1
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Sakander N, Ahmed A, Bhardwaj M, Kumari D, Nandi U, Mukherjee D. A path from synthesis to emergency use authorization of molnupiravir as a COVID-19 therapy. Bioorg Chem 2024; 147:107379. [PMID: 38643567 DOI: 10.1016/j.bioorg.2024.107379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/04/2024] [Accepted: 04/14/2024] [Indexed: 04/23/2024]
Abstract
Coronaviruses are a group of enveloped viruses with non-segmented, single-stranded, and positive-sense RNA genomes. It belongs to the 'Coronaviridae family', responsible for various diseases, including the common cold, SARS, and MERS. The COVID-19 pandemic, which began in March 2020, has affected 209 countries, infected over a million people, and claimed over 50,000 lives. Significant efforts have been made by repurposing several approved drugs including antiviral, to combat the COVID-19 pandemic. Molnupiravir is found to be the first orally acting efficacious drug to treat COVID-19 cases. It was approved for medical use in the UK in November 2021 and other countries, including USFDA, which granted approval an emergency use authorization (EUA) for treating adults with mild to moderate COVID-19 patients. Considering the importance of molnupiravir, the present review deals with its various synthetic strategies, pharmacokinetics, bio-efficacy, toxicity, and safety profiles. The comprehensive information along with critical analysis will be very handy for a wide range of audience including medicinal chemists in the arena of antiviral drug discovery especially anti-viral drugs against any variant of COVID-19.
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Affiliation(s)
- Norein Sakander
- Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ajaz Ahmed
- Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Mahir Bhardwaj
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Diksha Kumari
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Infectious Diseases Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Utpal Nandi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Debaraj Mukherjee
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Department of Chemical Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, WB, India.
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2
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Awad SM, Ali SM, Mansour YE, Fatahala SS. Synthesis and Evaluation of Some Uracil Nucleosides as Promising Anti-Herpes Simplex Virus 1 Agents. Molecules 2021; 26:2988. [PMID: 34069874 PMCID: PMC8157375 DOI: 10.3390/molecules26102988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/15/2021] [Accepted: 05/16/2021] [Indexed: 02/06/2023] Open
Abstract
Since herpes simplex virus type 1 (HSV-1) infection is so widespread, several antiviral drugs have been developed to treat it, among which are uracil nucleosides. However, there are major problems with the current medications such as severe side-effects and drug resistance. Here we present some newly synthesized cyclic and acyclic uracil nucleosides that showed very promising activity against HSV-1 compared to acyclovir.
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Affiliation(s)
- Samir Mohamed Awad
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Helwan University, Ain-Helwan, Cairo 11795, Egypt; (S.M.A.); (Y.E.M.)
| | - Shima Mahmoud Ali
- Department of Microbiology and Immunology, Faculty of Pharmacy, Helwan University, Ain-Helwan, Cairo 11795, Egypt;
| | - Yara Essam Mansour
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Helwan University, Ain-Helwan, Cairo 11795, Egypt; (S.M.A.); (Y.E.M.)
| | - Samar Said Fatahala
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Helwan University, Ain-Helwan, Cairo 11795, Egypt; (S.M.A.); (Y.E.M.)
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3
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Cartmell C, Abou Fayad A, Lynch R, Sharma SV, Hauck N, Gust B, Goss RJM. SynBio-SynChem Approaches to Diversifying the Pacidamycins through the Exploitation of an Observed Pictet-Spengler Reaction. Chembiochem 2021; 22:712-716. [PMID: 33058439 PMCID: PMC7898326 DOI: 10.1002/cbic.202000594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/12/2020] [Indexed: 11/09/2022]
Abstract
A nonenzymatic Pictet-Spengler reaction has been postulated to give rise to a subset of naturally occurring uridyl peptide antibiotics (UPAs). Here, using a combination of strain engineering and synthetic chemistry, we demonstrate that Pictet-Spengler chemistry may be employed to generate even greater diversity in the UPAs. We use an engineered strain to afford access to meta-tyrosine containing pacidamycin 4. Pictet-Spengler diversification of this compound using a small series of aryl-aldehydes was achieved with some derivatives affording remarkable diastereomeric control.
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Affiliation(s)
- Christopher Cartmell
- School of Chemistry and BSRCUniversity of St AndrewsSt AndrewsFife, KY16 9STUK
- Department of ChemistryUniversity of Prince Edward Island CharlottetownPrince Edward IslandC1A 4P3Canada
| | - Antoine Abou Fayad
- School of Chemistry and BSRCUniversity of St AndrewsSt AndrewsFife, KY16 9STUK
- Department of Experimental Pathology, Immunology and Microbiology Faculty of Medicine. Center of Infectious Disease Research (CIDR) WHO Collaborating Center for Reference and Research on Bacterial PathogensAmerican University of BeirutRiad El-Solh/Beirut1107 2020Lebanon
| | - Rosemary Lynch
- School of Chemistry and BSRCUniversity of St AndrewsSt AndrewsFife, KY16 9STUK
| | - Sunil V. Sharma
- School of Chemistry and BSRCUniversity of St AndrewsSt AndrewsFife, KY16 9STUK
| | - Nils Hauck
- Pharmazeutische Biologie, Pharmazeutisches InstitutEberhard-Karls-UniversitätAuf der Morgenstelle 872076TübingenGermany
| | - Bertolt Gust
- Pharmazeutische Biologie, Pharmazeutisches InstitutEberhard-Karls-UniversitätAuf der Morgenstelle 872076TübingenGermany
| | - Rebecca J. M. Goss
- School of Chemistry and BSRCUniversity of St AndrewsSt AndrewsFife, KY16 9STUK
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4
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Mitachi K, Kurosu SM, Eslamimehr S, Lemieux MR, Ishizaki Y, Clemons WM, Kurosu M. Semisynthesis of an Anticancer DPAGT1 Inhibitor from a Muraymycin Biosynthetic Intermediate. Org Lett 2019; 21:876-879. [PMID: 30698984 PMCID: PMC6447083 DOI: 10.1021/acs.orglett.8b03716] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have explored a method to convert a muraymycin biosynthetic intermediate 3 to an anticancer drug lead 2 for in vivo and thorough preclinical studies. Cu(OAc)2 forms a stable complex with the amide 4 and prevents electrophilic reactions at the 2-((3-aminopropyl)amino)acetamide moiety. Under the present conditions, the desired 5″-primary amine was selectively protected with (Boc)2O to yield 6. The intermediate 6 was converted to 2 in two steps with 90% yield.
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , 881 Madison Avenue , Memphis , Tennessee 38163 , United States
| | - Shou M Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , 881 Madison Avenue , Memphis , Tennessee 38163 , United States
| | - Shakiba Eslamimehr
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , 881 Madison Avenue , Memphis , Tennessee 38163 , United States
| | - Maddie R Lemieux
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , 881 Madison Avenue , Memphis , Tennessee 38163 , United States
| | - Yoshimasa Ishizaki
- Laboratory of Microbiology , Institute of Microbial Chemistry (BIKAKEN) , 3-14-23, Kamiosaki , Shinagawa-ku, Tokyo 141-0021 , Japan
| | - William M Clemons
- Division of Chemistry and Chemical Engineering , California Institute of Technology , 1200 E. California Boulevard , Pasadena , California 91125 , United States
| | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , 881 Madison Avenue , Memphis , Tennessee 38163 , United States
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5
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He XY, Wang J, Lu DD, Wang SQ. Synthesis and Antisense Properties of 2'β-F-Arabinouridine Modified Oligonucleotides with 4'- C-OMe Substituent. Molecules 2018; 23:molecules23092374. [PMID: 30227644 PMCID: PMC6225415 DOI: 10.3390/molecules23092374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 11/16/2022] Open
Abstract
A novel 2′-F,4′-C-OMe–arabinouridine (araU) was successfully synthesized and introduced into oligonucleotides. The oligonucleotide containing 2′-F,4′-C-OMe–araU exhibited improved nuclease resistance and RNA hybridizing selective ability relative to 2′-F–araU. In particular, when 2′-F,4′-C-OMe–araU inserted into C–H⋯F–C bonding-favorable 5′–uridine–purine–3′ steps, the modified oligonucleotide showed remarkable binding affinity and selectivity to RNA complements. Thus, 2′-F,4′-C-OMe–araU has valuable antisense properties and can be used as novel chemical modification for antisense therapeutic strategy.
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Affiliation(s)
- Xiao-Yang He
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Jing Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Dan-Dan Lu
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Sheng-Qi Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
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6
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Komor R, Pastuch-Gawolek G, Krol E, Szeja W. Synthesis and Preliminary Evaluation of Biological Activity of Glycoconjugates Analogues of Acyclic Uridine Derivatives. Molecules 2018; 23:molecules23082017. [PMID: 30104510 PMCID: PMC6222857 DOI: 10.3390/molecules23082017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/09/2018] [Accepted: 08/11/2018] [Indexed: 12/16/2022] Open
Abstract
Herein we present the methodology for obtaining glycosyltransferase inhibitors, analogues of natural enzyme substrates of donor-type: UDP-glucose and UDP-galactose. The synthesis concerned glycoconjugates, nucleoside analogues containing an acyclic ribose mimetic linked to a uracil moiety in their structure. The biological activity of the synthesised compounds was determined on the basis of their ability to inhibit the model enzyme action of β-1,4-galactosyltransferase from bovine milk. The obtained results allowed to expand and supplement the existing library of synthetic compounds that are able to regulate the biological activity of enzymes from the GT class.
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Affiliation(s)
- Roman Komor
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 4, 44-100 Gliwice, Poland.
| | - Gabriela Pastuch-Gawolek
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 4, 44-100 Gliwice, Poland.
- Biotechnology Center, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland.
| | - Ewelina Krol
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland.
| | - Wieslaw Szeja
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 4, 44-100 Gliwice, Poland.
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7
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Kim EK, Martin V, Krishnamurthy R. Orotidine-Containing RNA: Implications for the Hierarchical Selection (Systems Chemistry Emergence) of RNA. Chemistry 2017; 23:12668-12675. [PMID: 28708927 DOI: 10.1002/chem.201702912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 02/05/2023]
Abstract
The prebiotic synthesis of canonical nucleobases from HCN is a cornerstone for the RNA world hypothesis. However, their role in the primordial pathways to RNA is still debated. The very same process starting from HCN also gives rise to orotic acid, which (via orotidine) plays a crucial role in extant biology in the de novo synthesis of uridine and cytidine, the informational base-pairs in RNA. However, orotidine itself is absent in RNA. Given the prebiotic and biological relevance of orotic acid vis-à-vis uracil, we investigated orotidine-containing RNA oligonucleotides and show that they have severely compromised base-pairing properties. While not unexpected, these results suggest that the emergence of extant RNA cannot just be a consequence of the plausible prebiotic formation of its chemical constituents/building blocks. In combination with other investigations on alternative prebiotic nucleobases, sugars, and linkers, these findings imply that the selection of the components of extant RNA occurred at a higher hierarchical level of an oligomer/polymer based on its functional properties-pointing to a systems chemistry emergence of RNA from a library of precursors.
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Affiliation(s)
- Eun-Kyong Kim
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
| | - Vincent Martin
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550, North Torrey Pines Rd, La Jolla, Ca, 92037, USA
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8
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Chen S, Le BT, Rahimizadeh K, Shaikh K, Mohal N, Veedu RN. Synthesis of a Morpholino Nucleic Acid (MNA)-Uridine Phosphoramidite, and Exon Skipping Using MNA/2'-O-Methyl Mixmer Antisense Oligonucleotide. Molecules 2016; 21:molecules21111582. [PMID: 27879669 PMCID: PMC6274534 DOI: 10.3390/molecules21111582] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/11/2016] [Accepted: 11/16/2016] [Indexed: 01/14/2023] Open
Abstract
In this study, we synthesised a morpholino nucleoside-uridine (MNA-U) phosphoramidite and evaluated the potential of a MNA-modified antisense oligonucleotide (AO) sequences to induce exon 23 skipping in mdx mouse myotubes in vitro towards extending the applicability of morpholino chemistry with other nucleotide monomers. We designed, synthesised, and compared exon skipping efficiencies of 20 mer MNA-modified 2'-O-methyl RNA mixmer AO on a phosphorothioate backbone (MNA/2'-OMePS) to the corresponding fully modified 2'-O-methyl RNA AO (2'-OMePS) as a control. Our results showed that the MNA/2'-OMePS efficiently induced exon 23 skipping. As expected, the 2'-OMePS AO control yielded efficient exon 23 skipping. Under the applied conditions, both the AOs showed minor products corresponding to exon 22/23 dual exon skipping in low yield. As these are very preliminary data, more detailed studies are necessary; however, based on the preliminary results, MNA nucleotides might be useful in constructing antisense oligonucleotides.
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Affiliation(s)
- Suxiang Chen
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
- Western Australian Neuroscience Research Institute, Perth 6150, Australia.
| | - Bao T Le
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
- Western Australian Neuroscience Research Institute, Perth 6150, Australia.
| | - Kamal Rahimizadeh
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
| | - Khalil Shaikh
- GMK Research Laboratories Pvt. Ltd., Mallapur, Hyderabad 500 076, India.
| | - Narinder Mohal
- GMK Research Laboratories Pvt. Ltd., Mallapur, Hyderabad 500 076, India.
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia.
- Western Australian Neuroscience Research Institute, Perth 6150, Australia.
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9
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Anderson BA, Hrdlicka PJ. Synthesis and characterization of oligodeoxyribonucleotides modified with 2'-thio-2'-deoxy-2'-S-(pyren-1-yl)methyluridine. Bioorg Med Chem Lett 2015; 25:3999-4004. [PMID: 26254942 PMCID: PMC4540677 DOI: 10.1016/j.bmcl.2015.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 01/11/2023]
Abstract
Pyrene-functionalized oligonucleotides are intensively explored for applications in materials science and diagnostics. Here, we describe a short synthetic route to 2'-S-(pyren-1-yl)methyl-2'-thiouridine monomer S, its incorporation into oligodeoxyribonucleotides (ONs), and biophysical characterization thereof. Pseudorotational analysis reveals that the furanose ring of this monomer has a slight preference for South-type conformations. ONs modified with monomer S display high cDNA affinity but decreased binding specificity. Hybridization is associated with bathochromic shifts of pyrene absorption bands and quenching of pyrene fluorescence consistent with an intercalative binding mode of the pyrene moiety. Monomer S was also evaluated as a building block for mixed-sequence recognition of double-stranded DNA via the Invader strategy. However, probes with +1 interstrand arrangements of monomer S were found to be less efficient than Invader probes based on 2'-O-(pyren-1-yl)methyluridine or 2'-N-(pyren-1-yl)methyl-2'-N-methyl-2'-aminouridine.
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Affiliation(s)
- Brooke A Anderson
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, United States
| | - Patrick J Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, United States.
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10
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Paszkowska J, Kral K, Bieg T, Żaba K, Węgrzyk K, Jaśkowiak N, Molinaro A, Silipo A, Wandzik I. Synthesis and biological evaluation of 5'-glycyl derivatives of uridine as inhibitors of 1,4-β-galactosyltransferase. Bioorg Chem 2014; 58:18-25. [PMID: 25462623 DOI: 10.1016/j.bioorg.2014.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 12/13/2022]
Abstract
New 5'-glycyl derivatives of uridine containing fragments of varying lipophilicity were synthesized as analogues of natural peptidyl antibiotics. One of the studied compounds, 5'-O-(N-succinylglycyl)-2',3'-O-isopropylideneuridine (A4), showed moderate inhibition against 1,4-β-galactosyltransferase. However, additional studies showed that the observed inhibitory effect was due to binding to bovine serum albumin, which was used in assays as a stabilizer.
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Affiliation(s)
- Jadwiga Paszkowska
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Katarzyna Kral
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Tadeusz Bieg
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Karolina Żaba
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Katarzyna Węgrzyk
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Natalia Jaśkowiak
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Ilona Wandzik
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland.
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11
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Kumar P, Østergaard ME, Baral B, Anderson BA, Guenther DC, Kaura M, Raible DJ, Sharma PK, Hrdlicka PJ. Synthesis and biophysical properties of C5-functionalized LNA (locked nucleic acid). J Org Chem 2014; 79:5047-61. [PMID: 24825249 PMCID: PMC4049237 DOI: 10.1021/jo500614a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Indexed: 01/07/2023]
Abstract
Oligonucleotides modified with conformationally restricted nucleotides such as locked nucleic acid (LNA) monomers are used extensively in molecular biology and medicinal chemistry to modulate gene expression at the RNA level. Major efforts have been devoted to the design of LNA derivatives that induce even higher binding affinity and specificity, greater enzymatic stability, and more desirable pharmacokinetic profiles. Most of this work has focused on modifications of LNA's oxymethylene bridge. Here, we describe an alternative approach for modulation of the properties of LNA: i.e., through functionalization of LNA nucleobases. Twelve structurally diverse C5-functionalized LNA uridine (U) phosphoramidites were synthesized and incorporated into oligodeoxyribonucleotides (ONs), which were then characterized with respect to thermal denaturation, enzymatic stability, and fluorescence properties. ONs modified with monomers that are conjugated to small alkynes display significantly improved target affinity, binding specificity, and protection against 3'-exonucleases relative to regular LNA. In contrast, ONs modified with monomers that are conjugated to bulky hydrophobic alkynes display lower target affinity yet much greater 3'-exonuclease resistance. ONs modified with C5-fluorophore-functionalized LNA-U monomers enable fluorescent discrimination of targets with single nucleotide polymorphisms (SNPs). In concert, these properties render C5-functionalized LNA as a promising class of building blocks for RNA-targeting applications and nucleic acid diagnostics.
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Affiliation(s)
- Pawan Kumar
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Michael E. Østergaard
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Bharat Baral
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Brooke A. Anderson
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Dale C. Guenther
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Mamta Kaura
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Daniel J. Raible
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Pawan K. Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Patrick J. Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
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12
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Song L, Risseeuw MDP, Karalic I, Barrett MO, Brown KA, Harden TK, Van Calenbergh S. Synthesis of extended uridine phosphonates derived from an allosteric P2Y2 receptor ligand. Molecules 2014; 19:4313-25. [PMID: 24714193 PMCID: PMC6270895 DOI: 10.3390/molecules19044313] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 01/28/2023] Open
Abstract
In this study we report the synthesis of C5/C6-fused uridine phosphonates that are structurally related to earlier reported allosteric P2Y2 receptor ligands. A silyl-Hilbert-Johnson reaction of six quinazoline-2,4-(1H,3H)-dione-like base moieties with a suitable ribofuranosephosphonate afforded the desired analogues after full deprotection. In contrast to the parent 5-(4-fluoropheny)uridine phosphonate, the present extended-base uridine phosphonates essentially failed to modulate the P2Y2 receptor.
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Affiliation(s)
- Lijun Song
- Laboratory for Medicinal Chemistry, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium.
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium.
| | - Izet Karalic
- Laboratory for Medicinal Chemistry, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium.
| | - Matthew O Barrett
- Department of Pharmacology, University of North Carolina, School of Medicine, Chapel Hill, NC 27599-7365, USA.
| | - Kyle A Brown
- Department of Pharmacology, University of North Carolina, School of Medicine, Chapel Hill, NC 27599-7365, USA.
| | - T Kendall Harden
- Department of Pharmacology, University of North Carolina, School of Medicine, Chapel Hill, NC 27599-7365, USA.
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium.
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13
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Paszkowska J, Kral K, Bieg T, Nawrot U, Szeja W, Wandzik I. Synthesis and preliminary biological evaluations of 5'-substituted derivatives of uridine as glycosyltransferase inhibitors. Molecules 2013; 18:8018-27. [PMID: 23884133 PMCID: PMC6270623 DOI: 10.3390/molecules18078018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/26/2013] [Indexed: 11/20/2022] Open
Abstract
New derivatives of uridine which contain a β-ketoenol motif were synthesized, characterized and biologically tested. Synthesized compounds 1–4 showed no activity against bovine milk β-1,4-galactosyltransferase I at concentrations up to 2.0 mM and were not active against Candida albicans and Aspergilus fumigatus up to the maximum tested concentration of 1,000 µg/mL.
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Affiliation(s)
- Jadwiga Paszkowska
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland; E-Mails: (J.P.); (K.K.); (T.B.); (W.S.)
| | - Katarzyna Kral
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland; E-Mails: (J.P.); (K.K.); (T.B.); (W.S.)
| | - Tadeusz Bieg
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland; E-Mails: (J.P.); (K.K.); (T.B.); (W.S.)
| | - Urszula Nawrot
- Department of Microbiology, Wroclaw Medical University, T. Chałubińskiego 4, 50-368 Wrocław, Poland; E-Mail:
| | - Wiesław Szeja
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland; E-Mails: (J.P.); (K.K.); (T.B.); (W.S.)
| | - Ilona Wandzik
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland; E-Mails: (J.P.); (K.K.); (T.B.); (W.S.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +48-32-2372028; Fax: +48-32-2372094
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14
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Sajiki H, Iida Y, Ikawa K(Y, Sawama Y, Monguchi Y, Kitade Y, Maki Y, Inoue H, Hirota K. Development of diversified methods for chemical modification of the 5,6-double bond of uracil derivatives depending on active methylene compounds. Molecules 2012; 17:6519-46. [PMID: 22728351 PMCID: PMC6269048 DOI: 10.3390/molecules17066519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 05/21/2012] [Accepted: 05/21/2012] [Indexed: 11/22/2022] Open
Abstract
The reaction of 5-halogenouracil and uridine derivatives 1 and 7 with active methylene compounds under basic conditions produced diverse and selective C-C bond formation products by virtue of the nature of the carbanions. Three different types of reactions such as the regioselective C-C bond formation at the 5- and 6-positions of uracil and uridine derivatives (products 2, 5, 8, 17, 20 and 21), and the formation of fused heterocycle derivatives 2,4-diazabicyclo[4.1.0]heptane (15) and 2,4-diazabicyclo-[4.1.0]nonane (16) via dual C-C bond formations at both the 5- and 6-positions were due to the different active methylene compounds used as reagents.
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Affiliation(s)
- Hironao Sajiki
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu 501-1196, Japan
| | - Yusuke Iida
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu 501-1196, Japan
| | - Kanoko (Yasunaga) Ikawa
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu 501-1196, Japan
| | - Yoshinari Sawama
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu 501-1196, Japan
| | - Yasunari Monguchi
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu 501-1196, Japan
| | - Yukio Kitade
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu 501-1196, Japan
| | - Yoshifumi Maki
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu 501-1196, Japan
| | - Hideo Inoue
- Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Kosaku Hirota
- Laboratory of Organic Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu 501-1196, Japan
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15
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Lavergne T, Debart F, Vasseur JJ. Optimized fluoride ions treatment for release of base-sensitive 2'-O-modified oligoribonucleotides from various solid supports. ACTA ACUST UNITED AC 2010:321-2. [PMID: 18776383 DOI: 10.1093/nass/nrn162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
To synthesize oligoribonucleotides containing base-sensitive 2'-O-modifications, we used the Q-linker or a silyl linker anchored to CPG or polystyrene resin. A fluoride ions treatment was optimized to release oligoribonucleotides from the solid-support and to remove TBDMS groups without affecting 2'-O-acyloxymethyl groups.
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Affiliation(s)
- Thomas Lavergne
- IBMM, UMR 5247 CNRS-UM1-UM2, CC 1704, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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16
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Grec M, Swierk P, Pastuch G, Szeja W. Glycoconjugates, products of uridine derivatives phosphitylation and oxidation as glycosyltransferases potential inhibitors. Acta Pol Pharm 2010; 67:652-663. [PMID: 21229882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The title compounds, variously protected 5'-uridine derivatives connected with 1-thiosugar with thio-phosphoesters fragment (17-22) were synthesized in sequence of reactions: phosphitylation--reaction of 5'-hydroxyl group of selectively protected nucleoside with a phosphitylating agent (N,N-diisopropyl chlorophosphoamidite), connection an phosphoroamidites with 2-bromoethanol or 3-bromopropanol and secondary oxidation with sulfur presence and finally condensation reaction of obtained products with 1-thiosugar. Received glycoconjugates (17-22) had a structure which mimic to structure of natural glycosyltransferases substrates.
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Affiliation(s)
- Marta Grec
- Silesian University of Technology, Faculty of Chemistry, Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Krzywoustego 4, 44-100 Gliwice, Poland
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17
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Khomiakova EA, Kazanova EV, Zubin EM, Kubareva EA, Molochkov NV, Riazanova EM, Oretskaia TS. [2'-aldehyde oligonucleotides: synthesis and use for affinity modification of DNA-recognizing proteins]. Bioorg Khim 2010; 36:343-353. [PMID: 20644589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Oligonucleotides with 1,2-diol grouping were prepared from 2'-O-[2-(2,3-dihydroxypropyl)amino-2-oxo-ethyl]uridine 3'-phosphoramidite. The thermal stability of modified DNA duplexes and their ability to form complexes with the p50 subunit of the NF-kappaB transcription factor and (cytosine-5)-DNA methyltransferase SsoII were studied. The periodate oxidation of the l,2-diol grouping of the oligonucleotides resulted in reactive 2'-aldehyde derivatives. The opportunity of their use for the affinity modification of DNA-recognizing proteins was studied.
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18
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Kim RR, Illarionov B, Joshi M, Cushman M, Lee CY, Eisenreich W, Fischer M, Bacher A. Mechanistic insights on riboflavin synthase inspired by selective binding of the 6,7-dimethyl-8-ribityllumazine exomethylene anion. J Am Chem Soc 2010; 132:2983-90. [PMID: 20143812 PMCID: PMC2832097 DOI: 10.1021/ja908395r] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Riboflavin synthase catalyzes the transfer of a four-carbon fragment between two molecules of the substrate, 6,7-dimethyl-8-ribityllumazine, resulting in the formation of riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. Earlier, a pentacyclic adduct formed from two substrate molecules was shown to be a catalytically competent intermediate, but the mechanism of its formation is still poorly understood. The present study shows that the recombinant N-terminal domain of riboflavin synthase from Escherichia coli interacts specifically with the exomethylene-type anion of 6,7-dimethyl-8-ribityllumazine but not with any of the tricyclic adduct-type anions that dominate the complex anion equilibrium in aqueous solution. Whereas these findings can be implemented into previously published mechanistic hypotheses, we also present a novel, hypothetical reaction sequence that starts with the transfer of a hydride ion from the 6,7-dimethyl-8-ribityllumazine exomethylene anion to an electroneutral 6,7-dimethyl-8-ribityllumazine molecule. The pair of dehydrolumazine and dihydrolumazine molecules resulting from this hydride transfer is proposed to undergo a 4 + 2 cycloaddition, affording the experimentally documented pentacyclic intermediate. In contrast to earlier mechanistic concepts requiring the participation of a nucleophilic agent, which is not supported by structural and mutagenesis data, the novel concept has no such requirement. Moreover, it requires fewer reaction steps and is consistent with all experimental data.
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Affiliation(s)
- Ryu-Ryun Kim
- Institute of Biochemistry and Food Chemistry, Food Chemistry Division, University of Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
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19
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Affiliation(s)
- Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Japan.
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20
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Abstract
A facile method for preparation of uridine 2'-carbamate derivatives based on reaction of 3',5'-disilyl-protected uridine with 1,1'-carbonyldiimidazole followed by treatment with an aliphatic amine is presented. A phosphoramidite monomer suitable for automated oligonucleotide synthesis is obtained in a few steps. The compounds are useful for the introduction of various labels and modifications into an oligonucleotide chain. Although 2'-carbamate modification is somewhat destabilizing for DNA-DNA and DNA-RNA duplexes, it is suitable for the direction of ligands into the minor groove of duplexes or at non-base-paired sites (e.g., loops and bulges) of oligonucleotides. Pyrene-modified oligonucleotide 2'-carbamates show a considerable increase in fluorescence intensity upon hybridization to a complementary RNA (but not DNA).
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21
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Aljarah M, Mathé C, Périgaud C. Synthesis of some derivatives of 3'-C-methyl pyrimidine nucleosides. Nucleic Acids Symp Ser (Oxf) 2008; 52:547-548. [PMID: 18776496 DOI: 10.1093/nass/nrn277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Attempts for the synthesis of 2'-deoxy-2'-fluoro nucleoside derivative of 3'-C-methyluridine were reported. The corresponding parent nucleoside was chosen as the starting material. However, the 2'-deoxy-2'-fluoro nucleoside was not obtained. Nevertheless, the new and unexpected nucleoside derivatives obtained as well as some proposals of mechanism regarding their formation will be presented.
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Affiliation(s)
- Mohamed Aljarah
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-UM 1-UM 2, Université Montpellier 2, case courrier 1705, Place E. Bataillon, 34095 Montpellier cedex 05, France
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22
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Hirano S, Ichikawa S, Matsuda A. Design and synthesis of diketopiperazine and acyclic analogs related to the caprazamycins and liposidomycins as potential antibacterial agents. Bioorg Med Chem 2008; 16:428-36. [PMID: 17904373 DOI: 10.1016/j.bmc.2007.09.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2007] [Revised: 09/11/2007] [Accepted: 09/12/2007] [Indexed: 11/16/2022]
Abstract
A systematic simplification methodology of a class of 6'-N-alkyl-5'-O-aminoribosyl-glycyluridine antibiotics was shown to produce potential antibacterial agents having a novel mechanism of action. Diketopiperazines and acyclic analogs of the caprazamycins (CPZs) and liposidomycins (LPMs) were efficiently synthesized, and their antibacterial activity was evaluated. The diketopiperazine analog 11a and the acyclic analogs 12a and 16a having a palmitoyl group as a lipophilic side chain exhibited moderate antibacterial activities with MICs of 12.5-50 microg/mL. This approach could provide ready access to a range of analogs for the development of potential antibacterial agents.
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Affiliation(s)
- Shinpei Hirano
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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23
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Ghatnekar J, Hägerlöf M, Oredsson S, Alm K, Elmroth SKC, Persson T. Construction of polyamine-modified uridine and adenosine derivatives--evaluation of DNA binding capacity and cytotoxicity in vitro. Bioorg Med Chem 2007; 15:7426-33. [PMID: 17869123 DOI: 10.1016/j.bmc.2007.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 07/05/2007] [Accepted: 07/10/2007] [Indexed: 11/27/2022]
Abstract
We here report the synthesis of the two polyamine-based nucleoside derivatives 5-{[bis-(3-aminopropyl)amino]acetamido-1-propynyl}uridine and 2-{[bis-(3-aminopropyl)amino]-acetamido-1-propynyl}adenosine. The various polyamine derivatives have been used in thermal melting analysis using DNA from herring testes, and in cellular studies using four different cell lines. The compounds were all found to be non-toxic, thus holding good promise for future use as siRNA building blocks.
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Affiliation(s)
- Johannes Ghatnekar
- Organic Chemistry, Chemical Center, Lund Univesity, PO Box 124, SE-22100 Lund, Sweden
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24
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Abstract
Recently, a novel base-modified uridine derivative, 5-taurinomethyluridine (taum(5)U) was discovered from bovine and human mitochondrial tRNAs, and this modified ribonucleoside was found to existed at the first position of the anti-codon. We report efficient reactions for the synthesis of RNA oligomers including this base-modified ribonucleotide.
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Affiliation(s)
- Toshihiko Ogata
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The Universitiy of Tokyo, Bioscience Bldg 702, Kashiwa, Chiba 277-8562, Japan
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25
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Rai D, Johar M, Srivastav NC, Manning T, Agrawal B, Kunimoto DY, Kumar R. Inhibition of Mycobacterium tuberculosis, Mycobacterium bovis, and Mycobacterium avium by Novel Dideoxy Nucleosides. J Med Chem 2007; 50:4766-74. [PMID: 17696514 DOI: 10.1021/jm070391t] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The prevalence of tuberculosis (TB) and mutidrug-resistant tuberculosis (MDR-TB) has been increasing, leading to serious infections, high mortality, and a global health threat. Here, we report the identification of a novel class of dideoxy nucleosides as potent and selective inhibitors of Mycobacterium bovis, Mycobacterium tuberculosis, and drug-resistant Mycobacterium tuberculosis. A series of 5-acetylenic derivatives of 2',3'-dideoxyuridine (3-8) and 3'-fluoro-2',3'-dideoxyuridine (22-27) were synthesized and tested for their antimycobacterial activity against M. bovis, M. tuberculosis, and M. avium. 2',3'-Dideoxyuridine possessing 5-decynyl, 5-dodecynyl, 5-tridecynyl, and 5-tetradecynyl substituents (4-7) exhibited the highest antimycobacterial activity against all three mycobacteria. In contrast, in the 3'-fluoro-2',3'-dideoxyuridine series, a 5-tetradecynyl analogue (26) displayed the most potent activity against these mycobacteria. Among other derivatives, 5-bromo-2',3'-dideoxycytidine (11), 5-methyl-2',3'-dideoxycytidine (12), and 5-chloro-4-thio-2',3'-dideoxyuridine (19) exhibited modest inhibition of M. bovis and M. tuberculosis. In the series of dideoxy derivatives of adenosine, guanosine, and purines, 2-amino-6-mercaptoethyl-9-(2,3-dideoxy-beta-d-glyceropentofuranosyl)purine (32) and 2-amino-4-fluoro-7-(2,3-dideoxy-beta-d-glyceropentofuranosyl)pyrrolo[2,3-d]pyrimidine (35) were the most efficacious against M. bovis and M. tuberculosis, and M. avium, respectively.
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Affiliation(s)
- Dinesh Rai
- Department of Laboratory Medicine and Pathology, 1-71 Medical Sciences Building, University of Alberta, Edmonton, AB, T6G 2H7, Canada
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26
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Iwase R, Namie Y, Yamaoka T, Murakami A. Synthesis and properties of fluorescent-labeled oligonucleotides containing amide-linked dinucleoside with pyrene. ACTA ACUST UNITED AC 2007:75-6. [PMID: 17150485 DOI: 10.1093/nass/48.1.75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Oligonucleotides containing 2'-pyrene modified uridine (Upy) exhibit the increase of the pyrene monomer emission when hybridize with the complementary RNA. In order to examine the effect of restricted C3'-endoconformation of the Upy residue for the enhancement of the pyrene monomer emission, an oligodeoxyribonucleotide containing amide-linked dinucleoside with a pyrene group at the sugar residue (UapyODN) was synthesized by use of 3'-carboxymethyl-5'-O-dimethoxytrityl-2'-O-(1-pyrenylmethyl)-3'-deoxyuridine. NMR analysis indicated that the furanose ring of the uridine derivative was fixed to C3'-endo conformation. The UapyODN showed increase of fluorescence intensity to 7-fold at 375 nm when hybridized with complementary oligoribonucleotide. This result suggests that the UapyODN can detect the target RNA.
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Affiliation(s)
- Reiko Iwase
- Department of Polymer Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyoku, Kyoto 606-8585, Japan
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27
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Li NS, Lu J, Piccirilli JA. Efficient Synthesis of Methyl 3,5-Di-O-benzyl-α-d-ribofuranoside and Application to the Synthesis of 2‘-C-β-Alkoxymethyluridines. Org Lett 2007; 9:3009-12. [PMID: 17629285 DOI: 10.1021/ol071075b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyl 3,5-di-O-arylmethyl-alpha-D-ribofuranosides have been used extensively as synthons to construct 2'-C-branched ribonucleosides. Herein, we describe efficient access to methyl 3,5-di-O-arylmethyl-alpha-D-ribofuranosides (aryl: 2-ClC(6)H(4), 3-ClC(6)H(4), 4-ClC(6)H(4), 4-BrC(6)H(4), 2,4-Cl(2)C(6)H(3), Ph) in 72-82% yields from methyl D-ribofuranoside. We also demonstrate efficient access to the versatile precursor methyl 3,5-di-O-benzyl-alpha-D-ribofuranoside (3f) and the synthesis of 2'-C-beta-methoxymethyl- and 2'-C-beta-ethoxymethyluridine in six steps from 3f with overall yields of 18% and 32%, respectively.
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Affiliation(s)
- Nan-Sheng Li
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.
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28
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Cristofoli WA, Wiebe LI, De Clercq E, Andrei G, Snoeck R, Balzarini J, Knaus EE. 5-alkynyl analogs of arabinouridine and 2'-deoxyuridine: cytostatic activity against herpes simplex virus and varicella-zoster thymidine kinase gene-transfected cells. J Med Chem 2007; 50:2851-7. [PMID: 17518459 DOI: 10.1021/jm0701472] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A group of arabinouridines (TMSEAU, EAU, IEAU-TA) and 2'-deoxyuridines (TMSEDU, EDU, IEDU) having a variety of substituents at the uracil C-5 position (trimethylsilylethynyl, TMSE; ethynyl, E; or iodoethynyl, IE), and the sugar C-2' position (2'-arabino OH in arabinouridine, AU; or 2'-deoxyribo H in 2'-deoxyuridine, DU) were prepared to acquire antiviral structure-activity relationships. A broad-spectrum viral panel screen showed that these 5-alkynylarabino/deoxy-uridines exhibit moderate anti-HSV-1 activity, with no difference in potency between arabinouridines and 2'-deoxyuridines. The 2'-deoxyuridines TMSEDU, EDU, and IEDU, unlike the arabinouridines, exhibited potent antiviral activity against cytomegalovirus, but they were also highly cytostatic. The abilities of the 5-alkynylarabino/deoxy-uridines to inhibit nontransfected (wild-type or thymidine kinase-deficient, tk-) and viral gene transfected (HSV-1, HSV-2, or VZV thymidine kinase-positive, tk+) FM3A and OST (osteosarcoma) cells were determined. This group of 5-alkynylarabino/deoxy-uridines showed an enhanced ability to inhibit cells transfected with a viral thymidine kinase gene (HSV-1tk+, HSV-2tk+, VZVtk+) relative to wild-type or thymidine kinase-deficient (tk-) cells.
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Affiliation(s)
- Walter A Cristofoli
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2N8
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29
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Perrone P, Luoni GM, Kelleher MR, Daverio F, Angell A, Mulready S, Congiatu C, Rajyaguru S, Martin JA, Levêque V, Le Pogam S, Najera I, Klumpp K, Smith DB, McGuigan C. Application of the Phosphoramidate ProTide Approach to 4‘-Azidouridine Confers Sub-micromolar Potency versus Hepatitis C Virus on an Inactive Nucleoside. J Med Chem 2007; 50:1840-9. [PMID: 17367121 DOI: 10.1021/jm0613370] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the application of our phosphoramidate ProTide technology to the ribonucleoside analogue 4'-azidouridine to generate novel antiviral agents for the inhibition of hepatitis C virus (HCV). 4'-Azidouridine did not inhibit HCV, although 4'-azidocytidine was a potent inhibitor of HCV replication under similar assay conditions. However 4'-azidouridine triphosphate was a potent inhibitor of RNA synthesis by HCV polymerase, raising the question as to whether our phosphoramidate ProTide approach could effectively deliver 4'-azidouridine monophosphate to HCV replicon cells and unleash the antiviral potential of the triphosphate. Twenty-two phosphoramidates were prepared, including variations in the aryl, ester, and amino acid regions. A number of compounds showed sub-micromolar inhibition of HCV in cell culture without detectable cytotoxicity. These results confirm that phosphoramidate ProTides can deliver monophosphates of ribonucleoside analogues and suggest a potential path to the generation of novel antiviral agents against HCV infection. The generic message is that ProTide synthesis from inactive parent nucleosides may be a warranted drug discovery strategy.
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Affiliation(s)
- Plinio Perrone
- Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff CF10 3XF, UK
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30
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Bello AM, Poduch E, Fujihashi M, Amani M, Li Y, Crandall I, Hui R, Lee PI, Kain KC, Pai EF, Kotra LP. A potent, covalent inhibitor of orotidine 5'-monophosphate decarboxylase with antimalarial activity. J Med Chem 2007; 50:915-21. [PMID: 17290979 DOI: 10.1021/jm060827p] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) has evolved to catalyze the decarboxylation of orotidine 5'-monophosphate without any covalent intermediates. Active site residues in ODCase are involved in an extensive hydrogen-bonding network. We discovered that 6-iodouridine 5'-monophosphate (6-iodo-UMP) irreversibly inhibits the catalytic activities of ODCases from Methanobacterium thermoautotrophicum and Plasmodium falciparum. Mass spectral analysis of the enzyme-inhibitor complex confirms covalent attachment of the inhibitor to ODCase accompanied by the loss of two protons and the iodo moiety. The X-ray crystal structure (1.6 A resolution) of the complex of the inhibitor and ODCase clearly shows the covalent bond formation with the active site Lys-72 [corrected] residue. 6-Iodo-UMP inhibits ODCase in a time- and concentration-dependent fashion. 6-Iodouridine, the nucleoside form of 6-iodo-UMP, exhibited potent antiplasmodial activity, with IC50s of 4.4 +/- 1.3 microM and 6.2 +/- 0.7 microM against P. falciparum ItG and 3D7 isolates, respectively. 6-Iodouridine 5'-monophosphate is a novel covalent inhibitor of ODCase, and its nucleoside analogue paves the way to a new class of inhibitors against malaria.
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Affiliation(s)
- Angelica M Bello
- Center for Molecular Design and Preformulations, Toronto General Research Institute, Toronto General Hospital, Toronto, ON M5G 2C4 Canada
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31
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Abstract
Alkylbenzyltriazole units covalently bonded onto uridine nucleosides were synthesized and their suitability for water gelation compared with 2'-deoxyuridine derivatives was tested.
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Affiliation(s)
- Sun Min Park
- Laboratory for Modified Nucleic Acid Systems, Department of Chemistry, BK School of Molecular Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
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32
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Bag SS, Saito Y, Hanawa K, Hayasi K, Kodate S, Suzuka I, Saito I. Synthesis of perylene-labeled base-discriminating fluorescent (BDF) nucleoside and its fluorescence properties. ACTA ACUST UNITED AC 2006:179-80. [PMID: 17150876 DOI: 10.1093/nass/nrl089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We have synthesized perylene labeled BDF probe and its photophysical properties were explored. Perylene labeled oligonucleotide probe is capable of detecting cytosine from its target mismatch sequence by enhancement of fluorescence intensity.
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Affiliation(s)
- Subhendu Sekhar Bag
- Newcat Institute, School of Engineering, Nihon University, Tamura, Koriyama, Fukushima 963-8642, Japan
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33
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Oh CH, Kim JW, Hong JH. Simple synthesis and anti-HIV activity of novel 3'-vinyl branched apiosyl pyrimidine nucleosides. Nucleosides Nucleotides Nucleic Acids 2006; 25:871-8. [PMID: 16901819 DOI: 10.1080/15257770600793869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Novel vinyl branched apiosyl nucleosides were synthesized in this study. Apiosyl sugar moiety was constructed by sequential ozonolysis and reductions. The bases (uracil and thymine) were efficiently coupled by glycosyl condensation procedure (persilyated base and TMSOTf). The antiviral activities of the synthesized compounds were evaluated against the HIV-1, HSV-1, HSV-2, and HCMV. Compound 10beta displayed moderate anti-HIV activity (EC50 = 17.3 microg/mL) without exhibiting any cytotoxicity up to 100 microM.
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Affiliation(s)
- Chang Hyun Oh
- Medicinal Chemistry Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
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34
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Nowak I, Robins MJ. Addition of Difluorocarbene to 4‘,5‘-Unsaturated Nucleosides: Synthesis and Deoxygenation Reactions of Difluorospirocyclopropane Nucleosides1. J Org Chem 2006; 71:8876-83. [PMID: 17081018 DOI: 10.1021/jo061606u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic routes to 4'-(2,2-difluorospirocyclopropane) analogues of adenosine, cytidine, and uridine are described. Treatment of 2',3'-O-isopropylidene-4',5'-unsaturated compounds derived from adenosine and uridine with difluorocarbene (generated from PhHgCF3 and NaI) gave diastereomeric mixtures of the 2,2-difluorospirocyclopropane adducts. Stereoselectivity resulting from hindrance by the isopropylidene group favored addition at the beta face. Removal of base and sugar protecting groups gave new difluorospirocyclopropane nucleoside analogues. The protected uridine analogue was converted into its cytidine counterpart via a 4-(1,2,4-triazol-1-yl) intermediate. Stannyl radical-mediated deoxygenation of the 3'-O-TBS-2'-thionocarbamate derivatives gave the 2'-deoxy products of direct hydrogen transfer. In contrast, identical treatment of the 2'-O-TBS-3'-thionocarbamate isomers resulted in opening of the vicinal difluorocyclopropane ring upon generation of a C3' radical followed by homoallylic hydrogen transfer to give 4'-(1,1-difluoroethyl)-3',4'-unsaturated nucleoside derivatives. Structural aspects and biological effect considerations are discussed.
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Affiliation(s)
- Ireneusz Nowak
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700, USA
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35
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Salon J, Chen G, Portilla Y, Germann MW, Huang Z. Synthesis of a 2'-Se-uridine phosphoramidite and its incorporation into oligonucleotides for structural study. Org Lett 2006; 7:5645-8. [PMID: 16321012 PMCID: PMC3596769 DOI: 10.1021/ol052270y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[chemical reaction: see text]. We report here the synthesis of the 5'-[benzhydryloxybis(trimethylsilyloxy)]silyl-2'-methylseleno-2'-deoxyuridine phosphoramidite and its incorporation into oligonucleotides by solid-phase synthesis. The coupling yield of this phosphoramidite into oligonucleotides is higher than 99%. We also demonstrate that this 2'-methylselenophosphoramidite is compatible with the 5'-silyl-2'-ACE chemistry, for longer Se-RNA solid-phase synthesis. Our preliminary NMR study on the synthesized 2'-Se-DNA has revealed a U(Se)-A base pair and a duplex structure formation when its complementary strand was present.
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36
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Abstract
Some of nucleoside antibiotics include complex structures as well as sensitive functionality, which are challenging targets for organic chemists. Among complex nucleoside antibiotics, there are also good drug candidates because they possess a variety of interesting biological properties. Herbicidin B and fully protected tunicaminyluracil, which were undecose nucleoside antibiotics, were synthesized using a samarium diiodide (SmI(2)) mediated aldol reaction with the use of alpha-phenylthioketones as enolate sources. The characteristics of the SmI(2)-mediated aldol reaction are that the enolate can be regioselectively generated and the aldol reaction proceeds under near neutral condition. This reaction is proved to be a powerful reaction for the synthesis of complex nucleoside antibiotics. The synthesis of caprazol, the core structure of caprazamycins, was conducted by the strategy including beta-selective ribosylation without using a neighboring group participation and the construction of a diazepanone by a modified reductive amination. Our synthetic route would provide a range of key analogues with partial structures to define the pharmacophore, which can be a lead for the development of more effective anti-bacterial agents.
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Affiliation(s)
- Satoshi Ichikawa
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
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37
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Ogamino J, Mizunuma H, Kumamoto H, Haraguchi K, Tanaka H. Reaction of the 2'-silyl and 2'-stannyl derivatives of 6-(bromomethyl)dimethylsilyl-1',2'-unsaturated uridine under radical conditions. Nucleosides Nucleotides Nucleic Acids 2006; 24:1439-47. [PMID: 16438027 DOI: 10.1080/15257770500265687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The mode of cyclization (5-exo versus 6-endo) of 2-sila-5-hexen-1-yl radicals generated from 2'-tributylstannyl- and 2'-trimethylsilyl-6-(bromomethyl)dimethylsilyl-1',2'-unsaturated uridines (8 and 9) was investigated. Although the actual structure of the reaction products differ from each other reflecting the ease of elimination of the 2'-substituent, it was found that both substrates prefer the 5-exo-cyclization pathway.
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Affiliation(s)
- Junko Ogamino
- School of Pharmaceutical Sciences, Showa University, Shinagawa-ku, Tokyo, Japan
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38
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Watts JK, Sadalapure K, Choubdar N, Pinto BM, Damha MJ. Synthesis and Conformational Analysis of 2‘-Fluoro-5-methyl-4‘-thioarabinouridine (4‘S-FMAU). J Org Chem 2006; 71:921-5. [PMID: 16438502 DOI: 10.1021/jo051844+] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An improved synthesis of 2'-deoxy-2'-fluoro-5-methyl-4'-thioarabinouridine (4'S-FMAU) is described. Participation of the 3'-O-benzoyl protecting group in the thiosugar precursor influenced the stereochemistry of the N-glycosylation reaction in nonpolar solvents, permitting a higher beta/alpha ratio than previously observed for similar Lewis acid catalyzed glycosylations. Conformational analysis of the nucleoside using 3JHH and 3JHF NMR coupling constants together with the PSEUROT program showed that it adopted a predominantly northern conformation in contrast to 2'-deoxy-2'-fluoro-5-methylarabinouridine (FMAU), whose PSEUROT conformational analysis is presented here for the first time, which showed a dominantly southeast conformation. The sharp conformational switch attained by replacing the ring heteroatom is attributed to a decrease in relevant steric and stereoelectronic effects.
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Affiliation(s)
- Jonathan K Watts
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6
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39
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Al-Rawi S, Ahlborn C, Richert C. 3'-immobilized probes with 2'-caps: synthesis of oligonucleotides with 2'-N-methyl-2'-(anthraquinone carboxamido)uridine residues. Org Lett 2006; 7:1569-72. [PMID: 15816754 DOI: 10.1021/ol0502432] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] A synthesis for oligodeoxynucleotides with a 3'-terminal 2'-N-methyl-2'-acylamido-2'-deoxyuridine residue was developed. Unlike their unmethylated counterparts, these oligodeoxynucleotides can be stably immobilized on aldehyde-displaying glass surfaces to provide DNA microarrays. An anthraquinone carboxamido group as a 2'-substituent doubled the capture efficiency of an immobilized tetradecamer.
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Affiliation(s)
- Samy Al-Rawi
- Institute for Organic Chemistry, Universität Karlsruhe (TH), D-76131 Karlsruhe, Germany
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40
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Kodama T, Matsuda A, Shuto S. The first synthesis of 1'-fluoronucleosides. Nucleic Acids Symp Ser (Oxf) 2006:3-4. [PMID: 17150788 DOI: 10.1093/nass/nrl002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The first synthesis of 1'-fluoronucleosides, which has long been synthetic targets as the potential antimetabolites, was achieved. Electrophilic fluorination of the 1'-position of a 1'-ketouridine derivative, followed by reduction of the 2'-keto-moiety, gave the protected 1'-fluorouridine derivative and its arabino-type congener. Alternatively, nucleophilic fluorination of a 1'-phenyselenouridine derivative with DAST/NBS produced the protected 1'-fluorouridine and its alpha-anomer.
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Affiliation(s)
- Tetsuya Kodama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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41
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Zubin EM, Stetsenko DA, Zatsepin TS, Gait MJ, Oretskaya TS. Oligonucleotides containing 2'-O-[2-(2,3-dihydroxypropyl)amino-2-oxoethyl]uridine as suitable precursors of 2'-aldehyde oligonucleotides for chemoselective ligation. Bioorg Med Chem 2005; 13:4912-20. [PMID: 15993079 DOI: 10.1016/j.bmc.2005.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 05/16/2005] [Accepted: 05/20/2005] [Indexed: 11/30/2022]
Abstract
2'-O-[2-(2,3-Diacetoxypropyl)amino-2-oxoethyl]uridine 3'-phosphoramidite was prepared and used in solid-phase synthesis to obtain oligonucleotides containing a 1,2-diol group, which may then be converted into a 2'-aldehyde group. The oligonucleotides were conjugated efficiently to various molecules by chemoselective ligation that involves an addition-elimination reaction between the 2'-aldehyde group and a suitable nucleophile, such as a hydrazine, a O-alkylhydroxylamine or an 1,2-aminothiol. The method was applied successfully to the conjugation of peptides to oligonucleotides at the 2'-position.
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Affiliation(s)
- Eugeny M Zubin
- Department of Chemistry, M.V. Lomonossov Moscow State University, 1 Leninskie Gory, Moscow 119992, Russia
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42
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Sekine M, Aoyagi M, Ushioda M, Ohkubo A, Seio K. Chemically Stabilized Phenylboranylidene Groups Having a Dimethoxytrityl Group as a Colorimetrically Detectable Protecting Group Designed forcis-1,2-Diol Functions of Ribonucleosides in the Solid-Phase Synthesis of m22,2G5‘ppT. J Org Chem 2005; 70:8400-8. [PMID: 16209584 DOI: 10.1021/jo051202m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
To not only improve the inherently poor stability of the phenylboranylidene group as a protecting group of the 2',3'-cis-diol function of ribonucleosides but also introduce a colorimetrically detectable function into its mother structure, various 2-[(dialkylamino)methyl]phenylboronic acid derivatives having a [(4,4'-dimethoxytrityl)oxy]methyl group were synthesized. The reaction of uridine with these substituted phenylboronic acid derivatives gave the corresponding 2',3'-O-phenylboranylideneuridine derivatives. The stability of these phenylboranylidene groups was examined. As a result, it was shown that the steric hindrance around the amino group greatly influenced the stability of the 2-substituted phenylboranylidene groups. The 2-aminomethyl-5-[[(4,4'-dimethoxytrityl)oxy]methyl]phenylboranylidene group was the most stable. Its 2-dimethylamino counterpart, the 2-[(dimethylamino)methyl]-5-[[(4,4'-dimethoxytrityl)oxy]methyl]phenylboranylidene group, was the second most stable. When the most and second stable protecting groups were applied to the synthesis of m(2)(2,2)G(5)(')ppT on controlled pore glass, the second stable protecting group showed the best result. The use of this DMTr-containing protecting group enabled us to estimate colorimetrically the amount of the m(2)(2,2)G residue that was incorporated into the reactive site of the pT-loaded CPG resin.
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Affiliation(s)
- Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, Division of Collaborative Research for Bioscience and Biotechnology, Midoriku, Yokohama 226-8501, Japan.
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43
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Hrdlicka PJ, Andersen NK, Jepsen JS, Hansen FG, Haselmann KF, Nielsen C, Wengel J. Synthesis and biological evaluation of branched and conformationally restricted analogs of the anticancer compounds 3'-C-ethynyluridine (EUrd) and 3'-C-ethynylcytidine (ECyd). Bioorg Med Chem 2005; 13:2597-621. [PMID: 15755661 DOI: 10.1016/j.bmc.2005.01.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 01/13/2005] [Accepted: 01/18/2005] [Indexed: 10/25/2022]
Abstract
The synthesis of branched and conformationally restricted analogs of the anticancer nucleosides 3'-C-ethynyluridine (EUrd) and 3'-C-ethynylcytidine (ECyd) is presented. Molecular modeling and (1)H NMR coupling constant analysis revealed that the furanose rings of all analogs except the LNA analog are conformationally biased towards South conformation, and are thus mimicking the structure of ECyd. All target nucleosides were devoid of anti-HIV or anticancer activity.
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Affiliation(s)
- Patrick J Hrdlicka
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
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44
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Abstract
Thymidine and uridine were modified at the C2' and C5' ribose positions to form amine analogues of the nucleosides (1 and 4). Direct amination with NaBH(OAc)3 in DCE with the appropriate aldehydes yielded 1-{5-[(bis(pyridin-2-ylmethyl)amino)methyl]-4-hydroxytetrahydrofuran-2-yl}-5-methyl-1H-pyrimidine-2,4-dione (L1), 1-{5-[(bis(quinolin-2-ylmethyl)amino)methyl]-4-hydroxytetrahydrofuran-2-yl}-5-methyl-1H-pyrimidine-2,4-dione (L2), and 1-[3-(bis(pyridin-2-ylmethyl)amino)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-1H-pyrimidine-2,4-dione (L5), while standard coupling procedures of 1 and 4 with 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid (2) and 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid (3) in the presence of HOBT-EDCI in DMF provided a second novel series of bifunctional chelators: 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid [(3-hydroxy-5-(5-methyl-4-oxo-3,4-dihydro-2H-pyrimidin-1-yl)tetrahydrofuran-2-yl)methyl] amide (L3), 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid [(3-hydroxy-5-(5-methyl-4-oxo-3,4-dihydro-2H-pyrimidin-1-yl)tetrahydrofuran-2-yl)methyl] amide (L4), 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid [2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl] amide (L6), and 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid [2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl] amide (L7). The rhenium tricarbonyl complexes of L1-L4, L6, and L7, [Re(CO)3(LX)]Br (X=1-4, 6, 7: compounds 5-10, respectively), have been prepared by reacting the appropriate ligand with [NEt4][Re(CO)3Br3] in methanol. The ligands and their rhenium complexes were obtained in good yields and characterized by common spectroscopic techniques including 1D and 2D NMR, HRMS, IR, cyclic voltammetry, UV, and luminescence spectroscopy and X-ray crystallography. The crystal structure of complex 6.0.5NaPF6 displays a facial geometry of the carbonyl ligands. The nitrogen donors of the tridentate ligand complete the distorted octahedral spheres of the complex. Crystal data: monoclinic, C2, a = 24.618(3) A, b = 11.4787(11) A, c = 15.5902(15) A, beta = 112.422(4) degrees , Z = 4, D(calc) = 1.562 g/cm3.
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Affiliation(s)
- Lihui Wei
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, USA
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45
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Abstract
[reaction: see text] Silatranyluridine 1 and germatranyluridine 2 have been prepared in five steps from oxazolinouridine 3 in 27 and 29% yields, respectively. These compounds are novel transition-state analogues (TSAs) for RNA hydrolysis and offer a number of advantages over traditional vanadium- or rhenium-based TSAs. Germatrane 2 is completely stable in D(2)O at room temperature, and the half-life of silatrane 1 in D(2)O was found to be >7 days by (1)H NMR spectroscopy.
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Affiliation(s)
- Chad M Rink
- Department of Chemistry, Xavier University, 3800 Victory Parkway, Cincinnati, Ohio 45207, USA
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46
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Hrdlicka PJ, Jepsen JS, Nielsen C, Wengel J. Synthesis and biological evaluation of nucleobase-modified analogs of the anticancer compounds 3′-C-ethynyluridine (EUrd) and 3′-C-ethynylcytidine (ECyd). Bioorg Med Chem 2005; 13:1249-60. [PMID: 15670934 DOI: 10.1016/j.bmc.2004.11.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Accepted: 11/26/2004] [Indexed: 10/26/2022]
Abstract
A series of nucleobase-modified analogs of the anticancer compounds 3'-C-ethynyluridine (EUrd) and 3'-C-ethynylcytidine (ECyd) were designed to overcome the strict substrate specificity of the activating uridine-cytidine kinase. EUrd, ECyd and target nucleosides were obtained using a short convergent synthetic route utilizing diacetone-alpha-D-glucose as starting material. 5-Iodo-substituted EUrd was the most potent inhibitor among the novel nucleobase-modified analogs in in vitro assays against human adenocarcinoma breast and prostate cancer cells with IC50 values down to 35 nM.
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Affiliation(s)
- Patrick J Hrdlicka
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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47
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Ogamino J, Mizunuma H, Kumamoto H, Takeda S, Haraguchi K, Nakamura KT, Sugiyama H, Tanaka H. 5-Exo versus 6-Endo Cyclization of Nucleoside 2-Sila-5-hexenyl Radicals: Reaction of 6-(Bromomethyl)dimethylsilyl 1‘,2‘-Unsaturated Uridines. J Org Chem 2005; 70:1684-90. [PMID: 15730288 DOI: 10.1021/jo040260p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mode of cyclization of 2-sila-5-hexen-1-yl radicals generated from 6-(bromomethyl)dimethylsilyl-1',2'-unsaturated uridines was investigated. In contrast to the case of the 2'-unsubstituted 6-silicon-tethered substrate (4), which undergoes exclusive 6-endo-cyclization, reactions of the 2'-substituted (Me, CO2Me, OBz, and Cl) derivatives (14, 20, 22, and 24) uniformly proceeded in preferential or exclusive 5-exo-mode. The Tamao oxidation of the resulting cyclized products was also carried out to synthesize the corresponding 1'-C-hydroxymethyl derivatives.
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Affiliation(s)
- Junko Ogamino
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
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48
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Garg NK, Woodroofe CC, Lacenere CJ, Quake SR, Stoltz BM. A ligand-free solid-supported system for Sonogashira couplings: applications in nucleoside chemistry. Chem Commun (Camb) 2005:4551-3. [PMID: 16158111 DOI: 10.1039/b505737j] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mild heterogeneous, ligand-free protocol for Sonogashira and Heck couplings has been developed and used to access several biologically important deoxynucleoside derivatives in a facile manner.
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Affiliation(s)
- Neil K Garg
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 164-30, Pasadena, CA 91125, USA
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49
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Gottschaldt M, Koth D, Görls H. Synthesis and crystal structure of a salen-type copper(ii) complex derived from 3,5′-O-dimethyl-2′,3′-diamino-2′,3′-dideoxy-β-d-xylo-uridine. Org Biomol Chem 2005; 3:1170-1. [PMID: 15785801 DOI: 10.1039/b500785b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis of the first 2',3'-diamino substituted uridine derivative with xylo-configuration, its use as starting material for the synthesis of salen-type ligands and the first structurally characterised copper(II) complex thereof.
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Affiliation(s)
- Michael Gottschaldt
- Institute for Organic and Macromolecular Chemistry, FSU Jena, Humboldtstrasse 10, 07743, Jena, Germany.
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50
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Jiang XJ, Kalman TI. Synthesis of 4-formyl-4-imidazolin-2-one nucleosides, isomers of uridine and 2'-deoxyuridine. Nucleosides Nucleotides Nucleic Acids 2004; 23:307-16. [PMID: 15043156 DOI: 10.1081/ncn-120027837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The syntheses of the ribo- and deoxyribonucleoside derivatives of 4-formyl-4-imidazolin-2-one, isosteric isomers of uridine and 2'-deoxyuridine, respectively, were carried out by ring contraction of the corresponding 5-bromouracil nucleosides, followed by conversion of the carboxyl side-chain of the products to the respective carboxaldehyde derivatives.
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Affiliation(s)
- Xiang-Jun Jiang
- Department of Chemistry, University at Buffalo, Amherst, New York 14260, USA
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