The discovery and structural basis of two distinct state-dependent inhibitors of BamA

• Published in: Nature communications Vol. 15; no. 1; pp. 8718 - 15
• Main Authors: Sun, Dawei, Storek, Kelly M., Tegunov, Dimitry, Yang, Ying, Arthur, Christopher P., Johnson, Matthew, Quinn, John G., Liu, Weijing, Han, Guanghui, Girgis, Hany S., Alexander, Mary Kate, Murchison, Austin K., Shriver, Stephanie, Tam, Christine, Ijiri, Hiroshi, Inaba, Hiroko, Sano, Tatsuya, Yanagida, Hayato, Nishikawa, Junichi, Heise, Christopher E., Fairbrother, Wayne J., Tan, Man-Wah, Skelton, Nicholas, Sandoval, Wendy, Sellers, Benjamin D., Ciferri, Claudio, Smith, Peter A., Reid, Patrick C., Cunningham, Christian N., Rutherford, Steven T., Payandeh, Jian
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 08.10.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 101/28; 13; 14; 631/326; 631/535; 82/75; Anti-Bacterial Agents - chemistry; Anti-Bacterial Agents - pharmacology; Antibiotics; Assembly machines; Bacteria; Bacterial Outer Membrane Proteins - chemistry; Bacterial Outer Membrane Proteins - metabolism; Barrels; Binding Sites; Coliforms; Divalent cations; E coli; Escherichia coli - drug effects; Escherichia coli - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Gram-negative bacteria; Humanities and Social Sciences; In vitro methods and tests; Inhibitors; Inserts; Membrane proteins; Membranes; Models, Molecular; multidisciplinary; Peptide inhibitors; Peptides; Peptides - chemistry; Peptides - metabolism; Peptides - pharmacology; Protein Binding; Protein Conformation; Protein folding; Proteins; Science; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-52512-1

BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of Gram-negative bacteria. Despite recent advances in our mechanistic and structural understanding of BamA, there are few potent and selective tool molecules that can bind to and modulate BamA activity. Here, we explored in vitro selection methods and different BamA/BAM protein formulations to discover peptide macrocycles that kill Escherichia coli by targeting extreme conformational states of BamA. Our studies show that Peptide Targeting BamA-1 (PTB1) targets an extracellular divalent cation-dependent binding site and locks BamA into a closed lateral gate conformation. By contrast, PTB2 targets a luminal binding site and traps BamA into an open lateral gate conformation. Our results will inform future antibiotic discovery efforts targeting BamA and provide a template to prospectively discover modulators of other dynamic integral membrane proteins. BamA carries out the essential process of folding outer membrane β-barrels in Gram-negative bacteria and is a potential antibiotic target. Here, the authors discover macrocyclic peptide inhibitors that trap BamA in distinct structural conformations.