Solid-Phase Synthesis and Biological Evaluation of Des-hydroxy Pseudouridimycin Analogs

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Abstract
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 (1) and a chemically stabilized des-hydroxy analog of PUM (2a) bound to an Escherichia coli 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 para-substituted phenyl amidine analog (54) emerging as the most potent inhibitor (IC50 = 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.
Funding Information
  • University of Notre Dame
  • National Institute of General Medical Sciences (GM041376)
  • National Institute of General Medical Sciences (GM145773)
  • Welter Family Foundation

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