Side-chain conformational restriction in template-competitive inhibitors of E. coli DNA polymerase I Klenow fragment: Synthesis, structural characterization and inhibition activity

Michael B. Doughty, Karam Aboudehen, Garland Anderson, Ke Li, Bob Moore, Tina Poolson

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Nucleotide triphosphate α-(4-azidophenyl)-1,N6-etheno-dATP 3 and its monophosphate 3m were synthesized by condensation of 2-halo-2-(4-azidophenyl)acetaldehyes with dATP and dAMP, respectively. Structure analysis shows that the azidophenyl side chain is attached to the α-position of the etheno ring (i.e., the carbon attached to N1 of the purine), and conformation calculations show minima in the etheno-phenyl bond rotation at 50 and 130° where the bulk of the phenyl ring projects out from the plane of the etheno group. Like DNA Pol inhibitor 2-(4-azidophenacyl)thio- 2′-deoxyadenosine 5′-triphosphate 1, nucleotide 3 is a template-competitive DNA polymerase inhibitor (TCPI), with a competitive Ki for Pol I KF of 3.41 μM, but has only weak activity as an HIV RT inhibitor relative to the template-competitive reverse transcriptase inhibitor 2-(4-azidophenacyl)thio-1,N6-etheno-2′-deoxyadenosine 5′-triphosphate 2. Additionally, 3 photoinactivates KF in a time-dependent manner, confirming the kinetic data that 3 binds to the free form of KF. The TCPI activity of 3 provides evidence for an extended side chain conformational preference in the combined substrate polymerase inhibitors.

Original languageEnglish (US)
Pages (from-to)1751-1765
Number of pages15
JournalNucleosides, Nucleotides and Nucleic Acids
Volume23
Issue number11
DOIs
StatePublished - Dec 13 2004

Keywords

  • DNA polymerase inhibitors
  • Klenow fragment
  • Reverse transcriptase inhibitors

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