Adolfo M. Iribarren

National University of Quilmes, Quilmes, Provincia de Buenos Aires, Argentina

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Publications (64)141.62 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: The highly conserved untranslated regions of the hepatitis C virus (HCV) play a fundamental role in viral translation and replication and are therefore attractive targets for drug development. A set of modified DNAzymes carrying (2′R)-, (2′S)-2′-deoxy-2′-C-methyl- and -2′-O-methylnucleosides at various positions of the catalytic core were assayed against the 5′-internal ribosome entry site element (5′-IRES) region of HCV. Intracellular stability studies showed that the highest stabilization effects were obtained when the DNAzymes′ cores were jointly modified with 2′-C-methyl- and 2′-O-methylnucleosides, yielding an increase by up to fivefold in the total DNAzyme accumulation within the cell milieu within 48 h of transfection. Different regions of the HCV IRES were explored with unmodified 10–23 DNAzymes for accessibility. A subset of these positions was tested for DNAzyme activity using an HCV IRES-firefly luciferase translation-dependent RNA (IRES-FLuc) transcript, in the rabbit reticulocyte lysate system and in the Huh-7 human hepatocarcinoma cell line. Inhibition of IRES-dependent translation by up to 65 % was observed for DNAzymes targeting its 285 position, and it was also shown that the modified DNAzymes are as active as the unmodified one.
    ChemMedChem 07/2014; · 2.84 Impact Factor
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    ABSTRACT: Natural and modified nucleoside-5'-monophosphates and their precursors are valuable compounds widely used in biochemical studies. Bacterial nonspecific acid phosphatases (NSAPs) are a group of enzymes involved in the hydrolysis of phosphoester bonds, and some of them exhibit phosphotransferase activity. NSAP containing Enterobacter aerogenes and Raoultella planticola whole cells were evaluated in the phosphorylation of a wide range of nucleosides and nucleoside precursors using pyrophosphate as phosphate donor. To increase the productivity of the process, we developed two genetically modified strains of Escherichia coli which overexpressed NSAPs of E. aerogenes and R. planticola. These new recombinant microorganisms (E. coli BL21 pET22b-phoEa and E. coli BL21 pET22b-phoRp) showed higher activity than the corresponding wild-type strains. Reductions in the reaction times from 21 h to 60 min, from 4 h to 15 min, and from 24 h to 40 min in cases of dihydroxyacetone, inosine, and fludarabine, respectively, were obtained.
    Applied Microbiology and Biotechnology 08/2013; · 3.81 Impact Factor
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    ABSTRACT: N-Monoacetylated derivatives of ribo- (adenosine, guanosine) and 2'-deoxyribonucleosides (2'-deoxyadenosine and 2'-deoxyguanosine), useful as oligonucleotide building blocks, were obtained in 88-100% by enzymatic chemoselective hydrolysis of the corresponding peracetylated nucleosides. Among the tested hydrolases, most satisfactory results were found with acylase I from Aspergillus melleus and Candida antarctica lipase B. For acylase I, the observed chemoselectivity towards ester hydrolysis, without amide reaction, broadens the information about the selectivity of the enzyme and its synthetic applications in the field of nucleosides.
    Journal of Biotechnology 03/2013; · 3.18 Impact Factor
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    ABSTRACT: The use of nucleoside phosphorylases (NPs; EC 2.4.2.n) represents a convenient alternative to the chemical route for the synthesis of natural and modified nucleosides. We purified four recombinantly expressed nucleoside phosphorylases from the bacterial pathogens Citrobacter koseri, Clostridium perfringens, and Streptococcus pyogenes (CkPNPI, CkPNPII, CpUP, SpUP) and their substrate specificity was investigated towards either natural pyrimidine or purine nucleosides and some analogues, namely, arabinosyladenine (araA) and 2′,3′-dideoxyinosine (ddI). A 2–3 % activity towards these latter compounds (compared to the natural substrates) was observed. Enzyme activities were compared to the specificities obtained for the enzymes pyrimidine nucleoside phosphorylase from Bacillus subtilis (BsPyNP) and purine nucleoside phosphorylase from Aeromonas hydrophila (AhPNPII) previously reported by some of the authors. The enzymes displaying the suitable specificity for the synthesis of araA and ddI were immobilized on aldehyde–agarose. The immobilized preparations were highly stable at alkaline pH and in the presence of methanol or acetonitrile as cosolvent. They were used in the synthesis of araA and ddI by a one-pot, bienzymatic transglycosylation achieving 74 and 44 % conversion, respectively.
    ChemPlusChem 02/2013; 78(2).
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    ABSTRACT: The hybridization performance of a set of 12 mer RNA:RNA duplexes containing 2'-C-methyluridine, 5-bromo-2'-C-methyluridine or (2'S)-2'-deoxy-2'-C-methyluridine was analyzed. Melting point temperatures of the modified duplexes showed an important Tm decrease (-8.9 to -12.5ºC), while circular dichroism experiments indicated that the helix was still A-type, suggesting a localized disturbance disorder. Molecular dynamics simulations using AMBER were carried out in order to gain structural knowledge about the effect of the 2'-C-methyl modification in double stranded environments. On the other hand, in an attempt to explain the behavior of the 2'-deoxy-2'-C-methyl nucleosides in single stranded environments, like the 10-23 DNAzyme core, molecular dynamic simulations were performed, incorporating the modified analogs into single stranded reported stem-loop structures, studding the sugar conformations along the MD trajectories. It was observed that although their preferential conformational states, the 2'-C-methyl analogs are flexible enough to adopt a different puckering in single stranded environments.
    The Journal of Physical Chemistry B 12/2012; · 3.61 Impact Factor
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    ABSTRACT: Organocatalysis is assessed for the first time in the synthesis of purine and pyrimidine acyclic nucleosides providing high yields and straightforward work-up procedures. Nucleobases containing aldehydes are catalytically ligated (C–C bond formation) to acetone or to phosphonate-containing ketones by means of pyrrolidine or silica-immobilized piperazine as amine-based organocatalysts.
    Tetrahedron Letters 12/2012; 53(50):6797–6800. · 2.40 Impact Factor
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    ABSTRACT: Purine arabinosides are well known antiviral and antineoplastic drugs. Since their chemical synthesis is complex, time-consuming, and polluting, enzymatic synthesis provides an advantageous alternative. In this work, we describe the microbial whole cell synthesis of purine arabinosides through nucleoside phosphorylase-catalyzed transglycosylation starting from their pyrimidine precursors. By screening of our microbial collection, Citrobacter koseri (CECT 856) was selected as the best biocatalyst for the proposed biotransformation. In order to enlarge the scale of the transformations to 150 mL for future industrial applications, the biocatalyst immobilization by entrapment techniques and its behavior in different reactor configurations, considering both batch and continuous processes, were analyzed. C. koseri immobilized in agarose could be used up to 68 times and the storage stability was at least 9 months. By this approach, fludarabine (58% yield in 14 h), vidarabine (71% yield in 26 h) and 2,6-diaminopurine arabinoside (77% yield in 24 h), were prepared.
    Process Biochemistry. 12/2012; 47(12):2182–2188.
  • Esteban D. Gudiño, Adolfo M. Iribarren, Luis E. Iglesias
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    ABSTRACT: Methyl 2,3-di-O-acetyl-α,β-d-xylofuranoside was prepared as the sole regioisomer in 63–72% yield, according to the applied mass of substrate, through a Candida antarctica lipase B catalysed alcoholysis of methyl 2,3,5-tri-O-acetyl-α,β-d-xylofuranoside. The product is a potential synthetic precursor for 5-modified xylofuranosides and 5′-modified xylonucleosides.
    Biocatalysis and Biotransformation 09/2012; 30(4). · 0.90 Impact Factor
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    ABSTRACT: The catalytic core of a 10-23 DNAzyme was modified introducing conformationally restricted nucleosides such as (2'R)-, (2'S)-2'-deoxy-2'-C-methyluridine, (2'R)-, (2'S)-2'-deoxy-2'-C-methylcytidine, 2,2'-anhydrouridine and LNA-C, in one, two or three positions. Catalytic activities under pseudo first order conditions were compared at different Mg(2+) concentrations using a short RNA substrate. At low Mg(2+) concentrations, triple modified DNAzymes with similar kinetic performance to that displayed by the non-modified control were identified. In the search for a partial explanation of the obtained results, in silico studies were carried out in order to explore the conformational behavior of 2'-deoxy-2'-C-methylpyrimidines in the context of a loop structure, suggesting that at least partial flexibility is needed for the maintenance of activity. Finally, the modified 2'-C-methyl DNAzyme activity was tested assessing the inhibition of Stat3 expression and the decrease in cell proliferation using the human breast cancer cell line T47D.
    Bioorganic & medicinal chemistry 02/2012; 20(8):2581-6. · 2.82 Impact Factor
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    ABSTRACT: 2-deoxyribose 5-phosphate (DR5P) is a key intermediate in the biocatalyzed preparation of deoxyribonucleosides. Therefore, DR5P production by means of simpler, cleaner, and economic pathways becomes highly interesting. One strategy involves the use of bacterial whole cells containing DR5P aldolase as biocatalyst for the aldol addition between acetaldehyde and D: -glyceraldehyde 3-phosphate or glycolytic intermediates that in situ generate the acceptor substrate. In this work, diverse microorganisms capable of synthesizing DR5P were selected by screening several bacteria genera. In particular, Erwinia carotovora ATCC 33260 was identified as a new biocatalyst that afforded 14.1-mM DR5P starting from a cheap raw material like glucose.
    Applied biochemistry and biotechnology 11/2011; 166(2):300-8. · 1.94 Impact Factor
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    ABSTRACT: The synthesis of halogenated nucleosides and nucleobases is of interest due to their chemical and pharmacological applications. Herein, the enzymatic halogenation of nucleobases and analogues catalysed by microorganisms and by chloroperoxidase from Caldariomyces fumago has been studied. This latter enzyme catalysed the chlorination and bromination of indoline and uracil. Pseudomonas, Citrobacter, Aeromonas, Streptomyces, Xanthomonas, and Bacillus genera catalysed the chlorination and/or bromination of indole and indoline. Different products were obtained depending on the substrate, the biocatalyst and the halide used. In particular, 85% conversion from indole to 5-bromoindole was achieved using Streptomyces cetonii.
    Biotechnology Letters 06/2011; 33(10):1999-2003. · 1.85 Impact Factor
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    ABSTRACT: Abstract Microbial transglycosylation is useful as a green alternative in the preparation of purine nucleosides and analogues, especially for those that display pharmacological activities. In a search for new transglycosylation biocatalysts, two Aeromonas hydrophila strains were selected. The substrate specificity of both micro-organisms was studied and, as a result, several nucleoside analogues have been prepared. Among them, ribavirin, a broad spectrum antiviral, and the well-known anti HIV didanosine, were prepared, in 77 and 62% yield using A. hydrophila CECT 4226 and A. hydrophila CECT 4221, respectively. In order to scale-up the processes, the reaction conditions, product purification and biocatalyst preparation were analyzed and optimized.
    12/2010; 28(5-6):395-402.
  • Laura Robaldo, Javier M Montserrat, Adolfo M Iribarren
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    ABSTRACT: The catalytic core of a 10-23 DNAzyme was modified using (2'R), (2'S)-2'-deoxy-2'-C-methyluridine and LNA-T. Catalytic activities under pseudo first order conditions were compared at different Mg(2+) concentrations, indicating that certain 2'-C-methyl modified DNAzymes have significant activities. Resistance against MCF-7 cell lysate and endonuclease RQ1 was also measured, showing that the introduction of 2'-C-methyl-2'-deoxynucleosides increased the stability.
    Bioorganic & medicinal chemistry letters 08/2010; 20(15):4367-70. · 2.65 Impact Factor
  • Esteban D. Gudiño, Adolfo M. Iribarren, Luis E. Iglesias
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    ABSTRACT: Abstract Candida antarctica B lipase (CAL-B) catalysed alcoholysis of a series of peracetylated alkyl α, β-D-ribofuranosides was assayed. Methyl and ethyl 2,3-di-O-acetyl-α, β-D-ribofuranosides enriched in the α-anomer were regioselectively prepared through this enzymatic deacetylation in 33% and 43% yield, respectively, the latter being a new compound. Isopropyl 2,3,5-tri-O-acetyl-β-D-ribofuranoside gave the new isopropyl 2,3-di-O-acetyl-β-D-ribofuranoside in 24% yield. The anomeric substituent affects the regioselectivity of the reaction, since n-propyl and n-butyl α, β-D-ribofuranosides reacted without selectivity.
    06/2010; 28(4):267-271.
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    ABSTRACT: A new synthesis of 2'-C-methyluridine phosphoramidite is presented. Special emphasis is dedicated to the improvement of the protection of the tertiary 2'-hydroxyl group. Comparison to previous protecting strategies and analysis of stability under 5'-DMTr removing conditions are discussed. The synthetic incorporation of this modified nucleoside into the catalytic core of a hammerhead ribozyme against the estrogen receptor alpha protein (ER-alpha), and transfection experiments in MCF-7 cell line are also presented.
    Bioorganic & medicinal chemistry letters 03/2010; 20(9):2806-8. · 2.65 Impact Factor
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    ABSTRACT: Candida antarctica lipase B (CAL-B)-catalysed regioselective deacetylation of 2′,3′,5′-tri-O-acetyl-1-β-d-arabinofuranosyluracil (1) and 2′,3′,5′-tri-O-acetyl-9-β-d-arabinofuranosyladenine (2) was studied. The choice of the reaction medium allowed the regioselective formation of products bearing different degree of acetylation: in isopropanol, CAL-B catalysed the formation of the corresponding 2′-O-acetylated arabinonucleosides, while hydrolyses afforded the 2′,3′-di-O-acetylated products. In particular, the procedure herein described allows a simple and efficient preparation of the reported vidarabine prodrug 2′,3′-di-O-acetyl-9-β-d-arabinofuranosyladenine, avoiding the utilisation of protective groups. Moreover, to achieve full deacetylation of the assayed substrates, a set of commercial hydrolases and fungal keratinases from Doratomyces microsporus (DMK) and Paecilomyces marquandii (PMK) were tested. While only PMK and DMK catalysed the quantitative complete deacetylation of 1, DMK accomplished full deacetylation of 2 in shorter time than the other assayed enzymes.
    Journal of Molecular Catalysis B Enzymatic 03/2010; 62:225-229. · 2.82 Impact Factor
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    ABSTRACT: ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
    ChemInform 01/2010; 25(40).
  • Esteban D. Gudiño, Adolfo M. Iribarren, Luis E. Iglesias
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    ABSTRACT: Methyl 3-O-acetyl-2-deoxy-α-d-ribofuranoside, 1,3-di-O-acetyl-2-deoxy-α-d-ribofuranose and 1,2,3-tri-O-acetyl-α-d-arabinofuranose were diastereoselectively prepared (de=100%) from anomeric mixtures of the corresponding 5-acetylated compounds through Candida antarctica B lipase (CAL B)-catalysed alcoholysis.
    Tetrahedron Asymmetry 08/2009; 20(15):1813-1816. · 2.12 Impact Factor
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    ABSTRACT: Experimental conditions such as shaking (aeration) rate, concentration of reagents and extent of culture growth for the optimal synthesis of adenosine using Escherichia coli BL21 as biocatalyst were assessed, achieving 95% yield in 30 min of reaction using microorganisms harvested from late exponential phase. The ability of E. coli BL21 to synthesise purine nucleosides containing sugar residues such as 2'-deoxyribose, 2',3'-dideoxyribose and arabinose was also verified. 2'-Deoxyribo- and arabinonucleosides could be prepared in high yield, while the results obtained with 2',3'-dideoxyribonucleosides were not satisfactory. In the case of 2'-deoxyadenosine, using thymidine as a starting material, a yield of 94% was achieved at 45°C.
    Biocatalysis and Biotransformation 07/2009; 20(5):347-351. · 0.90 Impact Factor
  • Rosario Médici, Adolfo M Iribarren, Elizabeth S Lewkowicz
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    ABSTRACT: Unlike the preparation of other purine nucleosides, transglycosylation from a pyrimidine nucleoside and guanine is difficult because of the low solubility of this base. Thus, another strategy, based on the coupled action of two whole cell biocatalyzed reactions, transglycosylation and deamination, was used. Enterobacter gergoviae and Arthrobacter oxydans were employed to synthesize 9-beta-d-arabinofuranosylguanine (AraG), an efficient anti leukemic drug.
    Bioorganic & medicinal chemistry letters 06/2009; 19(15):4210-2. · 2.65 Impact Factor

Publication Stats

344 Citations
141.62 Total Impact Points


  • 2000–2013
    • National University of Quilmes
      • Department of Science and Technology
      Quilmes, Provincia de Buenos Aires, Argentina
  • 2005
    • University of Rome Tor Vergata
      Roma, Latium, Italy
  • 1990
    • European Molecular Biology Laboratory
      Heidelburg, Baden-Württemberg, Germany