Drug Binding to BamA Targets Its Lateral Gate.

Area of Science:

• Microbiology
• Structural Biology
• Biochemistry

Background:

• BamA is the central component of the β-barrel assembly machinery (BAM) complex, essential for inserting and folding outer-membrane proteins (OMPs) in Gram-negative bacteria.
• BamA is proposed to function via an asymmetric hybrid-barrel model involving lateral gate opening to facilitate OMP insertion through β-augmentation.

Purpose of the Study:

• To investigate the mechanism by which newly identified lead compounds interfere with BamA function.
• To determine how these compounds affect BamA's lateral gate dynamics and substrate OMP folding.

Main Methods:

• Molecular modeling and docking of lead compounds into BamA.
• 5 μs molecular dynamics simulations of BamA with docked compounds and BamA mutants.
• Analysis of lateral gate dynamics and compound-β-strand interactions.

Main Results:

• Docking compounds into extracellular loops prevented lateral gate opening.
• Docking compounds into the open lateral gate resulted in stable binding to the β16 strand, inhibiting substrate folding.
• Simulated BamA mutants showed altered lateral gate dynamics, correlating with compound resistance.

Conclusions:

• Lead compounds inhibit BamA by preventing lateral gate opening and/or substrate binding.
• These inhibitory mechanisms disrupt OMP folding and insertion, offering potential therapeutic strategies against Gram-negative bacteria.