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Khandazhinskaya A, Fateev I, Konstantinova I, Esipov R, Polyakov K, Seley-Radtke K, Kochetkov S, Matyugina E. Synthesis of New 5′-Norcarbocyclic Aza/Deaza Purine Fleximers - Noncompetitive Inhibitors of E.coli Purine Nucleoside Phosphorylase. Front Chem 2022; 10:867587. [PMID: 35601551 PMCID: PMC9114674 DOI: 10.3389/fchem.2022.867587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
A new series of flexible 5′-norcarbocyclic aza/deaza-purine nucleoside analogs were synthesized from 6-oxybicyclo[3.1.0.]hex-2-ene and pyrazole-containing fleximer analogs of heterocyclic bases using the Trost procedure. The compounds were evaluated as potential inhibitors of E. coli purine nucleoside phosphorylase. Analog 1-3 were found to be noncompetitive inhibitors with inhibition constants of 14–24 mM. From the data obtained, it can be assumed that the new 5′-norcarbocyclic nucleoside analogs interact with the active site of the PNP like natural heterocyclic bases. But at the same time the presence of a cyclopentyl moiety with 2′ and 3′ hydroxyls is necessary for the inhibitory properties, since compounds 8–10, without those groups did not exhibit an inhibitory effect under the experimental conditions.
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Affiliation(s)
| | - Ilja Fateev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Roman Esipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Polyakov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Katherine Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, United States
| | - Sergey Kochetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Elena Matyugina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Elena Matyugina,
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2
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Khandazhinskaya A, Eletskaya B, Fateev I, Kharitonova M, Konstantinova I, Barai V, Azhayev A, Hyvonen MT, Keinanen TA, Kochetkov S, Seley-Radtke K, Khomutov A, Matyugina E. Novel fleximer pyrazole-containing adenosine analogues: chemical, enzymatic and highly efficient biotechnological synthesis. Org Biomol Chem 2021; 19:7379-7389. [PMID: 34198312 DOI: 10.1039/d1ob01069g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nucleoside analogues have long served as key chemotherapeutic drugs for the treatment of viral infections and cancers. Problems associated with the development of drug resistance have led to a search for the design of nucleosides capable of bypassing point mutations in the target enzyme's binding site. As a possible answer to this, the Seley-Radtke group developed a flexible nucleoside scaffold (fleximers), where the heterocyclic purine base is split into its two components, i.e. pyrimidine and imidazole. Herein, we present a series of new pyrazole-containing flex-bases and the corresponding fleximer analogues of 8-aza-7-deaza nucleosides. Subsequent studies found that pyrazole-containing flex-bases are substrates of purine nucleoside phosphorylase (PNP). We have compared the chemical synthesis of fleximers and enzymatic approaches with both isolated enzymes and the use of E. coli cells overproducing PNP. The latter provided stereochemically pure pyrazole-containing β-d-ribo- and β-d-2'-deoxyribo-fleximers and are beneficial in terms of environmental issues, are more economical, and streamline the steps required from a chemical approach. The reaction is carried out in water, avoiding hazardous chemicals, and the products are isolated by ion-exchange chromatography using water/ethanol mixtures for elution. Moreover, the target nucleosides were obtained on a multi-milligram scale with >97-99% purity, and the reactions can be easily scaled up.
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Affiliation(s)
- Anastasia Khandazhinskaya
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
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3
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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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4
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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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5
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Chudinov MV. Nucleoside Analogs with Fleximer Nucleobase. Chem Heterocycl Compd (N Y) 2020; 56:636-643. [PMID: 32836313 PMCID: PMC7364132 DOI: 10.1007/s10593-020-02713-5] [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: 02/28/2020] [Accepted: 04/15/2020] [Indexed: 11/30/2022]
Abstract
This review article is devoted to the so-called fleximer nucleoside analogs, containing two or more planar moieties in the heterocyclic base, connected by a bond that permits rotation. Such analogs have been proposed as molecular probes for detecting enzyme–substrate interactions and studying the transcription and translation of nucleic acids, but subsequently have attracted the interest of researchers by their antiviral and antitumor activity. The methods used in the synthesis of such compounds, along with their structural features and also biological activity are considered in this review.
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Affiliation(s)
- Mikhail V. Chudinov
- MIREA - Russian Technological University, Lomonosov Institute of Fine Chemical Tehnology, 78 Vernadsky Ave, Moscow, 119454 Russia
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6
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Mattelaer HP, Van Hool AS, de Jong F, Van der Auweraer M, Van Meervelt L, Dehaen W, Herdewijn P. New metal-free route towards imidazole substituted uridine. European J Org Chem 2020; 2020:4022-4025. [PMID: 32837299 PMCID: PMC7283795 DOI: 10.1002/ejoc.202000563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Indexed: 01/24/2023]
Abstract
Nucleosides with a bi(hetero)aryl nucleobase have unique potential applications as antiviral drugs and molecular probes. The need for transition metal catalysis to synthetize these nucleosides from pre-functionalized building blocks and the use of nucleobase protection groups results in expensive and tedious syntheses. Herein we report that 5-imidazolyl-uracil can be obtained by scalable Van Leusen imidazole synthesis and regioselectively introduced on ribose to obtain the desired nucleoside in a 5 step synthesis (total yield 55%). The 5-imidazolyl moiety leads to improved fluorescence properties. The only side-product formed was characterized by 2D-NMR and X-ray crystallography and could be suppressed during synthesis in favor of the desired product.
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Affiliation(s)
| | - Anne-Sophie Van Hool
- Katholieke Universiteit Leuven Rega Institute for Medical Research Medicinal Chemistry BELGIUM
| | - Flip de Jong
- Katholieke Universiteit Leuven Chemistry Department BELGIUM
| | | | | | - Wim Dehaen
- Katholieke Universiteit Leuven Chemistry Department BELGIUM
| | - Piet Herdewijn
- Rega Institute for Medical Research Medicinal Chemistry Herestraat 49 - box 1030 3000 Leuven BELGIUM
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7
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Matyugina ES, Khandazhinskaya AL, Kochetkov SN, Seley-Radtke KL. Synthesis of 3-hetarylpyrroles by Suzuki–Miyaura cross-coupling. MENDELEEV COMMUNICATIONS 2020. [PMCID: PMC7241993 DOI: 10.1016/j.mencom.2020.03.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
1-[tert-Butyl(diphenyl)silyl]pyrrol-3-ylboronic acid was obtained from pyrrole in three steps. Its Suzuki–Miyaura cross-coupling with functionalized pyridinyl and pyrimidinyl bromides afforded new promising 3-hetaryl-1H-pyrroles.
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Affiliation(s)
- Elena S. Matyugina
- V. A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Anastasia L. Khandazhinskaya
- V. A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russian Federation
- Corresponding author.
| | - Sergey N. Kochetkov
- V. A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russian Federation
| | - Katherine L. Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
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8
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Vichier-Guerre S, Ku TC, Pochet S, Seley-Radtke KL. An Expedient Synthesis of Flexible Nucleosides through Enzymatic Glycosylation of Proximal and Distal Fleximer Bases. Chembiochem 2020; 21:1412-1417. [PMID: 31899839 PMCID: PMC7228337 DOI: 10.1002/cbic.201900714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Indexed: 01/24/2023]
Abstract
The structurally unique “fleximer” nucleosides were originally designed to investigate how flexibility in a nucleobase could potentially affect receptor–ligand recognition and function. Recently they have been shown to have low‐to‐sub‐micromolar levels of activity against a number of viruses, including coronaviruses, filoviruses, and flaviviruses. However, the synthesis of distal fleximers in particular has thus far been quite tedious and low yielding. As a potential solution to this issue, a series of proximal fleximer bases (flex‐bases) has been successfully coupled to both ribose and 2′‐deoxyribose sugars by using the N‐deoxyribosyltransferase II of Lactobacillus leichmannii (LlNDT) and Escherichia coli purine nucleoside phosphorylase (PNP). To explore the range of this facile approach, transglycosylation experiments on a thieno‐expanded tricyclic heterocyclic base, as well as several distal and proximal flex‐bases were performed to determine whether the corresponding fleximer nucleosides could be obtained in this fashion, thus potentially significantly shortening the route to these biologically significant compounds. The results of those studies are reported herein.
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Affiliation(s)
- Sophie Vichier-Guerre
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS UMR3523, 28, rue du Dr Roux, 75015, Paris, France
| | - Therese C Ku
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Sylvie Pochet
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS UMR3523, 28, rue du Dr Roux, 75015, Paris, France
| | - Katherine L Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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9
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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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10
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Elgemeie GH, Mohamed RA. Microwave chemistry: Synthesis of purine and pyrimidine nucleosides using microwave radiation. J Carbohydr Chem 2019. [DOI: 10.1080/07328303.2018.1543430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Galal H. Elgemeie
- Chemistry Department, Faculty of Science, Helwan University, Helwan, Cairo, Egypt
| | - Reham A. Mohamed
- Chemistry of Natural and Microbial Products Department, National Research Center, Dokki, Cairo, Egypt
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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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