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Westarp S, Benckendorff CMM, Motter J, Röhrs V, Sanghvi YS, Neubauer P, Kurreck J, Kurreck A, Miller GJ. Biocatalytic Nucleobase Diversification of 4'-Thionucleosides and Application of Derived 5-Ethynyl-4'-thiouridine for RNA Synthesis Detection. Angew Chem Int Ed Engl 2024; 63:e202405040. [PMID: 38785103 DOI: 10.1002/anie.202405040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
Nucleoside and nucleotide analogues have proven to be transformative in the treatment of viral infections and cancer. One branch of structural modification to deliver new nucleoside analogue classes explores replacement of canonical ribose oxygen with a sulfur atom. Whilst biological activity of such analogues has been shown in some cases, widespread exploration of this compound class is hitherto hampered by the lack of a straightforward and universal nucleobase diversification strategy. Herein, we present a synergistic platform enabling both biocatalytic nucleobase diversification from 4'-thiouridine in a one-pot process, and chemical functionalization to access new entities. This methodology delivers entry across pyrimidine and purine 4'-thionucleosides, paving a way for wider synthetic and biological exploration. We exemplify our approach by enzymatic synthesis of 5-iodo-4'-thiouridine on multi-milligram scale and from here switch to complete chemical synthesis of a novel nucleoside analogue probe, 5-ethynyl-4'-thiouridine. Finally, we demonstrate the utility of this probe to monitor RNA synthesis in proliferating HeLa cells, validating its capability as a new metabolic RNA labelling tool.
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Affiliation(s)
- Sarah Westarp
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstraße 76 ACK24, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstrasse 76, D-13355, Berlin, Germany
| | - Caecilie M M Benckendorff
- Centre for Glycoscience and School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Jonas Motter
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstraße 76 ACK24, D-13355, Berlin, Germany
| | - Viola Röhrs
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, TIB 4/3-2, D-13355, Berlin, Germany
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, California, 92024, USA
| | - Peter Neubauer
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstraße 76 ACK24, D-13355, Berlin, Germany
| | - Jens Kurreck
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, TIB 4/3-2, D-13355, Berlin, Germany
| | - Anke Kurreck
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstraße 76 ACK24, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstrasse 76, D-13355, Berlin, Germany
| | - Gavin J Miller
- Centre for Glycoscience and School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
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Benckendorff CMM, Sanghvi YS, Miller GJ. Preparation of a 4'-Thiouridine Building-Block for Solid-Phase Oligonucleotide Synthesis. Curr Protoc 2023; 3:e878. [PMID: 37747330 PMCID: PMC10946921 DOI: 10.1002/cpz1.878] [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] [Indexed: 09/26/2023]
Abstract
Starting from a commercially available thioether, we report a nine-step synthesis of a 4'-thiouridine phosphoramidite building-block. We install the uracil nucleobase using Pummerer-type glycosylation of a sulfoxide intermediate followed by a series of protecting group manipulations to deliver the desired phosphite. Notably, we introduce a 3',5'-O-di-tert-butylsilylene protecting group within a 4'-thiosugar framework, harnessing this to ensure regiospecific installation of the 2'-O-silyl protecting group. We envisage this methodology will be generally applicable to other 4'-thionucleosides and duly support the exploration of their inclusion within related nucleic acid syntheses. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: (2R,3S,4R)-2,3-O-Isopopropylidene-5-O-tert-butyldiphenylsilyl-1-(4-sulfinyl)cyclopentane: Sulfoxidation Basic Protocol 2: 2',3'-O-Isopropylidene-5'-O-tert-butyldiphenylsilyl-4'-thiouridine: Pummerer glycosylation Basic Protocol 3: 4'-Thiouridine: Deprotection Basic Protocol 4: 2'-O-tert-Butyldimethylsilyl-3',5'-di-tert-butylsiloxy-4'-thiouridine: 2',3',5'-O-silylation Basic Protocol 5: 2'-O-tert-Butyldimethylsilyl-4'-thiouridine: Selective 3'-5'-desilylation Basic Protocol 6: 2'-O-tert-Butyldimethylsilyl-5'-O-dimethoxytrityl-4'-thiouridine: 5'-O-dimethoxytritylation Basic Protocol 7: 2'-O-tert-butyldimethylsilyl-3'-O-[(2-cyanoethoxy)(N,N-diisopropylamino)phosphino]-5'-O-dimethoxytrityl-4'-thiouridine: 3'-O-phosphitylation.
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Affiliation(s)
- Caecilie M. M. Benckendorff
- Centre for GlycoscienceKeele UniversityKeeleStaffordshireUnited Kingdom
- Lennard‐Jones Laboratory, School of Chemical and Physical SciencesKeele UniversityKeeleStaffordshireUnited Kingdom
| | | | - Gavin J. Miller
- Centre for GlycoscienceKeele UniversityKeeleStaffordshireUnited Kingdom
- Lennard‐Jones Laboratory, School of Chemical and Physical SciencesKeele UniversityKeeleStaffordshireUnited Kingdom
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Hussain Z, A. Ibrahim M, M. El-Gohary N, A. Gabr Y, A. Allimony H, Badran AS. Utility of 6-Aminouracils for Building Substituted and Heteroannulated Pyrimidines: A Comprehensive Review. HETEROCYCLES 2023. [DOI: 10.3987/rev-23-1002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Katayama A, Jin Y, Nishiyama Y, Hosoya T, Yokoshima S. Substitution of α-Azido Sulfones with Thiolates to Form α-Azido Sulfides. Org Lett 2022; 24:7361-7365. [PMID: 36178802 DOI: 10.1021/acs.orglett.2c02895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Upon treatment of α-azido sulfones with a thiol in the presence of 1,1,3,3-tetramethylguanidine, substitution of the sulfonyl group with a thiolate occurred, resulting in the formation of α-azido sulfides. Based on experimental results and DFT calculations, a reaction mechanism that involves the addition of a thiolate to the azido group and generation of an alkylidene triazene is proposed.
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Affiliation(s)
- Akito Katayama
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yuan Jin
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshitake Nishiyama
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Takamitsu Hosoya
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Satoshi Yokoshima
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan
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Haraguchi K, Hannda N, Wakasugi M, Maruyama M, Ishii H, Nagano D, Kumamoto H. DAST-Mediated Fluorination of 1-[4-Thio-β-d-arabinofuranosyl]uracil: Investigation of Thiolane vs Thietane Formation and Stereoselective Synthesis of 4′-ThioFAC. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0040-1720042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
AbstractThe unprecedented DAST-mediated (DAST = diethylaminosulfur trifluoride) deoxygenative fluorination of benzoyl-, TBDPS-, and Bn-protected 1-(β-d-4-thioarabinofuranosyl)uracil at the sugar portion was examined. Three kinds of nucleoside (Ns) products were formed: target thiolane Ns, ring-contracted thietane Ns, and anhydro Ns products. The reaction pathway was determined by the electronic effect of the protecting groups at the sugar and base moieties. The benzoylated uracil starting material gave the 2,2′-anhydronucleoside (anhydro Ns) as a major product, whereas the silylated and benzylated starting materials furnished the corresponding fluorinated products, in which the ring-contracted thietanes predominantly formed. The desired thiolane Ns could be obtained as major product by the addition of a pyridine derivative as an additive. Upon reacting N
3-benzoylated 1-(β-d-4-thioarabinofuranosyl)uracil with DAST in the presence of 2,4,6-collidine, the target 2′-deoxy-2′-β-fluoro-4′-thiouracil nucleoside could be obtained in 72% isolated yield along with the corresponding thietane Ns (7%) and anhydro Ns (3%) (thiolane Ns/thietane Ns/anhydro Ns = 10.3:1.00:0.43), with recovery of the starting material (12%). In this study, the first stereoselective synthesis of the β-anomer of 1-(2-deoxy-2-fluoro-4-thio-β-d-arabino-pentofuranosyl)cytosine (4′-thioFAC) has been developed.
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Siry SA, Timoshenko VM, Rusanov EB, Schermolovich YG. Synthesis and oxidative transformations of 2-functionalized 2-trifluoromethyltetrahydrothiophenes. J Fluor Chem 2022. [DOI: 10.1016/j.jfluchem.2022.109999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Guinan M, Huang N, Hawes CS, Lima MA, Smith M, Miller GJ. Chemical synthesis of 4'-thio and 4'-sulfinyl pyrimidine nucleoside analogues. Org Biomol Chem 2022; 20:1401-1406. [PMID: 34806745 DOI: 10.1039/d1ob02097h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analogues of the canonical nucleosides required for nucleic acid synthesis have a longstanding presence and proven capability within antiviral and anticancer research. 4'-Thionucleosides, that incorporate bioisosteric replacement of furanose oxygen with sulfur, represent an important chemotype within this field. Established herein is synthetic capability towards a common 4-thioribose building block that enables access to thio-ribo and thio-arabino pyrimidine nucleosides, alongside their 4'-sulfinyl derivatives. In addition, this building block methodology is templated to deliver 4'-thio and 4'-sulfinyl analogues of the established anticancer drug gemcitabine. Cytotoxic capability of these new analogues is evaluated against human pancreatic cancer and human primary glioblastoma cell lines, with observed activities ranging from low μM to >200 μM; explanation for this reduced activity, compared to established nucleoside analogues, is yet unclear. Access to these chemotypes, with thiohemiaminal linkages, will enable a wider exploration of purine and triphosphate analogues and the application of such materials for potential resistance towards relevant hydrolytic enzymes within nucleic acid biochemistries.
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Affiliation(s)
- Mieke Guinan
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK.
- School of Life Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK
| | - Ningwu Huang
- Riboscience LLC, 428 Oakmead Pkwy, Sunnyvale, CA 94085, USA
| | - Chris S Hawes
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK.
| | - Marcelo A Lima
- School of Life Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK
- Centre for Glycoscience Research, Keele University, Keele, Staffordshire ST5 5BG, UK
| | - Mark Smith
- Riboscience LLC, 428 Oakmead Pkwy, Sunnyvale, CA 94085, USA
| | - Gavin J Miller
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK.
- Centre for Glycoscience Research, Keele University, Keele, Staffordshire ST5 5BG, UK
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Guinan M, Benckendorff C, Smith M, Miller GJ. Recent Advances in the Chemical Synthesis and Evaluation of Anticancer Nucleoside Analogues. Molecules 2020; 25:E2050. [PMID: 32354007 PMCID: PMC7248840 DOI: 10.3390/molecules25092050] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/20/2020] [Accepted: 04/25/2020] [Indexed: 12/12/2022] Open
Abstract
Nucleoside analogues have proven to be highly successful chemotherapeutic agents in the treatment of a wide variety of cancers. Several such compounds, including gemcitabine and cytarabine, are the go-to option in first-line treatments. However, these materials do have limitations and the development of next generation compounds remains a topic of significant interest and necessity. Herein, we discuss recent advances in the chemical synthesis and biological evaluation of nucleoside analogues as potential anticancer agents. Focus is paid to 4'-heteroatom substitution of the furanose oxygen, 2'-, 3'-, 4'- and 5'-position ring modifications and the development of new prodrug strategies for these materials.
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Affiliation(s)
- Mieke Guinan
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK; (M.G.); (C.B.)
| | - Caecilie Benckendorff
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK; (M.G.); (C.B.)
| | - Mark Smith
- Medicinal Chemistry Knowledge Center, Stanford ChEM-H, 290 Jane Stanford Way, Stanford, CA 94305, USA;
| | - Gavin J. Miller
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK; (M.G.); (C.B.)
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