Using computational method to identify the binding site of 8R-lipoxygenase for arachidonic acid

Lipoxygenases (LOX) play important roles in the biosynthesis of biologically active eicosanoids form polyunsaturated fatty acids. An understanding of the structure basis of LOX familiy is critical for the development of LOX specific inhibitors. In this study, a computational method, Internal Coordinate Mechanics (ICM) was applied to find the binding site of 8R-LOX for its substrate, arachidonic acid (AA). The docking simulation shows that the C-10 of AA is positioned against Fe, which is in favor of the catalytic process of 8R-LOX. A potential binding site is defined. The purpose of this study is to identify the binding site using computational method. The result helps model how the arachidonic acid binds in the active site of LOX super family.