Adolfo M. Iribarren

National University of Quilmes, Quilmes, Buenos Aires, Argentina

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Publications (63)132.54 Total impact


  • No preview · Article · Jan 2016 · European Journal of Organic Chemistry
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    María A. Dellafiore · Javier M. Montserrat · Adolfo M. Iribarren
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    ABSTRACT: A guanine-rich DNA oligonucleotide complexed with hemin was used to catalyze controlled oxygen transfer reactions to different sulfides for sulfoxide preparation in the presence of H2O2. Comparable activities were obtained when using fully modified L-DNA. In addition, oligonucleotide immobilization led to an active catalyst which could be successfully recoveredand reused without loss of activity. © 2015 Dellafiore et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
    Preview · Article · Jun 2015 · PLoS ONE
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    ABSTRACT: Nucleosides are valuable bioactive molecules, which display antiviral and antitumor activities. Diverse types of prodrugs are designed to enhance their therapeutic efficacy, however this strategy faces the troublesome selectivity issues of nucleoside chemistry. In this context, the aim of this review is to give an overview of the opportunities provided by biocatalytic procedures in the preparation of nucleoside prodrugs. The potential of biocatalysis in this research area will be presented through examples covering the different types of nucleoside prodrugs: nucleoside analogues as prodrugs, nucleoside lipophilic prodrugs and nucleoside hydrophilic prodrugs. Copyright © 2015. Published by Elsevier Inc.
    No preview · Article · Mar 2015 · Biotechnology advances
  • Ana Laura Valino · Adolfo M. Iribarren · Elizabeth Lewkowicz
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    ABSTRACT: Since the preparation of nucleoside 5′-diphosphates by classical methodologies is complex, multistep enzymatic systems were explored to synthesize pyrimidine nucleoside 5′-diphosphates starting from readily available reagents. Different strategies were combined to prepare uridine- and thymidine 5′-diphosphates as ribo- and deoxyribonucleoside models, respectively. For uridine 5′-diphosphate synthesis, conversions between 38 and 66% were achieved, using a simple methodology that involves commercial yeast extract as biocatalyst and biocatalytically in situ prepared uridine 5′-monophosphate. Corynebacterium ammoniagenes ATCC 19350 was used for the first time as biocatalyst to synthesize uridine 5′-monophosphate from uracil and orotic acid while Raoultella planticola was the selected biocatalyst for uridine 5′-monophosphate synthesis from uridine. The overall performances of all the tested approaches were similar but the use of uracil leads to a more suitable and cheaper process. Alternatively, for thymidine 5′-diphosphate synthesis two consecutive one pot multistep enzyme systems were assayed. In the first biotransformation, 2′-deoxyribose 5-phosphate was formed from glucose by Erwinia carotovora whole cells followed by the action of phosphopentomutase and thymidine phosphorylase affording thymidine in 85% conversion relative to 2′-deoxyribose 5-phosphate. Finally, in the second one pot reaction, the nucleoside was converted to thymidine 5′-diphosphate by the combined action of E. coli BL21 pET22b-phoRp and Saccharomyces cerevisiae.
    No preview · Article · Dec 2014 · Journal of Molecular Catalysis B Enzymatic
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    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.
    No preview · Article · Sep 2014 · ChemMedChem
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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.
    No preview · Article · Aug 2013 · Applied Microbiology and Biotechnology
  • Cyntia M Palacio · María B Sabaini · Adolfo M Iribarren · Luis E Iglesias
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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.
    No preview · Article · Mar 2013 · Journal of Biotechnology
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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.
    No preview · Article · Feb 2013 · ChemPlusChem
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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.
    Full-text · Article · Dec 2012 · The Journal of Physical Chemistry B
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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.
    No preview · Article · Dec 2012 · Tetrahedron Letters
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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.
    No preview · Article · Dec 2012 · PROCESS BIOCHEMISTRY
  • 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.
    No preview · Article · Sep 2012 · Biocatalysis and Biotransformation
  • Esteban D. Gudino · Adolfo M. Iribarren · Luis E. Iglesias

    No preview · Article · Mar 2012
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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.
    No preview · Article · Feb 2012 · Bioorganic & medicinal chemistry
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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.
    No preview · Article · Nov 2011 · Applied biochemistry and biotechnology
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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.
    No preview · Article · Jun 2011 · Biotechnology Letters
  • Matías Nóbile · Marco Terreni · Elizabeth Lewkowicz · Adolfo M. Iribarren
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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.
    No preview · Article · Dec 2010 · Biocatalysis and Biotransformation
  • 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.
    No preview · Article · Aug 2010 · Bioorganic & medicinal chemistry letters
  • 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.
    No preview · Article · Jun 2010 · Biocatalysis and Biotransformation
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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.
    Full-text · Article · Mar 2010 · Bioorganic & medicinal chemistry letters