Vinylogous ureas as a novel class of inhibitors of reverse transcriptase-associated ribonuclease H activity

ACS Chem Biol. 2008 Oct 17;3(10):635-44. doi: 10.1021/cb8001039. Epub 2008 Oct 3.

Abstract

High-throughput screening of National Cancer Institute libraries of synthetic and natural compounds identified the vinylogous ureas 2-amino-5,6,7,8-tetrahydro-4 H-cyclohepta[ b]thiophene-3-carboxamide (NSC727447) and N-[3-(aminocarbonyl)-4,5-dimethyl-2-thienyl]-2-furancarboxamide (NSC727448) as inhibitors of the ribonuclease H (RNase H) activity of HIV-1 and HIV-2 reverse transcriptase (RT). A Yonetani-Theorell analysis demonstrated that NSC727447, and the active-site hydroxytropolone RNase H inhibitor beta-thujaplicinol were mutually exclusive in their interaction with the RNase H domain. Mass spectrometric protein footprinting of the NSC727447 binding site indicated that residues Cys280 and Lys281 in helix I of the thumb subdomain of p51 were affected by ligand binding. Although DNA polymerase and pyrophosphorolysis activities of HIV-1 RT were less sensitive to inhibition by NSC727447, protein footprinting indicated that NSC727447 occupied the equivalent region of the p66 thumb. Site-directed mutagenesis using reconstituted p66/p51 heterodimers substituted with natural or non-natural amino acids indicates that altering the p66 RNase H primer grip significantly affects inhibitor sensitivity. NSC727447 thus represents a novel class of RNase H antagonists with a mechanism of action differing from active site, divalent metal-chelating inhibitors that have been reported.

Publication types

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

MeSH terms

  • Binding Sites
  • Combinatorial Chemistry Techniques
  • Furans / chemistry
  • Furans / pharmacology*
  • HIV Reverse Transcriptase / antagonists & inhibitors*
  • HIV Reverse Transcriptase / chemistry
  • Humans
  • Reverse Transcriptase Inhibitors / chemistry
  • Reverse Transcriptase Inhibitors / pharmacology*
  • Ribonuclease H, Human Immunodeficiency Virus / antagonists & inhibitors*
  • Ribonuclease H, Human Immunodeficiency Virus / chemistry
  • Thiophenes / chemistry
  • Thiophenes / pharmacology*
  • Urea / analogs & derivatives*

Substances

  • Furans
  • NSC 727447
  • NSC 727448
  • Reverse Transcriptase Inhibitors
  • Thiophenes
  • Urea
  • reverse transcriptase, Human immunodeficiency virus 1
  • reverse transcriptase, Human immunodeficiency virus 2
  • HIV Reverse Transcriptase
  • Ribonuclease H, Human Immunodeficiency Virus