Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Effective antibiotics typically permeate OM porins; thus, understanding porin permeation mechanisms would aid antibiotic development. Although molecular dynamics (MD) simulations can provide key structural information on molecular processes, simulating OM porin permeation is challenging due to its high dimensionality. Since OM porins spontaneously transition between open and closed states, an understanding of  (1) porin functional states regulating permeation and (2) antibiotic permeation pathways through porins is necessary. To investigate the first aspect, we sampled the conformational landscape of the apo porin using MD simulations and Markov state models, an advanced analysis technique. We found large-scale motion of the internal loop to opposing sides of the porin regulates transition between energetically stable open and closed functional states. Furthermore, mutations of key residues involved in the transition alter the dynamic equilibrium of the porin, as found in our MD simulations, and regulate antibiotic permeation inside the cell, as observed in our whole-cell accumulation assays. The identified open state of the porin was then used to investigate the high OM porin permeability of primary amine-appended antibiotics. We compared the permeation of aminated and amine-free antibiotic derivatives by incorporating MD simulation with our novel, Monte Carlo and graph theory-based algorithm designed to improve sampling of conformationally flexible drugs. We found that the primary amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and form favorable electrostatic interactions with highly-conserved charged residues of the internal loop. The importance of these interactions was validated with experimental mutagenesis and whole cell accumulation assays.  Overall, our study demonstrating the regulation of antibiotic permeation by porin dynamics and direct antibiotic-protein interactions could help design effective antibiotics against resistant bacteria.

Investigating molecular mechanisms of antibiotic permeation through outer membrane porins

Fall 2022 abstracts, posters, and presentations will launch in mid-September.

ACS Fall 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.