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Koplūnaitė M, Butkutė K, Stankevičiūtė J, Meškys R. Exploring the Mutated Kinases for Chemoenzymatic Synthesis of N4-Modified Cytidine Monophosphates. Molecules 2024; 29:3767. [PMID: 39202847 PMCID: PMC11357392 DOI: 10.3390/molecules29163767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
Nucleosides, nucleotides, and their analogues are an important class of molecules that are used as substrates in research of enzymes and nucleic acid, or as antiviral and antineoplastic agents. Nucleoside phosphorylation is usually achieved with chemical methods; however, enzymatic phosphorylation is a viable alternative. Here, we present a chemoenzymatic synthesis of modified cytidine monophosphates, where a chemical synthesis of novel N4-modified cytidines is followed by an enzymatic phosphorylation of the nucleosides by nucleoside kinases. To enlarge the substrate scope, multiple mutant variants of Drosophila melanogaster deoxynucleoside kinase (DmdNK) (EC:2.7.1.145) and Bacillus subtilis deoxycytidine kinase (BsdCK) (EC:2.7.1.74) have been created and tested. It has been determined that certain point mutations in the active sites of the kinases alter their substrate specificities noticeably and allow phosphorylation of compounds that had been otherwise not phosphorylated by the wild-type DmdNK or BsdCK.
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Affiliation(s)
| | | | | | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania; (K.B.); (J.S.)
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2
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Hoyos P, Perona A, Bavaro T, Berini F, Marinelli F, Terreni M, Hernáiz MJ. Biocatalyzed Synthesis of Glycostructures with Anti-infective Activity. Acc Chem Res 2022; 55:2409-2424. [PMID: 35942874 PMCID: PMC9454102 DOI: 10.1021/acs.accounts.2c00136] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Molecules containing carbohydrate moieties play essential roles in fighting a variety of bacterial and viral infections. Consequently, the design of new carbohydrate-containing drugs or vaccines has attracted great attention in recent years as means to target several infectious diseases.Conventional methods to produce these compounds face numerous challenges because their current production technology is based on chemical synthesis, which often requires several steps and uses environmentally unfriendly reactants, contaminant solvents, and inefficient protocols. The search for sustainable processes such as the use of biocatalysts and eco-friendly solvents is of vital importance. Therefore, their use in a variety of reactions leading to the production of pharmaceuticals has increased exponentially in the last years, fueled by recent advances in protein engineering, enzyme directed evolution, combinatorial biosynthesis, immobilization techniques, and flow biocatalysis. In glycochemistry and glycobiology, enzymes belonging to the families of glycosidases, glycosyltransferases (Gtfs), lipases, and, in the case of nucleoside and nucleotide analogues, also nucleoside phosphorylases (NPs) are the preferred choices as catalysts.In this Account, on the basis of our expertise, we will discuss the recent biocatalytic and sustainable approaches that have been employed to synthesize carbohydrate-based drugs, ranging from antiviral nucleosides and nucleotides to antibiotics with antibacterial activity and glycoconjugates such as neoglycoproteins (glycovaccines, GCVs) and glycodendrimers that are considered as very promising tools against viral and bacterial infections.In the first section, we will report the use of NPs and N-deoxyribosyltransferases for the development of transglycosylation processes aimed at the synthesis of nucleoside analogues with antiviral activity. The use of deoxyribonucleoside kinases and hydrolases for the modification of the sugar moiety of nucleosides has been widely investigated.Next, we will describe the results obtained using enzymes for the chemoenzymatic synthesis of glycoconjugates such as GCVs and glycodendrimers with antibacterial and antiviral activity. In this context, the search for efficient enzymatic syntheses represents an excellent strategy to produce structure-defined antigenic or immunogenic oligosaccharide analogues with high purity. Lipases, glycosidases, and Gtfs have been used for their preparation.Interestingly, many authors have proposed the use Gtfs originating from the biosynthesis of natural glycosylated antibiotics such as glycopeptides, macrolides, and aminoglycosides. These have been used in the chemoenzymatic semisynthesis of novel antibiotic derivatives by modification of the sugar moiety linked to their complex scaffold. These contributions will be described in the last section of this review because of their relevance in the fight against the spreading phenomenon of antibiotic resistance. In this context, the pioneering in vivo synthesis of novel derivatives obtained by genetic manipulation of producer strains (combinatorial biosynthesis) will be shortly described as well.All of these strategies provide a useful and environmentally friendly synthetic toolbox. Likewise, the field represents an illustrative example of how biocatalysis can contribute to the sustainable development of complex glycan-based therapies and how problems derived from the integration of natural tools in synthetic pathways can be efficiently tackled to afford high yields and selectivity. The use of enzymatic synthesis is becoming a reality in the pharmaceutical industry and in drug discovery to rapidly afford collections of new antibacterial or antiviral molecules with improved specificity and better metabolic stability.
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Affiliation(s)
- Pilar Hoyos
- Departamento
de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Almudena Perona
- Departamento
de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Teodora Bavaro
- Dipartimento
di Scienze del Farmaco, Università
di Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - Francesca Berini
- Dipartimento
di Biotecnologie e Scienze della Vita, Università
degli Studi dell’Insubria, Via Dunant 3, 21100 Varese, Italy
| | - Flavia Marinelli
- Dipartimento
di Biotecnologie e Scienze della Vita, Università
degli Studi dell’Insubria, Via Dunant 3, 21100 Varese, Italy
| | - Marco Terreni
- Dipartimento
di Scienze del Farmaco, Università
di Pavia, Viale Taramelli 12, 27100 Pavia, Italy
| | - María J. Hernáiz
- Departamento
de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain,
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3
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Acosta J, Nguyen K, Spitale RC, Fernández-Lucas J. Taylor-made production of pyrimidine nucleoside-5'-monophosphate analogues by highly stabilized mutant uracil phosphoribosyltransferase from Toxoplasma gondii. BIORESOURCE TECHNOLOGY 2021; 339:125649. [PMID: 34329899 DOI: 10.1016/j.biortech.2021.125649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Nowadays, enzymatic synthesis of nucleotides is an efficient and sustainable alternative to chemical methodologies. In this regard, after the biochemical characterization of wild-type and mutant uracil phosphoribosyltransferases from Toxoplasma gondii (TgUPRT, TgUPRT2, and TgUPRT3), TgUPRT2 was selected as the optimal candidate (69.5 IU mg-1, UMP synthesis) for structure-guided immobilization onto Ni2+ chelate (MNiUPRT2) and onto glutaraldehyde-activated microparticles (MGlUPRT2). Among resulting derivatives, MNiUPRT23 (6127 IU g-1biocat; 92% retained activity; 3-5 fold enhanced stability at 50-60 °C) and MGlUPRT2N (3711 IU g-1biocat; 27% retained activity; 8-20 fold enhanced stability at 50-60 °C) displayed the best operability. Moreover, the enzymatic synthesis of different pyrimidine NMPs was performed. Finally, the reusability of both derivatives in 5-FUMP synthesis (MNiUPRT23, 80% retained activity after 7 cycles, 5 min; MGlUPRT2N, 70% retained activity after 10 cycles, 20 min) was carried out at short times.
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Affiliation(s)
- Javier Acosta
- Applied Biotechnology Group, Universidad Europea de Madrid, Calle Tajo, s/n, Villaviciosa de Odón 28670, Spain
| | - Kim Nguyen
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, CA 92697, USA; Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92697, USA
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Calle Tajo, s/n, Villaviciosa de Odón 28670, Spain; Grupo Investigación Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, Calle 58 # 55-66. Barranquilla, Colombia.
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4
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Hellendahl KF, Fehlau M, Hans S, Neubauer P, Kurreck A. Semi-Automated High-Throughput Substrate Screening Assay for Nucleoside Kinases. Int J Mol Sci 2021; 22:11558. [PMID: 34768989 PMCID: PMC8584170 DOI: 10.3390/ijms222111558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 11/21/2022] Open
Abstract
Nucleoside kinases (NKs) are key enzymes involved in the in vivo phosphorylation of nucleoside analogues used as drugs to treat cancer or viral infections. Having different specificities, the characterization of NKs is essential for drug design and nucleotide analogue production in an in vitro enzymatic process. Therefore, a fast and reliable substrate screening method for NKs is of great importance. Here, we report on the validation of a well-known luciferase-based assay for the detection of NK activity in a 96-well plate format. The assay was semi-automated using a liquid handling robot. Good linearity was demonstrated (r² > 0.98) in the range of 0-500 µM ATP, and it was shown that alternative phosphate donors like dATP or CTP were also accepted by the luciferase. The developed high-throughput assay revealed comparable results to HPLC analysis. The assay was exemplarily used for the comparison of the substrate spectra of four NKs using 20 (8 natural, 12 modified) substrates. The screening results correlated well with literature data, and additionally, previously unknown substrates were identified for three of the NKs studied. Our results demonstrate that the developed semi-automated high-throughput assay is suitable to identify best performing NKs for a wide range of substrates.
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Affiliation(s)
- Katja F. Hellendahl
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (K.F.H.); (M.F.); (S.H.); (P.N.)
| | - Maryke Fehlau
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (K.F.H.); (M.F.); (S.H.); (P.N.)
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany
| | - Sebastian Hans
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (K.F.H.); (M.F.); (S.H.); (P.N.)
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (K.F.H.); (M.F.); (S.H.); (P.N.)
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (K.F.H.); (M.F.); (S.H.); (P.N.)
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany
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5
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Abstract
Phosphorylation is a reversible, enzyme-controlled posttranslational process affecting approximately one-third of all proteins in eukaryotic cells at any given time. Any deviation in the degree and/or site of phosphorylation leads to an abnormal conformation of proteins, resulting in a decline or loss of their function. Knowledge of phosphorylation-related pathways is essential for understanding the understanding of the disease pathogenesis and for the design of new therapeutic strategies. Recent availability of various kinases at an affordable price differs in activity, specificity, and stability and provides the opportunity of studying and modulating this reaction in vitro. We can exploit this knowledge for other applications. There is an enormous potential to produce fully decorated and active recombinant proteins, either for biomedical or cosmetic applications. Closely related is the possibility to exploit current achievements and develop new safe and efficacious vaccines, drugs, and immunomodulators. In this review, we outlined the current enzyme-based possibilities for in vitro phosphorylation of peptides and recombinant proteins and the added value that immobilized kinases provide.
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6
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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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7
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Wohlgemuth R. Key advances in biocatalytic phosphorylations in the last two decades: Biocatalytic syntheses in vitro and biotransformations in vivo (in humans). Biotechnol J 2020; 16:e2000090. [PMID: 33283467 DOI: 10.1002/biot.202000090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Indexed: 01/05/2023]
Abstract
Biocatalytic phosphorylation reactions provide several benefits, such as more direct, milder, more selective, and shorter access routes to phosphorylated products. Favorable characteristics of biocatalytic methodologies represent advantages for in vitro as well as for in vivo phosphorylation reactions, leading to important advances in the science of synthesis towards bioactive phosphorylated compounds in various areas. The scope of this review covers key advances of biocatalytic phosphorylation reactions over the last two decades, for biocatalytic syntheses in vitro and for biotransformations in vivo (in humans). From the origins of probiotic life to in vitro synthetic applications and in vivo formation of bioactive pharmaceuticals, the common purpose is to outline the importance, relevance, and underlying connections of biocatalytic phosphorylations of small molecules. Asymmetric phosphorylations attracting increased attention are highlighted. Phosphohydrolases, phosphotransferases, phosphorylases, phosphomutases, and other enzymes involved in phosphorus chemistry provide powerful toolboxes for resource-efficient and selective in vitro biocatalytic syntheses of phosphorylated metabolites, chiral building blocks, pharmaceuticals as well as in vivo enzymatic formation of biologically active forms of pharmaceuticals. Nature's large diversity of phosphoryl-group-transferring enzymes, advanced enzyme and reaction engineering toolboxes make biocatalytic asymmetric phosphorylations using enzymes a powerful and privileged phosphorylation methodology.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland.,Swiss Coordination Committee Biotechnology, Zurich, Switzerland
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8
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Fehlau M, Kaspar F, Hellendahl KF, Schollmeyer J, Neubauer P, Wagner A. Modular Enzymatic Cascade Synthesis of Nucleotides Using a (d)ATP Regeneration System. Front Bioeng Biotechnol 2020; 8:854. [PMID: 32903716 PMCID: PMC7438870 DOI: 10.3389/fbioe.2020.00854] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/02/2020] [Indexed: 12/14/2022] Open
Abstract
Nucleoside-5'-triphosphates (NTPs) and their analogs are building blocks of DNA and are important compounds in both pharmaceutical and molecular biology applications. Currently, commercially available base or sugar modified NTPs are mainly synthesized chemically. Since the chemical production of NTPs is time-consuming and generally inefficient, alternative approaches are under development. Here we present a simple, efficient and generalizable enzymatic synthesis method for the conversion of nucleosides to NTPs. Our one-pot method is modular, applicable to a wide range of natural and modified nucleotide products and accesses NTPs directly from cheap nucleoside precursors. Nucleoside kinases, nucleoside monophosphate (NMP) kinases and a nucleoside diphosphate (NDP) kinase were applied as biocatalysts. Enzymes with different substrate specificities were combined to produce derivatives of adenosine and cytidine triphosphate with conversions of 4 to 26%. The implementation of a (deoxy)ATP recycling system resulted in a significant increase in the conversion to all NTP products, furnishing 4 different NTPs in quantitative conversion. Natural (deoxy)NTPs were synthesized with 60 to >99% conversion and sugar- and base-modified NTPs were produced with 69 to >99% and 27 to 75% conversion, respectively. The presented method is suitable for the efficient synthesis of a wide range of natural and modified NTPs in a sustainable one-pot process.
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Affiliation(s)
- Maryke Fehlau
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany.,BioNukleo GmbH, Berlin, Germany
| | - Felix Kaspar
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany.,BioNukleo GmbH, Berlin, Germany
| | - Katja F Hellendahl
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany
| | - Julia Schollmeyer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany.,BioNukleo GmbH, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany
| | - Anke Wagner
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany.,BioNukleo GmbH, Berlin, Germany
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9
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Abstract
We here described a three-step multi-enzymatic reaction for the one-pot synthesis of vidarabine 5′-monophosphate (araA-MP), an antiviral drug, using arabinosyluracil (araU), adenine (Ade), and adenosine triphosphate (ATP) as precursors. To this aim, three enzymes involved in the biosynthesis of nucleosides and nucleotides were used in a cascade mode after immobilization: uridine phosphorylase from Clostridium perfringens (CpUP), a purine nucleoside phosphorylase from Aeromonas hydrophila (AhPNP), and deoxyadenosine kinase from Dictyostelium discoideum (DddAK). Specifically, CpUP catalyzes the phosphorolysis of araU thus generating uracil and α-d-arabinose-1-phosphate. AhPNP catalyzes the coupling between this latter compound and Ade to form araA (vidarabine). This nucleoside becomes the substrate of DddAK, which produces the 5′-mononucleotide counterpart (araA-MP) using ATP as the phosphate donor. Reaction conditions (i.e., medium, temperature, immobilization carriers) and biocatalyst stability have been balanced to achieve the highest conversion of vidarabine 5′-monophosphate (≥95.5%). The combination of the nucleoside phosphorylases twosome with deoxyadenosine kinase in a one-pot cascade allowed (i) a complete shift in the equilibrium-controlled synthesis of the nucleoside towards the product formation; and (ii) to overcome the solubility constraints of araA in aqueous medium, thus providing a new route to the highly productive synthesis of araA-MP.
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10
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Human Deoxycytidine Kinase Is a Valuable Biocatalyst for the Synthesis of Nucleotide Analogues. Catalysts 2019. [DOI: 10.3390/catal9120997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Natural ribonucleoside-5’-monophosphates are building blocks for nucleic acids which are used for a number of purposes, including food additives. Their analogues, additionally, are used in pharmaceutical applications. Fludarabine-5´-monophosphate, for example, is effective in treating hematological malignancies. To date, ribonucleoside-5’-monophosphates are mainly produced by chemical synthesis, but the inherent drawbacks of this approach have led to the development of enzymatic synthesis routes. In this study, we evaluated the potential of human deoxycytidine kinase (HsdCK) as suitable biocatalyst for the synthesis of natural and modified ribonucleoside-5’-monophosphates from their corresponding nucleosides. Human dCK was heterologously expressed in E. coli and immobilized onto Nickel-nitrilotriacetic acid (Ni-NTA) superflow. A screening of the substrate spectrum of soluble and immobilized biocatalyst revealed that HsdCK accepts a wide range of natural and modified nucleosides, except for thymidine and uridine derivatives. Upon optimization of the reaction conditions, HsdCK was used for the synthesis of fludarabine-5´-monophosphate using increasing substrate concentrations. While the soluble biocatalyst revealed highest product formation with the lowest substrate concentration of 0.3 mM, the product yield increased with increasing substrate concentrations in the presence of the immobilized HsdCK. Hence, the application of immobilized HsdCK is advantageous upon using high substrate concentration which is relevant in industrial applications.
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11
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Abstract
Dextran aldehyde (dexOx), resulting from the periodate oxidative cleavage of 1,2-diol moiety inside dextran, is a polymer that is very useful in many areas, including as a macromolecular carrier for drug delivery and other biomedical applications. In particular, it has been widely used for chemical engineering of enzymes, with the aim of designing better biocatalysts that possess improved catalytic properties, making them more stable and/or active for different catalytic reactions. This polymer possesses a very flexible hydrophilic structure, which becomes inert after chemical reduction; therefore, dexOx comes to be highly versatile in a biocatalyst design. This paper presents an overview of the multiple applications of dexOx in applied biocatalysis, e.g., to modulate the adsorption of biomolecules on carrier surfaces in affinity chromatography and biosensors design, to serve as a spacer arm between a ligand and the support in biomacromolecule immobilization procedures or to generate artificial microenvironments around the enzyme molecules or to stabilize multimeric enzymes by intersubunit crosslinking, among many other applications.
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Del Arco J, Galindo J, Clemente-Suárez VJ, Corrales A, Fernández-Lucas J. Sustainable synthesis of uridine-5'-monophosphate analogues by immobilized uracil phosphoribosyltransferase from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140251. [PMID: 31299354 DOI: 10.1016/j.bbapap.2019.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/21/2019] [Accepted: 07/02/2019] [Indexed: 01/01/2023]
Abstract
Nowadays enzymatic synthesis of nucleic acid derivatives is gaining momentum over traditional chemical synthetic processes. Biotransformations catalyzed by whole cells or enzymes offer an ecofriendly and efficient alternative to the traditional multistep chemical methods, avoiding the use of chemical reagents and organic solvents that are expensive and environmentally harmful. Herein we report for the first time the covalent immobilization a uracil phosphoribosyltransferase (UPRT). In this sense, UPRT from Thermus thermophilus HB8 was immobilized onto glutaraldehyde-activated MagReSyn®Amine magnetic iron oxide porous microparticles (MTtUPRT). According to the catalyst load experiments, MTtUPRT3 was selected as optimal biocatalyst for further studies. MTtUPRT3 was active and stable in a broad range of temperature (70-100 °C) and in the pH interval 6-8, displaying maximum activity at 100 °C and pH 7 (activity 968 IU/gsupport, retained activity 100%). In addition, MTtUPRT3 could be reused up to 8 times in the synthesis of uridine-5'-monophosphate (UMP). Finally, MTtUPRT3 was successfully applied in the sustainable synthesis of different 5-modified uridine-5'-monophosphates at short times. Taking into account these results, MTtUPRT3 would emerge as a valuable biocatalyst for the synthesis of nucleoside monophosphates through an efficient and environmentally friendly methodology.
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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, Villaviciosa de Odón 28670, Spain
| | - Javier Galindo
- Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, Villaviciosa de Odón 28670, Spain
| | - Vicente Javier Clemente-Suárez
- Faculty of Sport Science, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, Villaviciosa de Odón 28670, Spain; Grupo de Investigación en Cultura, Educación y Sociedad, Universidad de la Costa, CUC, Calle 58#55-66, Barranquilla, Colombia
| | - Amaira Corrales
- Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55 - 66, Barranquilla, Colombia
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, Villaviciosa de Odón 28670, 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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13
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Arco JD, Pérez E, Naitow H, Matsuura Y, Kunishima N, Fernández-Lucas J. Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5'-monophospate analogues. BIORESOURCE TECHNOLOGY 2019; 276:244-252. [PMID: 30640018 DOI: 10.1016/j.biortech.2018.12.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/26/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
The present work describes the functional and structural characterization of adenine phosphoribosyltransferase 2 from Thermus thermophilus HB8 (TtAPRT2). The combination of structural and substrate specificity data provided valuable information for immobilization studies. Dimeric TtAPRT2 was immobilized onto glutaraldehyde-activated MagReSyn®Amine magnetic iron oxide porous microparticles by two different strategies: a) an enzyme immobilization at pH 8.5 to encourage the immobilization process by N-termini (MTtAPRT2A, MTtAPRT2B, MTtAPRT2C) or b) an enzyme immobilization at pH 10.0 to encourage the immobilization process through surface exposed lysine residues (MTtAPRT2D, MTtAPRT2E, MTtAPRT2F). According to catalyst load experiments, MTtAPRT2B (activity: 480 IU g-1biocatalyst, activity recovery: 52%) and MTtAPRT2F (activity: 507 IU g-1biocatalyst, activity recovery: 44%) were chosen as optimal derivatives. The biochemical characterization studies demonstrated that immobilization process improved the thermostability of TtAPRT2. Moreover, the potential reusability of MTtAPRT2B and MTtAPRT2F was also tested. Finally, MTtAPRT2F was employed in the synthesis of nucleoside-5'-monophosphate analogues.
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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
| | - Elena Pérez
- Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670, Villaviciosa de Odón, Spain
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Naoki Kunishima
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - 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 Desarrollo Agroindustrial Sostenible, Universidad de la Costa, CUC, Calle 58 # 55 - 66, Barranquilla, Colombia.
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15
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One-Pot Multi-Enzymatic Production of Purine Derivatives with Application in Pharmaceutical and Food Industry. Catalysts 2018. [DOI: 10.3390/catal8010009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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16
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del Arco J, Acosta J, Pereira HM, Perona A, Lokanath NK, Kunishima N, Fernández-Lucas J. Enzymatic Production of Non-Natural Nucleoside-5′-Monophosphates by a Thermostable Uracil Phosphoribosyltransferase. ChemCatChem 2017. [DOI: 10.1002/cctc.201701223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jon del Arco
- Applied Biotechnology Group; Universidad Europea de Madrid; Urbanización El Bosque Calle Tajo s/n 28670 Villaviciosa de Odón Madrid) Spain
| | - Javier Acosta
- Applied Biotechnology Group; Universidad Europea de Madrid; Urbanización El Bosque Calle Tajo s/n 28670 Villaviciosa de Odón Madrid) Spain
| | - Humberto M. Pereira
- Instituto de Física de São Carlos; Universidade de São Paulo; CP369 13560-970 São Carlos SP Brazil
| | - Almudena Perona
- Applied Biotechnology Group; Universidad Europea de Madrid; Urbanización El Bosque Calle Tajo s/n 28670 Villaviciosa de Odón Madrid) Spain
| | - Neratur K. Lokanath
- Department of Studies in Physics; University of Mysore; Mysore 570 006 India
| | - Naoki Kunishima
- RIKEN SPring-8 Center; 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group; Universidad Europea de Madrid; Urbanización El Bosque Calle Tajo s/n 28670 Villaviciosa de Odón Madrid) Spain
- Grupo de Investigación en Desarrollo Agroindustrial Sostenible; Universidad de la Costa; CUC; Calle 58 # 55-66 Barranquilla Colombia
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17
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Serra I, Ubiali D, Piškur J, Munch-Petersen B, Bavaro T, Terreni M. Immobilization of Deoxyadenosine Kinase fromDictyostelium discoideum(DddAK) and Its Application in the 5’-Phosphorylation of Arabinosyladenine and Arabinosyl-2-fluoroadenine. ChemistrySelect 2017. [DOI: 10.1002/slct.201700558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Immacolata Serra
- Department of Drug Sciences; University of Pavia; Viale T. Taramelli 12 I-27100 Pavia Italy
- Department of Food, Environmental and Nutritional Science (DeFENS); University of Milan; Via L. Mangiagalli 25 I-20133 Milano Italy
| | - Daniela Ubiali
- Department of Drug Sciences; University of Pavia; Viale T. Taramelli 12 I-27100 Pavia Italy
- ISTM-CNR; Via C. Golgi 19 I-20133 Milano Italy
| | - Jure Piškur
- Department of Biology; Lund University; Lund 22362 Sweden
| | - Birgitte Munch-Petersen
- Department of Biology; Lund University; Lund 22362 Sweden
- Department of Science, Systems and Models; Roskilde University; Roskilde 4000 Denmark
| | - Teodora Bavaro
- Department of Drug Sciences; University of Pavia; Viale T. Taramelli 12 I-27100 Pavia Italy
| | - Marco Terreni
- Department of Drug Sciences; University of Pavia; Viale T. Taramelli 12 I-27100 Pavia Italy
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18
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Del Arco J, Cejudo-Sanches J, Esteban I, Clemente-Suárez VJ, Hormigo D, Perona A, Fernández-Lucas J. Enzymatic production of dietary nucleotides from low-soluble purine bases by an efficient, thermostable and alkali-tolerant biocatalyst. Food Chem 2017; 237:605-611. [PMID: 28764042 DOI: 10.1016/j.foodchem.2017.05.136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 05/16/2017] [Accepted: 05/28/2017] [Indexed: 11/17/2022]
Abstract
Traditionally, enzymatic synthesis of nucleoside-5'-monophosphates (5'-NMPs) using low water-soluble purine bases has been described as less efficient due to their low solubility in aqueous media. The use of enzymes from extremophiles, such as thermophiles or alkaliphiles, offers the potential to increase solubilisation of these bases by employing high temperatures or alkaline pH. This study describes the cloning, expression and purification of hypoxanthine-guanine-xanthine phosphoribosyltransferase from Thermus thermophilus (TtHGXPRT). Biochemical characterization indicates TtHGXPRT as a homotetramer with excellent activity and stability across a broad range of temperatures (50-90°C) and ionic strengths (0-500mMNaCl), but it also reveals an unusually high activity and stability under alkaline conditions (pH range 8-11). In order to explore the potential of TtHGXPRT as an industrial biocatalyst, enzymatic production of several dietary 5'-NMPs, such as 5'-GMP and 5'-IMP, was carried out at high concentrations of guanine and hypoxanthine.
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Affiliation(s)
- J Del Arco
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - J Cejudo-Sanches
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - I Esteban
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - V J Clemente-Suárez
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - D Hormigo
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - A Perona
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - J Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain; Grupo de Investigación en Desarrollo Agroindustrial Sostenible, Universidad de la Costa, CUC, Calle 58 # 55-66, Barranquilla, Colombia.
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19
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Del Arco J, Martinez M, Donday M, Clemente-Suarez VJ, Fernández-Lucas J. Cloning, expression and biochemical characterization of xanthine and adenine phosphoribosyltransferases from Thermus thermophilus HB8. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1313837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jon Del Arco
- Applied Biotechnology Group, Research and Doctoral School, European University of Madrid, Urbanización El Bosque, Madrid, Spain
| | - María Martinez
- Applied Biotechnology Group, Research and Doctoral School, European University of Madrid, Urbanización El Bosque, Madrid, Spain
| | - Manuel Donday
- Applied Biotechnology Group, Research and Doctoral School, European University of Madrid, Urbanización El Bosque, Madrid, Spain
| | - Vicente Javier Clemente-Suarez
- Applied Biotechnology Group, Research and Doctoral School, European University of Madrid, Urbanización El Bosque, Madrid, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Research and Doctoral School, European University of Madrid, Urbanización El Bosque, Madrid, Spain
- Grupo de Investigación en Desarrollo Agroindustrial Sostenible, Ingenieróa Agroindustrial, Universidad de la Costa, CUC, Barranquilla, Colombia
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20
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21
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Iglesias LE, Lewkowicz ES, Medici R, Bianchi P, Iribarren AM. Biocatalytic approaches applied to the synthesis of nucleoside prodrugs. Biotechnol Adv 2015; 33:412-34. [PMID: 25795057 DOI: 10.1016/j.biotechadv.2015.03.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 03/01/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Nucleosides are valuable bioactive molecules, which display antiviral and antitumour 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.
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Affiliation(s)
- Luis E Iglesias
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina
| | - Elizabeth S Lewkowicz
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina
| | - Rosario Medici
- Biocatalysis Group, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Paola Bianchi
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina
| | - Adolfo M Iribarren
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876 Bernal, Buenos Aires, Argentina; Laboratorio de Química de Ácidos Nucleicos, INGEBI-CONICET, Vuelta de Obligado 2490, 1428 Ciudad Autónoma de Buenos Aires, Argentina.
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22
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Slot Christiansen L, Munch-Petersen B, Knecht W. Non-Viral Deoxyribonucleoside Kinases--Diversity and Practical Use. J Genet Genomics 2015; 42:235-48. [PMID: 26059771 DOI: 10.1016/j.jgg.2015.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/04/2015] [Accepted: 01/05/2015] [Indexed: 12/30/2022]
Abstract
Deoxyribonucleoside kinases (dNKs) phosphorylate deoxyribonucleosides to their corresponding monophosphate compounds. dNks also phosphorylate deoxyribonucleoside analogues that are used in the treatment of cancer or viral infections. The study of the mammalian dNKs has therefore always been of great medical interest. However, during the last 20 years, research on dNKs has gone into non-mammalian organisms. In this review, we focus on non-viral dNKs, in particular their diversity and their practical applications. The diversity of this enzyme family in different organisms has proven to be valuable in studying the evolution of enzymes. Some of these newly discovered enzymes have been useful in numerous practical applications in medicine and biotechnology, and have contributed to our understanding of the structural basis of nucleoside and nucleoside analogue activation.
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Affiliation(s)
| | - Birgitte Munch-Petersen
- Department of Biology, Lund University, Lund 22362, Sweden; Department of Science, Systems and Models, Roskilde University, Roskilde 4000, Denmark
| | - Wolfgang Knecht
- Department of Biology, Lund University, Lund 22362, Sweden; Lund Protein Production Platform, Lund University, Lund 22362, Sweden.
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