Molecular simulations reveal the molecular basis of diffusion through porins; and allow designing potent antibiotics

Introduction: The increasing bacterial resistance to antibiotics poses significant threat in treatment of infectious diseases. This calls for designing antibiotics with improved permeation properties using a bottom- up approach, based on the knowledge of molecular mechanisms regulating resistance. Bacterial outer membrane contain general diffusion porins, such as OmpF, which constitute the main path of diffusion for antibiotics. A common mechanism by which bacterial strains become resistant is to introduce mutations modulating the permeation of the porins. Methods: To study the diffusion of antibiotics through OmpF at a molecular scale, we performed molecular dynamics (MD) simulations, combined with the metadynamic algorithm that accelerate rare events. Results: We simulated the wild type porin OmpF as well as variants with substitutions. We found that a mutation on the residue D113 (a residue at the constriction region) changes drastically the Ampicillin diffusion in terms of strength and localization of minima on the associated free energy map. Then led by these results, we used an antibiotic that potentially interact less with this residue, such as penicillin-G, and predicted the expected diffusion pathway. Conclusion: We further extended this investigation to other antibiotics, such as carbencillin and even fourth generation of cephalosporins, which are the most frequently prescribed class of antibiotics in the world. These findings are in good agreement with experimental results obtained by our collaborators (liposome swelling assays and electrophysiology) and demonstrate how theory and experiments can be combined to reveal the mechanism of antibiotic diffusion and designing potent antibiotics.