Correlation of docking energies with spectroscopic kinetic assays of potential xanthine oxidase substrates

Amy L Stockert,Tarek M Mahfouz,Brad Petersen,Oluwaseun L Fakunmoju

doi:10.4236/jbpc.2013.41003

Abstract

Here we present a docking model that ranks compounds according to their potential effectiveness as a potential substrate or inhibitor. We utilize xanthine oxidase (XO), a multi-cofactor oxido-reductase which converts hypoxanthine to xanthine and xanthine to uric acid. During the reductive half reaction, electrons flow from the molybdopterin, to each of two Fe/S centers, and finally to FAD. During the oxidative half reaction, electrons are passed from the FAD to O2. Under ideal physiological conditions, this reduction of oxygen generates H2O2 and, under multiple turnover conditions, superoxide in amounts which is regulated by catalase and superoxide dismutase. Utilizing computer modeling predictions of the docking orientations and energies of a group of purine based structures was selected. Correlating computer estimations with steady state kinetic data, a rapid screening process for inhibittor prediction was highlighted. This method allows educated selection of likely inhibitors, thereby decreasing the time and supplies required to complete a traditional kinetic analysis screening. Results demonstrate the functionality and reliability of this method and have proven particularly useful in understanding binding orienttations or poses of each compound.

Highlights

Docking is a method which predicts the preferred orientation of one molecule to a second molecule
In the neutral form, a hydrogen bond is preferred between the carboxylic acid group and the molybdopterin oxygen allowing the substituted group to have a greater interaction with the active moiety
In the ionized form, the hydrogen bond is formed between triazole nitrogen and the molybdopterin oxygen, which changed the orientation of the inhibitor so that it was opposite the neutralized form in the active site

Summary

Introduction

Docking is a method which predicts the preferred orientation of one molecule to a second molecule. It is a useful method of identifying different modes of binding for an inhibitor in an enzyme active site. One can identify which binding mode is more favorable and the results can be used to find inhibitors for target proteins and to design new drugs. We use Glide® (Grid-base Ligand Docking with Energetics) program to generate ligand poses to search for possible locations of ligand molecules in the active-site region of the receptor. Our goal was to develop a more effective and high throughput method of ranking compounds according to potential function as inhibitors to the enzyme. The similarities between bovine xanthine oxidase and human xanthine oxidase make the bovine enzyme an appropriate medical target [1,2,3,4,5,6,7,8,9]

Objectives

Methods

Results

Conclusion