The translocation kinetics of antibiotics through porin OmpC: Insights from structure‐based solvation mapping using WaterMap

Abstract

Poor permeability of the lipopolysaccharide-based outer membrane of Gram-negative bacteria is compensated by the existence of protein channels (porins) that selectively admit low molecular weight substrates, including many antibiotics. Improved understanding of the translocation mechanisms of porin substrates could help guide the design of antibiotics capable of achieving high intracellular exposure. Energy barriers to channel entry and exit govern antibiotic fluxes through porins. We have previously reported a hypothesis that the costs of transferring protein solvation to and from bulk medium underlie the barriers to protein-ligand association and dissociation, respectively, concomitant with the gain and loss of protein-ligand interactions during those processes. We have now applied this hypothesis to explain the published rates of entry (association) and exit (dissociation) of six antibiotics to/from reconstituted E. coli porin OmpC. WaterMap was used to estimate the total water transfer energies resulting from transient occupation by each antibiotic. Our results suggest that solvation within the porin cavity is highly energetically favorable, and the observed moderately fast entry rates of the antibiotics are consistent with replacement of protein-water H-bonds. The observed ultrafast exit kinetics is consistent with the lack of intrachannel solvation sites that convey unfavorable resolvation during antibiotic dissociation. These results are aligned with known general relationships between antibiotic efficacy and physicochemical properties, namely unusually low logP, reflecting an abundance of H-bond partners. We conclude that antibiotics figuratively "melt" their way through porin solvation at a rate determined by the cost of exchanging protein-solvent for protein-antibiotic H-bonds.

Molecular Basis of Filtering Carbapenems by Porins from β-Lactam-resistant Clinical Strains of Escherichia coli

“…In compensation, favorable enthalpic antibiotic-protein interactions (40, 41) ease the passage of the polar molecule. Furthermore, the release of protein (and antibiotic) hydration waters, upon formation of antibiotic-protein H-bonds, is accompanied by a favorable entropy increase (42,43). A very recent investigation showed how small changes to the "lateral chains" of these two carbapenems can modulate the penetration through specific channels in Pseudomonas aeruginosa (22).…”

Physical methods to quantify small antibiotic molecules uptake into Gram-negative bacteria

“…These variables, which functional combination can be defined as the approximated reaction coordinate, are biased to allow an efficient tough not complete exploration of the huge space of all possible conformations (ergodic hypothesis). The results obtained within these two approximations, the reduced space and the lack of a real ergodicity, can help only when complemented with experimental results coming from different techniques, such as electrophysiology, liposome swelling assays, enzymatic assay [33,34]. The use of modelling methods in supporting/clarifying experiments are becoming popular in different fields thanks also to the development of supercomputer centres accessible through national and international grants (see in Europe the PRACE consortium, http://www.prace-ri.eu/) and very recently to the use of cheaper GPU for accelerating calculations on local computer resources [35].…”

“…(For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.) binding and [32], (iii) a mechanism based on a prior dehydration of the pore induced by the permeating molecule [33]. The three mechanisms are not to be intended as mutually exclusive: in principle the mechanism with binding might require a partial dehydration of the pore.…”

Conventional Antibiotics – Revitalized by New Agents

“…In the case of fluoroquinolones, outer membrane proteins play a key part in helping these molecules to cross the membrane [49,50]. In contrast, passive diffusion is thought to be important for translocation of the inner membrane of Gram-negatives and the single membrane of Gram-positives [51,52,53,54].…”