Bifunctional Nitrone-Conjugated Secondary Metabolite Targeting the Ribosome

J Am Chem Soc. 2020 Oct 28;142(43):18369-18377. doi: 10.1021/jacs.0c04675. Epub 2020 Oct 19.

Abstract

Many microorganisms possess the capacity for producing multiple antibiotic secondary metabolites. In a few notable cases, combinations of secondary metabolites produced by the same organism are used in important combination therapies for treatment of drug-resistant bacterial infections. However, examples of conjoined roles of bioactive metabolites produced by the same organism remain uncommon. During our genetic functional analysis of oxidase-encoding genes in the everninomicin producer Micromonospora carbonacea var. aurantiaca, we discovered previously uncharacterized antibiotics everninomicin N and O, comprised of an everninomicin fragment conjugated to the macrolide rosamicin via a rare nitrone moiety. These metabolites were determined to be hydrolysis products of everninomicin P, a nitrone-linked conjugate likely the result of nonenzymatic condensation of the rosamicin aldehyde and the octasaccharide everninomicin F, possessing a hydroxylamino sugar moiety. Rosamicin binds the erythromycin macrolide binding site approximately 60 Å from the orthosomycin binding site of everninomicins. However, while individual ribosomal binding sites for each functional half of everninomicin P are too distant for bidentate binding, ligand displacement studies demonstrated that everninomicin P competes with rosamicin for ribosomal binding. Chemical protection studies and structural analysis of everninomicin P revealed that everninomicin P occupies both the macrolide- and orthosomycin-binding sites on the 70S ribosome. Moreover, resistance mutations within each binding site were overcome by the inhibition of the opposite functional antibiotic moiety binding site. These data together demonstrate a strategy for coupling orthogonal antibiotic pharmacophores, a surprising tolerance for substantial covalent modification of each antibiotic, and a potential beneficial strategy to combat antibiotic resistance.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aminoglycosides / chemistry
  • Aminoglycosides / metabolism
  • Binding Sites
  • Cryoelectron Microscopy
  • Erythromycin / chemistry
  • Erythromycin / metabolism
  • Leucomycins / chemistry
  • Leucomycins / metabolism
  • Micromonospora / genetics
  • Multigene Family
  • Nitrogen Oxides / chemistry*
  • Nitrogen Oxides / metabolism
  • Ribosomes / metabolism*

Substances

  • Aminoglycosides
  • Leucomycins
  • Nitrogen Oxides
  • nitrones
  • evernimicin
  • Erythromycin
  • rosaramicin

Supplementary concepts

  • Micromonospora aurantiaca
  • Micromonospora carbonacea