Theoretical and Computational Chemistry

Computational Characterization of the Inhibition Mechanism of Xanthine Oxidoreductase by Topiroxostat



Xanthine oxidase (XO) is a member of the molybdopterin-containing enzyme family. It interconverts xanthine to uric acid as the last step of purine catabolism in the human body. The high uric acid concentration in the blood directly leads to human diseases like gout and hyperuricemia. Therefore, drugs that inhibit the biosynthesis of uric acid by human XO have been clinically used for many years to decrease the concentration of uric acid in the blood. In this study, the inhibition mechanism of XO and a new promising drug, Topiroxostat (code: FYX-051), is investigated by employing molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. This drug has been reported to act as both a non-covalent and covalent inhibitor and undergoes a stepwise inhibition by all its hydroxylated metabolites, which include 2-hydroxy-FYX-051, dihydroxy-FYX-051, and trihydroxy-FYX-051. However, the detailed mechanism of inhibition of each metabolite remains elusive and can be useful for designing more effective drugs with similar inhibition functions. Hence, herein we present the computational investigation of the structural and dynamical effects of FYX-051 and the calculated reaction mechanism for all the oxidation steps catalyzed by the molybdopterin center in the active site. Calculated results for the proposed reaction mechanisms for each metabolite’s inhibition reaction in the enzyme’s active site, binding affinities, and the non-covalent interactions with surrounding amino acid residues are consistent with previously reported experimental findings. Analysis of the non-covalent interactions via EDA and NCI suggests residues L648, K771, E802, R839, L873, R880, R912, F914, F1009, L1014, and A1079 can be used as key interacting residues for further hybrid-type inhibitor development.


Thumbnail image of XO-manuscript.pdf

Supplementary material

Thumbnail image of XO-SI.pdf
Supporting Information
Detailed results of the Structural Analysis, Clustering Analysis, Binding Affinities, Relative QM/MM Energies for Consecutive Minima, Electron Localization Functions (ELF), Non-Covalent Interactions (NCI), and Energy Decomposition Analysis (EDA)