ArticleJournal of computer-aided molecular design2011
Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations.
Article in Journal of computer-aided molecular design, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Nano-(Q)SAR for Cytotoxicity Prediction of Engineered Nanomaterials.Molecules (Basel, Switzerland) · 2019Review
- The influence of the configuration of the (CJournal of molecular modeling · 2018Article
- Exploration of the binding affinities between ecdysone agonists and EcR/USP by docking and MM-PB/GBSA approaches.Journal of molecular modeling · 2017Article
- Exploring the drug resistance of V32I and M46L mutant HIV-1 protease to inhibitor TMC114: flap dynamics and binding mechanism.Journal of molecular graphics & modelling · 2015Article
- Molecular modeling in structural nano-toxicology: interactions of nano-particles with nano-machinery of cells.Advanced drug delivery reviews · 2013Review
- Binding of single walled carbon nanotube to WT and mutant HIV-1 proteases: analysis of flap dynamics and binding mechanism.Journal of molecular graphics & modelling · 2012Article
- Molecular simulation methods in drug discovery: a prospective outlook.Journal of computer-aided molecular design · 2012Article
- Advantages and limitations of classic and 3D QSAR approaches in nano-QSAR studies based on biological activity of fullerene derivatives.Journal of nanoparticle research : an interdisciplinary forum for nanoscale science and technologyArticle
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Authors and funding
6 authors.
Funding
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Abstract
The objectives of this study include the design of a series of novel fullerene-based inhibitors for HIV-1 protease (HIV-1 PR), by employing two strategies that can also be applied to the design of inhibitors for any other target. Additionally, the interactions which contribute to the observed exceptionally high binding free energies were analyzed. In particular, we investigated: (1) hydrogen bonding (H-bond) interactions between specific fullerene derivatives and the protease, (2) the regions of HIV-1 PR that play a significant role in binding, (3) protease changes upon binding and (4) various contributions to the binding free energy, in order to identify the most significant of them. This study has been performed by employing a docking technique, two 3D-QSAR models, molecular dynamics (MD) simulations and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. Our computed binding free energies are in satisfactory agreement with the experimental results. The suitability of specific fullerene derivatives as drug candidates was further enhanced, after ADMET (absorption, distribution, metabolism, excretion and toxicity) properties have been estimated to be promising. The outcomes of this study revealed important protein-ligand interaction patterns that may lead towards the development of novel, potent HIV-1 PR inhibitors.
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Registered trials
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