Understanding the translocation of fluoroquinolones through OmpC using the metadynamics

Abstract

The outer membrane of Gram-negative bacteria such as Escherichia coli acts as a selective permeable barrier between cell and external environment. Water filled outer membrane proteins called as porins were identified for exchange of hydrophilic solutes and hydrophilic antibiotics. One of the most abundant outer membrane porins in E. coli is OmpC and many studies revealed that down-regulation or mutation of this porin shows reduced accumulation of antibacterials in bacterial cells [1]. Fluoroquinolones, used since 1980, are the most common treatment for urinary tract infection caused by E. coli and today this treatment is ineffective in more than half of the patients globally due to widespread resistance. So far the influx kinetics of fluoroquinolones with OmpC has been characterized on free standing lipid bilayers formed on a glass substrate [2]. In particular, detailed analysis of antibiotic interaction with a single OmpC channel using electrophysiology can provide a kinetic description. Here we have investigated two fluoroquinolones, Ciprofloxacin and Enrofloxacin, using an advanced molecular dynamics technique, i.e., metadynamics [3,4]. These free energy calculations help to identify the most favorable paths and activation energies required for molecules to translocate through the OmpC channel. Furthermore, we have also investigated the translocation of the same molecules in the presence of different salts to understand the altered translocation kinetics [5]. Moreover, the identification of favorable interactions networks is important to determine the most prominent residues required for translocation.