Insights about the Translocation Kinetics of Antibiotics through the E. coli Porin OmpC Obtained from Solvation Mapping

Abstract

Molecular translocation through the outer membrane of Gram-negative bacteria is a key step in achieving antibiotic exposure and efficacy at intracellular targets. Understanding molecular translocation mechanisms is a prerequisite to the rational design of advanced antibiotics aimed at the treatment of resistant, as well as currently untreatable organisms. The outer membrane of Gram-negative bacteria such as E. coli, contain a large number of channels falling under the broad family of β-barrel membrane-bound porin proteins. Antibiotic penetration has been attributed to such channels. Translocation kinetics measured using electrophysiology was reported for six cephalosporin and fluoroquinolone antibiotic drugs through the E. coli porin OmpC. We previously hypothesized that the rates of association and dissociation between solute partners are determined by the energetic costs of transferring solvent to and from protein surfaces and bulk solvent during binding, respectively. We set about to test whether the measured kinetics of antibiotic translocation could be explained by the solvation properties of the antibiotic conduction pathway calculated using WaterMap. The results suggest that intra-channel solvation is highly stable relative to bulk water, and as such, the observed rapid entry of substrates requires replacement of water donor/acceptor H-bonds. The lack of unstable solvation is consistent with the observed rapid exit of OmpC substrates. We docked the six antibiotics into the crystal structure of porin OmpC, and compared the overlay between those molecules and the calculated solvation map. The results suggest that rapid OmpC translocation is limited to substrates with exposed polar groups capable of replacing several simultaneous water-protein and water-water H-bonds. This is consistent with the known physico-chemical properties of the majority of Gram-negative antibiotics, and in particular, the hydrophilic nature of these molecules.