Dissecting the effects of DNA polymerase and ribonuclease H inhibitor combinations on HIV-1 reverse-transcriptase activities

Biochemistry. 2005 Feb 8;44(5):1595-606. doi: 10.1021/bi0486740.


Although HIV-1 reverse transcriptase (RT) DNA polymerase and ribonuclease H (RNase H) activities reside in spatially distinct domains of the enzyme, inhibitors that bind in the RT polymerase domain can affect RNase H activity. We used both gel assays and a real-time FRET assay to analyze the impact of three mechanistically distinct RT polymerase inhibitors on RNase H activity in vitro. The nucleoside analogue 3'-azido-3'-deoxythymidine triphosphate (AZT-TP) had no effect, whereas the pyrophosphate analogue phosphonoformate (PFA) inhibited RNase H activity in a concentration-dependent manner. Nonnucleoside RT inhibitors (NNRTIs) enhanced RNase H catalysis, but the cleavage products differed substantially for RNA/DNA hybrid substrates of different lengths. A comparison of 61 different RT crystal structures revealed that NNRTI binding opened the angle between the polymerase and RNase H domains of the p66 subunit and reduced the relative motion of the thumb and RNase H regions, suggesting that NNRTI enhancement of RNase H cleavage may result from increased accessibility of the RNase H active site to the RNA/DNA hybrid duplex. We also examined the effects of combining a diketo acid (DKA) RNase H inhibitor with various RT polymerase inhibitors on polymerase-independent RNase H cleavage, RNA-dependent DNA polymerization, and in reverse-transcription assays. Interestingly, although the NNRTI decreased DKA potency in polymerase-independent RNase H assays, NNRTI/DKA combinations were synergistic in inhibiting reverse transcription overall, indicating that regimens incorporating both NNRTI and RNase H inhibitors may be therapeutically beneficial.

MeSH terms

  • Anti-HIV Agents / chemistry*
  • Anti-HIV Agents / pharmacology
  • Binding Sites
  • Butyrates / chemistry
  • Butyrates / pharmacology
  • Catalysis / drug effects
  • DNA-Directed DNA Polymerase / metabolism
  • Dideoxynucleotides
  • Drug Combinations
  • Drug Synergism
  • Foscarnet / chemistry
  • Foscarnet / pharmacology
  • HIV Reverse Transcriptase / antagonists & inhibitors*
  • HIV Reverse Transcriptase / metabolism*
  • Hydrolysis
  • Kinetics
  • Nucleic Acid Synthesis Inhibitors*
  • Oxazines / chemistry
  • Oxazines / pharmacology
  • Reverse Transcriptase Inhibitors / chemistry*
  • Reverse Transcriptase Inhibitors / pharmacology
  • Ribonuclease H / antagonists & inhibitors*
  • Ribonuclease H / metabolism
  • Thiophenes / chemistry
  • Thiophenes / pharmacology
  • Thymine Nucleotides / chemistry
  • Thymine Nucleotides / pharmacology
  • Zidovudine / analogs & derivatives*
  • Zidovudine / chemistry
  • Zidovudine / pharmacology


  • 4-(5-(benzoylamino)thien-2-yl)-2,4-dioxobutanoic acid
  • Anti-HIV Agents
  • Butyrates
  • Dideoxynucleotides
  • Drug Combinations
  • Nucleic Acid Synthesis Inhibitors
  • Oxazines
  • Reverse Transcriptase Inhibitors
  • Thiophenes
  • Thymine Nucleotides
  • ZM 260384
  • Foscarnet
  • Zidovudine
  • zidovudine triphosphate
  • HIV Reverse Transcriptase
  • DNA-Directed DNA Polymerase
  • Ribonuclease H