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β-Cyanuryl Ribose, β-Barbituryl Ribose, and 6-Azauridine as Uridine Mimetics.

Helaneh Salameh1, Michal Afri1, Hugo E Gottlieb1

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Summary
This summary is machine-generated.

New uridine mimetics, cyanuryl-ribose (CR), barbituryl-ribose (BR), and 6-azauridine (AU), show enhanced acidity and altered conformations. These analogs offer potential for tighter binding interactions in biochemical and pharmacological applications.

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Area of Science:

  • Biochemistry
  • Medicinal Chemistry
  • Molecular Biology

Background:

  • Uridine (U) mimetics are valuable tools for biochemical and pharmacological research.
  • Previous studies identified uridine recognition patterns by proteins.
  • Characterizing uridine analogs is crucial for developing improved molecular probes.

Purpose of the Study:

  • To characterize novel uridine mimetics: cyanuryl-ribose (CR), barbituryl-ribose (BR), and 6-azauridine (AU).
  • To identify analogs with potentially enhanced binding interactions compared to uridine.
  • To explore structural and electronic modifications for improved biomolecular interactions.

Main Methods:

  • Comparative analysis of hydrogen bonding patterns with adenosine and guanosine.
  • Measurement of acidity and ionization states at physiological pH.
  • Spectroscopic analysis (13C NMR) to determine electron density.
  • Conformational analysis including N-glycosidic bond and exocyclic methylol rotamer preferences.

Main Results:

  • CR, BR, and AU retain selective hydrogen bonds similar to uridine.
  • CR/AU and BR exhibit significantly higher acidity (100- and 10,000-fold) and ionization than uridine at physiological pH.
  • These analogs display altered electron density, reflected in NMR chemical shifts and ε values.
  • CR/AU and BR show a preference for the N-conformation and varied rotamer populations compared to uridine.

Conclusions:

  • Modifications at uridine's C6 or C5-C6 positions significantly alter ionization, electron density, and conformation.
  • These changes suggest potentially stronger binding interactions with target proteins or nucleic acids.
  • The characterized uridine mimetics hold promise for diverse biochemical and pharmacological applications.