Using the Protein Data Bank crystallographic model of paclitaxel with tubulin as reference, a comparative interaction study of the antitumor drug with known macromolecular targets such as β-cyclodextrin and Dickerson's DNA dodecamer was carried out by molecular modeling techniques. AMBER* united atoms was found to be the most appropriate force field for our study. Conformational search of paclitaxel was performed using a water environment. A large set of conformers was selected for automatic "quasi-flexible" docking calculations performed by the "in-house" software MOLINE. A proper docking protocol was based on a crystallographic model and validated by a remarkable low atomic coordinate deviation. Using this method, a similar pattern via benzamide interaction was established for molecular recognition of paclitaxel cyclodextrin and DNA. The results are supported by our previous observations and other author's experimental data
Docking experiments showing similar recognition patterns of paclitaxel when interacting with different macromolecular targets
ORTUSO F;ALCARO S
2003-01-01
Abstract
Using the Protein Data Bank crystallographic model of paclitaxel with tubulin as reference, a comparative interaction study of the antitumor drug with known macromolecular targets such as β-cyclodextrin and Dickerson's DNA dodecamer was carried out by molecular modeling techniques. AMBER* united atoms was found to be the most appropriate force field for our study. Conformational search of paclitaxel was performed using a water environment. A large set of conformers was selected for automatic "quasi-flexible" docking calculations performed by the "in-house" software MOLINE. A proper docking protocol was based on a crystallographic model and validated by a remarkable low atomic coordinate deviation. Using this method, a similar pattern via benzamide interaction was established for molecular recognition of paclitaxel cyclodextrin and DNA. The results are supported by our previous observations and other author's experimental dataI documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.