Removal of human ether-à-go-go related gene (hERG) K+ channel affinity through rigidity: a case of clofilium analogues

J Med Chem. 2013 Dec 12;56(23):9427-40. doi: 10.1021/jm4010434. Epub 2013 Nov 25.


Cardiotoxicity is a side effect that plagues modern drug design and is very often due to the off-target blockade of the human ether-à-go-go related gene (hERG) potassium channel. To better understand the structural determinants of this blockade, we designed and synthesized a series of 40 derivatives of clofilium, a class III antiarrhythmic agent. These were evaluated in radioligand binding and patch-clamp assays to establish structure-affinity relationships (SAR) for this potassium channel. Efforts were especially focused on studying the influence of the structural rigidity and the nature of the linkers composing the clofilium scaffold. It was shown that introducing triple bonds and oxygen atoms in the n-butyl linker of the molecule greatly reduced affinity without significantly modifying the pKa of the essential basic nitrogen. These findings could prove useful in the first stages of drug discovery as a systematic way of reducing the risk of hERG K(+) channel blockade-induced cardiotoxicity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Arrhythmia Agents / chemistry*
  • Ether-A-Go-Go Potassium Channels / drug effects*
  • Ether-A-Go-Go Potassium Channels / metabolism
  • HEK293 Cells
  • Humans
  • Molecular Docking Simulation
  • Patch-Clamp Techniques
  • Potassium Channel Blockers / chemistry
  • Quaternary Ammonium Compounds / chemical synthesis*
  • Quaternary Ammonium Compounds / chemistry
  • Quaternary Ammonium Compounds / metabolism*
  • Structure-Activity Relationship


  • Anti-Arrhythmia Agents
  • Ether-A-Go-Go Potassium Channels
  • Potassium Channel Blockers
  • Quaternary Ammonium Compounds
  • clofilium