Abstract
We investigated the binding mode of a set of dihydropyridine calcium channel antagonists to a synthetic Ca 2+ channel peptide with a force field computational procedure. Different conformers of each ligand were docked into the synthetic channel peptide to take into account that the ligand conformation at the receptor site may not correspond to the most stable one of the isolated molecule. In the docking procedure the molecular structure of the Ca 2+ channel was kept rigid while the ligands were assumed to be flexible. The ranking of the computed interaction energies correlated with the biological activity data (expressed as the IC 50 values for the blockage of Ca 2+ induced contraction of K + depolarized rat aorta). The computational procedure also discriminated between the S and R enantiomers of the ligand amlodipine, predicting a stronger interaction of the former with the Ca 2+ channel model.
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