Interaction of HIV-1 reverse transcriptase ribonuclease H with an acylhydrazone inhibitor

Chem Biol Drug Des. 2011 Jan;77(1):39-47. doi: 10.1111/j.1747-0285.2010.01052.x. Epub 2010 Nov 29.


HIV-1 reverse transcriptase is a bifunctional enzyme, having both DNA polymerase (RNA- and DNA-dependent) and ribonuclease H activities. HIV-1 reverse transcriptase has been an exceptionally important target for antiretroviral therapeutic development, and nearly half of the current clinically used antiretrovirals target reverse transcriptase DNA polymerase. However, no inhibitors of reverse transcriptase ribonuclease H are on the market or in preclinical development. Several drug-like small molecule inhibitors of reverse transcriptase ribonuclease H have been described, but little structural information is available about the interactions between reverse transcriptase ribonuclease H and inhibitors that exhibit antiviral activity. In this report, we describe NMR studies of the interaction of a new ribonuclease H inhibitor, BHMP07, with a catalytically active HIV-1 reverse transcriptase ribonuclease H domain fragment. We carried out solution NMR experiments to identify the interaction interface of BHMP07 with the ribonuclease H domain fragment. Chemical shift changes of backbone amide signals at different BHMP07 concentrations clearly demonstrate that BHMP07 mainly recognizes the substrate handle region in the ribonuclease H fragment. Using ribonuclease H inhibition assays and reverse transcriptase mutants, the binding specificity of BHMP07 was compared with another inhibitor, dihydroxy benzoyl naphthyl hydrazone. Our results provide a structural characterization of the ribonuclease H inhibitor interaction and are likely to be useful for further improvements of the inhibitors.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Amino Acid Substitution / genetics*
  • Benzoates / chemical synthesis*
  • Benzoates / metabolism*
  • Benzoates / pharmacology
  • Binding Sites
  • HIV Infections / drug therapy
  • HIV Reverse Transcriptase* / antagonists & inhibitors
  • HIV Reverse Transcriptase* / genetics
  • HIV Reverse Transcriptase* / metabolism
  • HIV-1 / chemistry
  • HIV-1 / drug effects
  • HIV-1 / enzymology
  • Humans
  • Hydrazones / chemical synthesis*
  • Hydrazones / metabolism*
  • Hydrazones / pharmacology
  • Kinetics
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Structure, Tertiary
  • Reverse Transcriptase Inhibitors / chemical synthesis*
  • Reverse Transcriptase Inhibitors / metabolism*
  • Reverse Transcriptase Inhibitors / pharmacology
  • Ribonuclease H* / antagonists & inhibitors
  • Ribonuclease H* / genetics
  • Ribonuclease H* / metabolism


  • Benzoates
  • Hydrazones
  • Reverse Transcriptase Inhibitors
  • reverse transcriptase, Human immunodeficiency virus 1
  • HIV Reverse Transcriptase
  • Ribonuclease H