pseudomonas aeruginosa. Some new psoralen derivatives were synthesized and evaluated as inhibitors of NF-κB/DNA interaction, with the aim to investigate the structural determinants required to inhibit this interaction. Starting from molecular docking studies, several possible protein binding sites were proposed and several three-dimensional quantitative structure-activity relationship (3D-QSAR) models were built using the docked poses of compound 29 (the most active psoralen in the series) as templates for alignment of the inhibitors. The selected best model was validated through the prediction of the activity of 17 novel compounds. All the experimental data agreed with the computational experiments, supporting the reliability of the computational approach. The hypothesis about the direct interaction with NF-κB was also supported by surface plasmon resonance (SPR) based assays using the biosensor BIAcore-100 and the compound 29 injected on a sensor chip carrying immobilized NF-κB. Moreover EMSA experiments agreed in indicating psoralen 29 as the most interesting NF-κB inhibitor. Finally, in order to determine the effects on IL-8 accumulation (one of the most expressed interleukins involved in inflammatory processes of cystic fibrosis), RT-PCR and Bio-plex assays were performed on IB3-1 cystic fibrosis cell line treated with this compound. The data obtained demonstrate that compound 29 is a strong inhibitor of TNF-alpha induced accumulation of IL-8 mRNA and release of IL-8. All obtained data identified the compound 29 as a potential candidate for the development of pharmaceutical strategies against the inflammatory phenotype of cystic fibrosis