Mechanisms of action of the antibiotic ciprofloxacin on the DNA-binding protein Dps detected by molecular modeling techniques

A comprehensive analysis of the effect of the antibiotic ciprofloxacin on the DNA-binding protein Dps of the bacterium Escherichia coli was carried out using three molecular modeling methods: docking, umbrella sampling for calculating mean force potential profiles and classical molecular dynamics. It was shown that ciprofloxacin can penetrate into the internal cavity of the protein, as well as adsorb to the surface, reducing the ability of the N-termini to bind DNA.