抗生素PPT课件（英文精品）Drug Action in the .pptVIP

Kelcey Anderson Bioinformatics and Bioengineering Summer Institute Virginia Commonwealth University August 10, 2010 Efflux Pumps Found in Gram-negative bacteria, including E. coli AcrAB-TolC Composed of three parts spanning both the inner and outer cell membranes Responsible for extruding a variety of mainly lipophilic substances Symmons, et al. 2009. PNAS 106:7173-78 AcrB Nature, 2006, 443, 173-179 AcrB has three protomers Protomers exist in either the access, binding, or extrusion state Substrates enter the access state near the inner membrane Why Study Efflux Pumps? Responsible for extrusion of antibiotics Multidrug resistant strains overexpress efflux pump proteins Development of new antibiotics Penicillin G Acriflavine Minocycline Drug Action in the Cell Cannon, et al. 2009. Clin. Microbiol. Rev. 22,2:291-321 Research Questions What factors would determine whether an antibiotic is likely to be extruded by the cell? Can we predict the antibiotics that are more likely to be extruded by the efflux pump? Experimental Data Knock out efflux pump genes Measure MIC values for different substances Ratio of normal vs. knocked out MIC values Is there a correlation between the ratio of efflux and the properties of the compounds? Literature Sources: Mazzariol et al. 2000 Nishino et al. 2003 Sulavik et al. 2001 Lee et al. 2000 Nikaido et al. 1998 Calculation of Molecular Parameters Molecular Width Molecular dynamics LogP Measure of hydrophobicity Can be determined experimentally or computationally Docking Place molecules into different areas of the pump apparatus in many positions Charged vs. neutral molecules Four significant areas contribute to model for efflux Neutral molecules in the binding state Charged molecules in the extrusion state Charged molecules in the intermonomer region (“AcrB hole”) Charged molecules in “Zone 3” of TolC Dock Compounds into Pump Score Docked Positions using HINT Hydropathic INTeractions (HINT) scores the strength of the interaction between