Structural and inhibition studies of the RNase H function of xenotropic murine leukemia virus-related virus reverse transcriptase

Antimicrob Agents Chemother. 2012 Apr;56(4):2048-61. doi: 10.1128/AAC.06000-11. Epub 2012 Jan 17.


RNase H inhibitors (RNHIs) have gained attention as potential HIV-1 therapeutics. Although several RNHIs have been studied in the context of HIV-1 reverse transcriptase (RT) RNase H, there is no information on inhibitors that might affect the RNase H activity of other RTs. We performed biochemical, virological, crystallographic, and molecular modeling studies to compare the RNase H function and inhibition profiles of the gammaretroviral xenotropic murine leukemia virus-related virus (XMRV) and Moloney murine leukemia virus (MoMLV) RTs to those of HIV-1 RT. The RNase H activity of XMRV RT is significantly lower than that of HIV-1 RT and comparable to that of MoMLV RT. XMRV and MoMLV, but not HIV-1 RT, had optimal RNase H activities in the presence of Mn²⁺ and not Mg²⁺. Using hydroxyl-radical footprinting assays, we demonstrated that the distance between the polymerase and RNase H domains in the MoMLV and XMRV RTs is longer than that in the HIV-1 RT by ∼3.4 Å. We identified one naphthyridinone and one hydroxyisoquinolinedione as potent inhibitors of HIV-1 and XMRV RT RNases H with 50% inhibitory concentrations ranging from ∼0.8 to 0.02 μM. Two acylhydrazones effective against HIV-1 RT RNase H were less potent against the XMRV enzyme. We also solved the crystal structure of an XMRV RNase H fragment at high resolution (1.5 Å) and determined the molecular details of the XMRV RNase H active site, thus providing a framework that would be useful for the design of antivirals that target RNase H.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Anti-HIV Agents / pharmacology*
  • Cell Survival / drug effects
  • Crystallography, X-Ray
  • DNA Footprinting
  • HIV Reverse Transcriptase / antagonists & inhibitors
  • Hydrazones / chemical synthesis
  • Hydrazones / pharmacology
  • Indicators and Reagents
  • Isoquinolines / chemical synthesis
  • Isoquinolines / pharmacology
  • Magnesium / pharmacology
  • Manganese / pharmacology
  • Microbial Sensitivity Tests
  • Models, Molecular
  • Molecular Sequence Data
  • Moloney murine leukemia virus / drug effects
  • Moloney murine leukemia virus / enzymology
  • Naphthyridines / chemical synthesis
  • Naphthyridines / pharmacology
  • Plasmids / genetics
  • RNA-Directed DNA Polymerase / chemistry*
  • Reverse Transcriptase Inhibitors / pharmacology*
  • Ribonuclease H / antagonists & inhibitors*
  • Ribonuclease H / chemistry*
  • Ribonuclease H / physiology*
  • Xenotropic murine leukemia virus-related virus / enzymology*


  • Anti-HIV Agents
  • Hydrazones
  • Indicators and Reagents
  • Isoquinolines
  • Naphthyridines
  • Reverse Transcriptase Inhibitors
  • Manganese
  • HIV Reverse Transcriptase
  • RNA-Directed DNA Polymerase
  • Ribonuclease H
  • Magnesium