Optimization of Efflux Avoidance and Inhibition For Antibiotic Development

Project SummaryFailures of antibiotic therapy occur with increasing frequency in clinics due to the spread of multidrug resistantbacterial pathogens. The major challenge are infections caused by Gram-negative bacteria that are protectedfrom antibiotics by the concerted action of multidrug efflux pumps and the low permeability barrier of outermembranes. Pseudomonas aeruginosa, an opportunistic human pathogen responsible for a variety of infectiousdiseases, is notorious for its antibiotic impermeability. A handful of clinical antibiotics used against this pathogenare beginning to fail due to the emergence of multidrug resistant strains. New antibiotics are needed to addressthis growing threat.Decades of antibiotic discovery and optimization perfected empirical approaches for improvement of antibioticaction and avoidance of class-specific resistance mechanisms. The current critical challenge is to developapproaches that will enable antibiotic penetration across non-specific permeability barriers of Gram-negativebacteria, which present an urgent and serious threat to public health. This project responds to this challenge andproposes the development of a new technology for optimization of efflux avoidance and inhibition in clinical andinvestigational antibacterial agents that will be effective against Gram-negative bacteria.The proposed approach targets simultaneously the multidrug efflux mechanism of P. aeruginosa and its outermembrane barrier and combines cutting edge technologies in experimental analyses of efflux inhibition and drugpenetration, kinetic modeling of drug accumulation, computer simulations of drug efflux and transmembranediffusion, synthetic chemistry and machine learning analyses. The central objective of the proposal is to createa mechanism-based predictive model that integrates physicochemical properties of compounds, kinetics of theirintracellular accumulation and transmembrane diffusion, and a molecular level description of the interaction ofefflux transporters with their substrates and inhibitors. The model will be validated by focused medicinalchemistry efforts to generate antibacterial agents that combine the traits of effective antibiotics and potent effluxpump inhibitors or avoiders.This multi-disciplinary approach is enabled by the collaborative efforts of PIs on the project: Helen Zgurskaya(biochemistry of drug uptake and efflux), Valentin Rybenkov (kinetic modeling), Paolo Ruggerone (computationalbiophysics of efflux), Gnanakaran (computational simulations of membrane permeation) and John Walker(medicinal chemistry).