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J Mol Graph Model. 2008 Sep;27(2):217-24. doi: 10.1016/j.jmgm.2008.04.008. Epub 2008 Apr 29.

Molecular recognition of docosahexaenoic acid by peroxisome proliferator-activated receptors and retinoid-X receptor alpha.

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Department of Pharmacology, Faculty of Medicine, Institute of Medical Biology, University of Tromsø, Tromsø, Norway.


The family of peroxisome proliferator-activated receptors (PPARs) is the molecular target of synthetic antidiabetic and hypolipidemic drugs. The side effects of these drugs are limiting their use in patients with high lipid levels. Natural compounds, like Docosahexaenoic acid (DHA) from fish oil, have beneficial effects in the treatment of metabolic diseases, and several DHA derivatives are known to activate PPAR genes. Experimental studies on affinities of DHA and its derivatives for PPARs are not available. In the present study we are therefore using computational docking, molecular dynamics simulation, and several scoring programs to predict affinities and binding modes of DHA for PPARs and retinoid-X receptor alpha, which is the DNA binding partner of PPARs. The calculations indicated that DHA binds to PPARs and the retinoid-X receptor alpha with high affinity, and that different PPARs exhibited different structural effects on the first four carbons atoms of DHA. Our data indicate that the beneficial health effects of DHA may be obtained by high affinity binding to the PPARs.

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