Insights into the Mechanism of Binding of Arachidonic Acid to Mammalian 15-Lipoxygenases

Abstract

Mammalian 15-lipoxygenases (15-LOs) are key pharmaceutical targets under strong investigation because of their implication in atherosclerosis and cancer. Here, we present an atomic-level study of the binding modes of arachidonic acid (AA) to rabbit reticulocyte 15-LO, with a particular insight into the 15-LO:AA complexes consistent with known catalytic activity. We take into account both ligand and protein flexibility, by combining protein-ligand docking techniques and molecular dynamics simulations. We have also performed in silico mutagenesis. Our results are in agreement with previous mutagenesis data, in particular with the importance of Arg403 on AA binding. Interestingly, our results also reveal a central role of Arg403 in the conformational change of the alpha2-helix observed upon ligand binding. That induced-fit effect could give a possible framework for the molecular explanation of the known allosteric effect and questions the suitability of the inhibitor-bound crystal structure for accepting AA. Accounting for these dynamical considerations might improve the drug design process.

Probing Dimerization and Structural Flexibility of Mammalian Lipoxygenases by Small-Angle X-ray Scattering

“…12 In contrast, such interdomain movement was not observed for s-LOX1. 9 (iii) Alternative molecular conformation: employing proteinligand docking techniques and molecular dynamics simulations, we have reevaluated the original X-ray coordinates for the r-12/15LOX-inhibitor complex, and the results suggested that the enzyme undergoes conformational changes upon ligand binding, 16 as reported by Choi et al…”

Structure of a Calcium-dependent 11R-Lipoxygenase Suggests a Mechanism for Ca2+ Regulation

“…Also, a cationic arginine near the entrance of the cavity has been shown to stabilize the carboxylate head of the fatty acid (13). Computational docking studies based on x-ray crystallography data further support the boot-shaped substrate channel (14,15). For some LOXs, carboxylate head-first binding has been suggested to explain differing specificity or double dioxygenation of AA (16,17).…”

“…First, the same orifice is used in rabbit 15S-LOX according to docking studies (14). For 11R-and 15S-specificity, the same hydrogen must be abstracted in the initial step of catalysis; thus, substrate binding should also be identical.…”

Catalytic Multiplicity of 15-Lipoxygenase-1 Orthologs (ALOX15) of Different Species

“…In contrast, arachidonic acid is preferred by the 12-lipoxygenating Ile410Ala mutant (15-H(p)ETE/13H(p)ODE ratio of 79:21). According to MD simulations [120,131] linoleic acid and arachidonic acid share a common overall orientation at the active site. However, arachidonic acid is bound closer to the active site helix α18 and has a limited degree of motional freedom.…”

“…However, arachidonic acid is bound closer to the active site helix α18 and has a limited degree of motional freedom. The tail of linoleic acid fluctuates more freely and adopts a number of energetically similar conformations at the active site [120,131].…”