Molecular simulations enlighten the binding mode of quercetin to lipoxygenase-3

Molecular docking and dynamic simulation studies of isoflavones inhibiting Lox-2 activity for reducing beany flavor in soybean seeds

Low-lipoxygenase soybean cultivars are highly desirable because lower lipoxygenase content in soybean seeds leads to better quality soybean-based products and oils that are free from off-flavor or beany flavor. The expression of the Lox-2 gene is mainly responsible for this flavor. Over the years, natural antioxidants have been tested biochemically to inhibit Lox-2 activity, but in-silico studies are still lacking. To investigate the structural basis of inhibition, site-specific docking, as well as molecular dynamics (MD) simulations, were performed. Molecular docking analysis revealed that daidzein and genistein could be effective Lox2 receptor inhibitors. Furthermore, docked complexes were subjected to 100 ns MD simulation studies to analyze the structural conformations and stability of the complex. The analysis demonstrated that daidzein formed a more stable complex with the Lox-2 receptor and showed a higher H-bond propensity with the Asp775 residue. We discovered that the initial conformation of Lox2-daidzein complex changed to a more stable conformation at the beginning of the MD simulation and remained stable until the end with minor fluctuations. Furthermore, our analysis suggested that daidzein acts as a potential Lox-2 inhibitor and is a better candidate compared to genistein, which could be used to solve the beany flavor problem in soybean.Communicated by Ramaswamy H. Sarma.

Inhibition of lipoxygenase by sesamol corroborates its potential anti-inflammatory activity

Reactive oxygen species, the byproducts of oxygenases reaction, when in excess, promote degenerative diseases like cardiovascular, cancer and arthritis. Sesame lignans- sesamin, sesamolin and the phenolic degradation product of sesamolin, sesamol, are empirically known for their health promoting properties like antioxidant, antimutagenic, antiaging and antiinflammatory activities. In the current study, the effect of sesamol on the inflammatory oxygenase - lipoxygenase (LOX) was investigated. Enzyme kinetics and spectroscopic techniques were used to understand the inhibition mechanism. Sesamol was a potent inhibitor of soy LOX-1. It inhibited soy LOX-1 in a dose dependent manner with IC50 value of 51.84μM and Ki of 4.9μM. Binding studies using circular dichroism and corroborated by surface plasmon resonance, revealed that sesamol does not bind or change the conformation of LOX. Further, sesamol prevented the conversion of inactive LOX (Fe2+) to active LOX (Fe3+) by arresting the oxidation state of iron and prolonging the lag phase by virtue of its ability to scavenge hydroperoxides. Understanding the mechanism of action of such molecules will help in their application and promotion as nutraceuticals.

Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations

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Structural model of rhamnosidase Ram2 of Pediococcus acidilactici.

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Calculated binding free energies of rutinose and p-NPR agree with experiments.

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Suggested binding poses of rutinose and p-NPR are distinctly different.

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Different binding poses of rutinose and p-NPR are supported by experiments.

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Active site residues are proposed for further mutagenesis studies

Ram2 from Pediococcus acidilactici is a rhamnosidase from the glycoside hydrolase family 78. It shows remarkable selectivity for rutinose rather than para-nitrophenyl-alpha-l-rhamnopyranoside (p-NPR). Molecular dynamics simulations were performed using a homology model of this enzyme, in complex with both substrates. Free energy calculations lead to predicted binding affinities of −34.4 and −30.6 kJ mol⁻¹ respectively, agreeing well with an experimentally estimated relative free energy of 5.4 kJ mol⁻¹. Further, the most relevant binding poses could be determined. While p-NPR preferably orients its rhamnose moiety toward the active site, rutinose interacts most strongly with its glucose moiety. A detailed hydrogen bond analysis confirms previously implicated residues in the active site (Asp217, Asp222, Trp226, Asp229 and Glu488) and quantifies the importance of individual residues for the binding. The most important amino acids are Asp229 and Phe339 which are involved in many interactions during the simulations. While Phe339 was observed in more simulations, Asp229 was involved in more persistent interactions (forming an average of at least 2 hydrogen bonds during the simulation). These analyses directly suggest mutations that could be used in a further experimental characterization of the enzyme. This study shows once more the strength of computer simulations to rationalize and guide experiments at an atomic level.

Binding of arachidonic acid and two flavonoid inhibitors to human 12- and 15-lipoxygenases: a steered molecular dynamics study

The lipoxygenases (LOX) are a family of non-heme iron-containing dioxygenases which catalyze the stereospecific insertion of molecular oxygen into arachidonic acid, leading to hydroxy derivatives as end products. In this work, we docked arachidonic acid and two of its competitive inhibitors, flavonoids baicalein and quercetin, into the binding pockets of human 12- and 15-lipoxygenase. Steered molecular dynamics (SMD) simulations were employed to study the unbinding processes of the substrate and inhibitors from the two isoforms.