BamA, the core component of the β-barrel assembly machinery (BAM) complex, is an outer membrane protein (OMP) in Gram-negative bacteria. Gram-negative bacteria themselves are difficult to treat due to their intrinsic resistance from the outer membrane (OM), a significant permeability barrier. However, BamA is an attractive target for novel antibiotic development due to its location in the OM and the fact that it is both universal and essential in Gram-negative bacteria. The BAM complex itself is composed of the β-barrel BamA and four lipoproteins, BamB-E. The function of BamA is to insert and fold substrate OMPs into the outer membrane. Evidence suggests that BamA follows the hybrid-barrel model where the first and last strands of the BamA separate, known as lateral gate opening, to allow nascent substrate OMP β-strands to sequentially fold through β-augmentation. Recently, multiple lead compounds that interfere with BamA function have been identified. We modeled and then docked one of these compounds into either the loops of BamA or the open lateral gate. With the compound docked in the loops of BamA, we found the lateral gate remains closed during a 1 μs molecular dynamics simulation. The same compound when docked in the open lateral gate stays bound to the β16 strand of BamA during the simulation, which would prevent substrate OMP folding. In addition, we simulated mutants of BamA that are resistant to one or more of the identified lead compounds for 20 μs each in aggregate, for a total time of 100 μs. In these simulations, we observed a notably larger degree and/or frequency of opening of BamA’s lateral gate, suggesting that the mutations grant resistance by making the gate more permissive. We conclude that the compounds act by inhibiting BamA lateral gate opening and, thus, subsequent OMP folding and insertion, validating that lateral gate opening is a mechanism of action to target in antibiotic development.

Drug binding to BamA targets lateral gate opening and OMP folding

ACS Spring Meeting 2021

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