The crystal structure of xanthine oxidoreductase during catalysis: implications for reaction mechanism and enzyme inhibition

Mechanistic insights into xanthine oxidoreductase from development studies of candidate drugs to treat hyperuricemia and gout

Xanthine oxidoreductase (XOR), which is widely distributed from humans to bacteria, has a key role in purine catabolism, catalyzing two steps of sequential hydroxylation from hypoxanthine to xanthine and from xanthine to urate at its molybdenum cofactor (Moco). Human XOR is considered to be a target of drugs not only for therapy of hyperuricemia and gout, but also potentially for a wide variety of other diseases. In this review, we focus on studies of XOR inhibitors and their implications for understanding the chemical nature and reaction mechanism of the Moco active site of XOR. We also discuss further experimental or clinical studies that would be helpful to clarify remaining issues.

Electronic structure contributions to reactivity in xanthine oxidase family enzymes

We review the xanthine oxidase (XO) family of pyranopterin molybdenum enzymes with a specific emphasis on electronic structure contributions to reactivity. In addition to xanthine and aldehyde oxidoreductases, which catalyze the two-electron oxidation of aromatic heterocycles and aldehyde substrates, this mini-review highlights recent work on the closely related carbon monoxide dehydrogenase (CODH) that catalyzes the oxidation of CO using a unique Mo-Cu heterobimetallic active site. A primary focus of this mini-review relates to how spectroscopy and computational methods have been used to develop an understanding of critical relationships between geometric structure, electronic structure, and catalytic function.

Novel insights into the inhibitory mechanism of kaempferol on xanthine oxidase

Xanthine oxidase (XO), a key enzyme in purine catabolism, is widely distributed in human tissues. It can catalyze xanthine to generate uric acid and cause hyperuricemia and gout. Inhibition kinetics assay showed that kaempferol inhibited XO activity reversibly in a competitive manner. Strong fluorescence quenching and conformational changes of XO were found due to the formation of a kaempferol-XO complex, which was driven mainly by hydrophobic forces. The molecular docking further revealed that kaempferol inserted into the hydrophobic cavity of XO to interact with some amino acid residues. The main inhibition mechanism of kaempferol on XO activity may be due to the insertion of kaempferol into the active site of XO occupying the catalytic center of the enzyme to avoid the entrance of the substrate and inducing conformational changes of XO. In addition, luteolin exhibited a stronger synergistic effect with kaempferol than did morin at the lower concentration.

Xanthine oxidoreductase reference values in platelet-poor plasma and platelets in healthy volunteers

Introduction. Xanthine oxidoreductase (XOR) is an enzyme belonging to the class of hydroxylases. XOR is stated, inter alia, in the kidneys, liver, and small intestine as well as in leukocytes and platelets and endothelial cells of capillaries. Its main role is to participate in the conversion of hypoxanthine to xanthine and the uric acid. It occurs in two isoforms: dehydrogenase (XD) and oxidase (XO), which is considered one of the sources of reactive oxygen species. Aim of the Study. Determination of reference values of xanthine oxidoreductase activity in PPP and platelets. Materials and Methods. Study group consisted of 70 healthy volunteers. The isoform activities of xanthine oxidoreductase were determined by kinetic spectrophotometry. Results. A statistically significant difference between the activity of the XOR in PPP and platelets (P < 0.001). The highest activity of XO was found in both PPP and blood platelets. Significant differences between the activity of the various isoforms in PPP (P = 0.0032) and platelets (P < 0.001) were also found. Conclusions. The healthy volunteers showed the highest activity XO (prooxidant) and the lowest XD (antioxidant), which indicates a slight oxidative stress and confirmed physiological effects of XOR.

Nitrite reductase activity of rat and human xanthine oxidase, xanthine dehydrogenase, and aldehyde oxidase: evaluation of their contribution to NO formation in vivo

Nitrite is presently considered a NO "storage form" that can be made available, through its one-electron reduction, to maintain NO formation under hypoxia/anoxia. The molybdoenzymes xanthine oxidase/dehydrogenase (XO/XD) and aldehyde oxidase (AO) are two of the most promising mammalian nitrite reductases, and in this work, we characterized NO formation by rat and human XO/XD and AO. This is the first characterization of human enzymes, and our results support the employment of rat liver enzymes as suitable models of the human counterparts. A comprehensive kinetic characterization of the effect of pH on XO and AO-catalyzed nitrite reduction showed that the enzyme's specificity constant for nitrite increase 8-fold, while the Km(NO2(-)) decrease 6-fold, when the pH decreases from 7.4 to 6.3. These results demonstrate that the ability of XO/AO to trigger NO formation would be greatly enhanced under the acidic conditions characteristic of ischemia. The dioxygen inhibition was quantified, and the Ki(O2) values found (24.3-48.8 μM) suggest that in vivo NO formation would be fine-tuned by dioxygen availability. The potential in vivo relative physiological relevance of XO/XD/AO-dependent pathways of NO formation was evaluated using HepG2 and HMEC cell lines subjected to hypoxia. NO formation by the cells was found to be pH-, nitrite-, and dioxygen-dependent, and the relative contribution of XO/XD plus AO was found to be as high as 50%. Collectively, our results supported the possibility that XO/XD and AO can contribute to NO generation under hypoxia inside a living human cell. Furthermore, the molecular mechanism of XO/AO-catalyzed nitrite reduction was revised.

The reductive half-reaction of xanthine dehydrogenase from Rhodobacter capsulatus: the role of Glu232 in catalysis

The kinetic properties of an E232Q variant of the xanthine dehydrogenase from Rhodobacter capsulatus have been examined to ascertain whether Glu(232) in wild-type enzyme is protonated or unprotonated in the course of catalysis at neutral pH. We find that kred, the limiting rate constant for reduction at high [xanthine], is significantly compromised in the variant, a result that is inconsistent with Glu(232) being neutral in the active site of the wild-type enzyme. A comparison of the pH dependence of both kred and kred/Kd from reductive half-reaction experiments between wild-type and enzyme and the E232Q variant suggests that the ionized Glu(232) of wild-type enzyme plays an important role in catalysis by discriminating against the monoanionic form of substrate, effectively increasing the pKa of substrate by two pH units and ensuring that at physiological pH the neutral form of substrate predominates in the Michaelis complex. A kinetic isotope study of the wild-type R. capsulatus enzyme indicates that, as previously determined for the bovine and chicken enzymes, product release is principally rate-limiting in catalysis. The disparity in rate constants for the chemical step of the reaction and product release, however, is not as great in the bacterial enzyme as compared with the vertebrate forms. The results indicate that the bacterial and bovine enzymes catalyze the chemical step of the reaction to the same degree and that the faster turnover observed with the bacterial enzyme is due to a faster rate constant for product release than is seen with the vertebrate enzyme.

Michael hydratase alcohol dehydrogenase or just alcohol dehydrogenase?

The Michael hydratase – alcohol dehydrogenase (MhyADH) from Alicycliphilus denitrificans was previously identified as a bi-functional enzyme performing a hydration of α,β-unsaturated ketones and subsequent oxidation of the formed alcohols. The investigations of the bi-functionality were based on a spectrophotometric assay and an activity staining in a native gel of the dehydrogenase. New insights in the recently discovered organocatalytic Michael addition of water led to the conclusion that the previously performed experiments to identify MhyADH as a bi-functional enzyme and their results need to be reconsidered and the reliability of the methodology used needs to be critically evaluated.

Effects of topiroxostat on the serum urate levels and urinary albumin excretion in hyperuricemic stage 3 chronic kidney disease patients with or without gout

Background

Topiroxostat, a selective xanthine oxidase inhibitor, shows effective reduction in the serum urate level in hyperuricemic patients with or without gout. The objective of this study was to evaluate the efficacy and safety of topiroxostat in hyperuricemic stage 3 chronic kidney disease patients with or without gout.

Methods

The study design was a 22-week, randomized, multicenter, double-blind study. The enrolled patients were randomly assigned to treatment with topiroxostat 160 mg/day (n = 62) or to the placebo (n = 61). The endpoints were the percent change in the serum urate level, change in the estimated glomerular filtration rate, the urinary albumin-to-creatinine ratio, the proportion of patients with serum urate levels of 356.88 μmol/L or less, blood pressure, and serum adiponectin.

Results

After 22 weeks, although the changes in the estimated glomerular filtration rate and blood pressure were not significant, the percent change in the serum urate level (−45.38 vs. −0.08 %, P < 0.0001) and the percent change in urinary albumin-to-creatinine ratio (−33.0 vs. −6.0 %, P = 0.0092) were found to have decreased in the topiroxostat as compared with the placebo. Although the incidence of ‘alanine aminotransferase increased’ was higher in the topiroxostat, serious adverse event rates were similar in the two groups.

Conclusion

Topiroxostat 160 mg effectively reduced the serum urate level in the hyperuricemic stage 3 chronic kidney disease patients with or without gout.

The ring opening reaction of 1,3-dithiol-2-one systems is fully reversible

The deprotection of a common precursor moiety in dithiolene chemistry was discovered to be fully reversible, which, besides being relevant for researchers working in very different fields with these non-innocent ligand systems, may even have an impact on CO₂ housekeeping, as the deprotected ligand acts as an efficient trap.

Chemical nature and reaction mechanisms of the molybdenum cofactor of xanthine oxidoreductase

Xanthine oxidoreductase (XOR), a complex flavoprotein, catalyzes the metabolic reactions leading from hypoxanthine to xanthine and from xanthine to urate, and both reactions take place at the molybdenum cofactor. The enzyme is a target of drugs for therapy of gout or hyperuricemia. We review the chemical nature and reaction mechanisms of the molybdenum cofactor of XOR, focusing on molybdenum-dependent reactions of actual or potential medical importance, including nitric oxide (NO) synthesis. It is now generally accepted that XOR transfers the water-exchangeable -OH ligand of the molybdenum atom to the substrate. The hydroxyl group at OH-Mo(IV) can be replaced by urate, oxipurinol and FYX-051 derivatives and the structures of these complexes have been determined by x-ray crystallography under anaerobic conditions. Although formation of NO from nitrite or formation of xanthine from urate by XOR is chemically feasible, it is not yet clear whether these reactions have any physiological significance since the reactions are catalyzed at a slow rate even under anaerobic conditions.

Predicting intrinsic clearance for drugs and drug candidates metabolized by aldehyde oxidase

Metabolism by aldehyde oxidase (AO) has been responsible for a number of drug failures in clinical trials. The main reason is the clearance values for drugs metabolized by AO are underestimated by allometric scaling from preclinical species. Furthermore, in vitro human data also underestimates clearance. We have developed the first in silico models to predict both in vitro and in vivo human intrinsic clearance for 8 drugs with just two chemical descriptors. These models explain a large amount of the variance in the data using two computational estimates of the electronic and steric features of the reaction. The in vivo computational models for human metabolism are better than in vitro preclinical animal testing at predicting human intrinsic clearance. Thus, it appears that AO is amenable to computational prediction of rates, which may be used to guide drug discovery, and predict pharmacokinetics for clinical trials.

Mutations associated with functional disorder of xanthine oxidoreductase and hereditary xanthinuria in humans

Xanthine oxidoreductase (XOR) catalyzes the conversion of hypoxanthine to xanthine and xanthine to uric acid with concomitant reduction of either NAD⁺ or O₂. The enzyme is a target of drugs to treat hyperuricemia, gout and reactive oxygen-related diseases. Human diseases associated with genetically determined dysfunction of XOR are termed xanthinuria, because of the excretion of xanthine in urine. Xanthinuria is classified into two subtypes, type I and type II. Type I xanthinuria involves XOR deficiency due to genetic defect of XOR, whereas type II xanthinuria involves dual deficiency of XOR and aldehyde oxidase (AO, a molybdoflavo enzyme similar to XOR) due to genetic defect in the molybdenum cofactor sulfurase. Molybdenum cofactor deficiency is associated with triple deficiency of XOR, AO and sulfite oxidase, due to defective synthesis of molybdopterin, which is a precursor of molybdenum cofactor for all three enzymes. The present review focuses on mutation or chemical modification studies of mammalian XOR, as well as on XOR mutations identified in humans, aimed at understanding the reaction mechanism of XOR and the relevance of mutated XORs as models to estimate the possible side effects of clinical application of XOR inhibitors.

Design and synthesis of aza-flavones as a new class of xanthine oxidase inhibitors

In an attempt to develop non-purine-based xanthine oxidase (XO) inhibitors, keeping in view the complications reported with the use of purine-based XO inhibitors, the flavone framework (a class possessing XO inhibitory potential) was used as lead structure for further optimization. By means of structure-based classical bioisosterism, quinolone was used as an isoster for chromone (a bicyclic unit present in flavones), owing to the bioactive potential and drug-like properties of quinolones. This type of replacement does not alter the shape and structural features required for XO inhibition, and also provides some additional interaction sites, without the loss of hydrogen bonding and hydrophobic and arene-arene interactions. In the present study, a series of 2-aryl/heteroaryl-4-quinolones (aza analogs of flavones) was rationally designed, synthesized and evaluated for in vitro XO inhibitory activity. Some notions about structure-activity relationships are presented indicating the influence of the nature of the 2-aryl ring on the inhibitory activity. Important interactions of the most active compound 3l (IC(50)  = 6.24 µM) with the amino acid residues of the active site of XO were figured out by molecular modeling.

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity

BACKGROUND

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents.

RESULTS

The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics.

CONCLUSION

Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures.

SIGNIFICANCE

The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

Identification of a xanthinuria type I case with mutations of xanthine dehydrogenase in an Afghan child

Xanthinuria due to xanthine dehydrogenase (XDH) deficiency is a rare genetic disorder characterized by hypouricemia and the accumulation of xanthine in the urine. We have identified an Afghan girl whose xanthinuria could be classified as type I xanthinuria based on an allopurinol loading test. Three mutations were identified in the XDH gene, 141insG, C2729T (T910M) and C3886T (R1296W). Site-directed mutagenesis followed by expression analysis in Escherichia coli revealed that not only the frame shift mutation 141insG impairs XDH activity, but also the missense mutation C2729T, while C3886T resulted in major residual activity of about 50% of the wild type. In this report, a case of xanthinuria type I with mutations of XDH was identified and characterized by expression studies.

Synthesis, biological evaluation, and molecular docking of N-{3-[3-(9-methyl-9H-carbazol-3-yl)-acryloyl]-phenyl}-benzamide/amide derivatives as xanthine oxidase and tyrosinase inhibitors

Claisen-Schmidt condensation of 3-formyl-9-methylcarbazole with various amides of 3-aminoacetophenone afforded N-{3-[3-(9-methyl-9H-carbazol-3-yl)-acryloyl]-phenyl}-benzamide/amide derivatives. All compounds were investigated for their in vitro xanthine oxidase (XO), tyrosinase and melanin production inhibitory activity. Most of the target compounds had more potent XO inhibitory activity than the standard drug (IC(50) = 4.3-5.6 μM). Interestingly, compound 7q bearing cyclopropyl ring was found to be the most potent inhibitor of XO (IC(50) = 4.3 μM). Molecular modelling study gave an insight into its binding modes with XO. Compounds 7a, 7d, 7e, 7g, and 7k were found to be potent inhibitors of tyrosinase (IC(50) = 14.01-17.52 μM). These results suggest the possible use of these compounds for the design and development of novel XO and tyrosinase inhibitors.

X-ray crystal structure of arsenite-inhibited xanthine oxidase: μ-sulfido,μ-oxo double bridge between molybdenum and arsenic in the active site

Xanthine oxidoreductase is a molybdenum-containing enzyme that catalyzes the hydroxylation reaction of sp(2)-hybridized carbon centers of a variety of substrates, including purines, aldehydes, and other heterocyclic compounds. The complex of arsenite-inhibited xanthine oxidase has been characterized previously by UV-vis, electron paramagnetic resonance, and X-ray absorption spectroscopy (XAS), and the catalytically essential sulfido ligand of the square-pyrimidal molybdenum center has been suggested to be involved in arsenite binding through either a μ-sulfido,μ-oxo double bridge or a single μ-sulfido bridge. However, this is contrary to the crystallographically observed single μ-oxo bridge between molybdenum and arsenic in the desulfo form of aldehyde oxidoreductase from Desulfovibrio gigas (an enzyme closely related to xanthine oxidase), whose molybdenum center has an oxo ligand replacing the catalytically essential sulfur, as seen in the functional form of xanthine oxidase. Here we use X-ray crystallography to characterize the molybdenum center of arsenite-inhibited xanthine oxidase and solve the structures of the oxidized and reduced inhibition complexes at 1.82 and 2.11 Å resolution, respectively. We observe μ-sulfido,μ-oxo double bridges between molybdenum and arsenic in the active sites of both complexes. Arsenic is four-coordinate with a distorted trigonal-pyramidal geometry in the oxidized complex and three-coordinate with a distorted trigonal-planar geometry in the reduced complex. The doubly bridged binding mode is in agreement with previous XAS data indicating that the catalytically essential sulfur is also essential for the high affinity of reduced xanthine oxidoreductase for arsenite.

Molybdenum enzymes in higher organisms

Recent progress in our understanding of the structural and catalytic properties of molybdenum-containing enzymes in eukaryotes is reviewed, along with aspects of the biosynthesis of the cofactor and its insertion into apoprotein.

Chalcogenidobis(ene-1,2-dithiolate)molybdenum(IV) complexes (chalcogenide E = O, S, Se): probing Mo≡E and ene-1,2-dithiolate substituent effects on geometric and electronic structure

New square-pyramidal bis(ene-1,2-dithiolate)MoSe complexes, [Mo(IV)Se(L)(2)](2-), have been synthesised along with their terminal sulfido analogues, [Mo(IV)S(L)(2)](2-), using alkyl (L(C(4)H(8))), phenyl (L(Ph)) and methyl carboxylate (L(COOMe)) substituted dithiolene ligands (L). These complexes now complete three sets of Mo(IV)O, Mo(IV)S and Mo(IV)Se species that are coordinated with identical ene-1,2-dithiolate ligands. The [alkyl substituted Mo(S/Se)(L(C(4)H(8)))(2)](2-) complexes were reported in prior investigations (H. Sugimoto, T. Sakurai, H. Miyake, K. Tanaka and H. Tsukube, Inorg. Chem. 2005, 44, 6927, H. Tano, R. Tajima, H. Miyake, S. Itoh and H. Sugimoto, Inorg. Chem. 2008, 47, 7465). The new series of complexes enable a systematic investigation of terminal chalcogenido and supporting ene-1,2-dithiolate ligand effects on geometric structure, electronic structure, and spectroscopic properties. X-ray crystallographic analysis of these (Et(4)N)(2)[MoEL(2)] (E = terminal chalocogenide) complexes reveals an isostructural Mo centre that adopts a distorted square pyramidal geometry. The M≡E bond distances observed in the crystal structures and the ν(M≡E) vibrational frequencies indicate that these bonds are weakened with an increase in L→Mo electron donation (L(COOMe) < L(Ph) < L(C(4)H(8))), and this order is confirmed by an electrochemical study of the complexes. The (77)Se NMR resonances in MoSeL complexes appear at lower magnetic fields as the selenido ion became less basic from MoSeL(C(4)H(8)), MoSeL(Ph) and MoSeL(COOMe). Electronic absorption and resonance Raman spectroscopies have been used to assign key ligand-field, MLCT, LMCT and intraligand CT bands in complexes that possess the L(COOMe) ligand. The presence of low-energy intraligand CT transition in these MoEL(COOMe) compounds directly probes the electron withdrawing nature of the -COOMe substituents, and this underscores the complex electronic structure of square pyramidal bis(ene-1,2-dithiolate)-Mo(IV) complexes that possess extended dithiolene conjugation.

Activity and stability of rat liver xanthine oxidase in the presence of pyridine

In the present study, rat liver xanthine oxidase activity and its thermostability in the presence of pyridine were investigated. The activity of the enzyme was determined by following the formation of uric acid spectrophotometrically. The thermal stability of the enzyme was studied in the presence of 0.0%–2.0% of pyridine in Sorenson’s buffer. Thermal stability parameters (half-life, inactivation constant, and activation energies for enzyme inactivation), thermodynamic constants (ΔH*, ΔS*, and ΔG*) and the kinetic parameters (Km and Vmax), were determined in pyridine-free and pyridine-containing buffer solution. A dramatic reduction was observed in xanthine oxidase activity in the presence of pyridine. However, the pyridine-treated enzyme showed a marked enhancement in thermal stability compared with the native enzyme. The ΔG values for the enzyme activity in the presence of pyridine were found to be about 1.5-fold larger than that calculated for the native enzyme, indicating that the enzyme becomes kinetically more stable in the presence of pyridine. The Km value for xanthine oxidase in the presence of 0.5% pyridine increased by 4.8-fold compared with the enzyme in the pyridine-free buffer solution; however, there was 1.8-fold reduction in the Vmax value in the hydro-organic solution compared with the enzyme activity in the buffer solution. As the stability of enzymes is one of the most difficult problems in protein chemistry, this thermostability property of xanthine oxidase could be of great value in developing novel strategies to improve and expand its application in various areas.

Purification, characterization, and cloning of a bifunctional molybdoenzyme with hydratase and alcohol dehydrogenase activity

A bifunctional hydratase/alcohol dehydrogenase was isolated from the cyclohexanol degrading bacterium Alicycliphilus denitrificans DSMZ 14773. The enzyme catalyzes the addition of water to α,β-unsaturated carbonyl compounds and the subsequent alcohol oxidation. The purified enzyme showed three subunits in SDS gel, and the gene sequence revealed that this enzyme belongs to the molybdopterin binding oxidoreductase family containing molybdopterins, FAD, and iron-sulfur clusters.