A model for identifying HERG K+ channel blockers

Acquired long QT syndrome (LQTS) occurs frequently as a side effect of blockade of cardiac HERG K+ channels by commonly used medications. A large number of structurally diverse compounds have been shown to inhibit K+ current through HERG. There is considerable interest in developing in silico tools to filter out potential HERG blockers early in the drug discovery process. We describe a binary classification model that combines a 21) topological similarity filter with a 3D pharmacophore ensemble procedure to discriminate between HERG actives and inactives with an overall accuracy of 82%, with false negative and false positive rates of 29% and 15%, respectively. This model should be generally applicable in virtual library counterscreening against HERG. (C) 2004 Elsevier Ltd. All rights reserved.