Binding conformers searching method for ligands according to the structures of their receptors and its application to thrombin inhibitors
Abstract
AIM: To develop a method of finding binding conformers for ligands according to
the three-dimensional structures of their receptors.
METHODS: Combining the systematic search method of ligand with the molecular
docking approach of ligand fitting into its receptor, we developed a binding
conformer searching method for ligands.
RESULTS: The binding conformers of phosphonopeptidyl thrombin inhibitors were
recognized. The binding (interaction) energies between these inhibitors and
thrombin were calculated with molecular mechanical method.
CONCLUSION: Both of the total binding energies and steric binding energies have
good correlations with the inhibitory activities of these thrombin inhibitors,
demonstrating that our approach is reasonable. It can also be used to explain the
inhibition mechanism of thrombin interacting with these inhibitors.
Keywords:
the three-dimensional structures of their receptors.
METHODS: Combining the systematic search method of ligand with the molecular
docking approach of ligand fitting into its receptor, we developed a binding
conformer searching method for ligands.
RESULTS: The binding conformers of phosphonopeptidyl thrombin inhibitors were
recognized. The binding (interaction) energies between these inhibitors and
thrombin were calculated with molecular mechanical method.
CONCLUSION: Both of the total binding energies and steric binding energies have
good correlations with the inhibitory activities of these thrombin inhibitors,
demonstrating that our approach is reasonable. It can also be used to explain the
inhibition mechanism of thrombin interacting with these inhibitors.