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Chem Biol Drug Des. 2008 Nov;72(5):360-9. doi: 10.1111/j.1747-0285.2008.00716.x.

Docking and quantitative structure-activity relationship studies for the bisphenylbenzimidazole family of non-nucleoside inhibitors of HIV-1 reverse transcriptase.

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Centre for Bioinformatics CBUC, Faculty of Biological Sciences, Pontificia Universidad Catolica de Chile, Portugal 49-Zocalo, Santiago 6513492, Chile.


Molecular docking studies on a set of bisphenylbenzimidazole derivatives were conducted to identify the compounds binding orientations within the HIV-1 reverse transcriptase non-nucleoside binding pocket. A good correlation between the calculated binding free energies and the experimental inhibitory activities suggests that the identified binding conformations of these inhibitors are reliable. Based on obtained bisphenylbenzimidazoles binding conformations, a predictive quantitative structure-activity relationship model based on radial distribution function descriptors was developed. The obtained quantitative structure-activity relationship model was predictive according to internal and external validation experiments and might provide guidelines for the design of novel non-nucleoside HIV-1 reverse transcriptase inhibitors based on the 1-benzyl-2-arylbenzimidazole scaffold.

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