- Escherichia coli Bl21: A useful biocatalyst for the synthesis purine nucleosides
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E. coli BL21 cells were able to synthesize several purine nucleosides from pyrimidine ones. Kinetics and yields of this reaction showed a strong dependence on pH, temperature, reagent concentrations and weight of wet cell paste. Yields over 90% were reached in the synthesis of adenosine.
- Rogert,Martinez,Porro,Lewkowicz,Iribarren
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- Abiotic synthesis of purine and pyrimidine ribonucleosides in aqueous microdroplets
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Aqueous microdroplets (a nucleobase (uracil, adenine, cytosine, or hypoxanthine) are electrosprayed from a capillary at +5 kV into a mass spectrometer at room temperature and 1 atm pressure with 3 mM divalent magnesium ion (Mg2+) as a catalyst. Mass spectra show the formation of ribonucleosides that comprise a four-letter alphabet of RNA with a yield of 2.5% of uridine (U), 2.5% of adenosine (A), 0.7% of cytidine (C), and 1.7% of inosine (I) during the flight time of ～50 μs. In the case of uridine, no catalyst is required. An aqueous solution containing guanine cannot be generated under the same conditions given the extreme insolubility of guanine in water. However, inosine can base pair with cytidine and thus substitute for guanosine. Thus, a full set of ribonucleosides to generate the purine–pyrimidine base pairs A-U and I-C are spontaneously generated in aqueous microdroplets under similar mild conditions.
- Nam, Inho,Nam, Hong Gil,Zare, Richard N.
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- A secreted enzyme reporter system for MRI
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(Figure Presented) Let's see what comes out: An extracellular enzymatic gene-reporter system for magnetic resonance imaging (MRI) yields strong, reversible contrast changes in response to the expression of secreted alkaline phosphatase (SEAP; see picture). Products of SEAP activity were specifically detected using an iron-oxide-based sensor. The contrast agent is not used up by the enzyme, cell delivery is not required, and multimodal detection is possible.
- Westmeyer, Gil G.,Durocher, Yves,Jasanoff, Alan
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- SYNTHESIS OF 2'-5',3'-5' LINKED TRIADENYLATES
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2'-5',3'-5' Linked triadenylates have been synthesized by direct bisadenylylation of adenosine 2' and 3' hydroxyls with an adenosine 5'-phosphorochloridite followed by oxidation.
- Hayakawa, Y.,Nobori, T.,Noyori, R.,Imai, J.
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- An enzyme-responsive polymeric superamphiphile
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Responding to treatment: A superamphiphile is formed between a double-hydrophilic polymer (methoxy-poly(ethylene glycol)-block-poly(L-lysine hydrochloride)) and a natural enzyme-responsive molecule (adenosine 5-triphosphate). The superamphiphile self-assembles into spherical aggregates, which, upon addition of enzymes, disassemble and release loaded molecules (see picture).
- Wang, Chao,Chen, Qishui,Wang, Zhiqiang,Zhang, Xi
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- Simultaneous High-Resolution Detection of Bioenergetic Molecules using Biomimetic-Receptor Nanopore
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A novel artificial receptor, heptakis-[6-deoxy-6-(2-hydroxy-3-trimethylammonion-propyl) amino]-beta-cyclomaltoheptaose, with similar functions of mitochondrial ADP/ATP carrier protein, was synthesized and harbored in the engineered α-HL (M113R)7 nanopore, forming a single-molecule biosensor for sensing bioenergetic molecules and their transformations. The strategy significantly elevates both selectivity and signal-to-noise, which enables simultaneous recognition and detection of ATP, ADP, and AMP by real-time single-molecule measurement.
- Su, Zhuoqun,Wei, Yongfeng,Kang, Xiao-Feng
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- Cleavage of short oligoribonucleotides by a Zn2+binding multi-nucleating azacrown conjugate
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A multi-nucleating azacrown conjugate (5a) consisting of two 3,5-bis(1,5,9-triazacyclododecan-3-yloxymethyl)benzyl groups attached to 1 and 7 sites of cyclen was prepared and tested as an artificial ribonuclease. The conjugate in the presence of five equivalents of zinc nitrate expectedly showed uridine selectivity comparable to that 1,3,5-tris(1,5,9-triazacyclododecan-3-yl)benzene (2), a compound known to bind to two adjacent uridine residues and cleave the intervening phosphodiester bond. 5a was, however, unable to discriminate between two and three adjacent uridine residues, but cleaved oligonucleotides containing a UpU and UpUpU site at a comparable rate, even when present at sub-saturating concentrations.
- Laine, Maarit,L?nnberg, Tuomas,Helkearo, Mia,L?nnberg, Harri
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- New nucleoside-based polymeric supports for the solid phase synthesis of ribose-modified nucleoside analogues
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New solid supports, linking protected pyrimidine and purine nucleoside derivatives through the nucleobase, have been prepared. The support, incorporating a suitable derivative of 2′-azido, 2′-deoxyuridine, allowed the simple and efficient solid-phase synthesis of ribose-modified nucleoside and nucleic acid analogues, particularly of aminoacyl derivatives of 2′-deoxy, 2′-amino-uridine, following methodologies well established in peptide and oligonucleotide chemistry.
- De Napoli, Lorenzo,Di Fabio, Giovanni,D'Onofrio, Jennifer,Montesarchio, Daniela
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- Simple and rapid colorimetric enzyme sensing assays using non-crosslinking gold nanoparticle aggregation
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Non-crosslinking gold nanoparticle (AuNP) aggregation induced by the loss (or screen) of surface charges is applied for enzymatic activity sensing and potentially inhibitor screening. The Royal Society of Chemistry.
- Zhao, Weian,Chiuman, William,Lam, Jeffrey C. F.,Brook, Michael A.,Li, Yingfu
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- Utilization of real-time electrospray ionization mass spectrometry to gain further insight into the course of nucleotide degradation by intestinal alkaline phosphatase
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RATIONALE Related with its ability to degrade nucleotides, intestinal alkaline phosphatase (iAP) is an important participant in intestinal pH regulation and inflammatory processes. However, its activity has been investigated mainly by using artificial non-nucleotide substrates to enable the utilization of conventional colorimetric methods. To capture the degradation of the physiological nucleotide substrate of the enzyme along with arising intermediates and the final product, the enzymatic assay was adapted to mass spectrometric detection. Therewith, the drawbacks associated with colorimetric methods could be overcome. METHODS Enzymatic activity was comparatively investigated with a conventional colorimetric malachite green method and a single quadrupole mass spectrometer with an electrospray ionization source using the physiological nucleotide substrates ATP, ADP or AMP and three different pH-values in either methodological approach. By this means the enzymatic activity was assessed on the one hand by detecting the phosphate release spectrometrically at defined time points of enzymatic reaction or on the other by continuous monitoring with mass spectrometric detection. RESULTS Adaption of the enzymatic assay to mass spectrometric detection disclosed the entire course of all reaction components - substrate, intermediates and product - resulting from the degradation of substrate, thereby pointing out a stepwise removal of phosphate groups. By calculating enzymatic substrate conversion rates a distinctively slower degradation of AMP compared to ADP or ATP was revealed together with the finding of a substrate competition between ATP and ADP at alkaline pH. CONCLUSIONS The comparison of colorimetric and mass spectrometric methods to elucidate enzyme kinetics and specificity clearly underlines the advantages of mass spectrometric detection for the investigation of complex multi-component enzymatic assays. The entire course of enzymatic substrate degradation was revealed with different nucleotide substrates, thus allowing a specific monitoring of intestinal alkaline phosphatase activity. Copyright 2014 John Wiley & Sons, Ltd. Copyright
- Kaufmann, Christine M.,Grassmann, Johanna,Treutter, Dieter,Letzel, Thomas
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- Hydrolysis of an RNA dinucleoside monophosphate by neomycin B
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Neomycin B is shown to accelerate the phosphodiester hydrolysis of adenylyl(3′-5′)adenosine (ApA) more effectively than a simple unstructured diamine.
- Kirk, Sarah R.,Tor, Yitzhak
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- Molecular commonality detection using an artificial enzyme membrane for in situ one-stop biosurveillance
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Biodetection and biosensing have been developed based on the concept of sensitivity toward specific molecules. However, current demand may require more levelheaded or far-sighted methods, especially in the field of biological safety and security. In the fields of hygiene, public safety, and security including fighting bioterrorism, the detection of biological contaminants, e.g., microorganisms, spores, and viruses, is a constant challenge. However, there is as yet no sophisticated method of detecting such contaminants in situ without oversight. The authors focused their attention on diphosphoric acid anhydride, which is a structure common to all biological phosphoric substances. Interestingly, biological phosphoric substances are peculiar substances present in all living things and include many different substances, e.g., ATP, ADP, dNTP, pyrophosphate, and so forth, all of which have a diphosphoric acid anhydride structure. The authors took this common structure as the basis of their development of an artificial enzyme membrane with selectivity for the structure common to all biological phosphoric substances and studied the possibility of its application to in situ biosurveillance sensors. The artificial enzyme membrane-based amperometric biosensor developed by the authors can detect various biological phosphoric substances, because it has a comprehensive molecular selectivity for the structure of these biological phosphoric substances. This in situ detection method of the common diphosphoric acid anhydride structure brings a unique advantage to the fabrication of in situ biosurveillance sensors for monitoring biological contaminants, e.g., microorganism, spores, and viruses, without an oversight, even if they were transformed.
- Ikeno, Shinya,Asakawa, Hitoshi,Haruyama, Tetsuya
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- H-Bond activated glycosylation of nucleobases: Implications for prebiotic nucleoside synthesis
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Glycosylation of nucleobases is achieved by heating metal free aqueous solution of nucleobase and sugar. It seems that abstraction of N 9/N1 H by C1′-OH promotes N 9/N1(nucleobase)-C1′ (sug
- Singh, Palwinder,Singh, Amrinder,Kaur, Jagroop,Holzer, Wolfgang
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- The mitochondrial amidoxime reducing component (mARC) is involved in detoxification of N-hydroxylated base analogues
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The mitochondrial Amidoxime Reducing Component (mARC) is the newly discovered fourth molybdenum enzyme in mammals. All hitherto analyzed mammals express two mARC proteins, referred to as mARC1 and mARC2. Together with their electron transport proteins cytochrome b5 and NADH cytochrome b5 reductase, they form a three-component enzyme system and catalyze the reduction of N-hydroxylated prodrugs. Here, we demonstrate the reductive detoxification of toxic and mutagenic N-hydroxylated nucleobases and their corresponding nucleosides by the mammalian mARC-containing enzyme system. The N-reductive activity was found in all tested tissues with the highest detectable conversion rates in liver, kidney, thyroid, and pancreas. According to the presumed localization, the N-reductive activity is most pronounced in enriched mitochondrial fractions. In vitro assays with the respective recombinant three-component enzyme system show that both mARC isoforms are able to reduce N-hydroxylated base analogues, with mARC1 representing the more efficient isoform. On the basis of the high specific activities with N-hydroxylated base analogues relative to other N-hydroxylated substrates, our data suggest that mARC proteins might be involved in protecting cellular DNA from misincorporation of toxic N-hydroxylated base analogues during replication by converting them to the correct purine or pyrimidine bases, respectively.
- Krompholz, Nina,Krischkowski, Carmen,Reichmann, Debora,Garbe-Schoenberg, Dieter,Mendel, Ralf-R.,Bittner, Florian,Clement, Bernd,Havemeyer, Antje
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- Prebiotic stereoselective synthesis of purine and noncanonical pyrimidine nucleotide from nucleobases and phosphorylated carbohydrates
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According to a current RNA first model for the origin of life, RNA emerged in some form on early Earth to become the first biopolymer to support Darwinism here. Threose nucleic acid (TNA) and other polyelectrolytes are also considered as the possible first Darwinian biopolymer(s). This model is being developed by research pursuing a Discontinuous Synthesis Model (DSM) for the formation of RNA and/or TNA from precursor molecules that might have been available on early Earth from prebiotic reactions, with the goal of making the model less discontinuous. In general, this is done by examining the reactivity of isolated products from proposed steps that generate those products, with increasing complexity of the reaction mixtures in the proposed mineralogical environments. Here, we report that adenine, diaminopurine, and hypoxanthine nucleoside phosphates and a noncanonical pyrimidine nucleoside (zebularine) phosphate can be formed from the direct coupling reaction of cyclic carbohydrate phosphates with the free nucleobases. The reaction is stereoselective, giving only the β-anomer of the nucleotides within detectable limits. For purines, the coupling is also regioselective, giving the N-9 nucleotide for adenine as a major product. In the DSM, phosphorylated carbohydrates are presumed to have been available via reactions explored previously [Krishnamurthy R, Guntha S, Eschenmoser A (2000) Angew Chem Int Ed 39:2281-2285], while nucleobases are presumed to have been available from hydrogen cyanide and other nitrogenous species formed in Earth's primitive atmosphere.
- Kim, Hyo-Joong,Benner, Steven A.
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- S-adenosyl-L-methionine:Hydroxide adenosyltransferase: A SAM enzyme
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(Chemical Equation Presented) Not so DUF: A DUF62 enzyme from the archaeon Pyrococcus horikoshii OT3 converts S-adenosyl-L-methionine (SAM) into adenosine through the nucleophilic attack of a hydroxide ion derived from water (see picture of the active site). The highly conserved nature of Asp68, Arg75, and His127 throughout the DUF62 protein superfamily suggests the wide-spread distribution of this novel catalytic activity in microorganisms. DUF = domain of unknown function.
- Deng, Hai,Botting, Catherine H.,Hamilton, John T. G.,Russell, Rupert J. M.,O'Hagan, David
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- Biochemical characterization of a recombinant acid phosphatase from Acinetobacter baumannii
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Genomic sequence analysis of Acinetobacter baumannii revealed the presence of a putative Acid Phosphatase (AcpA; EC 3.1.3.2). A plasmid construct was made, and recombinant protein (rAcpA) was expressed in E. coli. PAGE analysis (carried out under denaturing/ reducing conditions) of nickel-affinity purified protein revealed the presence of a nearhomogeneous band of approximately 37 kDa. The identity of the 37 kDa species was verified as rAcpA by proteomic analysis with a molecular mass of 34.6 kDa from the deduced sequence. The dependence of substrate hydrolysis on pH was broad with an optimum observed at 6.0. Kinetic analysis revealed relatively high affinity for PNPP (Km = 90 μM) with Vmax, kcat, and Kcat/Km values of 19.2 pmoles s-1, 4.80 s-1(calculated on the basis of 37 kDa), and 5.30 × 104 M-1s-1, respectively. Sensitivity to a variety of reagents, i.e., detergents, reducing, and chelating agents as well as classic acid phosphatase inhibitors was examined in addition to assessment of hydrolysis of a number of phosphorylated compounds. Removal of phosphate from different phosphorylated compounds is supportive of broad, i.e., 'nonspecific' substrate specificity; although, the enzyme appears to prefer phosphotyrosine and/or peptides containing phosphotyrosine in comparison to serine and threonine. Examination of the primary sequence indicated the absence of signature sequences characteristic of Type A, B, and C nonspecific bacterial acid phosphatases.
- Smiley-Moreno, Elizabeth,Smith, Douglas,Yu, Jieh-Juen,Cao, Phuong,Arulanandam, Bernard P.,Chambers, James P.
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- Interstrand Aminoacyl Transfer in a tRNA Acceptor Stem-Overhang Mimic
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Protein-catalyzed aminoacylation of the 3′-overhang of tRNA by an aminoacyl-adenylate could not have taken place prior to the advent of genetically coded peptide synthesis, and yet the latter process has an absolute requirement for aminoacyl-tRNA. There must therefore have been an earlier nonprotein-catalyzed means of generating aminoacyl-tRNA. Here, we demonstrate efficient interstrand aminoacyl transfer from an aminoacyl phosphate mixed anhydride at the 5′-terminus of a tRNA acceptor stem mimic to the 2′,3′-diol terminus of a short 3′-overhang. With certain five-base 3′-overhangs, the transfer of an alanyl residue is highly stereoselective with the l-enantiomer being favored to the extent of ～10:1 over the d-enantiomer and is much more efficient than the transfer of a glycyl residue. N-Acyl-aminoacyl residues are similarly transferred from a mixed anhydride with the 5′-phosphate to the 2′,3′-diol but with a different dependence of efficiency and stereoselectivity on the 3′-overhang length and sequence. Given a prebiotically plausible and compatible synthesis of aminoacyl phosphate mixed anhydrides, these results suggest that RNA molecules with acceptor stem termini resembling modern tRNAs could have been spontaneously aminoacylated, in a stereoselective and chemoselective manner, at their 2′,3′-diol termini prior to the onset of protein-catalyzed aminoacylation.
- Bjork, Samuel J.,Liu, Ziwei,Su, Meng,Sutherland, John D.,Wu, Long-Fei
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supporting information
p. 11836 - 11842
(2021/08/03)
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- Prebiotic Photochemical Coproduction of Purine Ribo- And Deoxyribonucleosides
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The hypothesis that life on Earth may have started with a heterogeneous nucleic acid genetic system including both RNA and DNA has attracted broad interest. The recent finding that two RNA subunits (cytidine, C, and uridine, U) and two DNA subunits (deoxyadenosine, dA, and deoxyinosine, dI) can be coproduced in the same reaction network, compatible with a consistent geological scenario, supports this theory. However, a prebiotically plausible synthesis of the missing units (purine ribonucleosides and pyrimidine deoxyribonucleosides) in a unified reaction network remains elusive. Herein, we disclose a strictly stereoselective and furanosyl-selective synthesis of purine ribonucleosides (adenosine, A, and inosine, I) and purine deoxynucleosides (dA and dI), alongside one another, via a key photochemical reaction of thioanhydroadenosine with sulfite in alkaline solution (pH 8-10). Mechanistic studies suggest an unexpected recombination of sulfite and nucleoside alkyl radicals underpins the formation of the ribo C2′-O bond. The coproduction of A, I, dA, and dI from a common intermediate, and under conditions likely to have prevailed in at least some primordial locales, is suggestive of the potential coexistence of RNA and DNA building blocks at the dawn of life.
- Xu, Jianfeng,Green, Nicholas J.,Russell, David A.,Liu, Ziwei,Sutherland, John D.
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supporting information
p. 14482 - 14486
(2021/09/18)
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- Meteorite-catalyzed intermoleculartrans-glycosylation produces nucleosides under proton beam irradiation
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Di-glycosylated adenines act as glycosyl donors in the intermoleculartrans-glycosylation of pyrimidine nucleobases under proton beam irradiation conditions. Formamide and chondrite meteorite NWA 1465 increased the yield and the selectivity of the reaction
- Bizzarri, Bruno Mattia,Fanelli, Angelica,Kapralov, Michail,Krasavin, Eugene,Saladino, Raffaele
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p. 19258 - 19264
(2021/06/03)
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- General Principles for Yield Optimization of Nucleoside Phosphorylase-Catalyzed Transglycosylations
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The biocatalytic synthesis of natural and modified nucleosides with nucleoside phosphorylases offers the protecting-group-free direct glycosylation of free nucleobases in transglycosylation reactions. This contribution presents guiding principles for nucleoside phosphorylase-mediated transglycosylations alongside mathematical tools for straightforward yield optimization. We illustrate how product yields in these reactions can easily be estimated and optimized using the equilibrium constants of phosphorolysis of the nucleosides involved. Furthermore, the varying negative effects of phosphate on transglycosylation yields are demonstrated theoretically and experimentally with several examples. Practical considerations for these reactions from a synthetic perspective are presented, as well as freely available tools that serve to facilitate a reliable choice of reaction conditions to achieve maximum product yields in nucleoside transglycosylation reactions.
- Kaspar, Felix,Giessmann, Robert T.,Hellendahl, Katja F.,Neubauer, Peter,Wagner, Anke,Gimpel, Matthias
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p. 1428 - 1432
(2020/02/05)
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- An enzymatic flow-based preparative route to vidarabine
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The bi-enzymatic synthesis of the antiviral drug vidarabine (arabinosyladenine, ara-A), catalyzed by uridine phosphorylase from Clostridium perfringens (CpUP) and a purine nucleoside phosphorylase fromAeromonas hydrophila (AhPNP), was re-designed under continuous-flow conditions. Glyoxyl-agarose and EziGTM1 (Opal) were used as immobilization carriers for carrying out this preparative biotransformation. Upon setting-up reaction parameters (substrate concentration and molar ratio, temperature, pressure, residence time), 1 g of vidarabine was obtained in 55% isolated yield and >99% purity by simply running the flow reactor for 1 week and then collecting (by filtration) the nucleoside precipitated out of the exiting flow. Taking into account the substrate specificity of CpUP and AhPNP, the results obtained pave the way to the use of the CpUP/AhPNP-based bioreactor for the preparation of other purine nucleosides.
- Annunziata, Francesca,Bavaro, Teodora,Calleri, Enrica,Conti, Paola,Pinto, Andrea,Previtali, Clelia,Rinaldi, Francesca,Speranza, Giovanna,Tamborini, Lucia,Terreni, Marco,Ubiali, Daniela
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- Use of nucleoside phosphorylases for the preparation of 5-modified pyrimidine ribonucleosides
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Enzymatic transglycosylation, a transfer of the carbohydrate moiety from one heterocyclic base to another, is catalyzed by nucleoside phosphorylases (NPs) and is being actively developed and applied for the synthesis of biologically important nucleosides. Here, we report an efficient one-step synthesis of 5-substitited pyrimidine ribonucleosides starting from 7-methylguanosine hydroiodide in the presence of nucleoside phosphorylases (NPs).
- Alexeev, Cyril S.,Drenichev, Mikhail S.,Dorinova, Evgeniya O.,Esipov, Roman S.,Kulikova, Irina V.,Mikhailov, Sergey N.
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- Preparation method for adenosine bulk drug
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The invention discloses a preparation method for an adenosine bulk drug. According to the method, firstly, inosine and tert-butyldiphenylchlorosilane react in the presence of a catalyst, and an obtained product reacts with vilsmeier reagent after being purified; after the reaction ends, a product is purified; then ammonolysis deprotection is performed; and refining is performed to obtain the finalproduct adenosine. According to the method, by employing the acid-resistant and alkali-resistant hydroxyl protecting agent tert-butyldiphenylchlorosilane with high molecular weight, an intermediate product is present in a solid form, and thus, further purification is facilitated, the purity of the intermediate product is increased, meanwhile, the stability of all intermediates in the reaction process is also enhanced, and process quality control is enhanced. Meanwhile, zinc powder and zinc chloride are employed as catalysts for a hydroxyl protection reaction in the method, and thus, the problems of high steric hindrance, long reaction time and low yield during reaction of the sterically hindered hydroxyl protecting agent tert-butyldiphenylchlorosilane and the inosine are overcome, and thereaction activity of the tert-butyldiphenylchlorosilane is improved.
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- Thermodynamic Reaction Control of Nucleoside Phosphorolysis
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Nucleoside analogs represent a class of important drugs for cancer and antiviral treatments. Nucleoside phosphorylases (NPases) catalyze the phosphorolysis of nucleosides and are widely employed for the synthesis of pentose-1-phosphates and nucleoside analogs, which are difficult to access via conventional synthetic methods. However, for the vast majority of nucleosides, it has been observed that either no or incomplete conversion of the starting materials is achieved in NPase-catalyzed reactions. For some substrates, it has been shown that these reactions are reversible equilibrium reactions that adhere to the law of mass action. In this contribution, we broadly demonstrate that nucleoside phosphorolysis is a thermodynamically controlled endothermic reaction that proceeds to a reaction equilibrium dictated by the substrate-specific equilibrium constant of phosphorolysis, irrespective of the type or amount of NPase used, as shown by several examples. Furthermore, we explored the temperature-dependency of nucleoside phosphorolysis equilibrium states and provide the apparent transformed reaction enthalpy and apparent transformed reaction entropy for 24 nucleosides, confirming that these conversions are thermodynamically controlled endothermic reactions. This data allows calculation of the Gibbs free energy and, consequently, the equilibrium constant of phosphorolysis at any given reaction temperature. Overall, our investigations revealed that pyrimidine nucleosides are generally more susceptible to phosphorolysis than purine nucleosides. The data disclosed in this work allow the accurate prediction of phosphorolysis or transglycosylation yields for a range of pyrimidine and purine nucleosides and thus serve to empower further research in the field of nucleoside biocatalysis. (Figure presented.).
- Kaspar, Felix,Giessmann, Robert T.,Neubauer, Peter,Wagner, Anke,Gimpel, Matthias
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p. 867 - 876
(2020/01/24)
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- A short de novo synthesis of nucleoside analogs
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Nucleoside analogs are commonly used in the treatment of cancer and viral infections. Their syntheses benefit from decades of research but are often protracted, unamenable to diversification, and reliant on a limited pool of chiral carbohydrate starting materials. We present a process for rapidly constructing nucleoside analogs from simple achiral materials. Using only proline catalysis, heteroaryl-substituted acetaldehydes are fluorinated and then directly engaged in enantioselective aldol reactions in a one-pot reaction. A subsequent intramolecular fluoride displacement reaction provides a functionalized nucleoside analog. The versatility of this process is highlighted in multigram syntheses of D- or L-nucleoside analogs, locked nucleic acids, iminonucleosides, and C2′- and C4′-modified nucleoside analogs. This de novo synthesis creates opportunities for the preparation of diversity libraries and will support efforts in both drug discovery and development.
- Adluri, Bharanishashank,Britton, Robert,Campeau, Louis-Charles,Cohen, Ryan,Lehmann, Johannes,Meanwell, Michael,Silverman, Steven M.,Wang, Yang
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p. 725 - 730
(2020/09/02)
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- DIVERSE AND FLEXIBLE CHEMICAL MODIFICATION OF NUCLEIC ACIDS
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The present invention provides a method for chemically modifying a nucleic acid molecule using sulfinate reagents to increase stability in vitro and in vivo. Screening methods for nucleobase modifications that reduce cleavage of a nucleic acid molecule by a nuclease are also provided.
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Paragraph 0124-0126; 0131; 0134
(2020/05/12)
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- Enzymatic Synthesis of 2-Deoxyribose 1-Phosphate and Ribose 1 Phosphate and Subsequent Preparation of Nucleosides
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α-Ribose-1-phosphate (Rib-p) and 2-deoxy-α-ribose-1-phosphate (dRib-p) are key intermediates in nucleoside metabolism and are important starting compounds for the enzymatic synthesis of various modified nucleosides. To date, chemical and enzymatic methods allowed the preparation of these compounds in rather low yields (11–37 %). This prevents their widespread use for the enzymatic synthesis of biologically active and practically important nucleosides. Here we propose to use 7-methyl-2′-deoxyguanosine (7-Me-dGuo) and 7-methylguanosine (7-Me-Guo) for the preparation of dRib-p and Rib-p. In this paper, we present the effective preparation of Rib-p and dRib-p starting from readily prepared 7-methylguanosine derivatives via their irreversible enzymatic phosphorolysis in the presence of purine nucleoside phosphorylase. Rib-p and dRib-P are obtained in nearly quantitative yields (HPLC analysis) and 74–96 % yields after their isolation and purification, which is much higher than previously reported.
- Kulikova, Irina V.,Drenichev, Mikhail S.,Solyev, Pavel N.,Alexeev, Cyril S.,Mikhailov, Sergey N.
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p. 6999 - 7004
(2019/11/13)
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- Identification of Flavin Mononucleotide as a Cell-Active Artificial N6-Methyladenosine RNA Demethylase
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N6-Methyladenosine (m6A) represents a common and highly dynamic modification in eukaryotic RNA that affects various cellular pathways. Natural dioxygenases such as FTO and ALKBH5 are enzymes that demethylate m6A residues in mRNA. Herein, the first identification of a small-molecule modulator that functions as an artificial m6A demethylase is reported. Flavin mononucleotide (FMN), the metabolite produced by riboflavin kinase, mediates substantial photochemical demethylation of m6A residues of RNA in live cells. This study provides a new perspective to the understanding of demethylation of m6A residues in mRNA and sheds light on the development of powerful small molecules as RNA demethylases and new probes for use in RNA biology.
- Xie, Li-Jun,Yang, Xiao-Ti,Wang, Rui-Li,Cheng, Hou-Ping,Li, Zhi-Yan,Liu, Li,Mao, Lanqun,Wang, Ming,Cheng, Liang
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supporting information
p. 5028 - 5032
(2019/03/17)
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- Structure-Guided Tuning of a Selectivity Switch towards Ribonucleosides in Trypanosoma brucei Purine Nucleoside 2′-Deoxyribosyltransferase
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The use of nucleoside 2′-deoxyribosyltransferases (NDTs) as biocatalysts for the industrial synthesis of nucleoside analogues is often hindered by their strict preference for 2′-deoxyribonucleosides. It is shown herein that a highly versatile purine NDT from Trypanosoma brucei (TbPDT) can also accept ribonucleosides as substrates; this is most likely because of the distinct role played by Asn53 at a position that is usually occupied by Asp in other NDTs. Moreover, this unusual activity was improved about threefold by introducing a single amino acid replacement at position 5, following a structure-guided approach. Biophysical and biochemical characterization revealed that the TbPDTY5F variant is a homodimer that displays maximum activity at 50 °C and pH 6.5 and shows a remarkably high melting temperature of 69 °C. Substrate specificity studies demonstrate that 6-oxopurine ribonucleosides are the best donors (inosine>guanosine?adenosine), whereas no significant preferences exist between 6-aminopurines and 6-oxopurines as base acceptors. In contrast, no transferase activity could be detected on xanthine and 7-deazapurines. TbPDTY5F was successfully employed in the synthesis of a wide range of modified ribonucleosides containing different purine analogues.
- Del Arco, Jon,Mills, Alberto,Gago, Federico,Fernández-Lucas, Jesús
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p. 2996 - 3000
(2019/11/11)
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- ADENOSINE ANALOG AND ITS USE IN REGULATING THE CIRCADIAN CLOCK
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Provided are a kind of nucleoside analogue compounds, and compositions comprising these compounds and pentostatin, their use for modulating circadian rhythm, preferably, for shifting circadian phase, and methods for modulating circadian rhythm, preferably, for shifting circadian phase via these compounds or the compositions.
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Paragraph 0113; 0126; 0127; 0206
(2018/08/12)
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- SOLID-PHASE PURIFICATION OF SYNTHETIC NUCLEIC ACID SEQUENCES
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The invention provides a compound of the formula (I), and a capture support of the formula (9), wherein R1, R2, R3, R6, A, B, D, E, J, K, Q, W, and Z are as defined herein. The invention also provides a method of purifying an oligonucleotide or an oligonucleotide analog composed of "b" nucleotides from a mixture comprising the oligonucleotide or oligonucleotide analog and at least one oligonucleotide or oligonucleotide analog composed of "a" nucleotides, wherein b ≠ a, comprising use of the compound and the capture support.
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Page/Page column 41; 45
(2018/09/25)
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- Quantitative Prediction of Yield in Transglycosylation Reaction Catalyzed by Nucleoside Phosphorylases
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Phosphorolytic transglycosylation catalyzed by nucleoside phosphorylases is an important biotechnological process. The reaction is reversible, and the yield of the target nucleoside depends on its concentration at the equilibrium state. We have shown that initial concentrations of the starting compounds and the phosphorolysis equilibrium constants of starting and final glycosides determine concentrations of all the components at the equilibrium state. Based on that, we developed a novel quantitative approach for the prediction of yields in transglycosylation reactions. This method simplifies the choice of reagent concentrations and their ratios for the maximization of the target nucleoside yield. It is advantageous over widely applied blind and cumbersome trial-and-error approach and can reduce the required chemical and energy resources. The described algorithm could also be applied for other equilibrium transfer reactions. (Figure presented.).
- Alexeev, Cyril S.,Kulikova, Irina V.,Gavryushov, Sergei,Tararov, Vitali I.,Mikhailov, Sergey N.
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supporting information
p. 3090 - 3096
(2018/08/06)
-
- Synthesis of Nucleosides through Direct Glycosylation of Nucleobases with 5-O-Monoprotected or 5-Modified Ribose: Improved Protocol, Scope, and Mechanism
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Simplifying access to synthetic nucleosides is of interest due to their widespread use as biochemical or anticancer and antiviral agents. Herein, a direct stereoselective method to access an expansive range of both natural and synthetic nucleosides up to a gram scale, through direct glycosylation of nucleobases with 5-O-tritylribose and other C5-modified ribose derivatives, is discussed in detail. The reaction proceeds through nucleophilic epoxide ring opening of an in situ formed 1,2-anhydrosugar (termed “anhydrose”) under modified Mitsunobu reaction conditions. The scope of the reaction in the synthesis of diverse nucleosides and other 1-substituted riboside derivatives is described. In addition, a mechanistic insight into the formation of this key glycosyl donor intermediate is provided.
- Downey, A. Michael,Pohl, Radek,Roithová, Jana,Hocek, Michal
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supporting information
p. 3910 - 3917
(2017/03/27)
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- Synthesis of Adenine Nucleosides by Transglycosylation using Two Sequential Nucleoside Phosphorylase-Based Bioreactors with On-Line Reaction Monitoring by using HPLC
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Uridine phosphorylase from Clostridium perfringens (CpUP, EC 2.4.2.3) was immobilized covalently in an aminopropylsilica monolithic column (25 mm×4.6 mm) upon functionalization with glutaraldehyde. Imino bonds that result from the reaction between the enzyme and the support were reduced chemically to afford a 66 % yield (13 mg) determined spectrophotometrically. The CpUP immobilized enzyme reactor (IMER) was connected to a silica particle-based IMER that contained a purine nucleoside phosphorylase from Aeromonas hydrophila (AhPNP, EC 2.4.2.1), which was developed previously and used successfully for the fast synthesis of some purine ribonucleosides by a “one-enzyme” transglycosylation. CpUP-IMER and AhPNP-IMER were connected to a HPLC system by a six-way switching valve. In this set-up, the synthesis of 2′-deoxyadenosine (dAdo, 8), adenosine (Ado, 9), and arabinosyladenine (araA, 10) by a “two-enzyme” transglycosylation is coupled directly to on-line reaction monitoring. Under the optimized transglycosylation conditions (2:1 ratio sugar donor/base acceptor; 10 mm phosphate buffer; pH 7.25; temperature 37 °C, flow rate 0.1 mL min?1), defined by a 2(5-2) III experimental design, the conversion of dAdo and Ado was approximately 90 %, and araA was synthesized in 20 % yield.
- Cattaneo, Giulia,Rabuffetti, Marco,Speranza, Giovanna,Kupfer, Tom,Peters, Benjamin,Massolini, Gabriella,Ubiali, Daniela,Calleri, Enrica
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p. 4614 - 4620
(2017/12/13)
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- SELECTIVE INHIBITORS OF PROTEIN ARGININE METHYLTRANSFERASE 5 (PRMT5)
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The disclosure is directed to compounds of Formula (I) and Formula (II). Methods of their use and preparation is other described.
- -
-
Paragraph 00168
(2018/01/20)
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- Photochemical demethylation method for N6-methyladenine
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The invention relates to a specific photochemical demethylation method for N6-methyladenine and application of N6-methyladenine. According to the method, light is used as an initiator; and under the existence of a solvent, N6-methyladenine as shown in the formula I or a derivative of N6-methyladenine reacts with a photosensitizer and an oxidant under an illumination condition, thus obtaining a demethylated product as shown in the formula II and realizing demethylation. By the use of the photochemical demethylation method for the N6-methyladenine and relevant compounds, chemical adjustment of nucleic acid under a non-enzymic condition can be adjusted. The invention provides an effective research method on nucleic acid demethylation for the field of researches on epigenetics and chemicobiology.
- -
-
Paragraph 0042; 0044; 0046; 0048; 0050; 0052; 0054-0058
(2017/08/29)
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- Visible-light-mediated oxidative demethylation of: N 6-methyl adenines
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We report a simple protocol that affords oxidative demethylation of N6-methyl groups in N6-methyl adenines (m6A). The biologically compatible photocatalyst riboflavin prompts a highly selective C-H abstraction from N6-methyl in adenines under the irradiation of a visible blue LED light, affording a novel and highly selective biomimetic demethylation of m6A and related N-methyl adenine analogues. andcopy; 2017 The Royal Society of Chemistry.
- Xie, Li-Jun,Wang, Rui-Li,Wang, Dong,Liu, Li,Cheng, Liang
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supporting information
p. 10734 - 10737
(2017/10/06)
-
- The Chemoenzymatic Synthesis of 2-Chloro- and 2-Fluorocordycepins
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Two approaches to the chemoenzymatic synthesis of 2-fluorocordycepin and 2-chlorocordycepin were studied: (i) the use of 3′-deoxyadenosine (cordycepin) and 3′-deoxyinosine (3′dIno) as donors of 3-deoxy- d -ribofuranose in the transglycosylation of 2-fluoro- (2F Ade) and 2-chloroadenine (2Cl Ade) catalyzed by the recombinant E. coli purine nucleoside phosphorylase (PNP), and (ii) the use of 2-fluoroadenosine and 3′-deoxyinosine as substrates of the cross-glycosylation and PNP as a biocatalyst. An efficient method for 3′-deoxyinosine synthesis starting from inosine was developed. However, the very poor solubility of 2Cl Ade and 2F Ade is the limiting factor of the first approach. The second approach enables this problem to be overcome and it appears to be advantageous over the former approach from the viewpoint of practical synthesis of the title nucleosides. The 3-deoxy-α- d -ribofuranose-1-phosphate intermediary formed in the 3′dIno phosphorolysis by PNP was found to be the weak and marginal substrate of E. coli thymidine (TP) and uridine (UP) phosphorylases, respectively. Finally, one-pot cascade transformation of 3-deoxy- d -ribose in cordycepin in the presence of adenine and E. coli ribokinase, phosphopentomutase, and PNP was tested and cordycepin formation in ca. 3.4% yield was proved.
- Denisova, Alexandra O.,Tokunova, Yulia A.,Fateev, Ilja V.,Breslav, Alexandra A.,Leonov, Vladimir N.,Dorofeeva, Elena V.,Lutonina, Olga I.,Muzyka, Inessa S.,Esipov, Roman S.,Kayushin, Alexey L.,Konstantinova, Irina D.,Miroshnikov, Anatoly I.,Stepchenko, Vladimir A.,Mikhailopulo, Igor A.
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p. 4853 - 4860
(2017/10/06)
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- The synthesis of nebularine and its analogs via oxidative desulfuration in aqueous nitric acid
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The synthesis of nebularine and its analogs has been achieved via oxidative desulfuration in H2O for the first time. With 50% HNO3as an oxidant and solvent, 18 products were obtained in good yields (70%–94%). The oxidative desulfuration system could tolerate different functional groups including fluoro, chloro, amino, alkyl, allyl, ribosyl, deoxyribosyl, and arabinofuranosyl groups.More importantly, the drug nebularine could be obtained successfully on a 20 g scale, which made this route more attractive for industrial applications.
- Xia, Ran,Sun, Li-Ping,Qu, Gui-Rong
-
-
- Enzymatic synthesis of ribo- and 2′-deoxyribonucleosides from glycofuranosyl phosphates: An approach to facilitate isotopic labeling
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Milligram quantities of α-D-ribofuranosyl 1-phosphate (sodium salt) (αR1P) were prepared by the phosphorolysis of inosine, catalyzed by purine nucleoside phosphorylase (PNPase). The αR1P was isolated by chromatography in >95% purity and characterized by 1H and 13C NMR spectroscopy. Aqueous solutions of αR1P were stable at pH 6.4 and 4 °C for several months. The isolated αR1P was N-glycosylated with different nitrogen bases (adenine, guanine and uracil) using PNPase or uridine phosphorylase (UPase) to give the corresponding ribonucleosides in high yield based on the glycosyl phosphate. This methodology is attractive for the preparation of stable isotopically labeled ribo- and 2′-deoxyribonucleosides because of the ease of product purification and convenient use and recycling of nitrogen bases. The approach eliminates the need for separate reactions to prepare individual furanose-labeled ribonucleosides, since only one ribonucleoside (inosine) needs to be labeled, if desired, in the furanose ring, the latter achieved by a high-yield chemical N-glycosylation. 2′-Deoxyribonucleosides were prepared from 2′-deoxyinosine using the same methodology with minor modifications.
- Zhang, Wenhui,Turney, Toby,Surjancev, Ivana,Serianni, Anthony S.
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p. 125 - 133
(2017/08/08)
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- PROCESS FOR PREPARATION OF NICOTINAMIDE RIBOSIDE (NR) AND COSMETIC COMPOSITION COMPRISING (NR AND A PHOSPHATE-BINDING AGENT
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Disclosed herein is a process for preparing nicotinamide riboside (NR) from an NR precursor and a phosphate-binding agent in a solvent. The reaction-derived mixture comprising NR may be further used without further processing in a variety of products, particularly in a cosmetic product.
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Page/Page column 28
(2017/09/15)
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- Vinyluridine as a Versatile Chemoselective Handle for the Post-transcriptional Chemical Functionalization of RNA
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The development of modular and efficient methods to functionalize RNA with biophysical probes is very important in advancing the understanding of the structural and functional relevance of RNA in various cellular events. Herein, we demonstrate a two-step bioorthogonal chemical functionalization approach for the conjugation of multiple probes onto RNA transcripts using a 5-vinyl-modified uridine nucleotide analog (VUTP). VUTP, containing a structurally noninvasive and versatile chemoselective handle, was efficiently incorporated into RNA transcripts by in vitro transcription reactions. Furthermore, we show for the first time the use of a palladium-mediated oxidative Heck reaction in functionalizing RNA with fluorogenic probes by reacting vinyl-labeled RNA transcripts with appropriate boronic acid substrates. The vinyl label also permitted the post-transcriptional functionalization of RNA by a reagent-free inverse electron demand Diels-Alder (IEDDA) reaction in the presence of tetrazine substrates. Collectively, our results demonstrate that the incorporation of VUTP provides newer possibilities for the modular functionalization of RNA with variety of reporters.
- George, Jerrin Thomas,Srivatsan, Seergazhi G.
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p. 1529 - 1536
(2017/05/29)
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- Chiral Nanozymes-Gold Nanoparticle-Based Transphosphorylation Catalysts Capable of Enantiomeric Discrimination
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Enantioselectivity in RNA cleavage by a synthetic metalloenzyme has been demonstrated for the first time. Thiols containing chiral ZnII-binding head groups have been self-assembled on the surface of gold nanoparticles. This results in the spontaneous formation of chiral bimetallic catalytic sites that display different activities (kcat) towards the enantiomers of an RNA model substrate. Substrate selectivity is observed when the nanozyme is applied to the cleavage of the dinucleotides UpU, GpG, ApA, and CpC, and remarkable differences in reactivity are observed for the cleavage of the enantiomerically pure dinucleotide UpU.
- Chen, Jack L.-Y.,Pezzato, Cristian,Scrimin, Paolo,Prins, Leonard J.
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supporting information
p. 7028 - 7032
(2016/05/19)
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- Efficient and green approach for the complete deprotection of O-acetylated biomolecules
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A simple, efficient and mild strategy for the complete O-deacetylation of different per-acetylated biomolecules in aqueous media has been described. Different lipases were tested but only the commercial Amano lipase A from Aspergillus Niger catalyzed the complete deprotection of peracetylated α-glucose to glucose in excellent yield. The experimental conditions were tested, in particular the pH effect. The reaction was performed at different pHs considering the only enzymatic process was evaluated at pH 5 and the combination of enzymatic and chemical migration process was evaluated at higher pHs. Finally pH 7 and 25 °C were selected as best conditions. Thus this lipase fully hydrolyzed different peracetylated α-glycopyranosides (glucose, mannose, glucal, galactal) with >99% yields, whereas very good deprotecting yields (75-80%) were achieved for different acetylated β-glycopyranosides (galactose, ribofuranose) under these mild conditions. This strategy was successfully extended to the fully O-selective deprotection of acetylated nucleosides where >99% yield was rapidly obtained. No selectivity was observed for the N-deacetylation in amino acids and peptides.
- Dunne, Anthony,Palomo, Jose M.
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p. 88974 - 88978
(2016/10/03)
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- A PHOTOLUMINESCENT PROBE
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The invention relates to organic long lifetime photoluminescent probes that contain no metal complexes and whose specific association with purine-binding proteins leads to increased emission of long wavelength luminescence with long lifetime (in microsecond region). This enables the time-gated discrimination of the signal over fluorescence present in the biological samples, either autofluorescence of cells or emission from other fluorophores. The invention concerns also the use of the improved method for monitoring activity of protein kinases in living cells, characterization of inhibitors of protein kinases, analysis of protein kinase-based disease biomarkers and other tasks of biological and medical importance.
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- Graphene oxide enhanced specificity at aptamer and its application to multiplexed enzymatic activity sensing
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We explore the effect of sufficient GO on the property of a dye labeled adenosine 5′-triphosphate (ATP) aptamer (P) which shows similar affinity and specificity for ATP and its analogues including adenosine 5′-diphosphate (ADP), adenosine 5′-monophosphate (AMP), and adenosine (AD). It is found that ATP and its analogues give rise to fluorescence recovery of GO-quenched P to a different extent (in the order of ATP > AD > ADP > AMP), and the difference becomes larger when increasing the concentration of GO in a certain range, implying an improvement of specificity of the ATP aptamer. Based on this finding, a fluorescence turn-on assay for alkaline phosphatase (ALP) and creatine kinase (CK) is proposed, by using AMP and ADP as the substrate, respectively. Specifically, the GO-quenched P system containing substrate shows low fluorescence intensity. In the presence of target enzyme, the substrate is converted into either AD or ATP which have higher affinity with P, resulting in stronger fluorescence of the mixture of P and GO. The entire assay is sensitive and selective. More importantly, the ability of GO with suitable concentration to improve the specificity of aptamers not only offers an exciting new way to detect protease, but also is valuable for developing the application of GO and aptamers in the biosensing field and is expected to be used in aptamer screening systems, to improve the specificity of screened aptamers.
- Xing, Xiaojing,Liu, Xueguo,Zhou, Ying,Xu, Dangdang,Pang, Daiwen,Tang, Hongwu
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p. 11815 - 11821
(2016/02/09)
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- N in RNA6 -Chemical demethylation method of methyl adenosine
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The invention relates to a chemical demethylation method of N-methyladenosine in RNA by using a chemical method specifically. The chemical demethylation method specifically comprises the following steps: hydrogen peroxide reacts with ammonium bicarbonate in a water phase to generate peroxy-carbonic acid HCO4, N atoms on the N site of N-methyladenosine is used as a nucleophilic reagent to attack HCO4, the intermediate products of NA), N-hydroxymethylcytosine (hmA) and N-formyl cytosine (fA), and finally demethylation is performed to generate adenosine.
- -
-
Paragraph 0018; 0019
(2017/04/11)
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- Protection of the 2′-Hydroxy Function of Ribonucleosides as an Iminooxymethyl Propanoate and Its 2′-O-Deprotection through an Intramolecular Decarboxylative Elimination Process
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The design and implementation of 2′-hydroxy protecting groups for ribonucleosides is still a daunting challenge to overcome when assembling RNA (ribonucleic acid) sequences for therapeutic applications. The reaction of 2′-O-aminooxymethylribonucleosides with ethyl pyruvate results in the formation of 2′-O-iminooxymethyl ethyl propanoates. The cleavage of this type of 2′-O-protecting groups is demonstrated through saponification of the esters to 2′-O-iminooxymethyl propanoate salts, which, when needed, decarboxylate quantitatively at 55 °C in the presence of tetra-n-butylammonium fluoride or chloride in dimethyl sulfoxide (DMSO) to produce all four native ribonucleosides.
- Cie?lak, Jacek,Grajkowski, Andrzej,Ausín, Cristina,Beaucage, Serge L.
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p. 5817 - 5821
(2016/12/18)
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- New (green) methodology for efficient hydrazine cleavage
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An efficient method for removal of the hydrazine group from (hetero)aromatic substrates has been developed. It can be realized both on a solid support and in solution by synthesis employing a low concentration solution of trimethylsilanolate in tetrahydrofuran or N,N-dimethylformamide. For water-soluble substrates, the reaction can be performed in water, highlighting the eco-friendly attributes of this methodology.
- Kubovi?ová, Lenka,Bürglová, Kristyna,Hlavá?, Jan
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supporting information
p. 4824 - 4828
(2016/06/13)
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- THERMOSTABLE BIOCATALYST COMBINATION FOR NUCLEOSIDE SYNTHESIS
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The present invention relates to a transglycosylation method for the preparation of natural and synthetic nucleosides using a uridine phosphorylase (PyNPase, E.C. 2.4.2.3), a purine nucleoside phosphorylase (PNPase, E.C. 2.4.2.1), or a combination thereof. These biocatalysts may be used as such, or by means of host cells transformed with vectors comprising recombinant DNA gene derived from hyperthermophilic archaea and encoding for the PyNPase and PNPase enzymes.
- -
-
Paragraph 0076
(2016/08/17)
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- PRODUCTION METHOD OF NUCLEOSIDE COMPOUND
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PROBLEM TO BE SOLVED: To provide a production method of a nucleoside compound by which an isotopic labeled nucleoside compound can be produced efficiently. SOLUTION: A production method of a nucleoside compound comprises obtaining a target nucleoside compound by the base exchange reaction of a raw material nucleoside compound and a base in the solution containing a phosphoric acid ion by a nucleoside phosphorylase, wherein the target nucleoside compound is labeled with a stable isotope or a radioisotope. COPYRIGHT: (C)2015,JPOandINPIT
- -
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Paragraph 0032-0033
(2017/03/24)
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- Deoxygenation of amine N-oxides using gold nanoparticles supported on carbon nanotubes
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Deoxygenation of a variety of aromatic and aliphatic amine N-oxides has been carried out in excellent yield using dimethylphenylsilane as the reducing agent under the catalytic influence of a carbon nanotube-gold nanohybrid at room temperature. Low catalyst loading, good TON and TOF values, and recyclability of the catalyst are some of the salient features of our methodology.
- Donck, Simon,Gravel, Edmond,Shah, Nimesh,Jawale, Dhanaji V.,Doris, Eric,Namboothiri, Irishi N. N.
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p. 50865 - 50868
(2015/06/25)
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- Ribonuclease activity of an artificial catalyst that combines a ligated CuII ion and a guanidinium group at the upper rim of a cone -Calix[4]arene platform
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A cone-calix[4]arene derivative, featuring a guanidinium group and a CuII ion ligated to a 1,4,7-triazacyclononane (TACN) ligand at the 1,3-distal positions of the upper rim, effectively catalyzes the cleavage of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) and a number of diribonucleoside 3′,5′-monophosphates (NpN′). Kinetic and potentiometric measurements support the operation of a general-base/general-acid mechanism and demonstrate that the hydroxo form of the ligated CuII ion is the sole catalytically active species. Rate enhancements relative to the background hydrolysis reaction at 1 mM catalyst concentration are 6 × 105-fold for HPNP and cluster around 107-fold with the most favorable catalyst-NpN′ combinations.
- Salvio, Riccardo,Volpi, Stefano,Cacciapaglia, Roberta,Casnati, Alessandro,Mandolini, Luigi,Sansone, Francesco
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p. 5887 - 5893
(2015/06/16)
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- Flow-Synthesis of Nucleosides Catalyzed by an Immobilized Purine Nucleoside Phosphorylase from Aeromonas hydrophila: Integrated Systems of Reaction Control and Product Purification
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A purine nucleoside phosphorylase from Aeromonas hydrophyla (AhPNP) was covalently immobilized in a pre-packed stainless steel column containing aminopropylsilica particles via Schiff base chemistry upon glutaraldehyde activation. The resulting AhPNP-IMER (Immobilized Enzyme Reactor, immobilization yield ≈50%) was coupled on-line through a 6-way switching valve to an HPLC apparatus containing an analytical or a semi-preparative chromatographic column. The synthesis of five 6-modified purine ribonucleosides was carried out by continuously pumping the reaction mixture through the AhPNP-IMER until the highest conversion was reached, and then directing the reaction mixture to chromatographic separation. The conditions of the AhPNP-catalyzed transglycosylations (2:1 ratio sugar donor:base acceptor; 10 mM phosphate buffer; pH 7.5; temperature 37 °C, flow rate 0.5 mL min-1) were optimized by a fractional factorial experimental design. Coupling the bioconversion step with the product purification in such an integrated platform resulted in a fast and efficient synthetic process (yield=52-89%; 10 mg) where sample handling was minimized. To date, AhPNP-IMER has retained completely its activity upon 50 reactions in 10 months.
- Calleri, Enrica,Cattaneo, Giulia,Rabuffetti, Marco,Serra, Immacolata,Bavaro, Teodora,Massolini, Gabriella,Speranza, Giovanna,Ubiali, Daniela
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p. 2520 - 2528
(2015/08/18)
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- Guanidine-based polymer brushes grafted onto silica nanoparticles as efficient artificial phosphodiesterases
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Polymer brushes grafted to the surface of silica nanoparticles were fabricated by atom-transfer radical polymerization (ATRP) and investigated as catalysts in the cleavage of phosphodiesters. The surfaces of silica nanoparticles were functionalized with an ATRP initiator. Surface-initiated ATRP reactions, in varying proportions, of a methacrylate moiety functionalized with a phenylguanidine moiety and an inert hydrophilic methacrylate species afforded hybrid nanoparticles that were characterized with potentiometric titrations, thermogravimetric analysis, and SEM. The activity of the hybrid nanoparticles was tested in the transesterification of the RNA model compound 2-hydroxypropyl para-nitrophenylphosphate (HPNP) and diribonucleoside monophosphates. A high catalytic efficiency and a remarkable effective molarity, thus overcoming the effective molarities previously observed for comparable systems, indicate the existence of an effective cooperation of the guanidine/guanidinium units and a high level of preorganization in the nanostructure. The investigated system also exhibits a marked and unprecedented selectivity for the diribonucleoside sequence CpA. The results presented open up the way for a novel and straightforward strategy for the preparation of supramolecular catalysts.
- Savelli, Claudia,Salvio, Riccardo
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p. 5856 - 5863
(2015/03/31)
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- Efficacy and site specificity of hydrogen abstraction from DNA 2-deoxyribose by carbonate radicals
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The carbonate radical anion CO3?- is a potent reactive oxygen species (ROS) produced in vivo through enzymatic one-electron oxidation of bicarbonate or, mostly, via the reaction of CO2 with peroxynitrite. Due to the vitally essential role of the carbon dioxide/bicarbonate buffer system in regulation of physiological pH, CO3?- is arguably one of the most important ROS in biological systems. So far, the studies of reactions of CO3?- with DNA have been focused on the pathways initiated by oxidation of guanines in DNA. In this study, low-molecular products of attack of CO3?- on the sugar-phosphate backbone in vitro were analyzed by reversed phase HPLC. The selectivity of damage in double-stranded DNA (dsDNA) was found to follow the same pattern C4′ > C1′ > C5′ for both CO3?- and the hydroxyl radical, though the relative contribution of the C1′ damage induced by CO3?- is substantially higher. In single-stranded DNA (ssDNA) oxidation at C1′ by CO3?- prevails over all other sugar damages. An approximately 2000-fold preference for 8-oxoguanine (8oxoG) formation over sugar damage found in our study identifies CO3?- primarily as a one-electron oxidant with fairly low reactivity toward the sugar-phosphate backbone.
- Roginskaya, Marina,Moore,Ampadu-Boateng,Razskazovskiy
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p. 1431 - 1437
(2015/11/09)
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- Direct One-Pot Synthesis of Nucleosides from Unprotected or 5-O-Monoprotected d -Ribose
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New, improved methods to access nucleosides are of general interest not only to organic chemists but to the greater scientific community as a whole due their key implications in life and disease. Current synthetic methods involve multistep procedures employing protected sugars in the glycosylation of nucleobases. Using modified Mitsunobu conditions, we report on the first direct glycosylation of purine and pyrimidine nucleobases with unprotected d-ribose to provide β-pyranosyl nucleosides and a one-pot strategy to yield β-furanosides from the heterocycle and 5-O-monoprotected d-ribose.
- Downey, A. Michael,Richter, Celin,Pohl, Radek,Mahrwald, Rainer,Hocek, Michal
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supporting information
p. 4604 - 4607
(2015/09/28)
-
- An efficient approach for conversion of 5-substituted 2-thiouridines built in RNA oligomers into corresponding desulfured 4-pyrimidinone products
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Abstract An efficient approach for the desulfuration of C5-substituted 2-thiouridines (R5S2U) bound in the RNA chain exclusively to 4-pyrimidinone nucleoside (R5H2U)-containing RNA products is proposed. This post-synthetic transformation avoids the preparation of a suitably protected H2U phosphoramidite, which otherwise would be necessary for solid-phase synthesis of the modified RNA. Optimization of the desulfuration, which included reaction stoichiometry, time and temperature, allowed to transform a set of ten R5S2U-RNAs into their R5H2U-RNA congeners in ca. 90% yield.
- Chwialkowska, Anna,Wielgus, Ewelina,Leszczynska, Grazyna,Sobczak, Milena,Mikolajczyk, Barbara,Sochacka, Elzbieta,Nawrot, Barbara
-
supporting information
p. 3100 - 3104
(2015/07/08)
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- Guanidine based self-assembled monolayers on Au nanoparticles as artificial phosphodiesterases
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Gold nanoparticles passivated with a long chain alkanethiol decorated with a phenoxyguanidine moiety were prepared and investigated as catalysts in the cleavage of the RNA model compound HPNP and diribonucleoside monophosphates. The catalytic efficiency and the high effective molarity value of the Au monolayer protected colloids points to a high level of cooperation between the catalytic groups.
- Salvio, Riccardo,Cincotti, Antonio
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p. 28678 - 28682
(2014/07/22)
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- Diguanidinocalix[4]arenes as effective and selective catalysts of the cleavage of diribonucleoside monophosphates
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Calix[4]arenes derivatives 1 and 2, featuring two guanidine units at the upper rim, catalyze the transesterification of diribonucleoside monophosphates much more effectively than that of HPNP. Rate accelerations relative to the background range from 10su
- Salvio, Riccardo,Cacciapaglia, Roberta,Mandolini, Luigi,Sansone, Francesco,Casnati, Alessandro
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p. 34412 - 34416
(2014/11/12)
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