Enzyme-catalyzed synthesis of nucleoside triphosphates from nucleoside monophosphates

Syntheses of adenosine 5′-triphosphate (ATP) from adenosine 5′-monophosphate (AMP) and ribavirin 5′-triphosphate (RTP) from ribavirin 5′-monophosphate (RMP) (1) were performed using enzymes as catalysts. Synthesis of ATP is based on acetyl phosphate as the phosphate donor, and acetate kinase (Bacillus stearothermophilus, EC 2.7.2.1), adenylate kinase (porcine muscle, EC 2.7.4.3), and inorganic pyrophosphatase (yeast, EC 2.6.1.1) as the catalysts. Three reactions on a 150-mmol scale provided ATP as its barium salt in 82% yield and 67% purity. Synthesis of RTP used phosphoenol pyruvate (PEP) as the phosphate donor, and pyruvate kinase (rabbit muscle, EC 2.7.1.40) and adenylate kinase (rabbit muscle) as the catalysts. A gram-scale reaction provided RTP as its barium salt in 93% yield and 97% purity. This work demonstrates the utility of the autoxidationresistant acetate kinase fromB. stearothermophilus, the value of pyrophosphatase in controlling the level of pyrophosphate in the reactions and the ability of adenylate kinase to accept at least one substrate other than a derivative of adenosine.     

Preparation of a mixture of nucleoside triphosphates suitable for use in synthesis of nucleotide phosphate sugars from ribonucleic acid using nuclease P1, a mixture of nucleoside monophosphokinases and acetate kinase

This paper (1) describes the enzymatic synthesis of a mixture of adenosine, guanosine, cytidine, and uridine triphosphates (ATP, GTP, CTP, and UTP) from ribonucleic acid (RNA). RNA was hydrolyzed by nuclease P1 to a mixture of 5'-nucleoside monophosphates. This mixture was converted to the nucleoside triphosphates using a mixture of nucleoside monophosphate kinases and acetate kinase, with acetyl phosphate as the ultimate phosphoryl donor. The nucleoside monophosphokinases were extracted from brewer's yeast in a four-step procedure. The specific activity of the yeast enzyme preparation after gel permeation chromatography was sufficiently high that the yeast kinases could be immobilized in volumes that were practical for laboratory scale syntheses. Conversions from NMP to NTP in a mixture containing 0.34 mol of total nucleoside phosphates were: ATP, 90%; GTP, 90%; CTP, 60%; and UTP, 40%.     

A facile electrophoretic technique to monitor phosphoenolpyruvate-dependent kinases

Phosphoenolpyruvate (PEP)-dependent kinases are central to numerous metabolic processes and mediate the production of adenosine triphosphate (ATP) by substrate-level phosphorylation (SLP). While pyruvate kinase (PK, EC: 2.7.1.40), the final enzyme of the glycolytic pathway is critical in the anaerobic synthesis of ATP from ADP, pyruvate phosphate dikinase (PPDK, EC: 2.7.9.1), and phosphoenolpyruvate synthase (PEPS, EC: 2.7.9.2) help generate ATP from AMP coupled to PEP as a substrate. Here we demonstrate an inexpensive and effective electrophoretic technology to determine the activities of these enzymes by blue-native polyacrylamide gel electrophoresis (BN-PAGE). The generation of pyruvate is linked to exogenous lactate dehydrogenase (LDH), and the oxidation of reduced nicotinamide adenine dinucleotide (NADH) coupled to 2,6-dichloroindophenol (DCIP) and iodonitrotetrazolium chloride (INT) results in a formazan precipitate which is easily quantifiable. The selectivity of the enzymes is ensured by including either AMP or ADP and pyrophosphate (PP(i) ) or inorganic phosphate (P(i) ). Activity bands were readily obtained after incubation in the respective reaction mixtures for 20-30 min. Cell-free extract concentrations as low as 20 μg protein equivalent yielded activity bands and substrate levels were manipulated to optimize sensitivity of this analytical technique. High-pressure liquid chromatography (HPLC), two-dimensional (2-D) SDS-PAGE (where SDS is sodium dodecyl sulfate), and immunoblot studies of the excised activity band help further characterize these PEP-dependent kinases. Furthermore, these enzymes were readily identified on the same gel by incubating it sequentially in the respective reaction mixtures. This technique provides a facile method to elucidate these kinases in biological systems.     

A two-stage one-pot enzymatic synthesis of TDP-L-mycarose from thymidine and glucose-1-phosphate

This report describes a procedure combining six enzymes native to Escherichia coli or Salmonella typhi, such as thymidine kinase (TK), thymidylate kinase (TMK), nucleoside diphosphate kinase (NDK), pyruvate kinase (PK; for ATP regeneration), TDP-glucose synthetase (RfbA), and TDP-glucose 4,6-dehydratase (RfbB), with five enzymes from Streptomyces fradiae, such as TylX3, TylC1, TylC3, TylK, and TylC2, that resulted in the biosynthesis of TDP-l-mycarose from glucose-1-phosphate and thymidine. This two-stage one-pot approach can be readily applied to the synthesis of other unusual sugars.     

Solid‐Phase Synthesis of (Poly)phosphorylated Nucleosides and Conjugates

Succinyl‐cycloSal‐phosphate triesters of ribo‐ and 2′‐deoxyribonucleosides were attached to aminomethyl polystyrene as an insoluble solid support and reacted with phosphate‐containing nucleophiles yielding nucleoside di‐ and triphosphates, nucleoside diphosphate sugars, and dinucleoside polyphosphates in high purity after cleavage from the solid support. Here, reactive cycloSal‐phosphate triesters were used as immobilized reagents that led to a generally applicable method for the efficient synthesis of phosphorylated biomolecules and phosphate‐bridged bioconjugates.     

Large-Scale Production of the Immunomodulator c-di-GMP from GMP and ATP by an Enzymatic Cascade

(3'-5')-Cyclic diguanylate (c-di-GMP) is a bacterial second messenger with immunomodulatory activities in mice suggesting potential applications as a vaccine adjuvant and as a therapeutic agent. Clinical studies in larger animals or humans will require larger doses that are difficult and expensive to generate by currently available chemical or enzymatic synthesis and purification methods. Here we report the production of c-di-GMP at the multi-gram scale from the economical precursors guanosine monophosphate (GMP) and adenosine triphosphate by a "one-pot" three enzyme cascade consisting of GMP kinase, nucleoside diphosphate kinase, and a mutated form of diguanylate cyclase engineered to lack product inhibition. The c-di-GMP was purified to apparent homogeneity by a combination of anion exchange chromatography and solvent precipitation and was characterized by reversed phase high performance liquid chormatography and mass spectrometry, nuclear magnetic resonance spectroscopy, and further compositional analyses. The immunomodulatory activity of the c-di-GMP preparation was confirmed by its potentiating effect on the lipopolysaccharide-induced interleukin 1β, tumor necrosis factor α, and interleukin 6 messenger RNA expression in J774A.1 mouse macrophages.     

Highly sensitive simultaneous bioluminescent measurement of acetate kinase and pyruvate phosphate dikinase activities using a firefly luciferase-luciferin reaction and its application to a tandem bioluminescent enzyme immunoassay.

We have developed a simultaneous bioluminescent measurement of acetate kinase (AK) and pyruvate phosphate dikinase (PPDK) activities and its application to a tandem enzyme immunoassay. The principle of the proposed assay is as follows. In the first step, AK generates ATP from ADP and acetylphosphate, and the ATP is determined by the firefly luciferase-luciferin reaction. In the second step, the bioluminescent intensity from AK is eliminated by adding glucose and ADP-dependent hexokinase, which forms AMP from ADP. At the same time, the PPDK catalyzes the interconversion of AMP, diphosphate, and phosphoenolpyruvate to ATP, phosphate and pyruvate. The ATP formed by PPDK is also determined by the firefly luciferase-luciferin reaction. The detection limits (at blank + 3SD) of AK and PPDK were 1.03 x 10(-20) and 2.05 x 10(-20) mol per assay, respectively. The method was applicable to a bioluminescent enzyme immunoassay for the assay of insulin and C-peptide in the same sample.     

An efficient synthesis of 2-amino-4-aryl-6,7,8,9-tetrahydro-5H-benzo[7]annulene-1,3-dicarbonitriles in THF with DBU as catalyst

An efficient and convenient multicomponent reaction for preparation of 2-amino-4-aryl-6,7,8,9-tetrahydro-5H-benzo[7]annulene-1,3-dicarbonitrile derivatives, in THF, with DBU as catalyst is reported. These compounds are typical acceptor–donor–acceptor (A–D–A) systems comprising one electron donor and two electron acceptors with different important chemical properties. Excellent yields and the simplicity of the reaction procedure make this one of the most efficient methods for synthesis of these types of compound.     

Efficient Solid‐Phase Synthesis of pppRNA by Using Product‐Specific Labeling

A novel solid‐phase synthesis and purification strategy for 5′‐triphosphate oligonucleotides by using lipophilic tagging of the triphosphate moiety is reported. This is based on triphosphate synthesis with 5′‐O‐cyclotriphosphate intermediates, whereby a lipophilic tag, such as decylamine, is introduced during the ring‐opening reaction to give a linear gamma‐phosphate‐tagged species. This method enables the highly efficient synthesis of 5′‐triphosphorylated RNA derivatives and their gamma‐phosphate‐substituted analogues and will especially facilitate the advancement of therapeutic approaches that make use of 5′‐triphosphate oligonucleotides as potent activators of the cytosolic immune sensor RIG‐I.     

Magnesium isotope effects in enzymatic phosphorylation

Recent discovery of magnesium isotope effect in the rate of enzymatic synthesis of adenosine triphosphate (ATP) offers a new insight into the mechanochemistry of enzymes as the molecular machines. The activity of phosphorylating enzymes (ATP-synthase, phosphocreatine, and phosphoglycerate kinases) in which Mg(2+) ion has a magnetic isotopic nucleus 25Mg was found to be 2-3 times higher than that of enzymes in which Mg(2+) ion has spinless, nonmagnetic isotopic nuclei 24Mg or 26Mg. This isotope effect demonstrates unambiguously that the ATP synthesis is a spin-dependent ion-radical process. The reaction schemes, suggested to explain the effect, imply a reversible electron transfer from the terminal phosphate anion of ADP to Mg(2+) ion as a first step, generating ion-radical pair with singlet and triplet spin states. The yields of ATP along the singlet and triplet channels are controlled by hyperfine coupling of unpaired electron in 25Mg+ ion with magnetic nucleus 25Mg. There is no difference in the ATP yield for enzymes with 24Mg and 26Mg; it gives evidence that in this reaction magnetic isotope effect (MIE) operates rather than classical, mass-dependent one. Similar effects have been also found for the pyruvate kinase. Magnetic field dependence of enzymatic phosphorylation is in agreement with suggested ion-radical mechanism.     

Synthesis of nucleoside tetraphosphates and dinucleoside pentaphosphates from nucleoside phosphoropiperidates via the activation of P(V)-N bond

A novel and efficient method for the preparation of nucleoside 5’-tetraphosphates has been developed by coupling nucleoside 5’-phosphoropiperidates with triphosphate reagent in the presence of 4,5-dicyanoimidazole(DCI) activator.Further coupling of the nucleoside 5’-tetraphosphates with nucleoside 5’-phosphoropiperidates via the P(V)-N activation strategy provided a reliable synthetic method for both symmetrical and asymmetrical dinucleoside pentaphosphates.     

Nucleotide recognition in water by a guanidinium-based artificial tweezer receptor

The water-soluble tweezer receptor 1 with two symmetric peptidic arms, which are connected by an aromatic scaffold and contain lysine, phenylalanine, and a guanidinium-based anion-binding site as headgroup, has been synthesized. UV/Vis-derived Job plots show that the receptor forms 1:1 complexes with nucleotides and phosphate in buffered water at neutral pH. Binding constants have been determined by fluorescence and UV/Vis spectroscopy. All nucleotides tested were bound very efficiently, even in pure water, with binding constants between 10(4) and 10(5) M(-1) . Interestingly, all mononucleotides were bound much stronger than phosphate by a factor of at least 5 to 10. Furthermore 1 favors the binding of adenosine monophosphate (AMP) over adenosine diphosphate (ADP) and adenosine triphosphate (ATP), which is unprecedented for artificial nucleotide receptors reported so far. According to NMR spectroscopy and molecular modeling studies, the efficient binding is a result of strong electrostatic contacts supported by π-π interactions with the nucleobase within the cavity-shaped receptor.     

Fe(III)-ion-catalysed non-enzymatic transformation of adenosine diphosphate into adenosine triphosphate part II. Evidence of catalytic nature of Fe ions

Non-enzymatic phosphorylation of adenosine diphosphate (ADP) to adenosine triphosphate (ATP) in aqueous solutions using acetyl phosphate has been studied extensively. The reaction proceeds in the presence of Fe(III) ions. Normally, the yield of ATP never exceeds the amount of Fe ions but, when a sufficient amount of Mg(II) ions is added to the reaction system, the yield of ATP increases beyond the amount of Fe ions. This is because the Fe(III) ion is tightly bound to not only ADP but also ATP, the phosphorylation product. When, however, the Fe(III) ion is liberated from ATP by exchanging with an Mg(II) ion, it regains catalytic activity and contributes to the surplus production of ATP. The Fe(II) ion with either a single molecule of 1,10-phenanthroline or 2,2′-bipyridyl exhibits a remarkably high catalytic activity. This suggests that the Fe(II) aquo ion should also be an excellent catalyst.     

Chaperones Are Necessary for the Expression of Catalytically Active Potato Apyrases in Prokaryotic Cells

NTPDases (nucleoside triphosphate diphosphohydrolases) (also called in plants apyrases) hydrolyze nucleoside 5′-tri- and/or diphosphate bonds producing nucleosides di or monophosphate and inorganic phosphate. For years, studies have been carried out to use both plant and animal enzymes for medicine. Therefore, there is a need to develop an efficient method for the quick production of large amounts of homogeneous proteins with high catalytic activity. Expression of proteins in prokaryotic cells is the most common way for the protein production. The aim of our study was to develop a method of expression of potato apyrase (StAPY4, 5, and 6) genes in bacterial cells under conditions that allowed the production of catalytically active form of these enzymes. Apyrase 4 and 6 were overexpressed in BL21-CodonPlus (DE3) bacteria strain but they were accumulated in inclusion bodies, regardless of the culture conditions and induction method. Co-expression of potato apyrases with molecular chaperones allowed the expression of catalytically active apyrase 5. However, its high nucleotidase activity could be toxic for bacteria and is therefore synthesized in small amounts in cells. Our studies show that each protein requires other conditions for maturation and even small differences in amino acid sequence can essentially affect protein folding regardless of presence of chaperones.     

Multidentate Europium Chelates as Luminoionophores for Anion Recognition: Impact of Ligand Design on Sensitivity and Selectivity,and Applicability to Enzymatic Assays

The design of photoluminescent molecular probes for the selective recognition of anions is a major challenge for the development of optical chemical sensors. The reversible binding of anions to lanthanide centers is one promising option for the realization of anion sensors, because it leads in some cases to a strong luminescence increase by the replacement of quenching water molecules. Yet, it is an open problem to gain control of the sensitivity and selectivity of the luminescence response. Primarily, the selective detection of (poly)phosphate species such as nucleotides has emerged as a demanding task, because they are involved in many biological processes and enzymatic reactions. We designed a series of pyridyl‐based multidentate europium complexes (seven‐, six‐, and five‐dentate) including sensitizing chromophores and studied their luminescence intensity and lifetime responses to different (poly)phosphates (adenosine triphosphate (ATP), adenosine diphosphate (ADP), adenosine monophosphate (AMP), cyclic adenosine monophosphate (cAMP), pyrophosphate, and phosphate anions), and carboxyanions (citrate, malate, oxalacetate, succinate, α‐ketoglutarate, pyruvate, oxalate, carbonate). The results reveal that the number of free coordination sites has a significant impact on the sensitivity and selectivity of the response. Because of its reversibility, the lanthanide probes can be applied to monitor the activity of ATP‐consuming enzymes such ATPases and apyrases, which is demonstrated by means of the five‐dentate complex.     

Stereoselective synthesis of PSI-352938: a β-D-2'-deoxy-2'-α-fluoro-2'-β-C-methyl-3',5'-cyclic phosphate nucleotide prodrug for the treatment of HCV

PSI-352938 is a novel 2'-deoxy-2'-α-fluoro-2'-β-C-methyl 3',5'-cyclic phosphate nucleotide prodrug currently under investigation for the treatment of hepatitis C virus (HCV) infection. PSI-352938 demonstrated superior characteristics in vitro that include broad genotype coverage, superior resistance profile, and high levels of active triphosphate in vivo in the liver compared to our first and second generation nucleoside inhibitors of this class. Consequently, PSI-352938 was selected for further development and an efficient and scalable synthesis was sought to support clinical development. We report an improved, diastereoselective synthesis of a key 1'-β-nucleoside intermediate 13 via S(N)2 displacement of 1-α-bromo ribofuranose sugar 16 with the potassium salt of 6-chloro-2-amino purine and an efficient method to prepare cis-Rp cyclic phosphate (PSI-352938) in a highly stereoselective manner without any chromatographic purification. The 1-α-bromo sugar 16 was stereospecifically prepared from the corresponding 1-β-lactol in high yield under mild bromination conditions using CBr(4)/PPh(3) (Appel reaction). The desired cis-Rp 3',5'-cyclic phosphate construction was accomplished using isopropyl phosphorodichloridate readily obtained from POCl(3) and isopropyl alcohol. The base combination of Et(3)N/NMI was identified as a key factor for producing PSI-352938 as the major (>95%) diastereomer (cis-Rp) in high yield after the final cyclization step. The current route described in this article was successfully used to produce PSI-352938 on multikilogram scale.     

Molecular Recognition of the Macrocyclic Polyamine for the Hydrolysis of Nucleotides in the Electrophoretic Condition

A 28-membered macrocyclic polyamine, 4,8,12,18,22,26-hexaaza-1,15-dioxacyclooctaeicosane ([28]ane-N₆O₂) with two dipropylenetriamine moieties bound together by diethylether unit was able to form polyprotonated, highly charged species in a wide pH region. It was covalently bonded on the inner surface of the fused silica capillary. The capillary showed reversed electroosmotic flow (EOF), allowing anions to be separated in the co-EOF mode. With the phosphate buffer (30 mM) and an applied voltage of –15 kV, the influence of buffer pH and temperature on the interaction between nucleotides and the bonded phase were investigated. The results indicated that a coordination reaction occurs between the analytes and the bonded phase, and this is followed by cleavage of the terminal phosphate. As a result we found three peaks for each nucleoside triphosphate and two peaks for the diphosphates after samples were injected at 35 °C, while only two peaks for the triphosphates and no splitting for the diphosphates at 20 °C were indicated. In other words, a significant effect of temperature on the hydrolysis was observed, and the bonded phase showed a preference for the binding of nucleoside triphosphate over nucleoside diphosphate.     

Synthesis of Deoxyoligonucleotides on an Isotactic Polymer Support

Abstract

An insoluble and noncross-linked polymer of isotactic polystyrene having a p-methoxytrityl group as part of its structure was chosen as a solid polymer support for deoxyribonucleotide synthesis. The p-methoxytrityl functional group was introduced into the isotactic polymer by benzoylation and Grignard reaction. Judging by the NMR spectra, the isotacticity of the polymer remains unaffected after the modifications. Deoxy-nucleosides were linked to the polymer via 5′ ether group. Condensation of the polymer-nucleoside derivative with 3′ protected nucleotides in the presence of mesitylene sulfonyl chloride resulted in 36-63% coupling to the bound nucleoside. Subsequent condensation gave the trinucleoside diphosphate in 25-57% conversion, based on polymer-bound dinucleoside phosphate. The limitation of the polymer support still lies in the low yield of the coupling step, but the value of an isotactic polymer backbone as a “dendritic” center for chain lengthening remains attractive.     

An Improved Approach for Practical Synthesis of 5-Hydroxymethyl-2′-deoxycytidine (5hmdC) Phosphoramidite and Triphosphate

5-Hydroxymethyl-2′-deoxycytidine (5hmdC) phosphoramidite and triphosphate are important building blocks in 5hmdC-containing DNA synthesis for epigenetic studies. However, efficient and practical methods for the synthesis of these compounds are still limited. The current research provides an intensively improved synthetic method that enables the preparation of commercially available cyanoethyl-protected 5hmdC phosphoramidite with an overall yield of 39% on 5 g scale. On the basis of facile and efficient accesses to cyanoethyl protected-5hmdU and 5hmdC intermediates, two efficient synthetic routes for 5hmdC triphosphate were also developed.     

Elucidating the site of protein-ATP binding by top-down mass spectrometry

A Fourier-transform ion cyclotron resonance (FT-ICR) top-down mass spectrometry strategy for determining the adenosine triphosphate (ATP)-binding site on chicken adenylate kinase is described. Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS), but the ability to detect protein-ligand complexes depends on their stability in the gas phase. Previously, we showed that collisionally activated dissociation (CAD) of protein-nucleotide triphosphate complexes yield products from the dissociation of a covalent phosphate bond of the nucleotide with subsequent release of the nucleotide monophosphate (Yin, S. et al., J. Am. Soc. Mass Spectrom. 2008, 19, 1199–1208). The intrinsic stability of electrostatic interactions in the gas phase allows the diphosphate group to remain noncovalently bound to the protein. This feature is exploited to yield positional information on the site of ATP-binding on adenylate kinase. CAD and electron capture dissociation (ECD) of the adenylate kinase-ATP complex generate product ions bearing monoand diphosphate groups from regions previously suggested as the ATP-binding pocket by NMR and crystallographic techniques. Top-down MS may be a viable tool to determine the ATP-binding sites on protein kinases and identify previously unknown protein kinases in a functional proteomics study.