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Jezuita A, Wieczorkiewicz PA, Szatylowicz H, Krygowski TM. Effect of the Solvent and Substituent on Tautomeric Preferences of Amine-Adenine Tautomers. ACS OMEGA 2021; 6:18890-18903. [PMID: 34337229 PMCID: PMC8320138 DOI: 10.1021/acsomega.1c02118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Adenine is one of the basic molecules of life; it is also an important building block in the synthesis of new pharmaceuticals, electrochemical (bio)sensors, or self-assembling molecular materials. Therefore, it is important to know the effects of the solvent and substituent on the electronic structure of adenine tautomers and their stability. The four most stable adenine amino tautomers (9H, 7H, 3H, and 1H), modified by substitution (C2- or C8-) of electron-withdrawing NO2 and electron-donating NH2 groups, are studied theoretically in the gas phase and in solvents of different polarities (1 ≤ ε < 109). Solvents have been modeled using the polarizable continuum model. Comparison of the stability of substituted adenine tautomers in various solvents shows that substitution can change tautomeric preferences with respect to the unsubstituted adenine. Moreover, C8 substitution results in slight energy differences between tautomers in polar solvents (<1 kcal/mol), which suggests that in aqueous solution, C8-X-substituted adenine systems may consist of a considerable amount of two tautomers-9H and 7H for X = NH2 and 3H and 9H for X = NO2. Furthermore, solvation enhances the effect of the nitro group; however, the enhancement strongly depends on the proximity effects. This enhancement for the NO2 group with two repulsive N···ON contacts can be threefold higher than that for the NO2 with one attractive NH···ON contact. The proximity effects are even more significant for the NH2 group, as the solvation may increase or decrease its electron-donating ability, depending on the type of proximity.
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Affiliation(s)
- Anna Jezuita
- Faculty of Science and Technology, Jan Dlugosz University in Czestochowa, Al. Armii Krajowej 113/15, 42-200 Czestochowa, Poland
| | | | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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2
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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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3
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Rinaldi F, Fernández-Lucas J, de la Fuente D, Zheng C, Bavaro T, Peters B, Massolini G, Annunziata F, Conti P, de la Mata I, Terreni M, Calleri E. Immobilized enzyme reactors based on nucleoside phosphorylases and 2'-deoxyribosyltransferase for the in-flow synthesis of pharmaceutically relevant nucleoside analogues. BIORESOURCE TECHNOLOGY 2020; 307:123258. [PMID: 32247276 DOI: 10.1016/j.biortech.2020.123258] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
In this work, a mono- and a bi-enzymatic analytical immobilized enzyme reactors (IMERs) were developed as prototypes for biosynthetic purposes and their performances in the in-flow synthesis of nucleoside analogues of pharmaceutical interest were evaluated. Two biocatalytic routes based on nucleoside 2'-deoxyribosyltransferase from Lactobacillus reuteri (LrNDT) and uridine phosphorylase from Clostridium perfrigens (CpUP)/purine nucleoside phosphorylase from Aeromonas hydrophila (AhPNP) were investigated in the synthesis of 2'-deoxy, 2',3'-dideoxy and arabinonucleoside derivatives. LrNDT-IMER catalyzed the synthesis of 5-fluoro-2'-deoxyuridine and 5-iodo-2'-deoxyuridine in 65-59% conversion yield, while CpUP/AhPNP-IMER provided the best results for the preparation of arabinosyladenine (60% conversion yield). Both IMERs proved to be promising alternatives to chemical routes for the synthesis of nucleoside analogues. The developed in-flow system represents a powerful tool for the fast production on analytical scale of nucleosides for preliminary biological tests.
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Affiliation(s)
- Francesca Rinaldi
- Department of Drug Sciences, Università degli Studi di Pavia, I-27100 Pavia, Italy
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Spain; Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, 080003 Barranquilla, Atlántico, Colombia
| | - Diego de la Fuente
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Changping Zheng
- CNRS, IPCM, UMR 8232, Sorbonne Université, 75005 Paris, France
| | - Teodora Bavaro
- Department of Drug Sciences, Università degli Studi di Pavia, I-27100 Pavia, Italy
| | - Benjamin Peters
- Instrumental Analytics R&D, Merck KGaA, DE-64271 Darmstadt, Germany
| | - Gabriella Massolini
- Department of Drug Sciences, Università degli Studi di Pavia, I-27100 Pavia, Italy
| | - Francesca Annunziata
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, I-20133 Milan, Italy
| | - Paola Conti
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, I-20133 Milan, Italy
| | - Isabel de la Mata
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Marco Terreni
- Department of Drug Sciences, Università degli Studi di Pavia, I-27100 Pavia, Italy
| | - Enrica Calleri
- Department of Drug Sciences, Università degli Studi di Pavia, I-27100 Pavia, Italy.
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4
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Szatylowicz H, Marek PH, Stasyuk OA, Krygowski TM, Solà M. Substituted adenine quartets: interplay between substituent effect, hydrogen bonding, and aromaticity. RSC Adv 2020; 10:23350-23358. [PMID: 35520336 PMCID: PMC9054646 DOI: 10.1039/d0ra04585c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 06/03/2020] [Indexed: 11/22/2022] Open
Abstract
Adenine, one of the components of DNA/RNA helices, has the ability to form self-organizing structures with cyclic hydrogen bonds (A4), similar to guanine quartets. Here, we report a computational investigation of the effect of substituents (X = NO2, Cl, F, H, Me, and NH2) on the electronic structure of 9H-adenine and its quartets (A4-N1, A4-N3, and A4-N7). DFT calculations were used to show the relationships between the electronic nature of the substituents, strength of H-bonds in the quartets, and aromaticity of five- and six-membered rings of adenine. We demonstrated how the remote substituent X modifies the proton-donating properties of the NH2 group involved in the H-bonds within quartets and how the position of the substituent and its electronic nature affect the stability of the quartets. We also showed the possible changes in electronic properties of the substituent and aromaticity of adenine rings caused by tetramer formation. The results indicate that the observed relationships depend on the A4 type. Moreover, the same substituent can both strengthen and weaken intermolecular interactions, depending on the substitution position. Substituent effects on hydrogen bonds in adenine quartets and aromaticity of adenine rings depend on the quartet type. A4-N3 and A4-N7 quartets are more responsive to the electronic nature of substituents than A4-N1.![]()
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Affiliation(s)
- Halina Szatylowicz
- Warsaw University of Technology, Faculty of Chemistry Noakowskiego 3 00-664 Warsaw Poland
| | - Paulina H Marek
- Warsaw University of Technology, Faculty of Chemistry Noakowskiego 3 00-664 Warsaw Poland .,University of Warsaw, Faculty of Chemistry Pasteura 1 02-093 Warsaw Poland
| | - Olga A Stasyuk
- Department of Chemistry, Institute of Computational Chemistry and Catalysis, University of Girona C/ M. Aurèlia Capmany, 69 17003 Girona Spain
| | | | - Miquel Solà
- Department of Chemistry, Institute of Computational Chemistry and Catalysis, University of Girona C/ M. Aurèlia Capmany, 69 17003 Girona Spain
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5
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Yehia H, Westarp S, Röhrs V, Kaspar F, Giessmann RT, Klare HF, Paulick K, Neubauer P, Kurreck J, Wagner A. Efficient Biocatalytic Synthesis of Dihalogenated Purine Nucleoside Analogues Applying Thermodynamic Calculations. Molecules 2020; 25:E934. [PMID: 32093094 PMCID: PMC7070685 DOI: 10.3390/molecules25040934] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/16/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023] Open
Abstract
The enzymatic synthesis of nucleoside analogues has been shown to be a sustainable and efficient alternative to chemical synthesis routes. In this study, dihalogenated nucleoside analogues were produced by thermostable nucleoside phosphorylases in transglycosylation reactions using uridine or thymidine as sugar donors. Prior to the enzymatic process, ideal maximum product yields were calculated after the determination of equilibrium constants through monitoring the equilibrium conversion in analytical-scale reactions. Equilibrium constants for dihalogenated nucleosides were comparable to known purine nucleosides, ranging between 0.071 and 0.081. To achieve 90% product yield in the enzymatic process, an approximately five-fold excess of sugar donor was needed. Nucleoside analogues were purified by semi-preparative HPLC, and yields of purified product were approximately 50% for all target compounds. To evaluate the impact of halogen atoms in positions 2 and 6 on the antiproliferative activity in leukemic cell lines, the cytotoxic potential of dihalogenated nucleoside analogues was studied in the leukemic cell line HL-60. Interestingly, the inhibition of HL-60 cells with dihalogenated nucleoside analogues was substantially lower than with monohalogenated cladribine, which is known to show high antiproliferative activity. Taken together, we demonstrate that thermodynamic calculations and small-scale experiments can be used to produce nucleoside analogues with high yields and purity on larger scales. The procedure can be used for the generation of new libraries of nucleoside analogues for screening experiments or to replace the chemical synthesis routes of marketed nucleoside drugs by enzymatic processes.
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Affiliation(s)
- Heba Yehia
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (H.Y.); (S.W.); (F.K.); (R.T.G.); (K.P.); (P.N.)
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (H.Y.); (S.W.); (F.K.); (R.T.G.); (K.P.); (P.N.)
- BioNukleo GmbH, Ackerstr. 76, 13355 Berlin, Germany
| | - Viola Röhrs
- Chair of Applied Biochemistry, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (V.R.); (J.K.)
| | - Felix Kaspar
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (H.Y.); (S.W.); (F.K.); (R.T.G.); (K.P.); (P.N.)
- BioNukleo GmbH, Ackerstr. 76, 13355 Berlin, Germany
| | - Robert T. Giessmann
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (H.Y.); (S.W.); (F.K.); (R.T.G.); (K.P.); (P.N.)
| | - Hendrik F.T. Klare
- Faculty II Mathematics and Natural Sciences, Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany;
| | - Katharina Paulick
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (H.Y.); (S.W.); (F.K.); (R.T.G.); (K.P.); (P.N.)
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (H.Y.); (S.W.); (F.K.); (R.T.G.); (K.P.); (P.N.)
| | - Jens Kurreck
- Chair of Applied Biochemistry, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (V.R.); (J.K.)
| | - Anke Wagner
- Chair of Bioprocess Engineering, Faculty III Process Sciences, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (H.Y.); (S.W.); (F.K.); (R.T.G.); (K.P.); (P.N.)
- BioNukleo GmbH, Ackerstr. 76, 13355 Berlin, Germany
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6
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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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7
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Chen YL, Wu DY, Tian ZQ. Theoretical Investigation on the Substituent Effect of Halogen Atoms at the C8 Position of Adenine: Relative Stability, Vibrational Frequencies, and Raman Spectra of Tautomers. J Phys Chem A 2016; 120:4049-58. [PMID: 27243104 DOI: 10.1021/acs.jpca.6b03604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have theoretically investigated the substituent effect of adenine at the C8 position with a substituent X = H, F, Cl, and Br by using the density functional theory (DFT) at the B3LYP/6-311+G(d, p) level. The aim is to study the substituent effect of halogen atoms on the relative stability, vibrational frequencies, and solvation effect of tautomers. Our calculated results show that for substituted adenine molecules the N9H8X tautomer to be the most stable structure in gas phase at the present theoretical level. Here N9H8X denotes the hydrogen atom binds to the N9 position of imidazole ring and X denotes H, F, Cl, and Br atoms. The influence of the induced attraction of the fluorine substituent is significantly larger than chlorine and bromine ones. The halogen substituent effect has a significant influence on changes of vibrational frequencies and Raman intensities.
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Affiliation(s)
- Yan-Li Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - De-Yin Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Zhong-Qun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
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8
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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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9
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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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10
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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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11
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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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12
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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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Ghanem M, Murkin AS, Schramm VL. Ribocation transition state capture and rebound in human purine nucleoside phosphorylase. ACTA ACUST UNITED AC 2010; 16:971-9. [PMID: 19778725 DOI: 10.1016/j.chembiol.2009.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 06/26/2009] [Accepted: 07/23/2009] [Indexed: 10/20/2022]
Abstract
Purine nucleoside phosphorylase (PNP) catalyzes the phosphorolysis of 6-oxy-purine nucleosides to the corresponding purine base and alpha-D-ribose 1-phosphate. Its genetic loss causes a lethal T cell deficiency. The highly reactive ribocation transition state of human PNP is protected from solvent by hydrophobic residues that sequester the catalytic site. The catalytic site was enlarged by replacing individual catalytic site amino acids with glycine. Reactivity of the ribocation transition state was tested for capture by water and other nucleophiles. In the absence of phosphate, inosine is hydrolyzed by native, Y88G, F159G, H257G, and F200G enzymes. Phosphorolysis but not hydrolysis is detected when phosphate is bound. An unprecedented N9-to-N3 isomerization of inosine is catalyzed by H257G and F200G in the presence of phosphate and by all PNPs in the absence of phosphate. These results establish a ribocation lifetime too short to permit capture by water. An enlarged catalytic site permits ribocation formation with relaxed geometric constraints, permitting nucleophilic rebound and N3-inosine isomerization.
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Affiliation(s)
- Mahmoud Ghanem
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Huard CN, Hutchinson DW. The Beneficial Effect of Organic Solvents on the Enzymatic Synthesis of Nucleoside Analogues Using N-Deoxyribosyltransferases fromLactobacillus leichmannii(E.C. 2.4.2.6). ACTA ACUST UNITED AC 2009. [DOI: 10.3109/10242429209014896] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Cecile N. Huard
- Chemistry Department, University of Warwick, Coventry, CV4 7AL, UK
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15
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Fernández-Lucas J, Condezo LA, Quezada MA, Sinisterra JV. Low-temperature synthesis of 2'-deoxyadenosine using immobilized psychrotrophic microorganisms. Biotechnol Bioeng 2008; 100:213-22. [PMID: 18098315 DOI: 10.1002/bit.21756] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Selective biocatalyzed synthesis of 2'-deoxyadenosine from 2'-deoxypyrimidine nucleosides was carried out using free or immobilized whole cells. The reaction was performed at 57 degrees C without secondary reactions. Two psychrotrophic microorganisms, Bacillus psychrosaccharolyticus and Psychrobacter immobilis, are described for the first time as active and specific strains for the synthesis of 2'-deoxyadenosine. Adenosine deaminase activity was not detected. Whole cells were immobilized in different matrixes. Calcium alginate and calcium pectate gave the best biocatalysts. The synthesis of 2'-deoxyadenosine follows an apparent first order kinetic expression. External mass transfer control was negligible as deduced from k(s), N(A), and Omega values. Internal mass transfer was the rate controlling step according to eta(T) and phi values.
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Affiliation(s)
- J Fernández-Lucas
- Biotransformations Group, Department of Organic & Pharmaceutical Chemistry, Faculty of Pharmacy, Universidad Complutense, 28040 Madrid, Spain
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16
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Kaminski PA, Dacher P, Dugué L, Pochet S. In vivo reshaping the catalytic site of nucleoside 2'-deoxyribosyltransferase for dideoxy- and didehydronucleosides via a single amino acid substitution. J Biol Chem 2008; 283:20053-9. [PMID: 18487606 DOI: 10.1074/jbc.m802706200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleoside 2'-deoxyribosyltransferases catalyze the transfer of 2-deoxyribose between bases and have been widely used as biocatalysts to synthesize a variety of nucleoside analogs. The genes encoding nucleoside 2'-deoxyribosyltransferase (ndt) from Lactobacillus leichmannii and Lactobacillus fermentum underwent random mutagenesis to select variants specialized for the synthesis of 2',3'-dideoxynucleosides. An Escherichia coli strain, auxotrophic for uracil and unable to use 2',3'-dideoxyuridine, cytosine, and 2',3'-dideoxycytidine as a source of uracil was constructed. Randomly mutated lactobacilli ndt libraries from two species, L. leichmannii and L. fermentum, were screened for the production of uracil with 2',3'-dideoxyuridine as a source of uracil. Several mutants suitable for the synthesis of 2',3'-dideoxynucleosides were isolated. The nucleotide sequence of the corresponding genes revealed a single mutation (G --> A transition) leading to the substitution of a small aliphatic amino acid by a nucleophilic one, A15T (L. fermentum) or G9S (L. leichmannii), respectively. We concluded that the "adaptation" of the nucleoside 2'-deoxyribosyltransferase activity to 2,3-dideoxyribosyl transfer requires an additional hydroxyl group on a key amino acid side chain of the protein to overcome the absence of such a group in the corresponding substrate. The evolved proteins also display significantly improved nucleoside 2',3'-didehydro-2',3'-dideoxyribosyltransferase activity.
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17
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Fernández-Lucas J, Condezo L, Martinez-Lagos F, Sinisterra J. Synthesis of 2′-deoxyibosylnucleosides using new 2′-deoxyribosyltransferase microorganism producers. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.08.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Bennett, Jr. LL, Chang CH, Allan PW, Adamson DJ, Rose LM, Brockman RW, Secrist III JA, Shortnacy A, Montgomery JA. Metabolism and Metabolic Effects of Halopurine Nucleosides in Tumor Cells in Culture. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328318508077834] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Ryu EK, Kim JN. The Oxidative Chlorination of Pyrimidine and Purine Bases, and Nucleosides Using Acyl Chloride-Dimethyl-Formamide-m-Chloroperbenzoic Acid System1. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328318908054157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Kaminski PA. Functional cloning, heterologous expression, and purification of two different N-deoxyribosyltransferases from Lactobacillus helveticus. J Biol Chem 2002; 277:14400-7. [PMID: 11836245 DOI: 10.1074/jbc.m111995200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lactobacillus helveticus contains two types of N-deoxyribosyltransferases: DRTase I catalyzes the transfer of 2'-deoxyribose between purine bases exclusively whereas DRTase II is able to transfer the 2'-deoxyribose between two pyrimidine or between pyrimidine and purine bases. An Escherichia coli strain, auxotrophic for guanine and unable to use deoxyguanosine as source of guanine, was constructed to clone the corresponding genes. By screening a genomic bank for the production of guanine, the L. helveticus ptd and ntd genes coding for DRTase I and II, respectively, were isolated. Although the two genes have no sequence similarity, the two deduced polypeptides display 25.6% identity, with most of the residues involved in substrate binding and the active site nucleophile Glu-98 being conserved. Overexpression and purification of the two proteins shows that DRTase I is specific for purines with a preference for deoxyinosine (dI) > deoxyadenosine > deoxyguanosine as donor substrates whereas DRTase II has a strong preference for pyrimidines as donor substrates and purines as base acceptors. Purine analogues were substrates as acceptor bases for both enzymes. Comparison of DRTase I and DRTase II activities with dI as donor or hypoxanthine as acceptor and colocalization of the ptd and add genes suggest a specific role for DRTase I in the metabolism of dI.
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Affiliation(s)
- Pierre Alexandre Kaminski
- Unité de Chimie Organique, CNRS Unité de Recherche Associée 2128, Institut Pasteur, 25-28 rue du Dr. Roux, 75724 Paris cedex 15, France.
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21
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Becker J, Brendel M. Rapid purification and characterization of two distinct N-deoxyribosyltransferases of Lactobacillus leichmannii. BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1996; 377:357-62. [PMID: 8839981 DOI: 10.1515/bchm3.1996.377.6.357] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Two distinct N-deoxyribosyltransferases of Lactobacillus leichmannii, designated as DRTase I and DRTase II, were separated and purified almost to homogeneity by one-step affinity chromatography. DRTase I is distinguished by specifically catalyzing the direct transfer of 2-deoxyribosyl residues from purine deoxyribonucleosides to free purine bases, whereas DRTase II has a rather broad substrate specificity and is able to transfer the deoxyribosyl moiety between pyrimidines and between purines and pyrimidines. Furthermore, in addition to the different substrate spectrum, we clearly differentiated the two enzymes by comparing their varying temperature/activity and pH/activity profiles, their kinetic constants, their behaviour in Western blot analysis, and their N-terminal amino acid sequences. Denaturing and non-denaturing DISK-PAGE revealed strong evidence that both intact enzymes consist of hexamers with subunit molecular weights of approximately 20,000 for DRTase I and 18,000 for DRTase II.
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Affiliation(s)
- J Becker
- Institut für Mikrobiologie, Johann Wolfgang Goethe-Universität, Frankfurt/Main, Germany
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22
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Short SA, Armstrong SR, Ealick SE, Porter DJ. Active site amino acids that participate in the catalytic mechanism of nucleoside 2'-deoxyribosyltransferase. J Biol Chem 1996; 271:4978-87. [PMID: 8617773 DOI: 10.1074/jbc.271.9.4978] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The importance of eight nucleoside 2'-deoxyribosyltransferase residues for catalysis was investigated by site-directed mutagenesis. Each residue was selected because of its proximity to nucleophile Glu-98 or on its potential contribution to intrinsic protein fluorescence. Mutation of Asp-72, Asp-92, Tyr-7, Trp-12, and Met-125 resulted in over a 90% activity loss whereas mutation of Tyr-157, Trp-64, and Trp-127 produced less than a 80% activity loss. The magnitude of the perturbation on catalysis by mutation, however, was dependent on donor substrate. The kcat values for dIno hydrolysis by these mutants were greater than 25% of that for native enzyme. Although mutant and native enzymes bound substrate analogues with comparable affinities, Km values for dIno hydrolysis varied over a 1000-fold range. The pH dependence of Glu-98 esterification by dCyd suggested that amino acids with pK values of 4.2 and 7.5 were relevant for catalysis. The intrinsic protein fluorescence was attributed primarily to Trp-127 (approximately 80%). Pre-steady-state kinetic parameters for deoxyribosylation of mutant enzymes by dCyd, dThd, and dAdo were determined by monitoring changes in enzyme fluorescence. Collectively, results from mutagenesis suggest that, depending upon substrate, either Asp-92 or Asp-72 functions as the general acid catalyst, and that this enzyme undergoes a change in conformation upon Glu-98 deoxyribosylation.
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Affiliation(s)
- S A Short
- Division of Biochemistry, Glaxo-Wellcome, Research Triangle Park, North Carolina 27709, USA
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23
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Armstrong SR, Cook WJ, Short SA, Ealick SE. Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site. Structure 1996; 4:97-107. [PMID: 8805514 DOI: 10.1016/s0969-2126(96)00013-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Nucleoside 2-deoxyribosyltransferase plays an important role in the salvage pathway of nucleotide metabolism in certain organisms, catalyzing the cleavage of beta-2'-deoxyribonucleosides and the subsequent transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base. The kinetics describe a ping-pong-bi-bi pathway involving the formation of a covalent enzyme-deoxyribose intermediate. The enzyme is produced by a limited number of microorganisms and its functions have been exploited in its use as a biocatalyst to synthesize nucleoside analogs of therapeutic interest. RESULTS We describe the crystal structure of the enzyme with and without bound ligand. The native structure was solved by the single isomorphous replacement with anomalous scattering method (SIRAS) and refined to 2.5 A resolution resulting in a crystallographic R factor of 16.6%. The enzyme comprises a single domain that belongs to the general class of doubly-wound alpha/beta proteins; it also exhibits a unique nucleoside-binding motif. X-ray analysis of enzyme-purine and enzyme-pyrimidine complexes presented here reveals that the active site lies in a cleft formed by the edge of the beta sheet and two alpha helices and contains side chains from two subunits. CONCLUSIONS These results indicate residues that may be important in substrate binding and catalysis and thus may serve as a framework for elucidating the mechanism of enzyme activity. In particular, the proposed nucleophile, Glu98, lies in the nucleoside-binding pocket at an appropriate position for nucleophilic attack. A comparison of the enzyme interactions with both a purine and pyrimidine ligand provides some insight into the structural basis for enzyme specificity.
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Affiliation(s)
- S R Armstrong
- Section of Biochemistry, Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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Porter DJ, Merrill BM, Short SA. Identification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98. J Biol Chem 1995; 270:15551-6. [PMID: 7797550 DOI: 10.1074/jbc.270.26.15551] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
2'-Fluoro-2'-deoxyarabinonucleosides are time-dependent inhibitors of nucleoside 2-deoxyribosyltransferase. 2,6-Diamino-9-(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl)-9H-purine (dFDAP) inhibited the enzyme by formation of a primary complex (Kd = 140 microM) that isomerized to a secondary complex with a first-order rate constant of 0.2 min-1. Inhibited enzyme contained stoichiometric amounts of covalently bound 2'-fluoro-2'-deoxyarabinosyl moiety, recovered less than 5% of its activity after storage for a week at 5 degrees C, but regained over 70% of the lost activity by treatment with 600 microM Ade. 6-Amino-9-(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl)-9H-purine (dFAdo) was a product of the reactivation reaction. Proteolysis of inhibited enzyme identified a modified fragment that spanned residues 82-107 which could not be sequenced past Gly-96. dFDAP-inhibited enzyme and enzyme reacted with normal substrates (i.e. dThd and dAdo) were hydrolyzed between Met-97 and Glu-98 by 0.1 M NaOH. These findings and model studies on the base lability of peptides containing glutamyl esters suggested that the gamma-carboxylate of Glu-98 was esterfied during catalysis. The role of Glu-98 was confirmed by changing this residue to alanine. The specific activity of wild-type enzyme was 3 orders of magnitude greater than that of the mutant enzyme. Collectively, chemical modification and mutagenesis studies have identified Glu-98 as the active site nucleophile of nucleoside 2-deoxyribosyltransferase.
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Affiliation(s)
- D J Porter
- Division of Experimental Therapy, Wellcome Research Laboratories, Research Triangle Park, North Carolina 27709, USA
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Porter DJ, Short SA. Nucleoside 2-deoxyribosyltransferase. Pre-steady-state kinetic analysis of native enzyme and mutant enzyme with an alanyl residue replacing Glu-98. J Biol Chem 1995; 270:15557-62. [PMID: 7797551 DOI: 10.1074/jbc.270.26.15557] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Nucleoside 2-deoxyribosyltransferase catalyzes cleavage of a 2'-deoxyribosylnucleoside (A) to a nucleobase (P) with deoxyribosylation of the enzyme. Substrates quenched the intrinsic fluorescence of native enzyme (E) and a catalytically inactive mutant enzyme (E98A enzyme). The time courses of these reactions were analyzed in terms of the following scheme where EX is the 2-deoxyribosyl ester of Glu-98. [formula: see text] The initial complexes between E and dAdo, dGuo, dIno, and dCyd or those between EX and the corresponding nucleobases were formed in a rapid equilibrium step. Native enzyme and E98A enzyme bound 2'-deoxyribosylnucleosides with similar affinities (k-1/k1). From a comparison of the time-dependent fluorescence changes associated with the reaction of native enzyme or E98A enzyme with these substrate, the kinetic step for 2-deoxyribosylation of Glu-98 was identified (k2 and k-2). dThd and dUrd quenched the fluorescence of native enzyme in a biphasic process. The late phase of this reaction was associated with 2-deoxyribosylation of Glu-98. The pre-steady-state kinetic constants calculated from fluorescence quenching data for dAdo and Cyt were consistent with the experimental values for the steady-state kinetic coefficients and the equilibrium constant of the reaction.
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Affiliation(s)
- D J Porter
- Division of Experimental Therapy, Wellcome Research Laboratories, Research Triangle Park, North Carolina 27709, USA
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26
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Steenkamp DJ, Hälbich TJ. Substrate specificity of the purine-2'-deoxyribonucleosidase of Crithidia luciliae. Biochem J 1992; 287 ( Pt 1):125-9. [PMID: 1417764 PMCID: PMC1133133 DOI: 10.1042/bj2870125] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The purine-2'-deoxyribonucleosidase of Crithidia luciliae catalyses an efficient deoxyribosyl transfer between a variety of purine bases, benzimidazole and 5,6-dimethylbenzimidazole. Since the deoxyriboside of a deoxyribosyl acceptor is necessarily also a substrate, the trans-N-deoxyribosylase activity of the enzyme allows a study of its specificity to be extended to a large number of purines and purine analogues. Amongst 27 different deoxyribosyl acceptors, only hypoxanthine gave rise to isomeric products. The introduction of methyl groups at appropriate positions in either purine or benzimidazole lowered the Michaelis constant, KB, for deoxyribosyl acceptors: by about 10-fold for 6-methylpurine (KB 351 +/- 87 microM) compared with purine (KB 3.91 +/- 0.8 mM) and by about 10(3)-fold for 5,6-dimethylbenzimidazole (KB 7.0 +/- 0.79 microM) compared with benzimidazole (Km,app. 7.8 +/- 2.4 mM). The maximal rates of deoxyribosyl transfer to different acceptors, on the other hand, varied by only 4.5-fold, and can be ascribed to decreases in the rate of release of the newly formed purine deoxyriboside from the enzyme.
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Affiliation(s)
- D J Steenkamp
- Department of Chemical Pathology, University of Cape Town Medical School, South Africa
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27
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Steenkamp DJ. The purine-2-deoxyribonucleosidase from Crithidia luciliae. Purification and trans-N-deoxyribosylase activity. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 197:431-9. [PMID: 2026165 DOI: 10.1111/j.1432-1033.1991.tb15929.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Crude extracts of Crithidia luciliae catalysed a deoxyribosyl transfer from purine deoxynucleosides to free purine bases. Fractionation of a 0-80% (NH4)2SO4 fraction from C. luciliae on DEAE-cellulose resulted in the separation of three nucleosidase activities. Two of these were ribonucleosidases, one specific for inosine, uridine and xanthosine and the other for inosine and guanosine, whereas the third activity was specific for purine deoxyribonucleosides. This pattern is similar to that found in Leishmania donovani. Significant deoxyribosyltransferase activity was, however, associated with the purine-2'-deoxyribonucleosidase from C. luciliae. The purine-2'-deoxyribonucleosidase was purified to homogeneity by a six-step procedure involving (NH4)2SO4 fractionation and chromatography on DEAE-cellulose, hydroxyapatite, Sephadex G-75, and a chromatofocusing resin. The purified enzyme migrated as a single band of 17 kDa on SDS/polyacrylamide gel electrophoresis. The enzyme catalysed the hydrolysis of deoxyinosine, deoxyguanosine and deoxyadenosine with Km values of 80 +/- 10.5 microM, 20.7 +/- 3.2 microM and 17.3 +/- 5.3 microM, respectively, and V values for these substrates in the ratio 1:0.5:0.39. The pH optimum for deoxyribosyl transfer from deoxyinosine to guanine was at pH 7.7, while deoxyinosine hydrolysis in the presence of guanine was optimal in the range pH 6-7. During the synthesis of deoxyinosine from hypoxanthine and deoxyadenosine two products were formed. One of these coeluted with deoxyinosine on HPLC, while the second was tentatively identified as the positional isomer, 7-(beta-D-2'-deoxyribofuranosyl)hypoxanthine.
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Affiliation(s)
- D J Steenkamp
- Department of Chemical Pathology, University of Cape Town Medical School, South Africa
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Betbeder D, Hutchinson DW. The Enzymatic Synthesis of Imidazole Deoxynucleosides: 1-β-D-2′-Deoxyribofuranosyl-5-aminoiinidazole-4-carboxamide and 1-β-D-2′-Deoxyribofuranosylbenzimidazole. ACTA ACUST UNITED AC 1990. [DOI: 10.1080/07328319008045188] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Birnbaum GI, Lassota P, Shugar D. 8-Chloroguanosine: solid-state and solution conformations and their biological implications. Biochemistry 1984; 23:5048-53. [PMID: 6498175 DOI: 10.1021/bi00316a034] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The three-dimensional structure of 8-chloroguanosine dihydrate was determined by X-ray crystallography. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), and the cell dimensions are a = 4.871 (1) A, b = 12.040 (1) A, and c = 24.506 (1) A. The structure was determined by direct methods, and least-squares refinement, which included all hydrogen atoms, converged at R = 0.031 for 1599 observed reflections. The conformation about the glycosidic bond is syn with chi CN = -131.1 degrees. The ribose ring has a C(2')-endo/C-(1')-exo (2T1) pucker, and the gauche+ conformation of the -CH2OH side chain is stabilized by an intramolecular O-(5')-H...N(3) hydrogen bond. Conformational analysis by means of 1H NMR spectroscopy showed that, in dimethyl sulfoxide, the sugar ring exhibits a marked preference for the C(2')-endo conformation (approximately 70%) and a conformation about the glycosidic bond predominantly syn (approximately 90%), hence similar to that in the solid state. However, the conformation of the exocyclic 5'-CH2OH group exhibits only a moderate preference for the gauche+ rotamer (approximately 40%), presumably due to the inability to form the intramolecular hydrogen bond to N(3) in a polar medium. The conformational features are examined in relation to the behavior of 8-substituted purine nucleosides in several enzymatic systems, with due account taken of the steric bulk and electronegativities of the 8-substituents.
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