A Multidisciplinary Approach toward Identification of Antibiotic Scaffolds for Acinetobacter baumannii

Area of Science:

• Microbiology and Molecular Biology
• Structural Biology
• Drug Discovery

Background:

• High attrition rates in antibiotic discovery for Gram-negative bacteria are linked to outer membrane (OM) permeability barriers and efflux systems.
• Overcoming OM permeability requires identifying small molecules that naturally utilize abundant OM channels as transport substrates.
• These natural substrates can serve as scaffolds for designing novel, efficiently permeating antibacterial agents.

Purpose of the Study:

• To identify potential small-molecule scaffolds that can overcome the outer membrane permeability barrier in Gram-negative bacteria.
• To focus on the pathogenic bacterium Acinetobacter baumannii as a model system for this investigation.

Main Methods:

• Utilized OM proteomics to identify DcaP as the most abundant OM channel in Acinetobacter baumannii during infection.
• Determined the X-ray crystal structure of DcaP, revealing a trimeric, porin-like structure.
• Employed electrophysiological experiments and all-atom molecular dynamics simulations to analyze substrate transport and permeation pathways.

Main Results:

• DcaP was identified as the most abundant OM channel in Acinetobacter baumannii during rodent infection.
• The crystal structure of DcaP suggests dicarboxylic acids as potential transport substrates.
• Simulations confirmed dicarboxylic acids as substrates and provided atomistic details on permeation pathways and energy barriers for small molecules, including a β-lactamase inhibitor.

Conclusions:

• DcaP is a key outer membrane channel in Acinetobacter baumannii, with dicarboxylic acids as likely natural substrates.
• The identified DcaP structure and substrate information provide a foundation for designing novel antibacterial agents.
• This strategy offers a promising approach to overcome OM permeability barriers and develop effective antibiotics against Gram-negative pathogens.