Uridine phosphorylase from rat liver

Spectral Unmixing-Based Reaction Monitoring of Transformations between Nucleosides and Nucleobases

The increased interest in (enzymatic) transformations between nucleosides and nucleobases has demanded the development of efficient analytical tools. In this report, we present an update and extension of our recently described method for monitoring these reactions by spectral unmixing. The presented method uses differences in the UV absorption spectra of nucleosides and nucleobases after alkaline quenching to derive their ratio based on spectral shape by fitting normalized reference spectra. It is applicable to a broad compound spectrum comprising more than 35 examples, offers HPLC-like accuracy, ease of handling and significant reductions in both cost and data acquisition time compared to other methods. This contribution details the principle of monitoring reactions by spectral unmixing, gives recommendations regarding solutions to common problems and applications that necessitate special sample treatment. We provide software, workflows and reference spectra that facilitate the straightforward and versatile application of the method.

A UV/Vis Spectroscopy-Based Assay for Monitoring of Transformations Between Nucleosides and Nucleobases

Efficient reaction monitoring is crucial for data acquisition in kinetic and mechanistic studies. However, for conversions of nucleosides to their corresponding nucleobases, as observed in enzymatically catalyzed nucleoside phosphorylation reactions, the current analytical arsenal does not meet modern requirements regarding cost, speed of analysis and high throughput. Herein, we present a UV/Vis spectroscopy-based assay employing an algorithm for spectral unmixing in a 96-well plate format. The algorithm relies on fitting of reference spectra of nucleosides and their bases to experimental spectra and allows determination of nucleoside/nucleobase ratios in solution with high precision. The experimental procedure includes appropriate dilution of a sample into aqueous alkaline solution, transfer to a multi-well plate, measurement of a UV/Vis spectrum and subsequent in silico spectral unmixing. This enables data collection in a high-throughput fashion and reduces costs compared to state-of-the-art HPLC analyses by approximately 5-fold while being 20-fold faster and offering comparable precision. Additionally, the method is robust regarding dilution and sample transfer errors as it only considers spectral form and not absolute intensity. It can be applied to all natural nucleosides and nucleobases and even unnatural ones as demonstrated by several examples.

Dynamic Modelling of Phosphorolytic Cleavage Catalyzed by Pyrimidine-Nucleoside Phosphorylase

Pyrimidine-nucleoside phosphorylases (Py-NPases) have a significant potential to contribute to the economic and ecological production of modified nucleosides. These can be produced via pentose-1-phosphates, an interesting but mostly labile and expensive precursor. Thus far, no dynamic model exists for the production process of pentose-1-phosphates, which involves the equilibrium state of the Py-NPase catalyzed reversible reaction. Previously developed enzymological models are based on the understanding of the structural principles of the enzyme and focus on the description of initial rates only. The model generation is further complicated, as Py-NPases accept two substrates which they convert to two products. To create a well-balanced model from accurate experimental data, we utilized an improved high-throughput spectroscopic assay to monitor reactions over the whole time course until equilibrium was reached. We examined the conversion of deoxythymidine and phosphate to deoxyribose-1-phosphate and thymine by a thermophilic Py-NPase from Geobacillus thermoglucosidasius. The developed process model described the reactant concentrations in excellent agreement with the experimental data. Our model is built from ordinary differential equations and structured in such a way that integration with other models is possible in the future. These could be the kinetics of other enzymes for enzymatic cascade reactions or reactor descriptions to generate integrated process models.

Metabolism of capecitabine, an oral fluorouracil prodrug: (19)F NMR studies in animal models and human urine

Capecitabine (Xeloda; CAP) is a recently developed oral antineoplastic prodrug of 5-fluorouracil (5-FU) with enhanced tumor selectivity. Previous studies have shown that CAP activation follows a pathway with three enzymatic steps and two intermediary metabolites, 5'-deoxy-5-fluorocytidine (5'-DFCR) and 5'-deoxy-5-fluorouridine (5'-DFUR), to form 5-FU preferentially in tumor tissues. In the present work, we investigated all fluorinated compounds present in liver, bile, and perfusate medium of isolated perfused rat liver (IPRL) and in liver, plasma, kidneys, bile, and urine of healthy rats. Moreover, data obtained from rat urine were compared with those from mice and human urine. According to a low cytidine deaminase (3.5.4.5) activity in rats, 5'-DFCR was by far the main product in perfusate medium from IPRL and plasma and urine from rats. Liver and circulating 5'-DFCR in perfusate and plasma equilibrated at the same concentration value in the range 25 to 400 microM, which supports the involvement of es-type nucleoside transporter in the liver. 5'-DFUR and alpha-fluoro-beta-ureidopropionic acid (FUPA) + alpha-fluoro-beta-alanine (FBAL) were the main products in urine of mice, making up 23 to 30% of the administered dose versus 3 to 4% in rat. In human urine, FUPA + FBAL represented 50% of the administered dose, 5'-DFCR 10%, and 5'-DFUR 7%. Since fluorine-19 nuclear magnetic resonance spectroscopy gives an overview of all the fluorinated compounds present in a sample, we observed the following unreported metabolites of CAP: 1) 5-fluorocytosine and its hydroxylated metabolite, 5-fluoro-6-hydroxycytosine, 2) fluoride ion, 3) 2-fluoro-3-hydroxypropionic acid and fluoroacetate, and 4) a glucuroconjugate of 5'-DFCR.

Enzymes of nucleotide metabolism: the significance of subunit size and polymer size for biological function and regulatory properties

The 72 enzymes in nucleotide metabolism, from all sources, have a distribution of subunit sizes similar to those from other surveys: an average subunit Mr of 47,900, and a median size of 33,300. The same enzyme, from whatever source, usually has the same subunit size (there are exceptions); enzymes having a similar activity (e.g., kinases, deaminases) usually have a similar subunit size. Most simple enzymes in all EC classes (except class 6, ligases/synthetases) have subunit sizes of less than 30,000. Since structural domains defined in proteins tend to be in the Mr range of 5,000 to 30,000, it may be that most simple enzymes are formed as single domains. Multifunctional proteins and ligases have subunits generally much larger than Mr 40,000. Analyses of several well-characterized ligases suggest that they also have two or more distinct catalytic sites, and that ligases therefore are also multifunctional proteins, containing two or more domains. Cooperative kinetics and evidence for allosteric regulation are much more frequently associated with larger enzymes: such complex functions are associated with only 19% of enzymes having a subunit Mr less than or equal to 29,000, and with 86% of all enzymes having a subunit Mr greater than 50,000. In general, larger enzymes have more functions. Only 20% of these enzymes appear to be monomers; the rest are homopolymers and rarely are they heteropolymers. Evidence for the reversible dissociation of homopolymers has been found for 15% of the enzymes. Such changes in quaternary structure are usually mediated by appropriate physiological effectors, and this may serve as a mechanism for their regulation between active and less active forms. There is considerable structural organization of the various pathways: 19 enzymes are found in various multifunctional proteins, and 13 enzymes are found in different types of multienzyme complexes.

Role of uridine phosphorylase in the anabolism of 5-fluorouracil

The activities of enzymes responsible for activating 5-fluorouracil (FUra) to 5-fluorouridine-5'-monophosphate (FUMP) were compared in normal and tumor tissues of rodents to assess the potential capacity of uridine phosphorylase to anabolize FUra to the nucleoside in the presence of ribose-1-phosphate (R-1-P). The activity of the alternative pathway to FUMP with a pyrimidine phosphoribosyltransferase [FUra + 1-pyrophosphoribosyl-5-phosphate (PPRP)] was approximately 15 to 17 nmoles/mg protein/hr in bone marrow from mice and rats and ranged from 28 to 47 nmoles/mg protein/hr in tumor tissues. Uridine phosphorylase [measured as the formation of 5-fluorouridine (FUrd) from FUra and R-1-P] was 35-230 nmoles/mg/hr in bone marrow and in two FUra-sensitive solid tumors, colon tumor No. 38 in mice and RPMI colon tumor in rats; the activity of uridine phosphorylase from L5178Y ascites leukemic cells was notably lower, 8 nmoles/mg/hr. Levels of uridine kinase ranged from 55 to 187 nmoles/mg protein/hr. Thus, the activities of the enzymes of the two-step FUra activating pathway were high compared to the PPRP-dependent activity in all tissues except L5178Y; also, the FUra-sensitive tumors yielded extracts with 1.5 to 6.5 times greater enzyme activity than the corresponding activity in bone marrow. Uridine phosphorylase was partially purified from rat liver, RPMI rat tumor and colon tumor No. 38; the apparent Km of FUra averaged 50 microM, almost 9-fold lower than that of uracil, and the apparent Km of R-1-P for condensation with FUra was 33 microM. The tissue concentration of R-1-P was greater than 70 microM in kidney and liver of rodents and somewhat less in spleen. Colon tumor No. 38 and RPMI colon tumor had 12 and 20 microM R-1-P, respectively, but these low values may reflect low tumor viability. The high levels of uridine phosphorylase and uridine kinase activities in normal tissues and even higher levels in tissues from FUra-sensitive tumors, as well as the sufficient concentration of R-1-P relative to its kinetic constant, suggest that FUra metabolism by the two-step pathway to FUMP may be a significant factor in the activity and selectivity of FUra.

The degradation of 5'-deoxy-5-fluorouridine by pyrimidine nucleoside phosphorylase in normal and cancer tissues

We describe an assay procedure for the quantification of pyrimidine nucleoside phosphorylase, the enzyme thought to degrade the pro-drug 5'-deoxy-5-fluorouridine to 5-fluorouracil. The method is based on the known differences in the ultraviolet absorption spectra in alkaline medium between pyrimidines and their nucleosides. Analogous to the cleavage of uridine by uridine phosphorylase, the enzymatic degradation of 5'-deoxy-5-fluorouridine in the presence of inorganic phosphate yields 5-fluorouracil and ribose-1-phosphate. We have shown that the rate of phosphorolysis of this pyrimidine nucleoside could be readily measured by spectrophotometry. The method described is simple, specific for the 'pro-drug' as well as reproducible. We have also applied this method to define tissue enzyme activities in extracts of human tumours, normal tissues of the same organ and tissues of mice.

Uridine phosphorylase from Novikoff rat hepatoma cells: purification, kinetic properties, and its role in uracil anabolism

Uridine phosphorylase activity was detected in sonic extracts of six different mammalian cell lines and, in conjunction with uridine kinase, provides a route for the conversion of uracil to UMP via uridine. Uracil phosphoribosyl transferase activity was not detected in any of eight different mammalian cell lines. Uridine phosphorylase was purified 5,330-fold from Novikoff rat hepatoma cells by ammonium sulfate precipitation, DEAE-Sephadex chromatography, hydroxyapatite chromatography, and Sephadex G-200 fractionation. The molecular weight of the enzyme by gel filtration was approximately 45,000. The kinetics of the purified enzyme were analyzed with respect to all four substrates at saturating cosubstrate concentration, yielding the parameters KmUra = 360 microM, KmRib-1-P = 88 microM, KmUrd = 16 micron, and KmPi = 130 microM. However, in intact cells the phosphorolysis of uridine proceeded with an apparent Km of 231 microM. Novikoff cells treated with 0.5 mM inosine exhibited an increase in uracil uptake rate which was proportional to an observed increase in intracellular ribose-1-phosphate. Nevertheless, in cells whose de novo synthesis of pyrimidines was blocked by pyrazofurin or N-(phosphonacetyl)-L-aspartate ("PALA"), the uptake of uracil was insufficient to support proliferation, even when enhanced by inosine. These observations are consistent with the kinetic characteristics of the enzyme and provide evidence that the intracellular level of ribose-1-phosphate plays a rate-limiting role in the uptake of uracil mediated by uridine phosphorylase.

Elucidation of pathways of 5-fluorouracil metabolism in xenografts of human colorectal adenocarcinoma

Hypoxanthine (Hx) and allopurinol (HPP) have been shown experimentally to reduce the conversion of 5-fluorouracil (FUra) to FUMP by orotate phosphoribosyltransferase (OPRTase). This study was designed to elucidate the major pathway by which FU ra was metabolized to ribonucleotides by human colorectal tumors. Consequently, the effect of Hx and HPP on the metabolism of [6-3H]-FUra was examined in 5 human colorectal adenocarcinomas maintained as xenografts in immune-deprived mice. In 2 tumors the formation of ribonucleotides from FUra was depressed by Hx and HPP in combination during the first hour after treatment, while in 3 other lines ribonucleotide concentrations were not reduced. The data suggested that these 5 xenograft lines may be divided into 2 groups: (1) group 1 tumors formed relatively high levels of FUrd and low levels of fluorinated ribonucleotides after the injection of FUra, with no decrease in ribonucleotide concentrations after the administration of Hx and HPP. These tumors possessed high ratios of uridine (Urd) phosphorylase/orotate phosphoribosyltransferase (OPRTase: 7-24) and ribose-1-phosphate (R-1-P)/5-phosphoribosyl-1-pyrophosphate (PRPP;5), and thus appeared to metabolize FUra by the U rd phosphorylase and U rd kinase pathway; (2) group 2 tumors formed low levels of FU rd, higher concentrations of fluorinated ribonucleotides and a reduction in levels of these nucleotides after administration of the purine combination. Group 2 tumors demonstrated a lower enzyme ratio (1-2), higher endogenous levels of PRPP, a lower R-1-P/PRPP ratio (1) and appeared to metabolize FUra predominantly by the activity of OPRTase. Hypoxanthine and HPP, alone or in combination, caused a rapid depletion of PRPP in each tumor line examined. In group 2 tumors this may be responsible for the decreased formation of FUra ribonucleotides observed.