New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies

Bioorg Med Chem. 2006 May 1;14(9):3160-73. doi: 10.1016/j.bmc.2005.12.032. Epub 2006 Jan 18.


We created a homology model of the homo-tetrameric pore domain of HERG using the crystal structure of the bacterial potassium channel, KvAP, as a template. We docked a set of known blockers with well-characterized effects on channel function into the lumen of the pore between the selectivity filter and extracellular entrance using a novel docking and refinement procedure incorporating Glide and Prime. Key aromatic groups of the blockers are predicted to form multiple simultaneous ring stacking and hydrophobic interactions among the eight aromatic residues lining the pore. Furthermore, each blocker can achieve these interactions via multiple docking configurations. To further interpret the docking results, we mapped hydrophobic and hydrophilic potentials within the lumen of each refined docked complex. Hydrophilic iso-potential contours define a 'propeller-shaped' volume at the selectivity filter entrance. Hydrophobic contours define a hollow 'crown-shaped' volume located above the 'propeller', whose hydrophobic 'rim' extends along the pore axis between Tyr652 and Phe656. Blockers adopt conformations/binding orientations that closely mimic the shapes and properties of these contours. Blocker basic groups are localized in the hydrophilic 'propeller', forming electrostatic interactions with Ser624 rather than a generally accepted pi-cation interaction with Tyr652. Terfenadine, cisapride, sertindole, ibutilide, and clofilium adopt similar docked poses, in which their N-substituents bridge radially across the hollow interior of the 'crown' (analogous to the hub and spokes of a wheel), and project aromatic/hydrophobic portions into the hydrophobic 'rim'. MK-499 docks with its longitudinal axis parallel to the axis of the pore and 'crown', and its hydrophobic groups buried within the hydrophobic 'rim'.

MeSH terms

  • Conserved Sequence
  • Ether-A-Go-Go Potassium Channels / antagonists & inhibitors*
  • Ether-A-Go-Go Potassium Channels / metabolism*
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Molecular Sequence Data
  • Potassium Channel Blockers / chemistry*
  • Protein Structure, Quaternary
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Structural Homology, Protein


  • Ether-A-Go-Go Potassium Channels
  • Potassium Channel Blockers