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Eletskaya BZ, Mironov AF, Fateev IV, Berzina MY, Antonov KV, Smirnova OS, Zatsepina AB, Arnautova AO, Abramchik YA, Paramonov AS, Kayushin AL, Khandazhinskaya AL, Matyugina ES, Kochetkov SN, Miroshnikov AI, Mikhailopulo IA, Esipov RS, Konstantinova ID. Enzymatic Transglycosylation Features in Synthesis of 8-Aza-7-Deazapurine Fleximer Nucleosides by Recombinant E. coli PNP: Synthesis and Structure Determination of Minor Products. Biomolecules 2024; 14:798. [PMID: 39062512 PMCID: PMC11275124 DOI: 10.3390/biom14070798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Enzymatic transglycosylation of the fleximer base 4-(4-aminopyridine-3-yl)-1H-pyrazole using recombinant E. coli purine nucleoside phosphorylase (PNP) resulted in the formation of "non-typical" minor products of the reaction. In addition to "typical" N1-pyrazole nucleosides, a 4-imino-pyridinium riboside and a N1-pyridinium-N1-pyrazole bis-ribose derivative were formed. N1-Pyrazole 2'-deoxyribonucleosides and a N1-pyridinium-N1-pyrazole bis-2'-deoxyriboside were formed. But 4-imino-pyridinium deoxyriboside was not formed in the reaction mixture. The role of thermodynamic parameters of key intermediates in the formation of reaction products was elucidated. To determine the mechanism of binding and activation of heterocyclic substrates in the E. coli PNP active site, molecular modeling of the fleximer base and reaction products in the enzyme active site was carried out. As for N1-pyridinium riboside, there are two possible locations for it in the PNP active site. The presence of a relatively large space in the area of amino acid residues Phe159, Val178, and Asp204 allows the ribose residue to fit into that space, and the heterocyclic base can occupy a position that is suitable for subsequent glycosylation. Perhaps it is this "upside down" arrangement that promotes secondary glycosylation and the formation of minor bis-riboside products.
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Affiliation(s)
- Barbara Z. Eletskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Anton F. Mironov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
- Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia Named after Patrice Lumumba, Miklukho-Maklaya St. 6, Moscow 117198, Russia
| | - Ilya V. Fateev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Maria Ya. Berzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Konstantin V. Antonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Olga S. Smirnova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexandra B. Zatsepina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexandra O. Arnautova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Yulia A. Abramchik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexander S. Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexey L. Kayushin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Anastasia L. Khandazhinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Elena S. Matyugina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Sergey N. Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Anatoly I. Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Igor A. Mikhailopulo
- Institute of Bioorganic Chemistry, National Academy of Sciences, Acad. Kuprevicha 5/2, 220141 Minsk, Belarus;
| | - Roman S. Esipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Irina D. Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
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2
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Stachelska-Wierzchowska A, Wierzchowski J. Chemo-Enzymatic Generation of Highly Fluorescent Nucleoside Analogs Using Purine-Nucleoside Phosphorylase. Biomolecules 2024; 14:701. [PMID: 38927104 PMCID: PMC11201700 DOI: 10.3390/biom14060701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Chemo-enzymatic syntheses of strongly fluorescent nucleoside analogs, potentially applicable in analytical biochemistry and cell biology are reviewed. The syntheses and properties of fluorescent ribofuranosides of several purine, 8-azapurine, and etheno-purine derivatives, obtained using various types of purine nucleoside phosphorylase (PNP) as catalysts, as well as α-ribose-1-phosphate (r1P) as a second substrate, are described. In several instances, the ribosylation sites are different to the canonical purine N9. Some of the obtained ribosides show fluorescence yields close to 100%. Possible applications of the new analogs include assays of PNP, nucleoside hydrolases, and other enzyme activities both in vitro and within living cells using fluorescence microscopy.
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Affiliation(s)
| | - Jacek Wierzchowski
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
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Westarp S, Brandt F, Neumair L, Betz C, Dagane A, Kemper S, Jacob CR, Neubauer P, Kurreck A, Kaspar F. Nucleoside Phosphorylases make N7-xanthosine. Nat Commun 2024; 15:3625. [PMID: 38684649 PMCID: PMC11058261 DOI: 10.1038/s41467-024-47287-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/26/2024] [Indexed: 05/02/2024] Open
Abstract
Modern, highly evolved nucleoside-processing enzymes are known to exhibit perfect regioselectivity over the glycosylation of purine nucleobases at N9. We herein report an exception to this paradigm. Wild-type nucleoside phosphorylases also furnish N7-xanthosine, a "non-native" ribosylation regioisomer of xanthosine. This unusual nucleoside possesses several atypical physicochemical properties such as redshifted absorption spectra, a high equilibrium constant of phosphorolysis and low acidity. Ultimately, the biosynthesis of this previously unknown natural product illustrates how even highly evolved, essential enzymes from primary metabolism are imperfect catalysts.
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Affiliation(s)
- Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Lena Neumair
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Christina Betz
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Amin Dagane
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Sebastian Kemper
- Institute for Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstrasse 76, 13355, Berlin, Germany.
- BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany.
| | - Felix Kaspar
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.
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Stachelska-Wierzchowska A, Wierzchowski J. Non-typical nucleoside analogs as fluorescent and fluorogenic indicators of purine-nucleoside phosphorylase activity in biological samples. Anal Chim Acta 2020; 1139:119-128. [PMID: 33190694 DOI: 10.1016/j.aca.2020.09.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Affiliation(s)
- A Stachelska-Wierzchowska
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, 4 Oczapowskiego St., PL-10-710, Olsztyn, Poland.
| | - J Wierzchowski
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, 4 Oczapowskiego St., PL-10-710, Olsztyn, Poland.
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Kaspar F, Giessmann RT, Westarp S, Hellendahl KF, Krausch N, Thiele I, Walczak MC, Neubauer P, Wagner A. Spectral Unmixing-Based Reaction Monitoring of Transformations between Nucleosides and Nucleobases. Chembiochem 2020; 21:2604-2610. [PMID: 32324971 PMCID: PMC7540295 DOI: 10.1002/cbic.202000204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/21/2020] [Indexed: 11/10/2022]
Abstract
The increased interest in (enzymatic) transformations between nucleosides and nucleobases has demanded the development of efficient analytical tools. In this report, we present an update and extension of our recently described method for monitoring these reactions by spectral unmixing. The presented method uses differences in the UV absorption spectra of nucleosides and nucleobases after alkaline quenching to derive their ratio based on spectral shape by fitting normalized reference spectra. It is applicable to a broad compound spectrum comprising more than 35 examples, offers HPLC-like accuracy, ease of handling and significant reductions in both cost and data acquisition time compared to other methods. This contribution details the principle of monitoring reactions by spectral unmixing, gives recommendations regarding solutions to common problems and applications that necessitate special sample treatment. We provide software, workflows and reference spectra that facilitate the straightforward and versatile application of the method.
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Affiliation(s)
- Felix Kaspar
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
| | - Robert T. Giessmann
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Sarah Westarp
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
| | - Katja F. Hellendahl
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Niels Krausch
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Isabel Thiele
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Miriam C. Walczak
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
| | - Peter Neubauer
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
| | - Anke Wagner
- Institute of Biotechnology, Chair of Bioprocess EngineeringTechnische Universität Berlin ACK 24Ackerstraße 7613355BerlinGermany
- BioNukleo GmbHAckerstraße 7613355BerlinGermany
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Jackson EK, Gillespie DG, Cheng D, Mi Z, Menshikova EV. Characterization of the N 6-etheno-bridge method to assess extracellular metabolism of adenine nucleotides: detection of a possible role for purine nucleoside phosphorylase in adenosine metabolism. Purinergic Signal 2020; 16:187-211. [PMID: 32367441 PMCID: PMC7367995 DOI: 10.1007/s11302-020-09699-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/08/2020] [Indexed: 12/11/2022] Open
Abstract
The goal of this study was to determine the validity of using N6-etheno-bridged adenine nucleotides to evaluate ecto-nucleotidase activity. We observed that the metabolism of N6-etheno-ATP versus ATP was quantitatively similar when incubated with recombinant CD39, ENTPD2, ENTPD3, or ENPP-1, and the quantitative metabolism of N6-etheno-AMP versus AMP was similar when incubated with recombinant CD73. This suggests that ecto-nucleotidases process N6-etheno-bridged adenine nucleotides similarly to endogenous adenine nucleotides. Four cell types rapidly (t1/2, 0.21 to 0.66 h) metabolized N6-etheno-ATP. Applied N6-etheno-ATP was recovered in the medium as N6-etheno-ADP, N6-etheno-AMP, N6-etheno-adenosine, and surprisingly N6-etheno-adenine; intracellular N6-etheno compounds were undetectable. This suggests minimal cellular uptake, intracellular metabolism, or deamination of these compounds. N6-etheno-ATP, N6-etheno-ADP, N6-etheno-AMP, N6-etheno-adenosine, and N6-etheno-adenine had little affinity for recombinant A1, A2A, or A2B receptors, for a subset of P2X receptors (3H-α,β-methylene-ATP binding to rat bladder membranes), or for a subset of P2Y receptors (35S-ATP-αS binding to rat brain membranes), suggesting minimal pharmacological activity. N6-etheno-adenosine was partially converted to N6-etheno-adenine in four different cell types; this was blocked by purine nucleoside phosphorylase (PNPase) inhibition. Intravenous N6-etheno-ATP was quickly metabolized, with N6-etheno-adenine being the main product in naïve rats, but not in rats pretreated with a PNPase inhibitor. PNPase inhibition reduced the urinary excretion of endogenous adenine and attenuated the conversion of exogenous adenosine to adenine in the renal cortex. The N6-etheno-bridge method is a valid technique to assess extracellular metabolism of adenine nucleotides by ecto-nucleotidases. Also, rats express an enzyme with PNPase-like activity that metabolizes N6-etheno-adenosine to N6-etheno-adenine.
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Affiliation(s)
- Edwin K. Jackson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 100 Technology Drive, Room 514, Pittsburgh, PA 15219 USA
| | - Delbert G. Gillespie
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 100 Technology Drive, Room 514, Pittsburgh, PA 15219 USA
| | - Dongmei Cheng
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 100 Technology Drive, Room 514, Pittsburgh, PA 15219 USA
| | - Zaichuan Mi
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 100 Technology Drive, Room 514, Pittsburgh, PA 15219 USA
| | - Elizabeth V. Menshikova
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 100 Technology Drive, Room 514, Pittsburgh, PA 15219 USA
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Kaspar F, Giessmann RT, Hellendahl KF, Neubauer P, Wagner A, Gimpel M. General Principles for Yield Optimization of Nucleoside Phosphorylase-Catalyzed Transglycosylations. Chembiochem 2020; 21:1428-1432. [PMID: 31820837 PMCID: PMC7318676 DOI: 10.1002/cbic.201900740] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Indexed: 11/29/2022]
Abstract
The biocatalytic synthesis of natural and modified nucleosides with nucleoside phosphorylases offers the protecting-group-free direct glycosylation of free nucleobases in transglycosylation reactions. This contribution presents guiding principles for nucleoside phosphorylase-mediated transglycosylations alongside mathematical tools for straightforward yield optimization. We illustrate how product yields in these reactions can easily be estimated and optimized using the equilibrium constants of phosphorolysis of the nucleosides involved. Furthermore, the varying negative effects of phosphate on transglycosylation yields are demonstrated theoretically and experimentally with several examples. Practical considerations for these reactions from a synthetic perspective are presented, as well as freely available tools that serve to facilitate a reliable choice of reaction conditions to achieve maximum product yields in nucleoside transglycosylation reactions.
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Affiliation(s)
| | - Robert T. Giessmann
- Department of BiotechnologyTechnical University of BerlinACK24, Ackerstrasse 7613355BerlinGermany
| | - Katja F. Hellendahl
- Department of BiotechnologyTechnical University of BerlinACK24, Ackerstrasse 7613355BerlinGermany
| | - Peter Neubauer
- Department of BiotechnologyTechnical University of BerlinACK24, Ackerstrasse 7613355BerlinGermany
| | - Anke Wagner
- BioNukleo GmbHAckerstrasse 7613355BerlinGermany
- Department of BiotechnologyTechnical University of BerlinACK24, Ackerstrasse 7613355BerlinGermany
| | - Matthias Gimpel
- Department of BiotechnologyTechnical University of BerlinACK24, Ackerstrasse 7613355BerlinGermany
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8
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Stachelska-Wierzchowska A, Wierzchowski J, Górka M, Bzowska A, Stolarski R, Wielgus-Kutrowska B. Tricyclic Nucleobase Analogs and Their Ribosides as Substrates and Inhibitors of Purine-Nucleoside Phosphorylases III. Aminopurine Derivatives. Molecules 2020; 25:E681. [PMID: 32033464 PMCID: PMC7037862 DOI: 10.3390/molecules25030681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 11/16/2022] Open
Abstract
Etheno-derivatives of 2-aminopurine, 2-aminopurine riboside, and 7-deazaadenosine (tubercidine) were prepared and purified using standard methods. 2-Aminopurine reacted with aqueous chloroacetaldehyde to give two products, both exhibiting substrate activity towards bacterial (E. coli) purine-nucleoside phosphorylase (PNP) in the reverse (synthetic) pathway. The major product of the chemical synthesis, identified as 1,N2-etheno-2-aminopurine, reacted slowly, while the second, minor, but highly fluorescent product, reacted rapidly. NMR analysis allowed identification of the minor product as N2,3-etheno-2-aminopurine, and its ribosylation product as N2,3-etheno-2-aminopurine-N2--D-riboside. Ribosylation of 1,N2-etheno-2-aminopurine led to analogous N2--d-riboside of this base. Both enzymatically produced ribosides were readily phosphorolysed by bacterial PNP to the respective bases. The reaction of 2-aminopurine-N9- -D-riboside with chloroacetaldehyde gave one major product, clearly distinct from that obtained from the enzymatic synthesis, which was not a substrate for PNP. A tri-cyclic 7-deazaadenosine (tubercidine) derivative was prepared in an analogous way and shown to be an effective inhibitor of the E. coli, but not of the mammalian enzyme. Fluorescent complexes of amino-purine analogs with E. coli PNP were observed.
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Affiliation(s)
| | - Jacek Wierzchowski
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Michał Górka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 5 Pasteura St., 02-093 Warsaw, Poland; (M.G.); (A.B.); (R.S.)
- Biological and Chemical Research Centre, University of Warsaw, 101 Zwirki i Wigury St., 02-089 Warsaw, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 5 Pasteura St., 02-093 Warsaw, Poland; (M.G.); (A.B.); (R.S.)
| | - Ryszard Stolarski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 5 Pasteura St., 02-093 Warsaw, Poland; (M.G.); (A.B.); (R.S.)
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 5 Pasteura St., 02-093 Warsaw, Poland; (M.G.); (A.B.); (R.S.)
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9
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Kaspar F, Giessmann RT, Krausch N, Neubauer P, Wagner A, Gimpel M. A UV/Vis Spectroscopy-Based Assay for Monitoring of Transformations Between Nucleosides and Nucleobases. Methods Protoc 2019; 2:E60. [PMID: 31311105 PMCID: PMC6789650 DOI: 10.3390/mps2030060] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 12/25/2022] Open
Abstract
Efficient reaction monitoring is crucial for data acquisition in kinetic and mechanistic studies. However, for conversions of nucleosides to their corresponding nucleobases, as observed in enzymatically catalyzed nucleoside phosphorylation reactions, the current analytical arsenal does not meet modern requirements regarding cost, speed of analysis and high throughput. Herein, we present a UV/Vis spectroscopy-based assay employing an algorithm for spectral unmixing in a 96-well plate format. The algorithm relies on fitting of reference spectra of nucleosides and their bases to experimental spectra and allows determination of nucleoside/nucleobase ratios in solution with high precision. The experimental procedure includes appropriate dilution of a sample into aqueous alkaline solution, transfer to a multi-well plate, measurement of a UV/Vis spectrum and subsequent in silico spectral unmixing. This enables data collection in a high-throughput fashion and reduces costs compared to state-of-the-art HPLC analyses by approximately 5-fold while being 20-fold faster and offering comparable precision. Additionally, the method is robust regarding dilution and sample transfer errors as it only considers spectral form and not absolute intensity. It can be applied to all natural nucleosides and nucleobases and even unnatural ones as demonstrated by several examples.
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Affiliation(s)
- Felix Kaspar
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany
| | - Robert T Giessmann
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany
| | - Niels Krausch
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany
| | - Peter Neubauer
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany
| | - Anke Wagner
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany.
- BioNukleo GmbH, Ackerstraße 76, D-13355 Berlin, Germany.
| | - Matthias Gimpel
- Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, D-13355 Berlin, Germany
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Stachelska-Wierzchowska A, Wierzchowski J, Górka M, Bzowska A, Wielgus-Kutrowska B. Tri-Cyclic Nucleobase Analogs and their Ribosides as Substrates of Purine-Nucleoside Phosphorylases. II Guanine and Isoguanine Derivatives. Molecules 2019; 24:E1493. [PMID: 30995785 PMCID: PMC6514686 DOI: 10.3390/molecules24081493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/27/2019] [Accepted: 04/09/2019] [Indexed: 11/17/2022] Open
Abstract
Etheno-derivatives of guanine, O6-methylguanine, and isoguanine were prepared and purified using standard methods. The title compounds were examined as potential substrates of purine-nucleoside phosphorylases from various sources in the reverse (synthetic) pathway. It was found that 1,N2-etheno-guanine and 1,N6-etheno-isoguanine are excellent substrates for purine-nucleoside phosphorylase (PNP) from E. coli, while O6-methyl-N2,3-etheno-guanine exhibited moderate activity vs. this enzyme. The latter two compounds displayed intense fluorescence in neutral aqueous medium, and so did the corresponding ribosylation products. By contrast, PNP from calf spleens exhibited only modest activity towards 1,N6-etheno-isoguanine; the remaining compounds were not ribosylated by this enzyme. The enzymatic ribosylation of 1,N6-etheno-isoguanine using two forms of calf PNP (wild type and N243D) and E. coli PNP (wild type and D204N) gave three different products, which were identified on the basis of NMR analysis and comparison with the product of the isoguanosine reaction with chloroacetic aldehyde, which gave an essentially single compound, identified unequivocally as N9-riboside. With the wild-type E. coli enzyme as a catalyst, N9--d- and N7--d-ribosides are obtained in proportion ~1:3, while calf PNP produced another riboside, tentatively identified as N6--d-riboside. The potential application of various forms of PNP for synthesis of the tri-cyclic nucleoside analogs is discussed.
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Affiliation(s)
- Alicja Stachelska-Wierzchowska
- Department of Physics and Biophysics, University of Varmia & Masuria in Olsztyn, 4 Oczapowskiego St., 10-719 Olsztyn, Poland.
| | - Jacek Wierzchowski
- Department of Physics and Biophysics, University of Varmia & Masuria in Olsztyn, 4 Oczapowskiego St., 10-719 Olsztyn, Poland.
| | - Michał Górka
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
- Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
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