5-(Hydroxymethyl)-2-furfural: a selective inhibitor of DNA polymerase lambda and terminal deoxynucleotidyltransferase

Arch Biochem Biophys. 2006 Feb 1;446(1):69-76. doi: 10.1016/j.abb.2005.11.015. Epub 2005 Dec 15.


5-(Hydroxymethyl)-2-furfural (HMF), a pyrolysate of carbohydrate isolated from instant coffee (Coffea arabica L.), selectively inhibits the activities of mammalian DNA polymerase lambda (pol lambda) and terminal deoxynucleotidyltransferase (TdT) which are family X pols, in vitro. The compound influenced neither the activities of replicative DNA polymerases such as alpha, delta, and epsilon, nor even the activity of pol beta which is from the same family and thought to have a very similar three-dimensional structure to the pol beta-like region of pol lambda. Since parts of HMF such as furan, furfuryl alcohol, and 2-furaldehyde did not influence the activities of any enzymes tested, the substituted form of furan with a hyroxymethyl group and a formyl group might be important for the inhibition of pol lambda and TdT. The inhibitory effect of HMF on intact pol lambda (i.e., residues 1-575), a truncated pol lambda lacking the N-terminal BRCA1 C-terminus domain (133-575, del-1 pol lambda) and another truncated pol lambda lacking the N-terminal proline-rich region (245-575, del-2 pol lambda) was dose-dependent, and 50% inhibition was observed at a concentration of 26.1, 10.3, and 4.6 microM, respectively. The IC(50) value of HMF for TdT was the same as that for del-2 pol lambda (5.5 microM). The HMF-induced inhibition of both pol lambda and TdT activities was competitive with respect to both the DNA template-primer and the dNTP substrate. On the basis of these results, HMF was suggested to bind to the pol beta-like region of pol lambda and TdT.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Cattle
  • DNA Nucleotidylexotransferase / antagonists & inhibitors*
  • DNA Nucleotidylexotransferase / metabolism
  • DNA Polymerase beta / antagonists & inhibitors*
  • DNA Polymerase beta / metabolism
  • DNA-Directed DNA Polymerase / metabolism
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology*
  • Furaldehyde / analogs & derivatives*
  • Furaldehyde / chemistry
  • Furaldehyde / pharmacology
  • Nucleic Acid Synthesis Inhibitors
  • Substrate Specificity
  • Templates, Genetic


  • Enzyme Inhibitors
  • Nucleic Acid Synthesis Inhibitors
  • 5-hydroxymethylfurfural
  • Furaldehyde
  • DNA polymerase beta2
  • DNA Nucleotidylexotransferase
  • DNA Polymerase beta
  • DNA-Directed DNA Polymerase