Molecular Model of Norfloxacin Translocation Through the <i>Yersinia pseudotuberculosis</i> OmpF Porin Channel

Abstract

The interaction of Yersinia pseudotuberculosis OmpF (YpOmpF) porin with the fluoroquinolone antibiotic norfloxacin (Nf) and its derivatives (mono- and dihydrochloride) was studied using methods based on the use of bilayer lipid membranes (BLM), molecular modeling, and antibacterial activity testing. Asymmetric behavior of charged Nf (NfH+1) and (Nf2H+2) molecules was found to move through the YpOmpF channel depending on the membrane voltage and the side of antibiotic addition. Electrophysiological data were confirmed by computer modeling. For charged forms of the antibiotic, the presence of two peripheral high-affinity binding sites (NBS1 and NBS2), as well as an asymmetric current blocking site near the channel constriction zone (NBS3), was detected. The NBS1 site located near the channel mouth has almost the same affinity for both charged forms of Nf, while the localization of the more energetically favorable NBS2 site for the two salt forms of the antibiotic differs significantly. Nf has only one binding site near the channel constriction zone, which is a cluster of sites with lower overall affinity compared to the peripheral binding sites mentioned above. Slight differences were found in the antibacterial activity of the three forms of Nf, which is likely due to their different charge states and, accordingly, different permeability and/or ability to bind within the YpOmpF channel.