Docking experiments showing similar recognition patterns of paclitaxel when interacting with different macromolecular targets.
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.
D000972:Antineoplastic Agents, Phytogenic / Q000737:chemistry*; D003460:Crystallization; D003505:Cyclodextrins / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D017239:Paclitaxel / Q000737:chemistry*; D011108:Polymers / Q000737:chemistry; D011485:Protein Binding; D014404:Tubulin / Q000737:chemistry; D047392:beta-Cyclodextrins
D000972:Antineoplastic Agents, Phytogenic; D003505:Cyclodextrins; D011108:Polymers; D014404:Tubulin; D047392:beta-Cyclodextrins; D004247:DNA; C031215:betadex; D017239:Paclitaxel