The pharmacophore hypotheses of I(Kr) potassium channel blockers: novel class III antiarrhythmic agents

Bioorg Med Chem Lett. 2004 Sep 20;14(18):4771-7. doi: 10.1016/j.bmcl.2004.06.070.


Predictive pharmacophore models were developed for a large series of I(Kr) potassium channel blockers as class III antiarrhythmic agents using HypoGen in Catalyst software. The pharmacophore hypotheses were generated using a training set consisting of 34 compounds carefully selected from documents. Their biological data, expressed as IC(50), spanned from 1.5 nM to 2.8 mM with 7 orders difference. The most predictive hypothesis (Hypo1), consisting of four features (one positive ionizable feature, two aromatic rings and one hydrophobic group), had a best correlation coefficient of 0.825, a lowest rms deviation of 1.612, and a highest cost difference (null cost-total cost) of 77.552, which represents a true correlation and a good predictivity. The hypothesis Hypo1 was then validated by a test set consisting of 21 compounds and by a cross-validation of 95% confidence level with randomizing the data using CatScramble program. Accordingly, our model has strong predictivity to identify structural diverse I(Kr) potassium channel blockers with desired biological activity by virtual screening

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Arrhythmia Agents / chemical synthesis
  • Anti-Arrhythmia Agents / chemistry*
  • Anti-Arrhythmia Agents / classification
  • Models, Biological
  • Models, Molecular
  • Potassium Channel Blockers / chemical synthesis
  • Potassium Channel Blockers / chemistry*
  • Potassium Channels / chemistry
  • Quantitative Structure-Activity Relationship
  • Technology, Pharmaceutical / methods


  • Anti-Arrhythmia Agents
  • Potassium Channel Blockers
  • Potassium Channels