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TitleA Natural Depsipeptide Antibiotic that Targets the E site of the Bacterial Ribosome.
Journal, issue, pagesRes Sq, Year 2025
Publish dateJul 3, 2025
AuthorsGerard Wright / Manpreet Kaur / Dmitrii Travin / Max Berger / Manoj Jangra / Martino Morici / Haaris Ahsan Safdari / Dorota Klepacki / Wenliang Wang / Michael Cook / Sommer Chou / Allison Guitor / Kalinka Koteva / Min Xu / Linda Ejim / Lesley Macneil / Nora Vázquez-Laslop / Alexander Mankin / Daniel Wilson /
PubMed AbstractA significant challenge in addressing the antibiotic resistance crisis is identifying new antimicrobial compounds. Although natural products produced by fungi and bacteria, particularly ...A significant challenge in addressing the antibiotic resistance crisis is identifying new antimicrobial compounds. Although natural products produced by fungi and bacteria, particularly actinomycetes, have been the source of most antibiotics discovered over the past 80 years, they have fallen out of favor due to the frequent rediscovery of known drug scaffolds. The current perception is that antibiotic-producing actinomycetes have been over-mined and possess little novelty left to yield. Here, we demonstrate that by using improved fractionation approaches that enrich previously overlooked minor products, even well-studied strains of antibiotic-producing actinomycetes can provide new chemical scaffolds with unique modes of action. By fractionating a library of natural product extracts from soil bacteria, we show that Streptomyces rimosus, the source of the well-known antibiotic oxytetracycline, produces a previously overlooked cyclic depsipeptide antibiotic that we called manikomycin. Manikomycin can kill multi-drug-resistant Enterobacteriaceae and is not susceptible to resistance associated with clinically used antibiotics. Biochemical, genetic, and structural analyses reveal that manikomycin binds in the 'exit' or E site of the large subunit of the bacterial ribosome preventing the entry of the 3' end of the tRNA into the E site and effectively hindering the translocation step of protein synthesis in a sequence context-specific manner. Manikomycin is the first antibacterial agent to target the critical but underexplored E site in the large ribosomal subunit, highlighting its value as a lead for developing new antibiotics.
External linksRes Sq / PubMed:40630547 / PubMed Central
MethodsEM (single particle)
Resolution2.4 - 2.45 Å
Structure data

53943

9rfw

EMDB-53943, PDB-9rfw:
Manikomycin bound to the Escherichia coli 50S ribosomal subunit
Method: EM (single particle) / Resolution: 2.4 Å

54009

9rja

EMDB-54009, PDB-9rja:
Manikomycin bound to the Escherichia coli 70S ribosome
Method: EM (single particle) / Resolution: 2.45 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-PAR:
PAROMOMYCIN / medication*YM

ChemComp-SPD:
SPERMIDINE

Source
  • escherichia coli bw25113 (bacteria)
  • streptomyces rimosus (bacteria)
KeywordsANTIBIOTIC / Dal2 / PrAMP / Ribosome / Translation / Initiation / Nascent polypeptide exit tunnel / Cryo-EM / Manikomycin / E-site / Elongation

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