Computational Insights into the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol

Xanthine oxidoreductase (XOR) is a molybdopterin-containing enzyme found in many living organisms. Its function is to convert hypoxanthine to xanthine and subsequently to urate, which are the final steps in purine elimination in humans. Elevated uric acid levels in the human body can cause gout and hyperuricemia. Therefore, drug development efforts targeting this enzyme are a primary focus not only to treat these conditions but also for other diseases. Oxipurinol, an analog of xanthine, was the drug that emerged as a “gold standard” inhibitor of XO in the late sixties. Crystallographic studies have shown direct coordination of oxipurinol to the molybdenum cofactor (MoCo). The proposed inhibition mechanism based on available crystal structures posits that the oxipurinol’s nitrogen replaces a water-exchangeable OH ligand of the Mo atom. However, the detailed steps involved in the inhibition mechanism remain undefined, which would provide important insights for designing more efficacious drugs with similar inhibition functions. In this study, the inhibition mechanism of XOR by oxipurinol is investigated via molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. The structural and dynamical effects of oxipurinol on the pre-catalytic structure of the metabolite-bound system are presented, as well as the modeled reaction mechanism catalyzed by the MoCo center in the active site. The kinetics and thermodynamics of the proposed reaction mechanism as well as the non-covalent interactions with the binding cavity align with experimental findings. Our results also suggest the suitability of the inhibition reaction via another tautomer of oxipurinol other than the experimentally predominant tautomer. This might suggest possible routes for designing new analogs of oxipurinol with a similar coordination mode to the latter tautomer, which could lead to more energetically favorable inhibitors.