Phylogeny-Informed Synthetic Biology Reveals Unprecedented Structural Novelty in Type V Glycopeptide Antibiotics

The rise and dissemination
of glycopeptide antibiotic (GPA)-resistant
pathogens in healthcare settings fuel efforts to discover GPAs that
can overcome resistance. Members of the type V subclass of GPAs can
evade common GPA resistance mechanisms and offer promise as new drug
leads. We characterize five new type V GPAsrimomycin-A/B/C
and misaugamycin-A/Bdiscovered through a phylogeny-guided
genome mining strategy coupled with heterologous production using
our GPAHex synthetic biology platform. Rimomycin is a heptapeptide
similar to kistamicin but includes an N-methyl-tyrosine
at amino acid 6 (AA6) and substitutes 4-hydroxy­phenylglycine
for tyrosine and 3,5-dihydroxy­phenylglycine at positions AA1
and AA3. Misaugamycin is characterized by an unprecedented N–C
cross-link between AA2 and AA4 and unique N-terminal acylation by
malonyl (misaugamycin-A) or 2-sulfoacetyl (misaugamycin-B) groups.
We demonstrate that rimomycin-A/B/C and misaugamycin-A/B are potent
antibiotics with activity against GPA-resistant clinical isolates
and that the mode of action is consistent with the inhibition of cell
division by the evasion of autolysin activity. These discoveries expand
the chemical diversity of the type V GPAs, offer new chemical scaffolds
for drug development, and demonstrate the application of the GPAHex
platform in mining GPA chemical “dark matter”.