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Xu L, Li HM, Lin J. Efficient synthesis of 2'-deoxyguanosine in one-pot cascade by employing an engineered purine nucleoside phosphorylase from Brevibacterium acetylicum. World J Microbiol Biotechnol 2023; 39:286. [PMID: 37606812 DOI: 10.1007/s11274-023-03721-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/02/2023] [Indexed: 08/23/2023]
Abstract
2'-deoxyguanosine is a key medicinal intermediate that could be used to synthesize anti-cancer drug and biomarker in type 2 diabetes. In this study, an enzymatic cascade using thymidine phosphorylase from Escherichia coli (EcTP) and purine nucleoside phosphorylase from Brevibacterium acetylicum (BaPNP) in a one-pot whole cell catalysis was proposed for the efficient synthesis of 2'-deoxyguanosine. BaPNP was semi-rationally designed to improve its activity, yielding the best triple variant BaPNP-Mu3 (E57A/T189S/L243I), with a 5.6-fold higher production of 2'-deoxyguanosine than that of wild-type BaPNP (BaPNP-Mu0). Molecular dynamics simulation revealed that the engineering of BaPNP-Mu3 resulted in a larger and more flexible substrate entrance channel, which might contribute to its catalytic efficiency. Furthermore, by coordinating the expression of BaPNP-Mu3 and EcTP, a robust whole cell catalyst W05 was created, capable of producing 14.8 mM 2'-deoxyguanosine (74.0% conversion rate) with a high time-space yield (1.32 g/L/h) and therefore being very competitive for industrial applications.
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Affiliation(s)
- Lian Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China.
| | - Hui-Min Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China
| | - Juan Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China.
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2
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Magnetic Multi-Enzymatic System for Cladribine Manufacturing. Int J Mol Sci 2022; 23:ijms232113634. [DOI: 10.3390/ijms232113634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Enzyme-mediated processes have proven to be a valuable and sustainable alternative to traditional chemical methods. In this regard, the use of multi-enzymatic systems enables the realization of complex synthetic schemes, while also introducing a number of additional advantages, including the conversion of reversible reactions into irreversible processes, the partial or complete elimination of product inhibition problems, and the minimization of undesirable by-products. In addition, the immobilization of biocatalysts on magnetic supports allows for easy reusability and streamlines the downstream process. Herein we have developed a cascade system for cladribine synthesis based on the sequential action of two magnetic biocatalysts. For that purpose, purine 2′-deoxyribosyltransferase from Leishmania mexicana (LmPDT) and Escherichia coli hypoxanthine phosphoribosyltransferase (EcHPRT) were immobilized onto Ni2+-prechelated magnetic microspheres (MagReSyn®NTA). Among the resulting derivatives, MLmPDT3 (activity: 11,935 IU/gsupport, 63% retained activity, operational conditions: 40 °C and pH 5–7) and MEcHPRT3 (12,840 IU/gsupport, 45% retained activity, operational conditions: pH 5–8 and 40–60 °C) emerge as optimal catalysts for further synthetic application. Moreover, the MLmPDT3/MEcHPRT3 system was biochemically characterized and successfully applied to the one-pot synthesis of cladribine under various conditions. This methodology not only displayed a 1.67-fold improvement in cladribine synthesis (compared to MLmPDT3), but it also implied a practically complete transformation of the undesired by-product into a high-added-value product (90% conversion of Hyp into IMP). Finally, MLmPDT3/MEcHPRT3 was reused for 16 cycles, which displayed a 75% retained activity.
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3
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Fernández-Lucas J, Acebrón I, Wu RY, Alfaro Y, Acosta J, Kaminski PA, Arroyo M, Joachimiak A, Nocek BP, De la Mata I, Mancheño JM. Biochemical and structural studies of two tetrameric nucleoside 2'-deoxyribosyltransferases from psychrophilic and mesophilic bacteria: Insights into cold-adaptation. Int J Biol Macromol 2021; 192:138-150. [PMID: 34624379 DOI: 10.1016/j.ijbiomac.2021.09.164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Nucleoside 2'-deoxyribosyltransferases (NDTs) catalyze the cleavage of glycosidic bonds of 2'-deoxynucleosides and the following transfer of the 2'-deoxyribose moiety to acceptor nucleobases. Here, we report the crystal structures and biochemical properties of the first tetrameric NDTs: the type I NDT from the mesophilic bacterium Enterococcus faecalis V583 (EfPDT) and the type II NDT from the bacterium Desulfotalea psychrophila (DpNDT), the first psychrophilic NDT. This novel structural and biochemical data permitted an exhaustive comparative analysis aimed to shed light into the basis of the high global stability of the psychrophilic DpNDT, which has a higher melting temperature than EfPDT (58.5 °C versus 54.4 °C) or other mesophilic NDTs. DpNDT possesses a combination of unusual structural motifs not present neither in EfPDT nor any other NDT that most probably contribute to its global stability, in particular, a large aliphatic isoleucine-leucine-valine (ILV) bundle accompanied by a vicinal disulfide bridge and also an intersubunit disulfide bridge, the first described for an NDT. The functional and structural features of DpNDT do not fit the standard features of psychrophilic enzymes, which lead us to consider the implication of (sub)cellular levels together with the protein level in the adaptation of enzymatic activity to low temperatures.
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Affiliation(s)
- Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain; Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55 66, Barranquilla, Colombia
| | - Iván Acebrón
- Department of Crystallography and Structural Biology, Institute Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain
| | - Ruiying Y Wu
- Bioscience Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Yohana Alfaro
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 2, 28040 Madrid, Spain
| | - Javier Acosta
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain
| | - Pierre A Kaminski
- Institut Pasteur, Unite ́Biologie des Bactéries Pathogènes à Gram-positif, CNRS URL3526, Paris, France
| | - Miguel Arroyo
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 2, 28040 Madrid, Spain
| | - Andrzej Joachimiak
- Department of Crystallography and Structural Biology, Institute Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain; Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60367, USA
| | - Boguslaw P Nocek
- Bioscience Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Isabel De la Mata
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Nováis 2, 28040 Madrid, Spain
| | - José M Mancheño
- Department of Crystallography and Structural Biology, Institute Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain.
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Teng H, Wu Z, Wang Z, Jin Z, Yang Y, Jin Q. Site-directed mutation of purine nucleoside phosphorylase for synthesis of 2'-deoxy-2'-fluoroadenosine. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Multi-Enzymatic Cascades in the Synthesis of Modified Nucleosides: Comparison of the Thermophilic and Mesophilic Pathways. Biomolecules 2021; 11:biom11040586. [PMID: 33923608 PMCID: PMC8073115 DOI: 10.3390/biom11040586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/02/2021] [Accepted: 04/04/2021] [Indexed: 01/22/2023] Open
Abstract
A comparative study of the possibilities of using ribokinase → phosphopentomutase → nucleoside phosphorylase cascades in the synthesis of modified nucleosides was carried out. Recombinant phosphopentomutase from Thermus thermophilus HB27 was obtained for the first time: a strain producing a soluble form of the enzyme was created, and a method for its isolation and chromatographic purification was developed. It was shown that cascade syntheses of modified nucleosides can be carried out both by the mesophilic and thermophilic routes from D-pentoses: ribose, 2-deoxyribose, arabinose, xylose, and 2-deoxy-2-fluoroarabinose. The efficiency of 2-chloradenine nucleoside synthesis decreases in the following order: Rib (92), dRib (74), Ara (66), F-Ara (8), and Xyl (2%) in 30 min for mesophilic enzymes. For thermophilic enzymes: Rib (76), dRib (62), Ara (32), F-Ara (<1), and Xyl (2%) in 30 min. Upon incubation of the reaction mixtures for a day, the amounts of 2-chloroadenine riboside (thermophilic cascade), 2-deoxyribosides (both cascades), and arabinoside (mesophilic cascade) decreased roughly by half. The conversion of the base to 2-fluoroarabinosides and xylosides continued to increase in both cases and reached 20-40%. Four nucleosides were quantitatively produced by a cascade of enzymes from D-ribose and D-arabinose. The ribosides of 8-azaguanine (thermophilic cascade) and allopurinol (mesophilic cascade) were synthesized. For the first time, D-arabinosides of 2-chloro-6-methoxypurine and 2-fluoro-6-methoxypurine were synthesized using the mesophilic cascade. Despite the relatively small difference in temperatures when performing the cascade reactions (50 and 80 °C), the rate of product formation in the reactions with Escherichia coli enzymes was significantly higher. E. coli enzymes also provided a higher content of the target products in the reaction mixture. Therefore, they are more appropriate for use in the polyenzymatic synthesis of modified nucleosides.
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Oukhrib R, Abdellaoui Y, Berisha A, Abou Oualid H, Halili J, Jusufi K, Ait El Had M, Bourzi H, El Issami S, Asmary FA, Parmar VS, Len C. DFT, Monte Carlo and molecular dynamics simulations for the prediction of corrosion inhibition efficiency of novel pyrazolylnucleosides on Cu(111) surface in acidic media. Sci Rep 2021; 11:3771. [PMID: 33580143 PMCID: PMC7881149 DOI: 10.1038/s41598-021-82927-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
Five novel pyrazolylnucleosides have been evaluated theoretically for their corrosion inhibition efficiency on the Cu(111) surface in acidic media. DFT calculations were carried out to exhibit the intrinsic properties such as lowest unoccupied (ELUMO) and highest occupied (EHOMO) molecular orbital energies, as well as energy gap (∆E), chemical hardness (η), chemical softness (σ), electronegativity (χ), electrophilicity (ω) and nucleophilicity (ε). The theoretical FT-IR spectra were recorded to indicate the presence of the specific bonds in the studied molecules. The surface interactions between the inhibitor molecules and the metal surface were investigated using molecular dynamics simulations and Monte Carlo (MC) simulations. As a result, we have found that the inhibitor pyrazolylnucleosides 5a-e have strong interactions with Cu(111) surface, and therefore have excellent predictive inhibition power against copper corrosion.
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Affiliation(s)
- Rachid Oukhrib
- Apply Chemistry-Physic Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Youness Abdellaoui
- Faculty of Engineering, Environmental Engineering Department, Autonomous University of Yucatan, Mérida, Mexico
| | - Avni Berisha
- Department of Chemistry, Faculty of Natural and Mathematics Science, University of Prishtina, 10000, Pristina, Kosovo
| | - Hicham Abou Oualid
- Laboratory of Biotechnology, Materials and Environment, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
- Green Enenrgy Park, IRESEN, Ben Guerir, Morocco
| | - Jeton Halili
- Department of Chemistry, Faculty of Natural and Mathematics Science, University of Prishtina, 10000, Pristina, Kosovo
| | - Kaltrina Jusufi
- Department of Chemistry, Faculty of Natural and Mathematics Science, University of Prishtina, 10000, Pristina, Kosovo
| | - Mustapha Ait El Had
- Laboratoire de Chimie Biomoléculaire, substances naturelles et Réactivité (URAC 16), Faculté des Sciences Semlalia, Université Cadi Ayyad, B.P. 2390, Marrakech, Morocco
- Laboratoire de Chimie Bioorganique et Macromoléculaire, Faculty of Sciences and Technics Marrakech (FSTMG), Université Cadi Ayyad, Marrakech, Morocco
| | - Hassan Bourzi
- Apply Chemistry-Physic Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Souad El Issami
- Apply Chemistry-Physic Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Fatmah Ali Asmary
- Chemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Virinder S Parmar
- Department of Chemistry and Environmental Science, Medgar Evers College, The City University of New York, 1638 Bedford Avenue, Brooklyn, NY, 11225, USA
| | - Christophe Len
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences, 11 rue Pierre et Marie Curie, 75005, Paris, France.
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Del Arco J, Acosta J, Fernández-Lucas J. New trends in the biocatalytic production of nucleosidic active pharmaceutical ingredients using 2'-deoxyribosyltransferases. Biotechnol Adv 2021; 51:107701. [PMID: 33515673 DOI: 10.1016/j.biotechadv.2021.107701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/27/2020] [Accepted: 01/21/2021] [Indexed: 12/16/2022]
Abstract
Nowadays, pharmaceutical industry demands competitive and eco-friendly processes for active pharmaceutical ingredients (APIs) manufacturing. In this context, enzyme and whole-cell mediated processes offer an efficient, sustainable and cost-effective alternative to the traditional multi-step and environmentally-harmful chemical processes. Particularly, 2'-deoxyribosyltransferases (NDTs) have emerged as a novel synthetic alternative, not only to chemical but also to other enzyme-mediated synthetic processes. This review describes recent findings in the development and scaling up of NDTs as industrial biocatalysts, including the most relevant and recent examples of single enzymatic steps, multienzyme cascades, chemo-enzymatic approaches, and engineered biocatalysts. Finally, to reflect the inventive and innovative steps of NDT-mediated bioprocesses, a detailed analysis of recently granted patents, with specific focus on industrial synthesis of nucleoside-based APIs, is hereunder presented.
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Affiliation(s)
- Jon Del Arco
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain
| | - Javier Acosta
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain; Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55 - 66, Barranquilla, Colombia.
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8
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Méndez MB, Trelles JA, Rivero CW. Decitabine bioproduction using a biocatalyst with improved stability by adding nanocomposites. AMB Express 2020; 10:173. [PMID: 32990767 PMCID: PMC7524979 DOI: 10.1186/s13568-020-01109-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/09/2020] [Indexed: 01/05/2023] Open
Abstract
A novel IDA-LaNDT derivative was able to reach the highest productivity in the biosynthesis of a well-known antitumoral agent called decitabine. However, the combination of two simple and inexpensive techniques such as ionic absorption and gel entrapment with the incorporation of a bionanocomposite such as bentonite significantly improved the stability of this biocatalyst. These modifications allowed the enhancement of storage stability (for at least 18 months), reusability (400 h of successive batches without significant loss of its initial activity), and thermal and solvent stability with respect to the non-entrapped derivative. Moreover, reaction conditions were optimized by increasing the solubility of 5-aza by dilution with dimethylsulfoxide. Therefore, a scale-up of the bioprocess was assayed using the developed biocatalyst, obtaining 221 mg/L·h of DAC. Finally, green parameters were calculated using the nanostabilized biocatalyst, whose results indicated that it was able to biosynthesize DAC by a smooth, cheap, and environmentally friendly methodology.![]()
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Rinaldi F, Fernández-Lucas J, de la Fuente D, Zheng C, Bavaro T, Peters B, Massolini G, Annunziata F, Conti P, de la Mata I, Terreni M, Calleri E. Immobilized enzyme reactors based on nucleoside phosphorylases and 2'-deoxyribosyltransferase for the in-flow synthesis of pharmaceutically relevant nucleoside analogues. BIORESOURCE TECHNOLOGY 2020; 307:123258. [PMID: 32247276 DOI: 10.1016/j.biortech.2020.123258] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
In this work, a mono- and a bi-enzymatic analytical immobilized enzyme reactors (IMERs) were developed as prototypes for biosynthetic purposes and their performances in the in-flow synthesis of nucleoside analogues of pharmaceutical interest were evaluated. Two biocatalytic routes based on nucleoside 2'-deoxyribosyltransferase from Lactobacillus reuteri (LrNDT) and uridine phosphorylase from Clostridium perfrigens (CpUP)/purine nucleoside phosphorylase from Aeromonas hydrophila (AhPNP) were investigated in the synthesis of 2'-deoxy, 2',3'-dideoxy and arabinonucleoside derivatives. LrNDT-IMER catalyzed the synthesis of 5-fluoro-2'-deoxyuridine and 5-iodo-2'-deoxyuridine in 65-59% conversion yield, while CpUP/AhPNP-IMER provided the best results for the preparation of arabinosyladenine (60% conversion yield). Both IMERs proved to be promising alternatives to chemical routes for the synthesis of nucleoside analogues. The developed in-flow system represents a powerful tool for the fast production on analytical scale of nucleosides for preliminary biological tests.
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Affiliation(s)
- Francesca Rinaldi
- Department of Drug Sciences, Università degli Studi di Pavia, I-27100 Pavia, Italy
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Spain; Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, 080003 Barranquilla, Atlántico, Colombia
| | - Diego de la Fuente
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Changping Zheng
- CNRS, IPCM, UMR 8232, Sorbonne Université, 75005 Paris, France
| | - Teodora Bavaro
- Department of Drug Sciences, Università degli Studi di Pavia, I-27100 Pavia, Italy
| | - Benjamin Peters
- Instrumental Analytics R&D, Merck KGaA, DE-64271 Darmstadt, Germany
| | - Gabriella Massolini
- Department of Drug Sciences, Università degli Studi di Pavia, I-27100 Pavia, Italy
| | - Francesca Annunziata
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, I-20133 Milan, Italy
| | - Paola Conti
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, I-20133 Milan, Italy
| | - Isabel de la Mata
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Marco Terreni
- Department of Drug Sciences, Università degli Studi di Pavia, I-27100 Pavia, Italy
| | - Enrica Calleri
- Department of Drug Sciences, Università degli Studi di Pavia, I-27100 Pavia, Italy.
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Acosta J, Del Arco J, Pisabarro V, Gago F, Fernández-Lucas J. N-Ribosyltransferase From Archaeoglobus veneficus: A Novel Halotolerant and Thermostable Biocatalyst for the Synthesis of Purine Ribonucleoside Analogs. Front Bioeng Biotechnol 2020; 8:593. [PMID: 32612982 PMCID: PMC7308715 DOI: 10.3389/fbioe.2020.00593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022] Open
Abstract
Nucleoside-2′-deoxyribosyl-transferases (NDTs) catalyze a transglycosylation reaction consisting of the exchange of the 2′-deoxyribose moiety between a purine and/or pyrimidine nucleoside and a purine and/or pyrimidine base. Because NDTs are highly specific for 2′-deoxyribonucleosides they generally display poor activity on modified C2′ and C3′ nucleosides and this limitation hampers their applicability as biocatalysts for the synthesis of modified nucleosides. We now report the production and purification of a novel NDT from Archaeoglobus veneficus that is endowed with native ribosyltransferase activity and hence it is more properly classified as an N-ribosyltransferase (AvNRT). Biophysical and biochemical characterization revealed that AvNRT is a homotetramer that displays maximum activity at 80°C and pH 6 and shows remarkably high stability at high temperatures (60–80°C). In addition, the activity of AvNRT was found to increase up to 2-fold in 4 M NaCl aqueous solution and to be retained in the presence of several water-miscible organic solvents. For completeness, and as a proof of concept for possible industrial applications, this thermophilic and halotolerant biocatalyst was successfully employed in the synthesis of different purine ribonucleoside analogs.
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Affiliation(s)
- Javier Acosta
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Madrid, Spain
| | - Jon Del Arco
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Madrid, Spain
| | - Victor Pisabarro
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Madrid, Spain
| | - Federico Gago
- Department of Biomedical Sciences and "IQM-CSIC Associated Unit", School of Medicine and Health Sciences University of Alcalá, Madrid, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Madrid, Spain.,Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Barranquilla, Colombia
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11
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Del Arco J, Jordaan J, Moral-Dardé V, Fernández-Lucas J. Sustainable production of nucleoside analogues by a high-efficient purine 2'-deoxyribosyltransferase immobilized onto Ni 2+ chelate magnetic microparticles. BIORESOURCE TECHNOLOGY 2019; 289:121772. [PMID: 31307865 DOI: 10.1016/j.biortech.2019.121772] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 06/10/2023]
Abstract
The present work aims to develop a magnetic biocatalyst for customized production of nucleoside analogues using mutant His-tagged purine 2'-deoxyribosyltransferase from Trypanosoma brucei (TbPDTV11S) immobilized onto Ni2+ chelate magnetic iron oxide porous microparticles (MTbPDTV11S). Biochemical characterization revealed MTbPDTV11S5 as optimal candidate for further studies (10,552 IU g-1; retained activity 54% at 50 °C and pH 6.5). Interestingly, MTbPDTV11S5 displayed the highest activity value described up to date for an immobilized NDT. Moreover, MTbPDTV11S5 was successfully employed in the one-pot, one-step production of different therapeutic nucleoside analogues, such as cladribine or 2'-deoxy-2-fluoroadenosine, among others. Finally, MTbPDTV11S5 proved to be stable when stored at 50 °C for 8 h and pH 6.0 and reusable up to 10 times without negligible loss of activity in the enzymatic production of the antitumor prodrug 2'-deoxy-2-fluoroadenosine.
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Affiliation(s)
- Jon Del Arco
- Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Spain
| | - Justin Jordaan
- ReSyn Biosciences, Meiring Naudé Road, Brummeria, Pretoria 0184, South Africa
| | - Verónica Moral-Dardé
- Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Spain; Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55 - 66, Barranquilla, Colombia.
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12
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Pérez E, Sánchez‐Murcia PA, Jordaan J, Blanco MD, Mancheño JM, Gago F, Fernández‐Lucas J. Enzymatic Synthesis of Therapeutic Nucleosides using a Highly Versatile Purine Nucleoside 2’‐DeoxyribosylTransferase from
Trypanosoma brucei. ChemCatChem 2018. [DOI: 10.1002/cctc.201800775] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Elena Pérez
- Applied Biotechnology GroupUniversidad Europea de Madrid Villaviciosa de Odón E-28670 Spain
| | - Pedro A. Sánchez‐Murcia
- Institute of Theoretical Chemistry Faculty of ChemistryUniversity of Vienna Vienna 1090 Austria
| | - Justin Jordaan
- Biotechnology Innovation CentreRhodes University Grahamstown 6140 South Africa
- ReSyn Biosciences Meiring Naudé Road Brummeria Pretoria 0184 South Africa
| | - María Dolores Blanco
- Department of Biochemistry and Molecular Biology III School of MedicineUniversidad Complutense Madrid E-28040 Spain
| | - José Miguel Mancheño
- Department of Crystallography and Structural BiologyRocasolano Institute (CSIC) Madrid E-28006 Spain
| | - Federico Gago
- Department of Biomedical Sciences and “U. A. IQM-CSIC” School of Medicine and Health SciencesUniversity of Alcalá Alcalá de Henares E-28805 Spain
| | - Jesús Fernández‐Lucas
- Applied Biotechnology GroupUniversidad Europea de Madrid Villaviciosa de Odón E-28670 Spain
- Grupo de Investigación en Desarrollo Agroindustrial SostenibleUniversidad de la Costa Barranquilla 080002 Colombia
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Méndez MB, Rivero CW, López-Gallego F, Guisán JM, Trelles JA. Development of a high efficient biocatalyst by oriented covalent immobilization of a novel recombinant 2′- N -deoxyribosyltransferase from Lactobacillus animalis. J Biotechnol 2018; 270:39-43. [DOI: 10.1016/j.jbiotec.2018.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 12/28/2017] [Accepted: 01/15/2018] [Indexed: 02/01/2023]
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Zhang J, Zhou Y, Liu K, Chu J, Zhang Y, He B. Ca2+-induced stabilization of the nucleoside 2′- deoxyribosyltransferase from Lactobacillus hilgardii ZJS01: Characteristics and application in nucleosides synthesis. Int J Biol Macromol 2018; 106:963-968. [DOI: 10.1016/j.ijbiomac.2017.08.104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 10/19/2022]
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15
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Mitsukawa Y, Hibi M, Matsutani N, Horinouchi N, Takahashi S, Ogawa J. Enzymatic synthesis of 2'-O-methylribonucleosides with a nucleoside hydrolase family enzyme from Lactobacillus buchneri LBK78. J Biosci Bioeng 2017; 123:659-664. [PMID: 28202305 DOI: 10.1016/j.jbiosc.2017.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/25/2016] [Accepted: 01/10/2017] [Indexed: 10/20/2022]
Abstract
2'-O-Methylribonucleosides (2'-OMe-NRs) are promising raw materials for the production of nucleic acid drugs. We previously reported that LbNH, a nucleoside hydrolase from Lactobacillus buchneri LBK78 (NITE P-01581), was the first enzyme found to act on 2'-OMe-NRs. In the present study, we determined that LbNH also has the transribosylation activity between 2'-OMe-NRs and nucleobases, in addition to the hydrolyzing activity towards 2'-OMe-NRs. When 2'-O-methyluridine (2'-OMe-UR) and adenine were reacted with LbNH, 2'-O-methyladenosine (2'-OMe-AR) was produced. LbNH preferred purine nucleobases as its acceptor substrates for the transribosylation with 2'-OMe-UR as a donor substrate. Kinetic analysis of LbNH revealed that adenine behaved as a mixed inhibitor of the hydrolysis of 2'-OMe-UR. Under the optimal reaction conditions, the maximum molar yield of enzymatic 2'-OMe-AR produced reached 0.97% towards 2'-OMe-UR, corresponding to 0.16 g/L.
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Affiliation(s)
- Yuuki Mitsukawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Makoto Hibi
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Narihiro Matsutani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Nobuyuki Horinouchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Satomi Takahashi
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
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Lapponi MJ, Rivero CW, Zinni MA, Britos CN, Trelles JA. New developments in nucleoside analogues biosynthesis: A review. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.08.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Biotransformation of halogenated nucleosides by immobilized Lactobacillus animalis 2′- N -deoxyribosyltransferase. J Fluor Chem 2016. [DOI: 10.1016/j.jfluchem.2016.04.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Fresco-Taboada A, Serra I, Arroyo M, Fernández-Lucas J, de la Mata I, Terreni M. Development of an immobilized biocatalyst based on Bacillus psychrosaccharolyticus NDT for the preparative synthesis of trifluridine and decytabine. Catal Today 2016. [DOI: 10.1016/j.cattod.2015.06.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Genome shuffling of Lactobacillus brevis for enhanced production of thymidine phosphorylase. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0617-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Fresco-Taboada A, Serra I, Fernández-Lucas J, Acebal C, Arroyo M, Terreni M, de la Mata I. Nucleoside 2'-deoxyribosyltransferase from psychrophilic bacterium Bacillus psychrosaccharolyticus--preparation of an immobilized biocatalyst for the enzymatic synthesis of therapeutic nucleosides. Molecules 2014; 19:11231-49. [PMID: 25090115 PMCID: PMC6270756 DOI: 10.3390/molecules190811231] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 11/16/2022] Open
Abstract
Nucleoside 2'-deoxyribosyltransferase (NDT) from the psychrophilic bacterium Bacillus psychrosaccharolyticus CECT 4074 has been cloned and produced for the first time. A preliminary characterization of the recombinant protein indicates that the enzyme is an NDT type II since it catalyzes the transfer of 2'-deoxyribose between purines and pyrimidines. The enzyme (BpNDT) displays a high activity and stability in a broad range of pH and temperature. In addition, different approaches for the immobilization of BpNDT onto several supports have been studied in order to prepare a suitable biocatalyst for the one-step industrial enzymatic synthesis of different therapeutic nucleosides. Best results were obtained by adsorbing the enzyme on PEI-functionalized agarose and subsequent cross-linking with aldehyde-dextran (20 kDa and 70% oxidation degree). The immobilized enzyme could be recycled for at least 30 consecutive cycles in the synthesis of 2'-deoxyadenosine from 2'-deoxyuridine and adenine at 37 °C and pH 8.0, with a 25% loss of activity. High conversion yield of trifluridine (64.4%) was achieved in 2 h when 20 mM of 2'-deoxyuridine and 10 mM 5-trifluorothymine were employed in the transglycosylation reaction catalyzed by immobilized BpNDT at 37 °C and pH 7.5.
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Affiliation(s)
- Alba Fresco-Taboada
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Novais 2, 28040 Madrid, Spain.
| | - Immacolata Serra
- Department of Drug Sciences and Italian Biocatalysis Center, Università degli Studi di Pavia, Via Taramelli 12, 27100 Pavia, Italy.
| | - Jesús Fernández-Lucas
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Novais 2, 28040 Madrid, Spain.
| | - Carmen Acebal
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Novais 2, 28040 Madrid, Spain.
| | - Miguel Arroyo
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Novais 2, 28040 Madrid, Spain.
| | - Marco Terreni
- Department of Drug Sciences and Italian Biocatalysis Center, Università degli Studi di Pavia, Via Taramelli 12, 27100 Pavia, Italy.
| | - Isabel de la Mata
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/José Antonio Novais 2, 28040 Madrid, Spain.
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Fernández-Lucas J, Harris R, Mata-Casar I, Heras A, de la Mata I, Arroyo M. Magnetic chitosan beads for covalent immobilization of nucleoside 2'-deoxyribosyltransferase: application in nucleoside analogues synthesis. J Ind Microbiol Biotechnol 2013; 40:955-66. [PMID: 23832437 DOI: 10.1007/s10295-013-1304-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/12/2013] [Indexed: 11/28/2022]
Abstract
Cross-linked magnetic chitosan beads were prepared in presence of epichlorohydrin under alkaline conditions, and subsequently incubated with glutaraldehyde in order to obtain an activated support for covalent attachment of nucleoside 2'-deoxyribosyltransferase from Lactobacillus reuteri (LrNDT). Changing the amount of magnetite (Fe(3)O(4)) and epichlorohydrin (EPI) led to different macroscopic beads to be used as supports for enzyme immobilization, whose morphology and properties were characterized by scanning electron microscopy, spin electron resonance (ESR), and vibrating sample magnetometry (VSM). Once activated with glutaraldehyde, the best support was chosen after evaluation of immobilization yield and product yield in the synthesis of thymidine from 2'-deoxyuridine and thymine. In addition, optimal conditions for highest activity of immobilized LrNDT on magnetic chitosan were determined by response surface methodology (RSM). Immobilized biocatalyst retained 50 % of its maximal activity after 56.3 h at 60 °C, whereas 100 % activity was observed after storage at 40 °C for 144 h. This novel immobilized biocatalyst has been successfully employed in the enzymatic synthesis of 2'-deoxyribonucleoside analogues as well as arabinosyl-nucleosides such as vidarabine (ara-A) and cytarabine (ara-C). Furthermore, this is the first report which describes the enzymatic synthesis of these arabinosyl-nucleosides catalyzed by an immobilized nucleoside 2'-deoxyribosyltransferase. Finally, the attached enzyme to magnetic chitosan beads could be easily recovered and recycled for 30 consecutive batch reactions with negligible loss of catalytic activity in the synthesis of 2,6-diaminopurine-2'-deoxyriboside and 5-trifluorothymidine.
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Affiliation(s)
- Jesús Fernández-Lucas
- Departamento de Bioquímica y Biología Molecular I. Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, c/José Antonio Novais 2, 28040, Madrid, Spain
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New insights on nucleoside 2'-deoxyribosyltransferases: a versatile biocatalyst for one-pot one-step synthesis of nucleoside analogs. Appl Microbiol Biotechnol 2013; 97:3773-85. [PMID: 23529679 DOI: 10.1007/s00253-013-4816-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 02/24/2013] [Accepted: 02/26/2013] [Indexed: 10/27/2022]
Abstract
In recent years, glycosiltransferases have arisen as standard biocatalysts for the enzymatic synthesis of a wide variety of natural and non-natural nucleosides. Such enzymatic synthesis of nucleoside analogs catalyzed by nucleoside phosphorylases and 2'-deoxyribosyltransferases (NDTs) has demonstrated to be an efficient alternative to the traditional multistep chemical methods, since chemical glycosylation reactions include several protection-deprotection steps. This minireview exhaustively covers literature reports on this topic with the final aim of presenting NDTs as an efficient option to nucleoside phosphorylases for the synthesis of natural and non-natural nucleosides. Detailed comments about structure and catalytic mechanism of described NDTs, as well as their possible biological role, substrate specificity, and advances in detection of new enzyme specificities towards different non-natural nucleoside synthesis are included. In addition, optimization of enzymatic transglycosylation reactions and their application in the synthesis of natural and non-natural nucleosides have been described. Finally, immobilization of NDTs is shown as a practical procedure which leads to the preparation of very interesting biocatalysts applicable to industrial nucleoside synthesis.
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Fernández-Lucas J, Fresco-Taboada A, de la Mata I, Arroyo M. One-step enzymatic synthesis of nucleosides from low water-soluble purine bases in non-conventional media. BIORESOURCE TECHNOLOGY 2012; 115:63-69. [PMID: 22197334 DOI: 10.1016/j.biortech.2011.11.127] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 11/28/2011] [Accepted: 11/29/2011] [Indexed: 05/31/2023]
Abstract
The effect of several water-miscible cosolvents on activity and stability of soluble and immobilized 2'-deoxyribosyltransferase from Lactobacillus reuteri on Sepabeads® has been studied in order to establish optimal conditions for enzymatic synthesis of nucleosides using purine bases with low solubility in aqueous buffer. As a rule of thumb, there was a general reduction of soluble enzyme activity when cosolvent content was gradually increased in reaction medium. In contrast, immobilized enzyme activity was enhanced 1.2-1.4-fold at 20% of methanol, ethanol, 2-propanol, diethylene glycol, and acetone; and at 10% and 30% acetonitrile. Likewise, highest increased activity (1.8-fold) was also obtained in presence of 20% acetonitrile. Immobilized enzyme was successfully used in the synthesis of 2'-deoxyxanthosine and 2'-deoxyguanosine using 2'-deoxyuridine as sugar donor and the corresponding poor water-soluble base in the presence of 30% of methanol, ethanol, 2-propanol, ethylene glycol, acetonitrile, and DMSO, giving high nucleoside yields at 4h.
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Affiliation(s)
- Jesús Fernández-Lucas
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
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