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

Stefano Alcaro·Danilo Battaglia·Francesco Ortuso
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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 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.

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Antineoplastic Agents, PhytogenicCrystallizationCyclodextrinsDNAModels, MolecularMolecular ConformationPaclitaxelPolymersProtein BindingTubulinbeta-CyclodextrinsComparative StudyJournal ArticleResearch Support, Non-U.S. Gov't

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Stefano Alcaro, Danilo Battaglia, Francesco Ortuso. 2003. Docking experiments showing similar recognition patterns of paclitaxel when interacting with different macromolecular targets.. https://doi.org/10.1016/s0014-827x(03)00108-3

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