1
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Tang P, Harding CJ, Dickson AL, da Silva RG, Harrison DJ, Czekster CM. Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase. ACS Catal 2024; 14:3090-3102. [PMID: 38449528 PMCID: PMC10913048 DOI: 10.1021/acscatal.3c06260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 03/08/2024]
Abstract
Nucleosides are ubiquitous to life and are required for the synthesis of DNA, RNA, and other molecules crucial for cell survival. Despite the notoriously difficult organic synthesis of nucleosides, 2'-deoxynucleoside analogues can interfere with natural DNA replication and repair and are successfully employed as anticancer, antiviral, and antimicrobial compounds. Nucleoside 2'-deoxyribosyltransferase (dNDT) enzymes catalyze transglycosylation via a covalent 2'-deoxyribosylated enzyme intermediate with retention of configuration, having applications in the biocatalytic synthesis of 2'-deoxynucleoside analogues in a single step. Here, we characterize the structure and function of a thermophilic dNDT, the protein from Chroococcidiopsis thermalis (CtNDT). We combined enzyme kinetics with structural and biophysical studies to dissect mechanistic features in the reaction coordinate, leading to product formation. Bell-shaped pH-rate profiles demonstrate activity in a broad pH range of 5.5-9.5, with two very distinct pKa values. A pronounced viscosity effect on the turnover rate indicates a diffusional step, likely product (nucleobase1) release, to be rate-limiting. Temperature studies revealed an extremely curved profile, suggesting a large negative activation heat capacity. We trapped a 2'-fluoro-2'-deoxyarabinosyl-enzyme intermediate by mass spectrometry and determined high-resolution structures of the protein in its unliganded, substrate-bound, ribosylated, 2'-difluoro-2'-deoxyribosylated, and in complex with probable transition-state analogues. We reveal key features underlying (2'-deoxy)ribonucleoside selection, as CtNDT can also use ribonucleosides as substrates, albeit with a lower efficiency. Ribonucleosides are the building blocks of RNA and other key intracellular metabolites participating in energy and metabolism, expanding the scope of use of CtNDT in biocatalysis.
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Affiliation(s)
- Peijun Tang
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Christopher J. Harding
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Alison L. Dickson
- School
of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, United Kingdom
| | - Rafael G. da Silva
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - David J. Harrison
- School
of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, United Kingdom
| | - Clarissa Melo Czekster
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
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2
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Rational Design of a Thermostable 2'-Deoxyribosyltransferase for Nelarabine Production by Prediction of Disulfide Bond Engineering Sites. Int J Mol Sci 2022; 23:ijms231911806. [PMID: 36233108 PMCID: PMC9570332 DOI: 10.3390/ijms231911806] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
One of the major drawbacks of the industrial implementation of enzymatic processes is the low operational stability of the enzymes under tough industrial conditions. In this respect, the use of thermostable enzymes in the industry is gaining ground during the last decades. Herein, we report a structure-guided approach for the development of novel and thermostable 2′-deoxyribosyltransferases (NDTs) based on the computational design of disulfide bonds on hot spot positions. To this end, a small library of NDT variants from Lactobacillus delbrueckii (LdNDT) with introduced cysteine pairs was created. Among them, LdNDTS104C (100% retained activity) was chosen as the most thermostable variant, displaying a six- and two-fold enhanced long-term stability when stored at 55 °C (t1/255 °C ≈ 24 h) and 60 °C (t1/260 °C ≈ 4 h), respectively. Moreover, the biochemical characterization revealed that LdNDTS104C showed >60% relative activity across a broad range of temperature (30−90 °C) and pH (5−7). Finally, to study the potential application of LdNDTS104C as an industrial catalyst, the enzymatic synthesis of nelarabine was successfully carried out under different substrate conditions (1:1 and 3:1) at different reaction times. Under these experimental conditions, the production of nelarabine was increased up to 2.8-fold (72% conversion) compared with wild-type LdNDT.
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3
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Wang H, Zhong YY, Xiao YC, Chen FE. Chemical and chemoenzymatic stereoselective synthesis of β-nucleosides and their analogues. Org Chem Front 2022. [DOI: 10.1039/d1qo01936h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
β-Nucleosides are fundamental building blocks of biological systems that are widely used as therapeutic agents for treating cancer and viral infections among others. In the last two years, nucleoside analogues...
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4
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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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5
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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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6
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Acosta J, Pérez E, Sánchez-Murcia PA, Fillat C, Fernández-Lucas J. Molecular Basis of NDT-Mediated Activation of Nucleoside-Based Prodrugs and Application in Suicide Gene Therapy. Biomolecules 2021; 11:biom11010120. [PMID: 33477716 PMCID: PMC7831932 DOI: 10.3390/biom11010120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 11/16/2022] Open
Abstract
Herein we report the first proof for the application of type II 2′-deoxyribosyltransferase from Lactobacillus delbrueckii (LdNDT) in suicide gene therapy for cancer treatment. To this end, we first confirm the hydrolytic ability of LdNDT over the nucleoside-based prodrugs 2′-deoxy-5-fluorouridine (dFUrd), 2′-deoxy-2-fluoroadenosine (dFAdo), and 2′-deoxy-6-methylpurine riboside (d6MetPRib). Such activity was significantly increased (up to 30-fold) in the presence of an acceptor nucleobase. To shed light on the strong nucleobase dependence for enzymatic activity, different molecular dynamics simulations were carried out. Finally, as a proof of concept, we tested the LdNDT/dFAdo system in human cervical cancer (HeLa) cells. Interestingly, LdNDT/dFAdo showed a pronounced reduction in cellular viability with inhibitory concentrations in the low micromolar range. These results open up future opportunities for the clinical implementation of nucleoside 2′-deoxyribosyltransferases (NDTs) in cancer treatment.
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Affiliation(s)
- Javier Acosta
- Applied Biotechnology Group, European University of Madrid, c/ Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain; (J.A.); (E.P.)
| | - Elena Pérez
- Applied Biotechnology Group, European University of Madrid, c/ Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain; (J.A.); (E.P.)
| | - Pedro A. Sánchez-Murcia
- Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria;
| | - Cristina Fillat
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08036 Barcelona, Spain
| | - Jesús Fernández-Lucas
- Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria;
- Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66 Barranquilla, Colombia
- Correspondence:
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7
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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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8
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Del Arco J, Perona A, González L, Fernández-Lucas J, Gago F, Sánchez-Murcia PA. Reaction mechanism of nucleoside 2'-deoxyribosyltransferases: free-energy landscape supports an oxocarbenium ion as the reaction intermediate. Org Biomol Chem 2020; 17:7891-7899. [PMID: 31397456 DOI: 10.1039/c9ob01315f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Insight into the catalytic mechanism of Lactobacillus leichmannii nucleoside 2'-deoxyribosyltransferase (LlNDT) has been gained by calculating a quantum mechanics-molecular mechanics (QM/MM) free-energy landscape of the reaction within the enzyme active site. Our results support an oxocarbenium species as the reaction intermediate and thus an SN1 reaction mechanism in this family of bacterial enzymes. Our mechanistic proposal is validated by comparing experimental kinetic data on the impact of the single amino acid replacements Tyr7, Glu98 and Met125 with Ala, Asp and Ala/norLeu, respectively, and accounts for the specificity shown by this enzyme on a non-natural substrate. This work broadens our understanding of enzymatic C-N bond cleavage and C-N bond formation.
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Affiliation(s)
- Jon Del Arco
- Applied Biotechnology Group, European University of Madrid, Villaviciosa de Odón, Spain
| | - Almudena Perona
- Applied Biotechnology Group, European University of Madrid, Villaviciosa de Odón, Spain
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, Währinger Str. 17, A-1090 University of Vienna, Vienna, Austria.
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, European University of Madrid, Villaviciosa de Odón, Spain and Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, Barranquilla, Colombia
| | - Federico Gago
- Department of Biomedical Sciences and "Unidad Asociada IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Spain
| | - Pedro A Sánchez-Murcia
- Institute of Theoretical Chemistry, Faculty of Chemistry, Währinger Str. 17, A-1090 University of Vienna, Vienna, Austria.
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9
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Del Arco J, Mills A, Gago F, Fernández-Lucas J. Structure-Guided Tuning of a Selectivity Switch towards Ribonucleosides in Trypanosoma brucei Purine Nucleoside 2'-Deoxyribosyltransferase. Chembiochem 2019; 20:2996-3000. [PMID: 31264760 DOI: 10.1002/cbic.201900397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Indexed: 01/21/2023]
Abstract
The use of nucleoside 2'-deoxyribosyltransferases (NDTs) as biocatalysts for the industrial synthesis of nucleoside analogues is often hindered by their strict preference for 2'-deoxyribonucleosides. It is shown herein that a highly versatile purine NDT from Trypanosoma brucei (TbPDT) can also accept ribonucleosides as substrates; this is most likely because of the distinct role played by Asn53 at a position that is usually occupied by Asp in other NDTs. Moreover, this unusual activity was improved about threefold by introducing a single amino acid replacement at position 5, following a structure-guided approach. Biophysical and biochemical characterization revealed that the TbPDTY5F variant is a homodimer that displays maximum activity at 50 °C and pH 6.5 and shows a remarkably high melting temperature of 69 °C. Substrate specificity studies demonstrate that 6-oxopurine ribonucleosides are the best donors (inosine>guanosine≫adenosine), whereas no significant preferences exist between 6-aminopurines and 6-oxopurines as base acceptors. In contrast, no transferase activity could be detected on xanthine and 7-deazapurines. TbPDTY5F was successfully employed in the synthesis of a wide range of modified ribonucleosides containing different purine analogues.
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Affiliation(s)
- Jon Del Arco
- Applied Biotechnology Group, Universidad Europea de Madrid, 28670, Villaviciosa de Odón, Madrid, Spain
| | - Alberto Mills
- Department of Biomedical Sciences and "U. A. IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, 28805, Alcalá de Henares, Madrid, Spain
| | - Federico Gago
- Department of Biomedical Sciences and "U. A. IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, 28805, Alcalá de Henares, Madrid, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, 28670, Villaviciosa de Odón, Madrid, Spain.,Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, 080002, Barranquilla, Colombia
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Li J, Yu L, Li J, Xie L, Zhang R, Wang H. Establishment of a high throughput-screening system for nucleoside deoxyribosyltransferase II mutant enzymes with altered substrate specificity. J Biosci Bioeng 2019; 128:22-27. [DOI: 10.1016/j.jbiosc.2019.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 12/23/2022]
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11
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Vichier-Guerre S, Dugué L, Pochet S. 2'-Deoxyribonucleoside 5'-triphosphates bearing 4-phenyl and 4-pyrimidinyl imidazoles as DNA polymerase substrates. Org Biomol Chem 2019; 17:290-301. [PMID: 30543241 DOI: 10.1039/c8ob02464b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed a versatile access to a series of 4-substituted imidazole 2'-deoxynucleoside triphosphate bearing functionalized phenyl or pyrimidinyl rings. 4-Iodo-1H-imidazole was enzymatically converted into the corresponding 2'-deoxynucleoside, which was then chemically derived into its 5'-triphosphate, followed by 4-arylation via Suzuki-Miyaura coupling using (hetero)arylboronic acids. Both KF (exo-) and Deep Vent (exo-) DNA polymerases incorporated these modified nucleotides in primer-extension assays, adenine being the preferred pairing partner in the template. The 4-(3-aminophenyl)imidazole derivative (3APh) was the most efficiently inserted opposite A by KF (exo-) with only a 37-fold lower efficiency (Vmax/KM) than that of the correct dTTP. No further extension occurred after the incorporation of a single aryl-imidazole nucleotide. Interestingly, the aryl-imidazole dNTPs were found to undergo successive incorporation by calf thymus terminal deoxynucleotidyl transferase with different tailing efficiencies among this series and with a marked preference for 2APyr polymerization.
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Affiliation(s)
- Sophie Vichier-Guerre
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS, UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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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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13
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Characterization of an atypical, thermostable, organic solvent- and acid-tolerant 2'-deoxyribosyltransferase from Chroococcidiopsis thermalis. Appl Microbiol Biotechnol 2018; 102:6947-6957. [PMID: 29872887 DOI: 10.1007/s00253-018-9134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/15/2018] [Accepted: 05/23/2018] [Indexed: 10/14/2022]
Abstract
In our search for thermophilic and acid-tolerant nucleoside 2'-deoxyribosyltransferases (NDTs), we found a good candidate in an enzyme encoded by Chroococcidiopsis thermalis PCC 7203 (CtNDT). Biophysical and biochemical characterization revealed CtNDT as a homotetramer endowed with good activity and stability at both high temperatures (50-100 °C) and a wide range of pH values (from 3 to 7). CtNDT recognizes purine bases and their corresponding 2'-deoxynucleosides but is also proficient using cytosine and 2'-deoxycytidine as substrates. These unusual features preclude the strict classification of CtNDT as either a type I or a type II NDT and further suggest that this simple subdivision may need to be updated in the future. Our findings also hint at a possible link between oligomeric state and NDT's substrate specificity. Interestingly from a practical perspective, CtNDT displays high activity (80-100%) in the presence of several water-miscible co-solvents in a proportion of up to 20% and was successfully employed in the enzymatic production of several therapeutic nucleosides such as didanosine, vidarabine, and cytarabine.
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2′-Deoxyribosyltransferase from Bacillus psychrosaccharolyticus: A Mesophilic-Like Biocatalyst for the Synthesis of Modified Nucleosides from a Psychrotolerant Bacterium. Catalysts 2018. [DOI: 10.3390/catal8010008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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15
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Crespo N, Sánchez-Murcia PA, Gago F, Cejudo-Sanches J, Galmes MA, Fernández-Lucas J, Mancheño JM. 2'-Deoxyribosyltransferase from Leishmania mexicana, an efficient biocatalyst for one-pot, one-step synthesis of nucleosides from poorly soluble purine bases. Appl Microbiol Biotechnol 2017; 101:7187-7200. [PMID: 28785897 DOI: 10.1007/s00253-017-8450-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/11/2022]
Abstract
Processes catalyzed by enzymes offer numerous advantages over chemical methods although in many occasions the stability of the biocatalysts becomes a serious concern. Traditionally, synthesis of nucleosides using poorly water-soluble purine bases, such as guanine, xanthine, or hypoxanthine, requires alkaline pH and/or high temperatures in order to solubilize the substrate. In this work, we demonstrate that the 2'-deoxyribosyltransferase from Leishmania mexicana (LmPDT) exhibits an unusually high activity and stability under alkaline conditions (pH 8-10) across a broad range of temperatures (30-70 °C) and ionic strengths (0-500 mM NaCl). Conversely, analysis of the crystal structure of LmPDT together with comparisons with hexameric, bacterial homologues revealed the importance of the relationships between the oligomeric state and the active site architecture within this family of enzymes. Moreover, molecular dynamics and docking approaches provided structural insights into the substrate-binding mode. Biochemical characterization of LmPDT identifies the enzyme as a type I NDT (PDT), exhibiting excellent activity, with specific activity values 100- and 4000-fold higher than the ones reported for other PDTs. Interestingly, LmPDT remained stable during 36 h at different pH values at 40 °C. In order to explore the potential of LmPDT as an industrial biocatalyst, enzymatic production of several natural and non-natural therapeutic nucleosides, such as vidarabine (ara A), didanosine (ddI), ddG, or 2'-fluoro-2'-deoxyguanosine, was carried out using poorly water-soluble purines. Noteworthy, this is the first time that the enzymatic synthesis of 2'-fluoro-2'-deoxyguanosine, ara G, and ara H by a 2'-deoxyribosyltransferase is reported.
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Affiliation(s)
- N Crespo
- Department of Crystallography and Structural Biology, Institute Rocasolano (CSIC), Serrano 119, E-28006, Madrid, Spain.,Applied Biotechnology Group, European University of Madrid, E-28670, Villaviciosa de Odón, Madrid, Spain
| | - P A Sánchez-Murcia
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, 1090, Vienna, Austria.,Department of Biomedical Sciences and "Unidad Asociada IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, E-28871, Alcalá de Henares, Spain
| | - F Gago
- Department of Biomedical Sciences and "Unidad Asociada IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, E-28871, Alcalá de Henares, Spain
| | - J Cejudo-Sanches
- Applied Biotechnology Group, European University of Madrid, E-28670, Villaviciosa de Odón, Madrid, Spain
| | - M A Galmes
- Applied Biotechnology Group, European University of Madrid, E-28670, Villaviciosa de Odón, Madrid, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, European University of Madrid, E-28670, Villaviciosa de Odón, Madrid, Spain. .,Grupo de Investigación en Desarrollo Agroindustrial Sostenible, Department of Agroindustrial Engineering, School of Environmental Sciences, Universidad de la Costa, Cra. 55 #58-66, Barranquilla, Colombia.
| | - José Miguel Mancheño
- Department of Crystallography and Structural Biology, Institute Rocasolano (CSIC), Serrano 119, E-28006, Madrid, Spain.
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16
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Vichier-Guerre S, Dugué L, Bonhomme F, Pochet S. An expedient synthesis of flexible nucleosides via a regiocontrolled enzymatic glycosylation of functionalized imidazoles. Org Biomol Chem 2017; 15:8193-8203. [DOI: 10.1039/c7ob01850a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A versatile two-step synthesis of C4- and C5-arylated 2′-deoxyribosylimidazoles was elaborated by enzymaticN-transglycosylation followed by microwave-assisted Pd-catalysed arylation reactions.
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Affiliation(s)
- S. Vichier-Guerre
- Unité de Chimie et Biocatalyse
- Institut Pasteur
- CNRS
- UMR3523
- 75724 Paris Cedex 15
| | - L. Dugué
- Unité de Chimie et Biocatalyse
- Institut Pasteur
- CNRS
- UMR3523
- 75724 Paris Cedex 15
| | - F. Bonhomme
- Unité de Chimie et Biocatalyse
- Institut Pasteur
- CNRS
- UMR3523
- 75724 Paris Cedex 15
| | - S. Pochet
- Unité de Chimie et Biocatalyse
- Institut Pasteur
- CNRS
- UMR3523
- 75724 Paris Cedex 15
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17
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Vichier-Guerre S, Dugué L, Bonhomme F, Pochet S. Expedient and generic synthesis of imidazole nucleosides by enzymatic transglycosylation. Org Biomol Chem 2016; 14:3638-53. [PMID: 26986701 DOI: 10.1039/c6ob00405a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A straightforward route to original imidazole-based nucleosides that makes use of an enzymatic N-transglycosylation step is reported in both the ribo- and deoxyribo-series. To illustrate the scope of this approach, a diverse set of 4-aryl and 4-heteroaryl-1H-imidazoles featuring variable sizes and hydrogen-bonding patterns was prepared using a microwave-assisted Suzuki-Miyaura cross-coupling reaction. These imidazole derivatives were examined as possible substrates for the nucleoside 2'-deoxyribosyltransferase from L. leichmannii and the purine nucleoside phosphorylase from E. coli. The optimum transglycosylation conditions, including the use of co-adjuvants to address solubility issues, were defined. Enzymatic conversion of 4-(hetero)arylimidazoles to 2'-deoxyribo- or ribo-nucleosides proceeded in good to high conversion yields, except bulky hydrophobic imidazole derivatives. Nucleoside deoxyribosyltransferase of class II was found to convert the widest range of functionalized imidazoles into 2'-deoxyribonucleosides and was even capable of bis-glycosylating certain heterocyclic substrates. Our findings should enable chemoenzymatic access to a large diversity of flexible nucleoside analogues as molecular probes, drug candidates and original building blocks for synthetic biology.
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Affiliation(s)
- S Vichier-Guerre
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS, UMR3523, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.
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18
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Ye W, Paul D, Gao L, Seckute J, Sangaiah R, Jayaraj K, Zhang Z, Kaminski PA, Ealick SE, Gold A, Ball LM. Ethenoguanines undergo glycosylation by nucleoside 2'-deoxyribosyltransferases at non-natural sites. PLoS One 2014; 9:e115082. [PMID: 25521390 PMCID: PMC4270796 DOI: 10.1371/journal.pone.0115082] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/18/2014] [Indexed: 11/19/2022] Open
Abstract
Deoxyribosyl transferases and functionally related purine nucleoside phosphorylases are used extensively for synthesis of non-natural deoxynucleosides as pharmaceuticals or standards for characterizing and quantitating DNA adducts. Hence exploring the conformational tolerance of the active sites of these enzymes is of considerable practical interest. We have determined the crystal structure at 2.1 Å resolution of Lactobacillus helveticus purine deoxyribosyl transferase (PDT) with the tricyclic purine 8,9-dihydro-9-oxoimidazo[2,1-b]purine (N2,3-ethenoguanine) at the active site. The active site electron density map was compatible with four orientations, two consistent with sites for deoxyribosylation and two appearing to be unproductive. In accord with the crystal structure, Lactobacillus helveticus PDT glycosylates the 8,9-dihydro-9-oxoimidazo[2,1-b]purine at N7 and N1, with a marked preference for N7. The activity of Lactobacillus helveticus PDT was compared with that of the nucleoside 2'-deoxyribosyltransferase enzymes (DRT Type II) from Lactobacillus leichmannii and Lactobacillus fermentum, which were somewhat more effective in the deoxyribosylation than Lactobacillus helveticus PDT, glycosylating the substrate with product profiles dependent on the pH of the incubation. The purine nucleoside phosphorylase of Escherichia coli, also commonly used in ribosylation of non-natural bases, was an order of magnitude less efficient than the transferase enzymes. Modeling based on published active-site structures as templates suggests that in all cases, an active site Phe is critical in orienting the molecular plane of the purine derivative. Adventitious hydrogen bonding with additional active site residues appears to result in presentation of multiple nucleophilic sites on the periphery of the acceptor base for ribosylation to give a distribution of nucleosides. Chemical glycosylation of O9-benzylated 8,9-dihydro-9-oxoimidazo[2,1-b]purine also resulted in N7 and N1 ribosylation. Absent from the enzymatic and chemical glycosylations is the natural pattern of N3 ribosylation, verified by comparison of spectroscopic and chromatographic properties with an authentic standard synthesized by an unambiguous route.
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Affiliation(s)
- Wenjie Ye
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Debamita Paul
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Lina Gao
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jolita Seckute
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Ramiah Sangaiah
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Karupiah Jayaraj
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Zhenfa Zhang
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Avram Gold
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Louise M. Ball
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
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19
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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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20
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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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21
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Kaminski PA, Labesse G. Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis. J Biol Chem 2013; 288:6534-41. [PMID: 23325804 DOI: 10.1074/jbc.m112.446492] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A large number of nucleoside analogues and 2'-deoxynucleoside triphosphates (dNTP) have been synthesized to interfere with DNA metabolism. However, in vivo the concentration and phosphorylation of these analogues are key limiting factors. In this context, we designed enzymes to switch nucleobases attached to a deoxyribose monophosphate. Active chimeras were made from two distantly related enzymes: a nucleoside deoxyribosyltransferase from lactobacilli and a 5'-monophosphate-2'-deoxyribonucleoside hydrolase from rat. Then their unprecedented activity was further extended to deoxyribose triphosphate, and in vitro biosyntheses could be successfully performed with several base analogues. These new enzymes provide new tools to synthesize dNTP analogues and to deliver them into cells.
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22
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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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23
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Lin Y, Zhang W, Zhu F, Su J, Fang D, Yang Y, Zhang G, Xie L, Zhang R, Wang H. Subcellular localization of N-deoxyribosyltransferase in Lactobacillus fermentum: cell surface association of an intracellular nucleotide metabolic enzyme. FEMS Microbiol Lett 2011; 323:132-41. [DOI: 10.1111/j.1574-6968.2011.02369.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 07/19/2011] [Accepted: 07/22/2011] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yin Lin
- School of Life Sciences; Tsinghua University; Beijing; China
| | - Wenquan Zhang
- School of Life Sciences; Tsinghua University; Beijing; China
| | - Fangjie Zhu
- School of Life Sciences; Tsinghua University; Beijing; China
| | - Jingtan Su
- School of Life Sciences; Tsinghua University; Beijing; China
| | - Dong Fang
- School of Life Sciences; Tsinghua University; Beijing; China
| | - Yang Yang
- School of Life Sciences; Tsinghua University; Beijing; China
| | - Guiyou Zhang
- School of Life Sciences; Tsinghua University; Beijing; China
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24
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Fernández-Lucas J, Fresco-Taboada A, Acebal C, de la Mata I, Arroyo M. Enzymatic synthesis of nucleoside analogues using immobilized 2'-deoxyribosyltransferase from Lactobacillus reuteri. Appl Microbiol Biotechnol 2011; 91:317-27. [PMID: 21476139 DOI: 10.1007/s00253-011-3221-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/23/2011] [Accepted: 03/02/2011] [Indexed: 11/29/2022]
Abstract
Covalent attachment of recombinant Lactobacillus reuteri 2'-deoxyribosyltransferase to Sepabeads EC-EP303 leads to the immobilized biocatalyst SLrNDT4, which displayed an enzymatic activity of 65.4 IU/g of wet biocatalyst in 2'-deoxyadenosine synthesis from 2'-deoxyuridine and adenine at 40°C and pH 6.5. Response surface methodology was employed for the optimization of SLrNDT4 activity. Optimal conditions for SLrNDT4 highest activity were observed at 40°C and pH 6.5. Immobilized biocatalyst retained 50% of its maximal activity after 17.9 h at 60°C, whereas 96% activity was observed after storage at 40°C for 110 h. This novel immobilized biocatalyst has been successfully employed in the enzymatic synthesis of different natural and therapeutic nucleosides effective against cancer and viral diseases. Among these last products, enzymatic synthesis of therapeutic nucleosides such as 5-ethyl-2'-deoxyuridine and 5-trifluorothymidine has been carried out for the first time. Importantly for its potential application, SLrNDT4 could be recycled for 26 consecutive batch reactions in the synthesis of 2,6-diaminopurine-2'-deoxyriboside with negligible loss of catalytic activity.
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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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25
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Biologically important nucleosides: modern trends in biotechnology and application. MENDELEEV COMMUNICATIONS 2011. [DOI: 10.1016/j.mencom.2011.03.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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26
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Nannemann DP, Kaufmann KW, Meiler J, Bachmann BO. Design and directed evolution of a dideoxy purine nucleoside phosphorylase. Protein Eng Des Sel 2010; 23:607-16. [PMID: 20525731 DOI: 10.1093/protein/gzq033] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Purine nucleoside phosphorylase (PNP) catalyzes the synthesis and phosphorolysis of purine nucleosides, interconverting nucleosides with their corresponding purine base and ribose-1-phosphate. While PNP plays significant roles in human and pathogen physiology, we are interested in developing PNP as a catalyst for the formation of nucleoside analog drugs of clinical relevance. Towards this aim, we describe the engineering of human PNP to accept 2',3'-dideoxyinosine (ddI, Videx((R))) as a substrate for phosphorolysis using a combination of site-directed mutagenesis and directed evolution. In human PNP, we identified a single amino acid, Tyr-88, as a likely modulator of ribose selectivity. RosettaLigand was employed to calculate binding energies for substrate and substrate analog transition state complexes for single mutants of PNP where Tyr-88 was replaced with another amino acid. In parallel, these mutants were generated by site-directed mutagenesis, expressed and purified. A tyrosine to phenylalanine mutant (Y88F) was predicted by Rosetta to improve PNP catalytic activity with respect to ddI. Kinetic characterization of this mutant determined a 9-fold improvement in k(cat) and greater than 2-fold reduction in K(M). Subsequently, we used directed evolution to select for improved variants of PNP-Y88F in Escherichia coli cell extracts resulting in an additional 3-fold improvement over the progenitor strain. The engineered PNP may form the basis for catalysts and pathways for the biosynthesis of ddI.
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Affiliation(s)
- David P Nannemann
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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27
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Fernández-Lucas J, Acebal C, Sinisterra JV, Arroyo M, de la Mata I. Lactobacillus reuteri 2'-deoxyribosyltransferase, a novel biocatalyst for tailoring of nucleosides. Appl Environ Microbiol 2010; 76:1462-70. [PMID: 20048065 PMCID: PMC2832402 DOI: 10.1128/aem.01685-09] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 12/26/2009] [Indexed: 11/20/2022] Open
Abstract
A novel type II nucleoside 2'-deoxyribosyltransferase from Lactobacillus reuteri (LrNDT) has been cloned and overexpressed in Escherichia coli. The recombinant LrNDT has been structural and functionally characterized. Sedimentation equilibrium analysis revealed a homohexameric molecule of 114 kDa. Circular dichroism studies have showed a secondary structure containing 55% alpha-helix, 10% beta-strand, 16% beta-sheet, and 19% random coil. LrNDT was thermostable with a melting temperature (T(m)) of 64 degrees C determined by fluorescence, circular dichroism, and differential scanning calorimetric studies. The enzyme showed high activity in a broad pH range (4.6 to 7.9) and was also very stable between pH 4 and 7.9. The optimal temperature for activity was 40 degrees C. The recombinant LrNDT was able to synthesize natural and nonnatural nucleoside analogues, improving activities described in the literature, and remarkably, exhibited unexpected new arabinosyltransferase activity, which had not been described so far in this kind of enzyme. Furthermore, synthesis of new arabinonucleosides and 2'-fluorodeoxyribonucleosides was carried out.
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Affiliation(s)
- Jesús Fernández-Lucas
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/ José Antonio Nováis 2, 28040 Madrid, Spain, Industrial Biotransformations Service, Scientific Park of Madrid, C/Santiago Grisolía n°2, 28760 Tres Cantos, Madrid, Spain
| | - Carmen Acebal
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/ José Antonio Nováis 2, 28040 Madrid, Spain, Industrial Biotransformations Service, Scientific Park of Madrid, C/Santiago Grisolía n°2, 28760 Tres Cantos, Madrid, Spain
| | - José V. Sinisterra
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/ José Antonio Nováis 2, 28040 Madrid, Spain, Industrial Biotransformations Service, Scientific Park of Madrid, C/Santiago Grisolía n°2, 28760 Tres Cantos, Madrid, Spain
| | - Miguel Arroyo
- Department of Biochemistry and Molecular Biology I, Faculty of Biology, Complutense University of Madrid, C/ José Antonio Nováis 2, 28040 Madrid, Spain, Industrial Biotransformations Service, Scientific Park of Madrid, C/Santiago Grisolía n°2, 28760 Tres Cantos, Madrid, Spain
| | - 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, Industrial Biotransformations Service, Scientific Park of Madrid, C/Santiago Grisolía n°2, 28760 Tres Cantos, Madrid, Spain
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