Open Access Research article

Rehabilitating drug-induced long-QT promoters: In-silico design of hERG-neutral cisapride analogues with retained pharmacological activity

Serdar Durdagi12*, Trevor Randall1, Henry J Duff3, Adam Chamberlin1 and Sergei Y Noskov14*

Author Affiliations

1 Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada

2 Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey

3 Libin Cardiovascular Institute of Alberta, Department of Cardiac Sciences, University of Calgary, Calgary, Canada

4 Center for Molecular Simulations, Department of Biological Sciences, BI-447, University of Calgary, 2500 University Drive, NW, Calgary T3A2T3, Canada

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BMC Pharmacology and Toxicology 2014, 15:14  doi:10.1186/2050-6511-15-14

Published: 8 March 2014



The human ether-a-go-go related gene 1 (hERG1), which codes for a potassium ion channel, is a key element in the cardiac delayed rectified potassium current, IKr, and plays an important role in the normal repolarization of the heart’s action potential. Many approved drugs have been withdrawn from the market due to their prolongation of the QT interval. Most of these drugs have high potencies for their principal targets and are often irreplaceable, thus “rehabilitation” studies for decreasing their high hERG1 blocking affinities, while keeping them active at the binding sites of their targets, have been proposed to enable these drugs to re-enter the market.


In this proof-of-principle study, we focus on cisapride, a gastroprokinetic agent withdrawn from the market due to its high hERG1 blocking affinity. Here we tested an a priori strategy to predict a compound’s cardiotoxicity using de novo drug design with molecular docking and Molecular Dynamics (MD) simulations to generate a strategy for the rehabilitation of cisapride.


We focused on two key receptors, a target interaction with the (adenosine) receptor and an off-target interaction with hERG1 channels. An analysis of the fragment interactions of cisapride at human A2A adenosine receptors and hERG1 central cavities helped us to identify the key chemical groups responsible for the drug activity and hERG1 blockade. A set of cisapride derivatives with reduced cardiotoxicity was then proposed using an in-silico two-tier approach. This set was compared against a large dataset of commercially available cisapride analogs and derivatives.


An interaction decomposition of cisapride and cisapride derivatives allowed for the identification of key active scaffolds and functional groups that may be responsible for the unwanted blockade of hERG1.

hERG K channel; A2A adenosine receptor; 5HT-4 receptor; Molecular docking; Molecular dynamics simulations; Drug design; Drug databases