Exploring bacterial outer membrane barrier to combat bad bugs

Abstract

One of the main fundamental mechanisms of antibiotic resistance in Gram-negative bacteria comprises an effective change in the membrane permeability to antibiotics. The Gram-negative bacterial complex cell envelope comprises an outer membrane that delimits the periplasm from the exterior environment. The outer membrane contains numerous protein channels, termed as porins or nanopores, which are mainly involved in the influx of hydrophilic compounds, including antibiotics. Bacterial adaptation to reduce influx through these outer membrane proteins (Omps) is one of the crucial mechanisms behind antibiotic resistance. Thus to interpret the molecular basis of the outer membrane permeability is the current challenge. This review attempts to develop a state of knowledge pertinent to Omps and their effective role in antibiotic influx. Further, it aims to study the bacterial response to antibiotic membrane permeability and hopefully provoke a discussion toward understanding and further exploration of prospects to improve our knowledge on physicochemical parameters that direct the translocation of antibiotics through the bacterial membrane protein channels.

Keywords: Gram-negative bacteria; antibiotic resistance; antibiotics; cell envelope; influx; nanopores; protein channels.

Figure 1

(A) Antibiotic resistance (an overview). (B) Various mechanisms of antibiotic resistance employed by Gram-negative bacteria (an overview). (C) Structural representation of outer membrane vesicles. Abbreviation: Omps, outer membrane proteins.

Figure 2

Antibiotic resistance mechanism associated with Omps modification. Antibiotic β-lactam molecules are represented by green stars, and Omps as trimers by gray cylinder. The width of the straight arrows imitating the level of β-lactam penetration via Omps. The curved arrows exemplify the uptake failure/reduce uptake occurring with the following: B: decrease in the level of wild-type Omps expression; C: expression of restricted-channel Omps; D: mutation or modification of the functional properties of a porin channel; and E: synthesis of modified Omps with significant constriction. Abbreviation: Omps, outer membrane proteins.

Figure 3

(A) Current recorded using staircase electrophysiology. A graphical representation depicting insertion of Omp over real time under applied potential. Recording time: 18 seconds. (B) Current histogram for the trace with each peak resembling a single Omp, showing, in total, approximately 45 Omps. (C) OmpF single channel–substrate interaction comparison: without substrate (blank), substrate 1 depicting no blockages, and substrate 2 inducing well-resolved channel blockage; a clear difference between the two substrates can be seen. Abbreviation: Omp, outer membrane protein.

Figure 4

(A) Intrinsic depiction of the two-dimensional free energy of translocation of β-lactamase inhibitor (avibactam), reassembled from metadynamic simulations. (B) Lateral view and (C) topmost view of the avibactam inside OmpF pore in the two lowest minima near the constriction region and at the subsequent transition state. Reprinted with permission from Ghai I, Pira A, Scorciapino MA, et al. General method to determine the flux of charged molecules through nanopores applied to beta-lactamase inhibitors and OmpF. J Phys Chem Lett. 2017;8(6):1295–1301. Copyright (2017) American Chemical Society.