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TitleComputational identification of a systemic antibiotic for gram-negative bacteria.
Journal, issue, pagesNat Microbiol, Vol. 7, Issue 10, Page 1661-1672, Year 2022
Publish dateSep 26, 2022
AuthorsRyan D Miller / Akira Iinishi / Seyed Majed Modaresi / Byung-Kuk Yoo / Thomas D Curtis / Patrick J Lariviere / Libang Liang / Sangkeun Son / Samantha Nicolau / Rachel Bargabos / Madeleine Morrissette / Michael F Gates / Norman Pitt / Roman P Jakob / Parthasarathi Rath / Timm Maier / Andrey G Malyutin / Jens T Kaiser / Samantha Niles / Blake Karavas / Meghan Ghiglieri / Sarah E J Bowman / Douglas C Rees / Sebastian Hiller / Kim Lewis /
PubMed AbstractDiscovery of antibiotics acting against Gram-negative species is uniquely challenging due to their restrictive penetration barrier. BamA, which inserts proteins into the outer membrane, is an ...Discovery of antibiotics acting against Gram-negative species is uniquely challenging due to their restrictive penetration barrier. BamA, which inserts proteins into the outer membrane, is an attractive target due to its surface location. Darobactins produced by Photorhabdus, a nematode gut microbiome symbiont, target BamA. We reasoned that a computational search for genes only distantly related to the darobactin operon may lead to novel compounds. Following this clue, we identified dynobactin A, a novel peptide antibiotic from Photorhabdus australis containing two unlinked rings. Dynobactin is structurally unrelated to darobactins, but also targets BamA. Based on a BamA-dynobactin co-crystal structure and a BAM-complex-dynobactin cryo-EM structure, we show that dynobactin binds to the BamA lateral gate, uniquely protruding into its β-barrel lumen. Dynobactin showed efficacy in a mouse systemic Escherichia coli infection. This study demonstrates the utility of computational approaches to antibiotic discovery and suggests that dynobactin is a promising lead for drug development.
External linksNat Microbiol / PubMed:36163500 / PubMed Central
MethodsEM (single particle) / X-ray diffraction / EM (electron crystallography)
Resolution1.05 - 3.6 Å
Structure data

14242

7r1w

EMDB-14242, PDB-7r1w:
E. coli BAM complex (BamABCDE) bound to dynobactin A
Method: EM (single particle) / Resolution: 3.6 Å

PDB-7r1v:
Crystal structure of E.coli BamA beta-barrel in complex with dynobactin A
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-7t3h:
MicroED structure of Dynobactin
Method: ELECTRON CRYSTALLOGRAPHY / Resolution: 1.05 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • escherichia coli k-12 (bacteria)
  • photorhabdus australis (bacteria)
  • escherichia coli o157:h7 (bacteria)
KeywordsMEMBRANE PROTEIN / Beta-Barrel / outer membrane / protein insertion / protein folding / protein maturation / antibiotic / natural product / cyclized peptide / antibiotics / drug development / Bam A / MicroED

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