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TitleSolid-phase synthesis and biological evaluation of des-hydroxy pseudouridimycin analogs.
Journal, issue, pagesACS Med Chem Lett, Year 2026
Publish dateMar 11, 2026
AuthorsAvraz F Anwar / Linlin You / David Degen / Katie J Burns / Michael J Garza / Richard H Ebright / Juan R Del Valle /
PubMed AbstractPseudouridimycin (PUM) is a C-nucleoside/peptide antibiotic that selectively inhibits bacterial RNA polymerase (RNAP) and exhibits potent activity against drug-resistant pathogens. However, PUM ...Pseudouridimycin (PUM) is a C-nucleoside/peptide antibiotic that selectively inhibits bacterial RNA polymerase (RNAP) and exhibits potent activity against drug-resistant pathogens. However, PUM suffers from chemical instability due to self-immolative cleavage of its central hydroxamate bond. Here, we employed cryo-electron microscopy to determine structures of PUM () and a chemically stabilized des-hydroxy analog of PUM () bound to an RNAP transcription complex. Guided by the observed bound conformation, we developed an efficient solid-phase synthesis of 50 des-hydroxy PUM analogs modified at the Gln residue and Gdn-Gly tail. Several analogs retained low-micromolar RNAP-inhibitory activity, with a -substituted phenyl amidine analog () emerging as the most potent inhibitor (IC = 0.95 μM). These results establish a versatile synthetic platform and structural framework for optimizing stabilized PUM derivatives and provide a foundation for the development of RNAP-targeted therapeutics against resistant bacterial pathogens.
External linksACS Med Chem Lett / PubMed:41890570 / PubMed Central
MethodsEM (single particle)
Resolution3.06 - 3.32 Å
Structure data

73220

9ynp

EMDB-73220, PDB-9ynp:
Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and pseudouridimycin (PUM)
Method: EM (single particle) / Resolution: 3.06 Å

73221

9ynq

EMDB-73221, PDB-9ynq:
Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and des-hydroxy pseudouridimycin (des-hydroxy PUM)
Method: EM (single particle) / Resolution: 3.32 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-PUM:
(1S)-1,4-anhydro-5-[(N-carbamimidoylglycyl-N~2~-hydroxy-L-glutaminyl)amino]-5-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol / antibiotic*YM


PDB Unreleased entry

PDB-1cyh: Unknown entry

Source
  • escherichia coli str. k-12 substr. mg1655 (bacteria)
KeywordsTRANSCRIPTION / TRANSFERASE/DNA/RNA/INHIBITOR / Transcription initiation complex / Pseudouridimycin (PUM) / Inhibitor / Antibacterial agent / TRANSFERASE-DNA-RNA-INHIBITOR complex / Des-hydroxy pseudouridimycin (des-hydroxy PUM)

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