Defining a process operating window for the synthesis of 5-methyluridine by transglycosylation of guanosine and thymine

This paper describes a high yielding coupled enzymatic reaction using Bacillus halodurans purine nucleoside phosphorylase (PNP) and E. coli uridine phosphorylase (UP) for synthesis of 5-methyluridine (5-MU) by transglycosylation. Key parameters such as reaction temperature, pH, reactant loading, reactor configuration and enzyme loading were investigated. A guanosine conversion of 95% and a 5-MU yield of 85% were achieved at 1 l scale, with a productivity of 10 g l⁻¹ h⁻¹.     

A New Synthesis of Hepialone [(R)-2-Ethyl-6-methyl-2,3-dihydro-4H-pyran-4-one], the Principal Component from Male Sex Scales of the Ghost Moth,Hepialus californicus B

Microorganisms that produce 5-methyluridine (ribothymidine) directly from purine nucleosides and thymine were screened from our stock cultures. Of the 400 strains tested, Erwinia carotovora AJ- 2992 was found to possess the most potent ability as to production of 5-methyluridine from guanosine and thymine. In the presence of intact cells of Er. carotovora AJ-2992 as the enzyme source, 222 mm 5-methyluridine was produced from 300 mm guanosine and 300 mm thymine at 60°C on 48 hr incubation. The enzymatic production of 5-methyluridine by Er. carotovora AJ-2992 was found to involve the following two successive reactions via ribose-1-phosphate as an intermediate: phosphorolysis of purine nucleosides to ribose-1-phosphate and purine bases by purine nucleoside phosphorylase, followed by condensation of ribose-1-phosphate and thymine into 5-methyluridine by pyrimidine nucleoside phosphorylase.     

Two-step efficient synthesis of 5-methyluridine via two thermostable nucleoside phosphorylase from Aeropyrum pernix

5-Methyluridine has been synthesized in high yield using guanosine and thymine as starting materials in the presence of highly thermostable recombinant purine nucleoside phosphorylase (PNP) and uridine phosphorylase (UP) obtained from hyperthermophilic aerobic crenarchaeon Aeropyrum pernix. Key reaction parameters such as pH, temperature, concentration of buffer and substrates were investigated. At the optimal conditions, 5-methyluridine was achieved in yield 85% with a guanosine conversion of 96% in 10ml scale. The process can be performed at high temperature, which will highly increase the solubility of substrates, therefore, this process is suitable for the industry application.     

Bioengineering and Application of Novel Glucose Polymers

Abstract

Glucan phosphorylase, branching enzyme, and 4-α-glucanotransferase were employed to produce glucose polymers with controlled molecular size and structures. Linear or branched glucan was produced from glucose-1-phosphate by glucan phosphorylase alone or together with bracnhing enzyme, where the molecular weight of linear glucan was strictly controlled by the glucose-1-phosphate/primer molar ratio, and the branching pattern by the relative branching enzyme/glucan phosphorylase activity ratio. Cyclic glucans were produced by the cyclization reaction of 5-αglucanotransferases and branching enzyme on amylose and amylopectin. Molecular size and structure of cyclic glucan was controlled by the type of enyzyme and substrate chosen and by the reaction conditions. This in vitro approach can be used to manufacture novel glucose polymers with applicable value.     

Synthesis of 1-(2,3-Dideoxy-β-d-glycero-pent-2-enofuranosyl)thymine (d4T; Stavudine) from 5-Methyluridine

Abstract

A practical synthetic method of d4T (3) from 5-methyluridine (2a) was developed. The Marumoto-Mansuri method was modified using 2′,3′-O-methoxy-ethylidene-5-methyluridine (10) as an intermediate to afford 1-(3,5-di-O-acetyl-2-bromo-2-deoxy-β-D-ribofuranosyl)thymine (6a) in high yield with less formation of by-products. The reaction mechanism was also discussed.

     

Probing enzyme–substrate interactions at the catalytic subsite of Leuconostoc mesenteroides sucrose phosphorylase with site-directed mutagenesis: the roles of Asp49 and Arg395

Abstract

Sucrose phosphorylase is a bacterial α-transglucosidase that catalyses glucosyl transfer from sucrose to phosphate, releasing d-fructose and α-d-glucose 1-phosphate as the product of the first (enzyme glucosylation) and second (enzyme deglucosylation) step of the enzymatic reaction, respectively. The transferred glucosyl moiety of sucrose is accommodated at the catalytic subsite of the phosphorylase through a network of charged hydrogen bonds whereby a highly conserved residue pair of Asp and Arg points towards the equatorial hydroxyl at C₄. To examine the role of this ‘hyperpolar’ binding site for the substrate 4-OH, we have mutated Asp⁴⁹ and Arg³⁹⁵ of Leuconostoc mesenteroides sucrose phosphorylase individually to Ala (D49A) and Leu (R395L), respectively, and also prepared an ‘uncharged’ double mutant harbouring both site-directed substitutions. The efficiency for enzyme glucosylation from sucrose was massively decreased in purified preparations of D49A (10⁷-fold) and R395L (10⁵-fold) as compared to wild-type enzyme. The double mutant was not active above the detection limit. Enzyme deglucosylation to phosphate proceeded relatively efficient in D49A as well as R395L, about 500-fold less than in the wild-type phosphorylase. Substrate inhibition by phosphate and a loss in selectivity for reaction with phosphate as compared to water were new features in the two mutants. Asp⁴⁹ and Arg³⁹⁵ are both essential in the catalytic reaction of L. mesenteroides sucrose phosphorylase.     

Complete and regioselective deacetylation of peracetylated uridines using a lipase

Lipase-catalysed alcoholysis and hydrolysis of 2',3',5'-tri-O-acetyluridine (1a) and 2',3',5'-tri-O-acetyl-2'-C-methyluridine (1b) were studied. Conditions for full and regioselective deacetylation of 1aand 1b are shown in the present work. New compound 2',3'-di-O-acetyl-2'-C-methyluridine (3b) was prepared by regioselective lipase-catalysed deacetylation.     

Glycogen phosphorylase from flight muscle of the hawk moth,Manduca sexta: purification and properties of three interconvertible forms and the effect of flight on their interconversion

Glycogen phosphorylase (EC 2.4.1.1) of Manduca sexta flight muscle was separated into three distinct peaks of activity on diethylaminoethyl-Sephacel. The three fractions of phosphorylase activity were further purified by affinity chromatography on AMP-Sepharose and shown to have the same relative molecular mass (=178000) on polyacrylamide gradient gel electrophoresis under non-denaturating conditions and to produce subunits of molecular mass =92000 on SDS gelelectrophoresis. On the basis of their kinetic properties with respect to the activator AMP and the inhibitor caffeine, the three fractions of phosphorylase activity were assigned as follows: peak 1=phosphorylase b (unphosphorylated form), peak 3=phosphorylase a (phosphorylated form); peak 2 represented a phospho-dephospho hybrid in which only one subunit of the dimeric enzyme was phosphorylated. This hypothesis was corroborated as the various forms could be interconverted in vitro by either dephosphorylation by an endogenous protein phosphatase producing the b form, or by phosphorylation catalyzed by purified phosphorylase kinase from rabbit muscle producing phosphorylase ab and a. From muscle of resting moths more phosphorylase was isolated in the b form (41%) than in the forms ab (28%) and a (31%), respectively. This proportion was changed in favour of the fully phosphorylated a form after a brief interval of flight when 68% of the phosphorylase activity was represented by the a form and only 13% by the b form. Unlike the phosphorylated forms a and ab of phosphorylase, the b form had low affinities for the substrates and for the activator AMP, and was virtually inactive if near-physiological concentrations of substrates and effectors were employed in the assays. The results demonstrate that in Manduca flight muscle three forms of phosphorylase coexist and that their interconversion is a mechanism for regulating phosphorylase activity in vivo.Abbreviations DEAE diethylaminoethyl - EDTA ethylenediamine tetraacetate - EGTA ethyleneglycol-bis(-aminoethylether)N,N-tetra-acetic acid - M _r relative molecular mass - NMR nuclear magnetic resonance - PAGGE polyacrylamide gradient gel electrophoresis - P_i morganic phosphate - SDS sodium dodecylsulphate - TRIS tris(hydroxymethyl)-aminomethane - V _max maximum activity     

Sucrose phosphorylase: a powerful transglucosylation catalyst for synthesis of α-D-glucosides as industrial fine chemicals

Abstract

Sucrose phosphorylase is a bacterial transglucosidase that catalyzes conversion of sucrose and phosphate into α-D-glucose-1-phosphate and D-fructose. The enzyme utilizes a glycoside hydrolase-like double displacement mechanism that involves a catalytically competent β-glucosyl enzyme intermediate. In addition to reaction with phosphate, glucosylated sucrose phosphorylase can undergo hydrolysis to yield α-D-glucose or it can decompose via glucosyl transfer to a hydroxy group in suitable acceptor molecules, giving new α-D-glucosidic products. The glucosyl acceptor specificity of sucrose phosphorylase is reviewed, focusing on applications of the enzyme in glucoside synthesis. Polyhydroxylated compounds such as sugars and sugar alcohols are often glucosylated efficiently. Aryl alcohols and different carboxylic acids also serve as acceptors for enzymatic transglucosylation. The natural osmolyte 2-O-(α-D-glucopyranosyl)-sn-glycerol (GG) was prepared by regioselective glucosylation of glycerol from sucrose using the phosphorylase from Leuconostoc mesenteroides. An industrial process for production of GG as active ingredient of cosmetic formulations has been recently developed. General advantages of sucrose phosphorylase as a transglucosylation catalyst lie in the use of sucrose as a high-energy glucosyl donor and the usually weak hydrolase activity of the enzyme towards substrate and product.     

A convenient synthesis of novel pyranosyl homo-C-nucleosides and their antidiabetic activities

A series of pyranosyl homo-C-nucleosides have been synthesized by reaction of butenonyl C-glycosides (5a–5j, and 8) and cyanoacetamide in presence of t-BuOK followed by further modifications. The reaction proceeds by Michael addition of cyanoacetamide to the butenonyl C-glycosides and subsequent dehydrative cyclization and oxidative aromatization to give glycosylmethyl pyridones (6a–6j, 7a–7j, 9, and 10). The glycosylmethyl pyridones (6a–6e) on reaction with POCl₃ under reflux gave respective glycosylmethyl pyridines (11a–11e and 12a–12e) in good yields. The synthesized compounds were screened for their in vitro α-glucosidase, glucose-6-phosphatase and glycogen phosphorylase inhibitory activities. One of the pyridylmethyl homo-C-nucleoside, compound 11d, displayed 52% inhibition of glucose-6-phosphatase as compared to the standard drug sodium orthovanadate while compound 12a showed a significant antihyperglycemic effect of 17.1% in the diabetic rats as compared to the standard drug metformin.     

Roles of Ala-149 in the catalytic activity of diadenosine tetraphosphate phosphorylase from Mycobacterium tuberculosis H37Rv

Diadenosine 5′,5′′′-P¹,P⁴-tetraphosphate (Ap₄A) phosphorylase from Mycobacterium tuberculosis H37Rv (MtAPA) belongs to the histidine triad motif (HIT) superfamily, but is the only member with an alanine residue at position 149 (Ala-149). Enzymatic analysis revealed that the Ala-149 deletion mutant displayed substrate specificity for diadenosine 5′,5′′′-P¹,P⁵-pentaphosphate and was inactive on Ap₄A and other substrates that are utilized by the wild-type enzyme.     

Substrate specificity of E. coli uridine phosphorylase. Further evidences of high-syn conformation of the substrate in uridine phosphorolysis

Twenty five uridine analogues have been tested and compared with uridine with respect to their potency to bind to E. coli uridine phosphorylase. The kinetic constants of the phosphorolysis reaction of uridine derivatives modified at 2′-, 3′- and 5′-positions of the sugar moiety and 2-, 4-, 5- and 6-positions of the heterocyclic base were determined. The absence of the 2′- or 5′-hydroxyl group is not crucial for the successful binding and phosphorolysis. On the other hand, the absence of both the 2′- and 5′-hydroxyl groups leads to the loss of substrate binding to the enzyme. The same effect was observed when the 3′-hydroxyl group is absent, thus underlining the key role of this group. Our data shed some light on the mechanism of ribo- and 2′-deoxyribonucleoside discrimination by E. coli uridine phosphorylase and E. coli thymidine phosphorylase. A comparison of the kinetic results obtained in the present study with the available X-ray structures and analysis of hydrogen bonding in the enzyme-substrate complex demonstrates that uridine adopts an unusual high-syn conformation in the active site of uridine phosphorylase.     

Syntheses of 1-[2-(Phosphonomethoxy)Alkyl]Thymine Monophosphates and an Evaluation of their Inhibitory Activity Toward Human Thymidine Phosphorylase

A series of new monophosphates of 1-[2-(phosphonomethoxy)alkyl]thymines, such as PMPTp_, 3-MeO-PMPTp, HPMPTp, and FPMPTp, were synthesized and tested for their ability to inhibit human thymidine phosphorylase. Kinetic measurements of enzyme activity were performed using thymidine and inorganic phosphate as the substrates. The data show that some monophosphates provide a considerable increase of the multisubstrate inhibitory effect. The highest inhibitory potency was found with (R)-FPMPTp 4c (K _i ^dT = 4.09 ± 0.47 μM, K _i(P_i) = 2.13 ± 0.29 μM) and (R) 3-MeO-PMPTp 4d (K _i ^dT = 5.78 ± 0.71 μM, K _i(P_i) = 2.71 ± 0.37 μM).     

Discovery profiling and bioinformatics analysis of serum microRNA in Mitochondrial NeuroGastroIntestinal Encephalomyopathy (MNGIE)

Abstract

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is a rare and fatal inherited metabolic disorder due to mutations in the nuclear TYMP gene and leads to a deficiency in the enzyme thymidine phosphorylase. This results in an accumulation of the deoxynucleosides, thymidine and deoxyuridine in the cellular and extracellular compartments, ultimately leading to mitochondrial failure. The understanding of the precise molecular mechanisms that underlie the disease pathology is limited, being hampered by the rarity of the disorder. Expression profiling of serum based mircoRNAs and subsequent bioinformatical analyses provide an approach to facilitate the identity of dysregulated genes and signalling pathways potentially involved in the pathogenesis of MNGIE.     

Binding of Substrates by Purine Nucleoside Phosphorylase (PNP) from Cellulomonas Sp. - Kinetic and Spectrofluorimetric Studies

Abstract

Dissociation constants and stoichiometry of binding for interaction of Cellulomonas sp. purine nucleoside phosphorylase with its substrates: inosine/guanosine, orthophosphate, guanine/hypoxanthine and D-ribose-1-phosphate were studied by kinetic and spectrofluorimetric methods.     

Preparation and functional characterization of a catalytically active fragment of phosphorylase kinase

Limited proteolysis of rabbit muscle phosphorylase kinase catalyzed by chymotrypsin generates a 33 kD product whose kinase activity is independent of both calcium and pH over the range of 6.8 to 8.3 (Malencik, D.A. & Fischer, E.H.Calcium and Cell Function III: 161–188, 1982). This active preparation consists of three related species containing residues 1–290, 1–296, and 1–298 of the 44.7 kD -subunit of phosphorylase kinase (Harris, W.R., Malencik, D.A., Johnson, C.M., Carr, S.A., Roberts, G.D., Byles, C.E., Anderson, S.R., Heilmeyer, L.M.G., Fischer, E.H. & Crabb, J.W.J. Biol. Chem. 265:11740–11745, 1991). Good recoveries of catalytic activity — with varying degrees of calcium dependence — result upon the digestion of phosphorylase kinase with assorted proteases. However, especially high yields of the chymotryptic fragment are obtainable, with purification on an Ultrogel-34 column and a DEAE Sepharose CL-6B column giving 23% of the maximum possible protein.Physical characterization shows that the 33 kD chymotryptic fragment is globular, withs _20,w=2.9S, and that it has an isoelectric point of 5.3. Our continuous catalytic assay, based on differences in the binding of the fluorescent dye 1-anilinonaphthalene-8-sulfonate by phosphorylasea andb, shows that, on a molar basis, the activity of the fragment is 2.8 fold greater than that of phosphorylase kinase (Malencik, D.A., Zhao, Z. and Anderson, S.R.Biochem. Biophys. Res. Comm. 174: 344–350, 1991). The active fragment also undergoes autophosphorylation. Incubation with Mg[-P³²] ATP results in the reaction of 0.7 mol³²P/mol fragment. When the catalytic subunit of the cAMP-dependent protein kinase is also present, the amount of³²P incorporated increases to 1.1 mol/mol. In the former case, phosphorylation occurs primarily at Ser³⁰ while in the latter an additional reaction takes place at Ser⁸¹. The phosphopeptides correspond to sequences occurring in the -subunit of phosphorylase kinase.Abbreviations cAMP adenosine 3(,5(-cyclic monophosphate - NaDodSO₄ sodium dodecyl sulfate - Mops 3-(N-morpholino)propanesulfonic acid - Tris tris(hydroxymethyl)aminomethane - EDTA ethylenediaminetetraacetic acid - EGTA ethylene glycol bis(-aminoethyl ether)-N,N,N(,N(-tetraacetic acid - ANS 1-anilinonapththalene-8-sulfonate - TPCK N-tosyl phenylalanyl chloromethyl ketone - TLCK N-tosyllysyl chloromethyl ketone - PTH phenylthiohydantoin The expected two to three fold increases in fluorescence intensity occur when assays are conducted with solutions containing 20 mM Tris chloride and no glycerophosphate.     

A kinetic,modeling and mechanistic re-analysis of thymidine phosphorylase and some related enzymes

Thymidine phosphorylase (TP) is an important target enzyme for cancer chemotherapy but currently available inhibitors lack in vivo potency. Related enzymes also are therapeutic targets. A greater understanding of enzyme structure and mechanism may help in the design of improved drugs and this work assists in that regard. Also important is the correct identification of the ionization states and tautomeric forms of substrates and products when bound to the enzyme and during the course of the reaction. Approximate methods for estimating some ΔpK_as between aqueous and protein-bound substrates are exemplified for nucleobases and nucleosides. The estimates demonstrate that carbonyl-protonated thymidine and hydroxy tautomers of thymine are not involved in TP's actions. Other estimates indicate that purine nucleoside phosphorylase binds inosine and guanosine as zwitterionic tautomers and that phosphorolysis proceeds through these forms. Extensive molecular modeling based on an X-ray structure of human TP indicates that TP is likely to be mechanistically similar to all other natural members of the class in proceeding through a α-oxacarbenium-like transition state or states.     

Reciprocal regulation of glycogen phosphorylase and glycogen synthase by insulin involving phosphatidylinositol-3 kinase and protein phosphatase-1 in HepG2 cells

The effect of insulin on glycogen synthesis and key enzymes of glycogen metabolism, glycogen phosphorylase and glycogen synthase, was studied in HepG2 cells. Insulin stimulated glycogen synthesis 1.83-3.30 fold depending on insulin concentration in the medium. Insulin caused a maximum of 65% decrease in glycogen phosphorylase 'a' and 110% increase in glycogen synthase activities in 5 min. Although significant changes in enzyme activities were observed with as low as 0.5 nM insulin level, the maximum effects were observed with 100 nM insulin. There was a significant inverse correlation between activities of glycogen phosphorylase 'a' and glycogen synthase 'a' (R² = 0.66, p < 0.001). Addition of 30 mM glucose caused a decrease in phosphorylase 'a' activity in the absence of insulin and this effect was additive with insulin up to 10 nM concentration. The inactivation of phosphorylase 'a' by insulin was prevented by wortmannin and rapamycin but not by PD98059. The activation of glycogen synthase by insulin was prevented by wortmannin but not by PD98059 or rapamycin. In fact, PD98059 slightly stimulated glycogen synthase activation by insulin. Under these experimental conditions, insulin decreased glycogen synthase kinase-3 activity by 30-50% and activated more than 4-fold particulate protein phosphatase-1 activity and 1.9-fold protein kinase B activity; changes in all of these enzyme activities were abolished by wortmannin. The inactivation of GSK-3 and activation of PKB by insulin were associated with their phosphorylation and this was also reversed by wortmannin. The addition of protein phosphatase-1 inhibitors, okadaic acid and calyculin A, completely abolished the effects of insulin on both enzymes. These data suggest that stimulation of glycogen synthase by insulin in HepG2 cells is mediated through the PI-3 kinase pathway by activating PKB and PP-1G and inactivating GSK-3. On the other hand, inactivation of phosphorylase by insulin is mediated through the PI-3 kinase pathway involving a rapamycin-sensitive p70^s6k and PP-1G. These experiments demonstrate that insulin regulates glycogen phosphorylase and glycogen synthase through (i) a common signaling pathway at least up to PI-3 kinase and bifurcates downstream and (ii) that PP-1 activity is essential for the effect of insulin.     

Development and validation of a quantitative method for thymidine phosphorylase activity in peripheral blood mononuclear cells

Abstract

The enzyme thymidine phosphorylase (TP) is important for activation of capecitabine and 5-fluorouracil. Assessment of TP phenotype might be suitable for identification of patients at risk of fluoropyrimidine-induced toxicity. In this paper, we describe the development and validation an assay for TP activity in peripheral blood mononuclear cells (PBMCs). The assay was based on ex vivo conversion of the TP substrate thymidine to thymine. The amount of thymine formed was determined by high-performance liquid chromatography – ultraviolet detection (HPLC-UV) with 5-bromouracil as internal standard. Lymphocytes and monocytes were purified from isolated PBMCs to examine cell-specific TP activity. TP activity in PBMCs demonstrated Michaelis-Menten kinetics. The lower limit of quantification was 2.3?µg PBMC protein and assay linearity was demonstrated up to 22.7?µg PBMC protein. Within-day and between-day precisions were ≤9.2% and ≤6.0%, respectively. Adequate stability TP activity was demonstrated after long-term storage of PBMC dry pellets and lysates at ?80?°C. In monocytes, TP activity was approximately 3 times higher than in lymphocytes. Clinical applicability was demonstrated in samples that were collected from five cancer patients. A simple, precise and sensitive HPLC-UV assay for quantification of TP activity in PBMCs was developed that can be applied for clinical research.     

Formation of partially phosphorylated phosphorylase in isoproterenol stimulated rat hearts

Summary Phosphorylase ab hybrid was demonstrated in perfused rat hearts and during the in vitro conversion of purified rat heart phosphorylase b. Phosphorylase ab hybrid was determined in rat heart extracts by the activating effect of AMP in the presence of caffeine. These results were confirmed by the quantitative determination of incorporated ³²P in vitro and through the characteristic inhibition of ab hybrid by glucose-6-phosphate.As shown by our results, in aerobically perfused control hearts only the ab hybrid represents the active form of phosphorylase, its activity reaching about 20% of the total. In response to isoproterenol (5–1000 ng), the amount of ab hybrid rose to about 30–40%, preceding the rise of the a form, which increased in a dose-dependent manner up to 45% of the total.The great sensitivity of the ab form to AMP activation and glucose-6-phosphate inhibition supports its physiological significance in heart under in vivo conditions as well. Our results strongly suggest that the activity ratio -AMP/+AMP reflects rather the percentage ratio of phosphorylated subunits than that of the activated (partially or totally phosphorylated) phosphorylase molecules.