Insights on Antibiotic Translocation through Bacterial Porin from Molecular Dynamics Simulations .
Amit Kumar , Eric Hajjar, Enrico Spiga , Francesca Collu, Paolo Ruggerone & Matteo Ceccarelli
Department of Physics , University of Cagliari . Italy .
Bacterial resistance continues to grow and poses threats to the society today. To reach the bacteria the antibiotics diffuse through general diffusion porins such as OmpF present in large abundance in the outer membrane of the bacteria. When exposed to an antibiotic bacteria become resistance either by introducing mutations such that the antibiotic can no longer diffuse through the porins . The diffusion of antibiotics through the Outer membrane protein (OmpF) is process controlled mainly by the interactions at molecular scale. Molecular Dynamic (MD) Simulations not only provide a microscopic description of the diffusion process but also allow quantification of process in terms of free energy . We use several computational methods to investigate how different Beta lactam antibiotics diffuse through OmpF which is a partially cationic selective channel.
Electro-physiological experiments (BLM) done by our partners in Bremen relate the interruption in ionic current with blockage of antibiotic in channel and further relate blockage to translocation according to free energy model : 2 Blockage 1 translocation .
The question we raise is does no blockage imply no translocation . Our simulation results suggest that no blockage does not necessarily imply no translocation .
In depth analysis for carbenicillin (charged -2 ) with wild type (WT) and double mutant D113N_E117Q (DM) will discussed , highlighting the mechanisms as to why carbenicillin does not translocate with WT but does so with DM . The Liposome swelling assays experiments done by our partners in Bremen compliment well with our simulation results for mutant R132A and D113N . Experimental results for carbeniciilin in DM is not yet available. We investigated the antibiotics of Floroquinolones family Moxifloxacin (charge 0) and Enrofloxacin (charge 0 ) characterized by their hydrophobicity. Finally we show translocation results for new antibiotics of cephalosporins family Cefpirome (CFR) ( charge 0 ) , Cefepime (charge 0 ) and initial results for Cefetamet (CFT) (charge -1 ). Summing up, we propose for the antibiotics in study a reaction pathway for the translocation process , with an effort to rationalize with the experimental findings provided by our partners in Bremen, Marseille, Porto and Basilea Pharmaceutica.