General diffusion porins such as OmpF and OmpC, located in the outer membrane of bacteria, represent the main entry point for different classes of antibiotics. Bacteria can resist the action of antibiotics by underexpressing and/or mutating porins. Nowadays the problem of bacterial resistance calls for new antibiotics. Another way bacteria exhibit resistance is by expressing enzymes that degrade antibiotics, such as β-lactamase that act on β-lactam antibiotics. Inhibitors of such enzymes are prescribed in combination with antibiotics to block β-lactamase and let antibiotics to reach their target. Again, β-lactamase inhibitors have to diffuse through porins in order to reach their target. Understanding how antibiotics and β-lactamase inhibitors diffuse through porins would help to design new molecules with improved permeation properties, solving this problem of resistance. To investigate the diffusion process of molecules through bacterial porins we used classical MD simulations using OmpF in monomeric and trimeric form. Indeed, as showed experimentally, diffusion is controlled mainly by interaction at the molecular scale. However the high level of accuracy of MD represents also a limitation for simulations to reach the typical time scale of diffusion, from microsecond to millisecond. To overcome this problem we used an acceleration scheme, metadynamics, that allow extending simulations time to biological time scale. From MD simulations we identified the structural determinants that play a key role in the diffusion process : (i) Flexibility of the molecule diffusing and porin (ii) particular localisation of charged residues (iii) presence of hydrophobic pockets. Further, we observed reciprocal influence of each monomer, in particular in the external loops and the constriction region. We compared diffusion of different antibiotics through various classes of porins, to understand better the problem of bacterial resistance to antibiotics.
Structural determinants of antibiotic and β-lactamase diffusion through bacterial porins
Kumar A;RUGGERONE, PAOLO;CECCARELLI, MATTEO
2009-01-01
Abstract
General diffusion porins such as OmpF and OmpC, located in the outer membrane of bacteria, represent the main entry point for different classes of antibiotics. Bacteria can resist the action of antibiotics by underexpressing and/or mutating porins. Nowadays the problem of bacterial resistance calls for new antibiotics. Another way bacteria exhibit resistance is by expressing enzymes that degrade antibiotics, such as β-lactamase that act on β-lactam antibiotics. Inhibitors of such enzymes are prescribed in combination with antibiotics to block β-lactamase and let antibiotics to reach their target. Again, β-lactamase inhibitors have to diffuse through porins in order to reach their target. Understanding how antibiotics and β-lactamase inhibitors diffuse through porins would help to design new molecules with improved permeation properties, solving this problem of resistance. To investigate the diffusion process of molecules through bacterial porins we used classical MD simulations using OmpF in monomeric and trimeric form. Indeed, as showed experimentally, diffusion is controlled mainly by interaction at the molecular scale. However the high level of accuracy of MD represents also a limitation for simulations to reach the typical time scale of diffusion, from microsecond to millisecond. To overcome this problem we used an acceleration scheme, metadynamics, that allow extending simulations time to biological time scale. From MD simulations we identified the structural determinants that play a key role in the diffusion process : (i) Flexibility of the molecule diffusing and porin (ii) particular localisation of charged residues (iii) presence of hydrophobic pockets. Further, we observed reciprocal influence of each monomer, in particular in the external loops and the constriction region. We compared diffusion of different antibiotics through various classes of porins, to understand better the problem of bacterial resistance to antibiotics.
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
