Docking experiments showing similar recognition patterns of paclitaxel when interacting with different macromolecular...

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 beta-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.