1. An automated docking protocol for hERG channel blockers.
- Author
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Di Martino GP, Masetti M, Ceccarini L, Cavalli A, and Recanatini M
- Subjects
- Automation, ERG1 Potassium Channel, Ether-A-Go-Go Potassium Channels chemistry, Humans, Potassium Channel Blockers chemistry, Protein Conformation, Solvents chemistry, Structure-Activity Relationship, Thermodynamics, Ether-A-Go-Go Potassium Channels antagonists & inhibitors, Ether-A-Go-Go Potassium Channels metabolism, Molecular Docking Simulation methods, Potassium Channel Blockers metabolism, Potassium Channel Blockers pharmacology
- Abstract
A docking protocol aimed at obtaining a consistent qualitative and quantitative picture of binding for a series of hERG channel blockers is presented. To overcome the limitations experienced by standard procedures when docking blockers at hERG binding site, we designed a strategy that explicitly takes into account the conformations of the channel, their possible intrinsic symmetry, and the role played by the configurational entropy of ligands. The protocol was developed on a series of congeneric sertindole derivatives, allowing us to satisfactorily explain the structure-activity relationships for this set of blockers. In addition, we show that the performance of structure-based models relying on multiple-receptor conformations statistically increases when the protein conformations are chosen in such a way as to capture relevant structural features at the binding site. The protocol was then successfully applied to a series of structurally unrelated blockers.
- Published
- 2013
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