title: Toward screening for antibiotics with enhanced permeation properties through bacterial porins.
abstract: Gram-negative bacteria are protected by an outer membrane barrier, and to reach their periplasmic target, penicillins have to diffuse through outer membrane porins such as OmpF. Here we propose a structure-dynamics-based strategy for improving such antibiotic uptake. Using a variety of experiments (high-resolution single channel recording, Minimum Inhibitory Concentration (MIC), liposome swelling assay) and accelerated molecular simulations, we decipher the subtle balance of interactions governing ampicillin diffusion through the porin OmpF. This suggests mutagenesis of a hot spot residue of OmpF for which additional simulations reveal drastic changes in the molecular and energetic pathway of ampicillin's diffusion. Inverting the problem, we predict and describe how benzylpenicillin diffuses with a lower effective energy barrier by interacting differently with OmpF. The thorough comparison between the theoretical predictions and the three independent experiments, which were set up to measure the kinetics of transport and biological activity, gives insights on how to combine such different investigation techniques with the aim of providing complementary validation. Our study illustrates the importance of microscopic interactions at the constriction region of the biological channel to control the antibiotic flux through it. We conclude by providing a complete inventory of the channel and antibiotic hot spots and discuss the implications in terms of antibacterial screening and design.
authors.affiliation: SLACS, Istituto Officina dei Materiali del CNR, c/o Department of Physics, University of Cagliari, I-09042 Monserrato (CA), Italy.
authors.forename: Eric
authors.initials: E
authors.lastname: Hajjar
authors.forename: Andrey
authors.initials: A
authors.lastname: Bessonov
authors.forename: Alexander
authors.initials: A
authors.lastname: Molitor
authors.forename: Amit
authors.initials: A
authors.lastname: Kumar
authors.forename: Kozhinjampara R
authors.initials: KR
authors.lastname: Mahendran
authors.forename: Mathias
authors.initials: M
authors.lastname: Winterhalter
authors.forename: Jean-Marie
authors.initials: JM
authors.lastname: Pagès
authors.forename: Paolo
authors.initials: P
authors.lastname: Ruggerone
authors.forename: Matteo
authors.initials: M
authors.lastname: Ceccarelli
mesh_terms: D000667:Ampicillin / Q000378:metabolism / Q000494:pharmacology; D000900:Anti-Bacterial Agents / Q000378:metabolism* / Q000494:pharmacology; D004594:Electrophysiology; D008826:Microbial Sensitivity Tests; D010400:Penicillin G / Q000378:metabolism / Q000494:pharmacology; D010406:Penicillins / Q000378:metabolism / Q000494:pharmacology; D018272:Porins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017433:Protein Structure, Secondary
chemical_list: D000900:Anti-Bacterial Agents; C109237:OmpF protein; D010406:Penicillins; D018272:Porins; D000667:Ampicillin; D010400:Penicillin G