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Pfeiffer M, Ribar A, Nidetzky B. A selective and atom-economic rearrangement of uridine by cascade biocatalysis for production of pseudouridine. Nat Commun 2023; 14:2261. [PMID: 37081027 PMCID: PMC10116470 DOI: 10.1038/s41467-023-37942-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
As a crucial factor of their therapeutic efficacy, the currently marketed mRNA vaccines feature uniform substitution of uridine (U) by the corresponding C-nucleoside, pseudouridine (Ψ), in 1-N-methylated form. Synthetic supply of the mRNA building block (1-N-Me-Ψ-5'-triphosphate) involves expedient access to Ψ as the principal challenge. Here, we show selective and atom-economic 1N-5C rearrangement of β-D-ribosyl on uracil to obtain Ψ from unprotected U in quantitative yield. One-pot cascade transformation of U in four enzyme-catalyzed steps, via D-ribose (Rib)-1-phosphate, Rib-5-phosphate (Rib5P) and Ψ-5'-phosphate (ΨMP), gives Ψ. Coordinated function of the coupled enzymes in the overall rearrangement necessitates specific release of phosphate from the ΨMP, but not from the intermediary ribose phosphates. Discovery of Yjjg as ΨMP-specific phosphatase enables internally controlled regeneration of phosphate as catalytic reagent. With driving force provided from the net N-C rearrangement, the optimized U reaction yields a supersaturated product solution (∼250 g/L) from which the pure Ψ crystallizes (90% recovery). Scale up to 25 g isolated product at enzyme turnovers of ∼105 mol/mol demonstrates a robust process technology, promising for Ψ production. Our study identifies a multistep rearrangement reaction, realized by cascade biocatalysis, for C-nucleoside synthesis in high efficiency.
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Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, A-8010, Graz, Austria
| | - Andrej Ribar
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, A-8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria.
- Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, A-8010, Graz, Austria.
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Shanmugasundaram M, Senthilvelan A, Kore AR. An efficient green synthesis of UNA-nucleoside-5′-triphosphates: a versatile synthon for RNA modification with broad therapeutic potential. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
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Shanmugasundaram M, Senthilvelan A, Kore AR. An Efficient Gram-Scale Chemical Synthesis of Purine Locked Nucleic Acid Nucleoside-5'-O-Triphosphates. Curr Protoc 2022; 2:e436. [PMID: 35723503 DOI: 10.1002/cpz1.436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This article presents a simple, reliable, straight-forward, general, and efficient chemical method for the gram-scale synthesis of purine locked nucleic acid (LNA) nucleotides, such as LNA guanosine-5'-O-triphosphate (LNA-GTP) and LNA adenosine-5'-O-triphosphate (LNA-ATP), starting from the corresponding nucleoside. The reaction pathway employs an improved protection-free "one-pot, three-step" Ludwig synthetic strategy. The first step involves monophosphorylation of nucleoside with phosphorus oxychloride followed by reaction with tributylammonium pyrophosphate and subsequent hydrolysis of the resulting cyclic intermediate to furnish the corresponding LNA nucleotide in good yields. It is noteworthy that the reaction affords high-purity (>99.5%) LNA nucleotide after diethylaminoethyl Sepharose column purification. © 2022 Wiley Periodicals LLC. Basic Protocol: Synthesis of LNA nucleoside-5'-O-triphosphates.
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas
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Shanmugasundaram M, Senthilvelan A, Kore AR. An improved protection-free one-pot chemical synthesis of purine locked nucleic acid nucleoside-5'-triphosphates. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2021; 41:36-44. [PMID: 34696692 DOI: 10.1080/15257770.2021.1994992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 10/20/2022]
Abstract
A simple, reliable, straightforward, and efficient method for the gram-scale chemical synthesis of purine locked nucleic acid (LNA) nucleotides such as LNA-guanosine-5'-triphosphate (LNA-GTP) and LNA-adenosine-5'-triphosphate (LNA-ATP) starting from the corresponding nucleoside is described. The overall reaction utilizes an improved "one-pot, three-step" Ludwig synthetic strategy that involves the monophosphorylation of LNA nucleoside, followed by the reaction with tributylammonium pyrophosphate and subsequent hydrolysis of the resulting cyclic intermediate using water to furnish the corresponding purine LNA nucleotide in good yield with high purity (>99.5%).
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas, USA
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Shanmugasundaram M, Senthilvelan A, Kore AR. Highly regioselective 1,3-dipolar cycloaddition of 3'- O-propargyl guanosine with nitrile oxide: An efficient method for the synthesis of guanosine containing isoxazole moiety. Tetrahedron Lett 2020; 61:152464. [PMID: 32981977 PMCID: PMC7501312 DOI: 10.1016/j.tetlet.2020.152464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/10/2020] [Accepted: 09/13/2020] [Indexed: 12/28/2022]
Abstract
The 1,3-dipolar cycloaddition reaction of 3'-O-propargyl guanosine with various in-situ generated nitrile oxides in the presence of DMF as a solvent is described. It is noteworthy that the reaction is highly regioselective that affords biologically important guanosine containing isoxazole moiety in good yields with high purities.
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Affiliation(s)
- Muthian Shanmugasundaram
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, USA
| | - Annamalai Senthilvelan
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, USA
| | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, USA
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Senthilvelan A, Shanmugasundaram M, Kore AR. Highly regioselective methylation of inosine nucleotide: an efficient synthesis of 7-methylinosine nucleotide. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1011-1019. [PMID: 32189563 DOI: 10.1080/15257770.2020.1738457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A facile, straightforward, reliable, and an efficient chemical synthesis of inosine nucleotides such as 7-methylinosine 5'-O-monophosphate, 7-methylinosine 5'-O-diphosphate, and 7-methylinosine 5'-O-triphosphate, starting from the corresponding inosine nucleotide is delineated. The present methylation reaction of inosine nucleotide utilizes dimethyl sulfate as a methylating agent and water as a solvent at room temperature. It is noteworthy that the present methylation reaction proceeds smoothly under aqueous conditions that is highly regioselective to afford exclusive 7-methylinosine nucleotide in good yields with high purity (>99.5%).
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas, USA
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Senthilvelan A, Shanmugasundaram M, Kore AR. An efficient protection-free chemical synthesis of inosine 5'-nucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:829-837. [PMID: 31997708 DOI: 10.1080/15257770.2019.1708388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A facile, straightforward, reliable, and efficient chemical synthesis of inosine nucleotides such as inosine-5'-monophosphate, inosine-5'-diphosphate, and inosine-5'-triphosphate, starting from inosine is delineated. The inosine-5'-monophosphate is achieved by the highly regioselective monophosphorylation of inosine using the Yoshikawa procedure. The inosine-5'-diphosphate is obtained by the coupling reaction of tributylammonium phosphate with an activated inosine-5'-monophosphate using zinc chloride as a catalyst. The inosine-5'-triphosphate is efficiently achieved by the improved "one-pot, three-step" Ludwig synthetic strategy. In all the cases, the resulting final product is isolated in good yields with high purity (>99.5%).
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, TX, USA
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Shanmugasundaram M, Senthilvelan A, Kore AR. Highly regio- and stereoselective Michael addition of pseudouridine with propiolates: An efficient method for the synthesis of (E)-pseudouridine-N1-acrylate. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2018.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Shanmugasundaram M, Senthilvelan A, Kore AR. Gram-Scale Chemical Synthesis of Base-Modified Ribonucleoside-5'-O-Triphosphates. ACTA ACUST UNITED AC 2016; 67:13.15.1-13.15.10. [PMID: 27911496 DOI: 10.1002/cpnc.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This unit delineates a simple, reliable, straight-forward, general, and efficient chemical method for the synthesis of modified nucleoside-5'-O-triphosphates such as 5-methylcytidine-5'-O-triphosphate (5-Me-CTP), pseudouridine-5'-O-triphosphate (pseudo-UTP), and N1 -methylpseudouridine-5'-O-triphosphate (N1 -methylpseudo-UTP), starting from the corresponding nucleoside. The reaction utilizes an improved protection-free "one-pot, three-step" Ludwig synthetic strategy that involves the monophosphorylation of the nucleoside with phosphorous oxychloride followed by reaction with tributylammonium pyrophosphate and subsequent hydrolysis of the resulting cyclic intermediate to furnish the corresponding ribonucleoside triphosphate (NTP) in moderate yields. It is noteworthy that the reaction affords high purity (>99.5%) NTPs after DEAE Sepharose column purification. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas
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Abstract
Focusing on the recent literature (since 2000), this review outlines the main synthetic approaches for the preparation of 5'-mono-, 5'-di-, and 5'-triphosphorylated nucleosides, also known as nucleotides, as well as several derivatives, namely, cyclic nucleotides and dinucleotides, dinucleoside 5',5'-polyphosphates, sugar nucleotides, and nucleolipids. Endogenous nucleotides and their analogues can be obtained enzymatically, which is often restricted to natural substrates, or chemically. In chemical synthesis, protected or unprotected nucleosides can be used as the starting material, depending on the nature of the reagents selected from P(III) or P(V) species. Both solution-phase and solid-support syntheses have been developed and are reported here. Although a considerable amount of research has been conducted in this field, further work is required because chemists are still faced with the challenge of developing a universal methodology that is compatible with a large variety of nucleoside analogues.
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Affiliation(s)
- Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Christian Périgaud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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