Using Molecular Simulations to Screen for Antibiotics with Enhanced Permeation Properties through Bacterial Pores

Gram-negative bacteria are protected by an outer membrane and to function, antibiotics have to diffuse through outer membrane channels, or porins, such as OmpF. Previously, we revealed the complete permeation pathways of β-lactams antibiotics, such as ampicillin, using all atom accelerated molecular dynamic simulations and found remarkable agreement with experimental results(1). Here we follow the paradigm for selecting antibiotics with better permeation properties via computer simulations. In-depth analysis of the simulations revealed the key determinants for the diffusion of ampicillin through OmpF: a subtle balance of interactions at the constriction region of the channel compensates the loss of entropy of the antibiotic and facilitates its diffusion. The simulations were then repeated using porins mutated in their key interacting residues, such as Asp113, and the drastic changes found in ampicillin permeation confirmed our hypothesis. Guided by these results, we then predict that an antibiotic that would interact differently with OmpF, such as penicillin-G that lacks the ampicillin positive group, would translocate faster. This is confirmed by the calculation of the effective energy barriers for translocation, and importantly, we are able to validate the predictions by a wide range of experiments using electrophysiology, spectroscopy and swelling assays techniques. We conclude by drawing, the complete inventory of the rate-limiting interactions and map them on both the porin and antibiotics structure. Finally we show how our multi-scale approach can help rational antibiotics design and screening as we extend it to (i) novel antibiotics of pharmaceutical and therapeutical interest and (ii) homology modeled porins from novel pathogenic strains which shows interesting antibiotic resistance profiles.1. Hajjar, E., et. al. Bridging time and length scales: from macroscopic flux to molecular mechanism of antibiotics diffusion through porins. Biophys. J. (minor revisions).