Bis-ketol nucleoside triesters as prodrugs of the antiviral nucleoside triphosphate analogues of 3'-deoxythymidine and 3'-deoxy-2',3'-didehydrothymidine

Derivatives of 3'-deoxythymidine (ddT) and 3'-deoxy-2',3'-didehydrothymidine (d4T) were prepared in which the 5'-hydroxyl group of the nucleoside was esterified to a bis-ketol phosphate. The resulting phosphate triesters are postulated to be prodrugs of the corresponding 5'-mononucleotides, which are formed intracellularly by the hydrolysis of the two ketol ester groups. The triesters were tested for anti-HIV activity with the result that those derived from ddT showed enhanced antiviral activity when compared to the parent nucleoside.     

A novel non-radioactive method for detection of nucleoside analog phosphorylation by 5'-nucleotidase.

Cytosolic 5'-nucleotidase has been implicated in the phosphorylation of certain nucleosides of therapeutic interest. In vitro, IMP and GMP serve as the optimal phosphate donors for this nucleoside phosphotransferase reaction. Existing assays for nucleoside phosphorylation effected by 5'-nucleotidase require a radiolabeled nucleoside as the phosphate acceptor and separation of the substrate-nucleoside from product-nucleotide has been accomplished either by a filter binding method or HPLC. However, detection of the phosphorylation of unlabeled nucleoside by HPLC is difficult since the ultraviolet absorbance of the phosphate donor, IMP, frequently obscures the absorbance of newly formed nucleotide. The use of ribavirin 5'-phosphate (RMP, 1,2,4-triazole-3-carboxamide riboside 5-monophosphate) as the phosphate donor obviates this difficulty since this triazole heterocycle does not significantly absorb at the wavelengths used to detect most nucleoside analogs. Using this procedure, a 5'-nucleotidase activity from the 100,000 x g supernatant fraction of human T-lymphoblasts deficient in adenosine kinase, hypoxanthine-guanine phosphoribosyltransferase, and deoxycytidine kinase, was characterized with regard to structure-activity relationships for certain inosine and guanosine analogs.     

Physiological correlation between nucleoside-diphosphate kinases and the 21-kDa guanine-nucleotide binding proteins copurified with the enzymes from the cell membrane fractions of Ehrlich ascites tumor cells

The physiological correlation between nucleoside-diphosphate kinases (NDP-kinases) and the 21-kDa guanine nucleotide-binding proteins (G1 and G2) which are copurified with the enzymes from the cell membrane fractions of Ehrlich ascites tumor cells has been biochemically investigated in vitro. We found that: incubation of the phosphoenzyme (enzyme-bound high-energy phosphate intermediate) of NDP-kinases (F-I and F-II) with one of the nucleoside 5'-diphosphates in the presence of 1 mM Mg2+ or 0.25 mM Ca2+ results in the rapid formation of nucleoside 5'-triphosphates without strict base specificity; GDP on the guanine nucleotide-binding proteins (G1, G2 and recombinant v-rasH p21) acts as a phosphate acceptor for the high-energy phosphates of the phosphoenzyme in the presence of 0.25 mM Ca2+; and [32P]GTP is preferentially formed from the 32P-labelled phosphoenzyme F-I and GDP-bound G1 or GDP-bound recombinant v-rasH p21 protein, even if any other nucleoside 5'-diphosphates are present in the reaction mixture. Although [32P]GTP formed was bound with the guanine nucleotide-binding proteins, it was immediately hydrolyzed by the proteins themselves in the presence of 5 mM Mg2+, but not in the presence of 0.25 mM Ca2+. Available evidence suggests that NDP-kinase may be responsible for the activation of the guanine nucleotide-binding proteins (G1, G2 and p21 proteins) through phosphate transfer by the enzyme.     

A new RNA helicase isolated from HeLa cells that catalytically translocates in the 3' to 5' direction.

We have purified an RNA helicase to near homogeneity from nuclear extracts of HeLa cells. The enzyme migrated as a 130-kDa protein upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and exhibited a sedimentation coefficient of 6.4 on glycerol gradient centrifugation. The enzyme translocated in a 3' to 5' direction and acted catalytically, displacing at least a 4-fold molar excess of duplex RNA compared with the enzyme added. All eight common nucleoside triphosphates supported RNA helicase activity at relatively low concentrations (Km in values in the 15-20 microM level). In the presence of RNA and some single-stranded DNAs, the RNA helicase hydrolyzed all nucleoside triphosphates to nucleoside diphosphates and inorganic phosphate. The enzyme displaced deoxyribooligonucleotides provided they were hydrogen-bonded to RNA possessing 3' single-stranded regions, but it did not displace ribooligonucleotides hydrogen-bonded to DNA containing 3' single-stranded regions. The enzyme, in the absence of ATP, binds to both single-stranded RNA and DNA, but the amount of complex formed with RNA was 20-fold greater than the complex formed with DNA. In both cases, the complex formed in the absence of ATP was rapidly reversed by the addition of ATP and not by adenyl-5'-yl (beta,gamma-methylene)-diphosphate. We propose that the enzyme can bind to both single-stranded RNA and DNA and hydrolyze ATP, but by virtue of its greater stability on RNA, the enzyme can only translocate on RNA possessing 3' single-stranded regions.     

Recent advances in structure and function of cytosolic IMP-GMP specific 5′nucleotidase II (cN-II)

Cytosolic 5′ nucleotidase II (cN-II) catalyses both the hydrolysis of a number of nucleoside monophosphates (e.g., IMP + H₂O→ inosine + Pi), and the phosphate transfer from a nucleoside monophosphate donor to the 5′ position of a nucleoside acceptor (e.g., IMP + guanosine → inosine + GMP). The enzyme protein functions through the formation of a covalent phosphoenzyme intermediate, followed by the phosphate transfer either to water (phosphatase activity) or to a nucleoside (phosphotransferase activity). It has been proposed that cN-II regulates the intracellular concentration of IMP and GMP and the production of uric acid. The enzyme might also have a potential therapeutic importance, since it can phosphorylate some anti-tumoral and antiviral nucleoside analogues that are not substrates of known kinases. In this review we summarise our recent studies on the structure, regulation and function of cN-II. Via a site-directed mutagenesis approach, we have identified the amino acids involved in the catalytic mechanism and proposed a structural model of the active site. A series of in vitro studies suggests that cN-II might contribute to the regulation of 5-phosphoribosyl-1-pyrophosphate (PRPP) level, through the so-called oxypurine cycle, and in the production of intracellular adenosine, formed by ATP degradation.     

Reactions at the termini of tRNA with T4 RNA ligase.

T4 RNA ligase will catalyze the addition of nucleoside 3', 5'-bisphosphates onto the 3' terminus of tRNA resulting in tRNA molecule one nucleotide longer with a 3' terminal phosphate. Under appropriate conditions the reaction is quantitative and, if high specific radioactivity bisphosphates are used, it provides an efficient means for in vitro labeling of tRNA. Although the 3' terminal hydroxyl is a good acceptor, the 5' terminal phosphate in most tRNA's is not an effective donor in the RNA ligase reaction. This poor reactivity is due to the secondary structure of the 5' terminal nucleotide. If E. Coli tRNAf Met is used, the 5' phosphate is reactive and the major product with RNA ligase is the cyclic tRNA.     

Ribose 1-phosphate and inosine activate uracil salvage in rat brain

The purpose of this study was to determine the mechanism by which inosine activates pyrimidine salvage in CNS. The levels of cerebral inosine, hypoxanthine, uridine, uracil, ribose 1-phosphate and inorganic phosphate were determined, to evaluate the Gibbs free energy changes (deltaG) of the reactions catalyzed by purine nucleoside phosphorylase and uridine phosphorylase, respectively. A deltaG value of 0.59 kcal/mol for the combined reaction inosine+uracil <==> uridine+hypoxanthine was obtained, suggesting that at least in anoxic brain the system may readily respond to metabolite fluctuations. If purine nucleoside phosphorolysis and uridine phosphorolysis are coupled to uridine phosphorylation, catalyzed by uridine kinase, whose activity is relatively high in brain, the three enzyme activities will constitute a pyrimidine salvage pathway in which ribose 1-phosphate plays a pivotal role. CTP, presumably the last product of the pathway, and, to a lesser extent, UTP, exert inhibition on rat brain uridine nucleotides salvage synthesis, most likely at the level of the kinase reaction. On the contrary ATP and GTP are specific phosphate donors.     

Proton polarizability of poly(L-tyrosine)–hydrogen phosphate hydrogen bonds as a function of alkali cations

We studied films of poly(L -tyrosine) with hydrogen phosphate (residue/phosphate, 1:1) by ir spectroscopy. The influences of the alkali cations (Li⁺, Na⁺, K⁺) and of the degree of hydration were clarified. If Li⁺ ions are present, the OH ?^?OP hydrogen bonds formed in the dried films between the tyrosine OH groups and hydrogen phosphate are asymmetrical. The formation of hydrogen phosphate–hydrogen phosphate hydrogen bonds is prevented by the presence of the Li⁺ ions. With an increase in the degree of hydration, the tyrosine–phosphate bonds are not broken but become slightly stronger. Completely different behaviour is found if K⁺ ions are present. In dry films, the OH ?^?OP ? O^? ?HOP hydrogen bonds formed between tyrosine and hydrogen phosphate show large proton polarizability. The tyrosine proton has a noticeable residence time at the acceptor O atom of the phosphate. The difference in the behaviour of the system with K⁺ ions when compared to the system with Li⁺ ions can be explained, since the hydrogen acceptor O atom of phosphate ions is more negatively charged due to the weaker influence of the K⁺ ions. Furthermore, POH ?^?OP hydrogen bonds between hydrogen phosphate molecules are formed. With an increase in the degree of hydration, the tyrosine–hydrogen phosphate hydrogen bonds are broken, all tyrosine protons are found at the tyrosine residues, and the -PO₃^? groupings are in a symmetrical environment, indicating that the K⁺ ions are removed from these groupings. If the degree of hydration increases further, hydrogen-bonded systems such as hydrogen phosphate–water–hydrogen phosphate are formed that show large proton polarizability due to collective proton motion. When Na⁺ ions are present, the OH ?^?OP ? O^? ?HOP hydrogen bonds formed in dry films still show proton polarizability, but the residence time of the tyrosine proton at the phosphate is very short.     

Hexamere purine nucleoside phosphorylase from Escherichia coli K-12. Kinetic analysis and mechanism of reaction

A kinetic analysis of the phosphorolytic reaction catalyzed by hexameric purine nucleoside phosphorylase II from E. coli K-12 in the presence and absence of reaction products was carried out. The results of the kinetic analysis are consistent with a rapid equilibrium random Bi-Bi mechanism, in which a dead-end ternary (enzyme.purine base.phosphate) complex is formed.     

Diastereomer Separation of Azobenzene-Tethered Oligodeoxyribonucleotides and Determination of Their Absolute Configurations by Enzymatic Digestion

Two diastereomers were produced by the introduction of azobenzene-tethering prochiral linker (2,2-bis(hydroxymethyl)propionic acid) in the modified ODN, which had been used for the photoregulation of DNA functions. We found that this modified ODN with sequence 5′-…pNpXpN…-3′ (p = phosphate; N = nucleoside; X = azobenzene residue) could be digested to pX (the phosphate at the 5′ side of X was left) by an over excess of Phosphodiesterase I. By comparing the retention time of pX from the separated diastereomer with that of authentic R- or S-pX on chiral HPLC, absolute configuration could be easily determined.     

Diastereomer separation of azobenzene-tethered oligodeoxyribonucleotides and determination of their absolute configurations by enzymatic digestion.

Two diastereomers were produced by the introduction of azobenzene-tethering prochiral linker (2,2-bis(hydroxymethyl)propionic acid) in the modified ODN, which had been used for the photoregulation of DNA functions. We found that this modified ODN with sequence 5'-...pNpXpN...-3' (p = phosphate; N = nucleoside; X = azobenzene residue) could be digested to pX (the phosphate at the 5' side of X was left) by an over excess of Phosphodiesterase I. By comparing the retention time of pX from the separated diastereomer with that of authentic R- or S-pX on chiral HPLC, absolute configuration could be easily determined.     

Enzymatic Synthesis of 5-Methyluridine from Adenosine and Thymine with High Efficiency

5-Methyluridine (5MU) was synthesized efficiently from adenosine, thymine, and phosphate by a combination of adenosine deaminase (ADA), purine nucleoside phosphorylase (PUNP), pyrimidine nucleoside phosphorylase (PYNP), and xanthine oxidase (XOD). Adenosine was converted into inosine first by ADA. 5MU and hypoxanthine were synthesized from inosine and thymine by PUNP and PYNP. The hypoxanthine formed was converted into urate via xanthine by XOD. After inosine was completely consumed, an equilibrium state, in which 5MU, thymine, ribose-1-phosphate, and phosphate were involved, was achieved. At the equilibrium state, the maximum yield of 5MU was obtained. The yield of 5MU was 74%, when the initial concentrations of adenosine, thymine, and phosphate were 5 mM each. On the other hand, in the absence of ADA or XOD the yield of 5MU was 1.8%. Several kinds of nucleosides were also synthesized with high yield by the same method.     

Measurement of nucleoside kinases in crude tissue extracts

The measurements of deoxyadenosine kinase, adenosine kinase, and deoxycytidine kinase were examined in human placental cytosol to achieve a valid and reliable assay linear with time and protein. Our studies confirm the need to inhibit deaminase enzymes, since deoxyadenosine and deoxycytidine undergo extensive deamination and phosphorolysis. The use of a uniformly labeled nucleoside substrate introduced an artifact because the chromatographic behavior of the deoxyribose-1-phosphate, formed during the assay, was difficult to distinguish from the deoxynucleoside phosphate product. Accurate product identification was also essential. Finally, the substitution of GTP in place of ATP as the phosphate donor, the addition of a sulfhydryl reducing agent and a monovalent cation need to be considered when an assay is optimized. The use of these methods have lead to valid assays in placental cytosol that are linear with time and protein. Consideration of these important principles are necessary when establishing a valid and reliable nucleoside kinase assay in a crude tissue preparation.     

The mechanism of the chemical synthesis of oligonucleotides and its synthetic consequences.

The data obtained mainly by pulsed NMR spectroscopy on phosphorus nuclei on the mechanism of the internucleotide phosphodiester (PDE) group formation are summarised. With arylsulphonyl chloride as condensing reagent monomeric nucleotide derivative B (nucleoside metaphosphate or its pyridinium adduct) is the highly reactive intermediate. In the presence of PDE groups in nucleoside or nucleotide component the significantly less reactive derivatives with trisubstituted pyrophosphoryl residues are formed both with arylsulphonyl chloride and dicyclohexylcarbodiimide (DCC). The reactive B form of nucleotide component may be obtained using greater excess of arylsulphonyl chloride with simultaneous convertion of PDE groups to tetrasubstituted pyrophosphates amenable to side reactions. The convertion of PDE groups to easily hydrolysable dicyclohexylurea derivatives by reaction with DCC is proposed to reversible blocking of PDE groups of nucleoside component. The B type derivatives of mononucleotides or oligonucleotides with blocked PDE groups seems to be the best nucleotide components.     

Interrelations of NAD and adenosine transformation in the rat liver

The interrelationship of NAD and adenosine (inosine) conversions in the rat liver is investigated. The ratio of products of NAD+ conversions (ADP-ribose, inosine, hypoxanthine and ribose phosphates) are established. AMP and adenosine are not detected, which indicates an availability of different activities of the corresponding enzymes. It is shown that under conditions of the high inorganic phosphate concentration (33 mM) ribose-1-phosphate, formed in the purine nucleoside phosphorylase reaction, is accumulated due to the phosphoribomutase inhibition, but in the presence of NAD+ the utilization of ribose phosphate increases significantly. Nicotinamide inhibits the NAD+-glycohydrolase reaction in the system containing 33 mM phosphate, NAD+ and adenosine and simultaneously it lowers the utilization of ribose.     

Chromate, molybdate, tungstate and vanadate behave as substrates of yeast diadenosine 5',5'-p1,p4-tetraphosphate alpha, beta-phosphorylase

Diadenosine 5',5'-p1,p4-tetraphosphate (Ap4A) alpha, beta-phosphorylase from yeast Saccharomyces cerevisiae catalyzes two reactions: Ap4A cleavage and nucleoside diphosphate--phosphate (NDP-Pi) exchange. In both reactions phosphate can be substituted by arsenate, chromate, molybdate, tungstate or vanadate. In the presence of each anion, nucleoside 5'-monophosphate (NMP) always accumulates as a product of the reaction. This indicates that an unstable NMP anion is formed as an intermediate.     

Effect of nucleotides on potential and pH changes across the thylakoid membrane of spinach chloroplasts.

With appropriate preparations of spinish chloroplasts we observe three distinct effects of the nucleotides: 1. An accelaration of the dark decay of the light induced 520 nm absorbance change after ATP addition. 2. An acidification of the internal space of the thylakoids after ATP addition in darkness. 3. A dark ATPase activity which is regulated by the deltapH across the membrane. We conclude that the effect of the nucleoside triphosphates on the 520 nm signal is linked to a change of the proton conductivity of the membrane, induced by the formation of a deltapH across the membrane in consequence of the dark ATPase activity. The mode of action of the nucleoside diphosphates in the presence of inorganic phosphate on the 520 nm signal is discussed. It is proposed that the effects observed are linked to the hydrolysis of the newly formed nucleoside triphosphates.     

Pentose phosphates in nucleoside interconversion and catabolism

Ribose phosphates are either synthesized through the oxidative branch of the pentose phosphate pathway, or are supplied by nucleoside phosphorylases. The two main pentose phosphates, ribose-5-phosphate and ribose-1-phosphate, are readily interconverted by the action of phosphopentomutase. Ribose-5-phosphate is the direct precursor of 5-phosphoribosyl-1-pyrophosphate, for both de novo and 'salvage' synthesis of nucleotides. Phosphorolysis of deoxyribonucleosides is the main source of deoxyribose phosphates, which are interconvertible, through the action of phosphopentomutase. The pentose moiety of all nucleosides can serve as a carbon and energy source. During the past decade, extensive advances have been made in elucidating the pathways by which the pentose phosphates, arising from nucleoside phosphorolysis, are either recycled, without opening of their furanosidic ring, or catabolized as a carbon and energy source. We review herein the experimental knowledge on the molecular mechanisms by which (a) ribose-1-phosphate, produced by purine nucleoside phosphorylase acting catabolically, is either anabolized for pyrimidine salvage and 5-fluorouracil activation, with uridine phosphorylase acting anabolically, or recycled for nucleoside and base interconversion; (b) the nucleosides can be regarded, both in bacteria and in eukaryotic cells, as carriers of sugars, that are made available though the action of nucleoside phosphorylases. In bacteria, catabolism of nucleosides, when suitable carbon and energy sources are not available, is accomplished by a battery of nucleoside transporters and of inducible catabolic enzymes for purine and pyrimidine nucleosides and for pentose phosphates. In eukaryotic cells, the modulation of pentose phosphate production by nucleoside catabolism seems to be affected by developmental and physiological factors on enzyme levels.     

A continuous spectrophotometric assay for mitogen-activated protein kinase kinases

We describe a convenient and simple continuous spectrophotometric method for the determination of mitogen-activated protein kinase (MAPK) kinase activity with its protein substrate. The assay relies on the measurement of phosphoprotein product generated in the first step of the MAPK kinase reaction. Dephosphorylation of the phosphoprotein is coupled to a MAPK phosphatase to generate phosphate, which is then used as the substrate of purine nucleoside phosphorylase to catalyze the N-glycosidic cleavage of 2-amino 6-mercapto 7-methyl purine ribonucleoside. Of the reaction products ribose 1-phosphate and 2-amino 6-mercapto 7-methylpurine, the latter has a high absorbance at 360nm relative to the nucleoside and, hence, provides a spectrophotometric signal that can be continuously followed. In the presence of excess phosphatase, the phosphorylated protein substrate molecules undergo dephosphorylation almost immediately after their formation; the steady-state use of the resultant inorganic phosphate is a reflection of the constant initial velocity of the exchange reaction. The validity of this method has been confirmed by using it to measure the activities of MEK1 (MAPK/ERK kinase 1) and MKK6 (MAPK kinase 6) toward their physiological substrates. Our findings of the MAPK kinases in the current study provide evidence that the substrate binding affinities of this subfamily of protein kinases are at the submicromolar concentration.     

The Use of Nucleoside Phosphotransferase and (P) p-Nitrophenyl Phosphate in the Determination of the 5'-Linked Termini of Ribosomal RNA

A method for the identification of the 5′-linked termini of ribosomal RNA is described. The method involves the phosphorylation of the nucleosides released from the 5′-linked termini after hydrolysis of the ribonucleic acid chain with alkali. The radioactive 5′-nucleotide derivatives are formed by a nucleoside phosphotransferase mediated phosphoryl transfer from (³²P) p-nitrophenyl phosphate to the nucleosides. The sensitivity of the method allows the use of small amounts of ribosomal RNA.