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Eymard C, Manchoju A, Almazloum A, Dostie S, Prévost M, Nemer M, Guindon Y. Synthesis of 4'-Thionucleoside Analogues Bearing a C2' Stereogenic All-Carbon Quaternary Center. Molecules 2024; 29:1647. [PMID: 38611926 PMCID: PMC11013827 DOI: 10.3390/molecules29071647] [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: 03/21/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
The design of novel 4'-thionucleoside analogues bearing a C2' stereogenic all-carbon quaternary center is described. The synthesis involves a highly diastereoselective Mukaiyama aldol reaction, and a diastereoselective radical-based vinyl group transfer to generate the all-carbon stereogenic C2' center, along with different approaches to control the selectivity of the N-glycosidic bond. Intramolecular SN2-like cyclization of a mixture of acyclic thioaminals provided analogues with a pyrimidine nucleobase. A kinetic bias favoring cyclization of the 1',2'-anti thioaminal furnished the desired β-D-4'-thionucleoside analogue in a 7:1 ratio. DFT calculations suggest that this kinetic resolution originates from additional steric clash in the SN2-like transition state for 1',4'-trans isomers, causing a significant decrease in their reaction rate relative to 1',4'-cis counterparts. N-glycosylation of cyclic glycosyl donors with a purine nucleobase enabled the formation of novel 2-chloroadenine 4'-thionucleoside analogues. These proprietary molecules and other derivatives are currently being evaluated both in vitro and in vivo to establish their biological profiles.
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Affiliation(s)
- Carla Eymard
- Bioorganic Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada; (C.E.); (A.M.); (S.D.)
- Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Amarender Manchoju
- Bioorganic Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada; (C.E.); (A.M.); (S.D.)
| | - Abir Almazloum
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (A.A.); (M.N.)
| | - Starr Dostie
- Bioorganic Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada; (C.E.); (A.M.); (S.D.)
| | - Michel Prévost
- Bioorganic Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada; (C.E.); (A.M.); (S.D.)
| | - Mona Nemer
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (A.A.); (M.N.)
| | - Yvan Guindon
- Bioorganic Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada; (C.E.); (A.M.); (S.D.)
- Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (A.A.); (M.N.)
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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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Benckendorff CMM, Slyusarchuk VD, Huang N, Lima MA, Smith M, Miller GJ. Synthesis of fluorinated carbocyclic pyrimidine nucleoside analogues. Org Biomol Chem 2022; 20:9469-9489. [PMID: 36408761 DOI: 10.1039/d2ob01761j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Analogues of the canonical nucleosides have a longstanding presence and proven capability within medicinal chemistry and drug discovery research. The synthesis reported herein successfully replaces furanose oxygen with CF2 and CHF in pyrimidine nucleosides, granting access to an alternative pharmacophore space. Key diastereoselective conjugate addition and fluorination methodologies are developed from chiral pool materials, establishing a robust gram-scale synthesis of 6'-(R)-monofluoro- and 6'-gem-difluorouridines. Vital intermediate stereochemistries are confirmed using X-ray crystallography and NMR analysis, providing an indicative conformational preference for these fluorinated carbanucleosides. Utilising these 6'-fluorocarbauridine scaffolds enables synthesis of related cytidine, ProTide and 2'-deoxy analogues alongside a preliminary exploration of their biological capabilities in cancer cell viability assays. This synthetic blueprint offers potential to explore fluorocarbanucleoside scaffolds, indicatively towards triphosphate analogues and as building blocks for oligonucleotide synthesis.
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Affiliation(s)
- Caecilie M M Benckendorff
- Centre for Glycosciences, Keele University, Keele, Staffordshire, ST5 5BG, UK. .,Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Valentyna D Slyusarchuk
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Ningwu Huang
- Riboscience LLC, 428 Oakmead Pkwy, Sunnyvale, CA 94085, USA
| | - Marcelo A Lima
- Centre for Glycosciences, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Mark Smith
- Riboscience LLC, 428 Oakmead Pkwy, Sunnyvale, CA 94085, USA
| | - Gavin J Miller
- Centre for Glycosciences, Keele University, Keele, Staffordshire, ST5 5BG, UK. .,Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
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Guinan M, Huang N, Smith M, Miller GJ. Design, chemical synthesis and antiviral evaluation of 2'-deoxy-2'-fluoro-2'-C-methyl-4'-thionucleosides. Bioorg Med Chem Lett 2022; 61:128605. [PMID: 35123007 DOI: 10.1016/j.bmcl.2022.128605] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 11/02/2022]
Abstract
Nucleoside analogues represent an historically accomplished class of antiviral drug. Notwithstanding this, new molecular scaffolds are required to overcome their limitations and evolve pharmacophore space within this established field. Herein, we develop concise synthetic access to a new 2'-deoxy-2'-fluoro-2'-C-methyl-4'-thionucleoside chemotype, including the ProTide form of the uridine analogue. Biological evaluation of these materials in the Hepatitis C replicon assay shows little activity for the canonical pyrimidine forms, but the phosphoramidate of 2'-deoxy-2'-fluoro-2'-C-methyl-β-d-4'-thiouridine has an EC50 of 2.99 μM. Direct comparison to the established Hepatitis C drug Sofosbuvir shows a 100-fold drop in activity upon substituting the furanose chalcogen; the reasons for this are as yet unclear.
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Affiliation(s)
- Mieke Guinan
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom; Centre for Glycoscience Research, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Ningwu Huang
- Riboscience LLC, 428 Oakmead Pkwy, Sunnyvale, CA 94085, USA
| | - 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, United Kingdom; Centre for Glycoscience Research, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom.
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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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Drug Discovery of Nucleos(t)ide Antiviral Agents: Dedicated to Prof. Dr. Erik De Clercq on Occasion of His 80th Birthday. Molecules 2021; 26:molecules26040923. [PMID: 33572409 PMCID: PMC7916218 DOI: 10.3390/molecules26040923] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/20/2021] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleoside and nucleotide analogues are essential antivirals in the treatment of infectious diseases such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), herpes simplex virus (HSV), varicella-zoster virus (VZV), and human cytomegalovirus (HCMV). To celebrate the 80th birthday of Prof. Dr. Erik De Clercq on 28 March 2021, this review provides an overview of his contributions to eight approved nucleos(t)ide drugs: (i) three adenosine nucleotide analogues, namely tenofovir disoproxil fumarate (Viread®) and tenofovir alafenamide (Vemlidy®) against HIV and HBV infections and adefovir dipivoxil (Hepsera®) against HBV infections; (ii) two thymidine nucleoside analogues, namely brivudine (Zostex®) against HSV-1 and VZV infections and stavudine (Zerit®) against HIV infections; (iii) two guanosine analogues, namely valacyclovir (Valtrex®, Zelitrex®) against HSV and VZV and rabacfosadine (Tanovea®-CA1) for the treatment of lymphoma in dogs; and (iv) one cytidine nucleotide analogue, namely cidofovir (Vistide®) for the treatment of HCMV retinitis in AIDS patients. Although adefovir dipivoxil, stavudine, and cidofovir are virtually discontinued for clinical use, tenofovir disoproxil fumarate and tenofovir alafenamide remain the most important antivirals against HIV and HBV infections worldwide. Overall, the broad-spectrum antiviral potential of nucleos(t)ide analogues supports their development to treat or prevent current and emerging infectious diseases worldwide.
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