Inhibitory Effect of Carboxylic Acid Group on hERG Binding

Bioorg Med Chem Lett. 2006 Nov 1;16(21):5507-12. doi: 10.1016/j.bmcl.2006.08.039. Epub 2006 Aug 22.


Drug-induced QT prolongation arising from drugs' blocking of hERG channel activity presents significant challenges in drug development. Many, but not all, of our benzamidine-containing factor Xa inhibitors were found to have high hERG binding propensity. However, incorporation of a carboxylic acid group into these benzamidine molecules generally leads to hERG inactive compounds regardless where the carboxyl group is tethered within the molecules. The inhibitory effect of a carboxylic acid group on hERG binding has also been observed in many series of diverse structural scaffolds (including non-amidines). These findings suggest that the negatively charged carboxylate group causes unfavorable interaction within hERG channel binding cavity by electrostatic interaction.

MeSH terms

  • Benzamidines / metabolism*
  • Carboxylic Acids / metabolism*
  • Ether-A-Go-Go Potassium Channels / antagonists & inhibitors*
  • Ether-A-Go-Go Potassium Channels / metabolism*
  • Factor Xa Inhibitors
  • Humans


  • Benzamidines
  • Carboxylic Acids
  • Ether-A-Go-Go Potassium Channels
  • Factor Xa Inhibitors
  • benzamidine