1
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Vavřina Z, Perlíková P, Milisavljević N, Chevrier F, Smola M, Smith J, Dejmek M, Havlíček V, Buděšínský M, Liboska R, Vaneková L, Brynda J, Boura E, Řezáčová P, Hocek M, Birkuš G. Design, Synthesis, and Biochemical and Biological Evaluation of Novel 7-Deazapurine Cyclic Dinucleotide Analogues as STING Receptor Agonists. J Med Chem 2022; 65:14082-14103. [PMID: 36201304 PMCID: PMC9620234 DOI: 10.1021/acs.jmedchem.2c01305] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Indexed: 11/28/2022]
Abstract
Cyclic dinucleotides (CDNs) are second messengers that activate stimulator of interferon genes (STING). The cGAS-STING pathway plays a promising role in cancer immunotherapy. Here, we describe the synthesis of CDNs containing 7-substituted 7-deazapurine moiety. We used mouse cyclic GMP-AMP synthase and bacterial dinucleotide synthases for the enzymatic synthesis of CDNs. Alternatively, 7-(het)aryl 7-deazapurine CDNs were prepared by Suzuki-Miyaura cross-couplings. New CDNs were tested in biochemical and cell-based assays for their affinity to human STING. Eight CDNs showed better activity than 2'3'-cGAMP, the natural ligand of STING. The effect on cytokine and chemokine induction was also evaluated. The best activities were observed for CDNs bearing large aromatic substituents that point above the CDN molecule. We solved four X-ray structures of complexes of new CDNs with human STING. We observed π-π stacking interactions between the aromatic substituents and Tyr240 that are involved in the stabilization of CDN-STING complexes.
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Affiliation(s)
- Zdeněk Vavřina
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Pavla Perlíková
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Technicka 5, Prague 166 28, Czech Republic
| | - Nemanja Milisavljević
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Florian Chevrier
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Miroslav Smola
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Joshua Smith
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- First
Faculty of Medicine, Charles University, Katerinska 1660/32, Prague 121 08, Czech Republic
| | - Milan Dejmek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Vojtěch Havlíček
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 00, Czech Republic
| | - Miloš Buděšínský
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Radek Liboska
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Lenka Vaneková
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
- Department
of Cell Biology, Faculty of Science, Charles
University, Vinicna 1594/7, Prague 128 43, Czech Republic
| | - Jiří Brynda
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Evzen Boura
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Pavlína Řezáčová
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
| | - Gabriel Birkuš
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo Namesti 542, Prague 166 10, Czech Republic
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2
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Moorthy R, Kennelly SA, Rodriguez DJ, Harki DA. An efficient synthesis of RNA containing GS-441524: the nucleoside precursor of remdesivir. RSC Adv 2021; 11:31373-31376. [PMID: 35496844 PMCID: PMC9041347 DOI: 10.1039/d1ra06589k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/14/2021] [Indexed: 01/18/2023] Open
Abstract
Remdesivir is an antiviral nucleoside phosphoramidate with activity against multiple viruses, including SARS-CoV-2. To enable studies of viral polymerases with RNA containing remdesivir, we report an efficient synthesis of a phosphoramidite of GS-441524, the nucleoside precursor of remdesivir, and its incorporation into RNA using automated solid-phase RNA synthesis.
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Affiliation(s)
- Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota 2231 6th Street S.E. Minneapolis MN 55455 USA
| | - Samantha A Kennelly
- Department of Medicinal Chemistry, University of Minnesota 2231 6th Street S.E. Minneapolis MN 55455 USA
| | - Deborah J Rodriguez
- Department of Medicinal Chemistry, University of Minnesota 2231 6th Street S.E. Minneapolis MN 55455 USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota 2231 6th Street S.E. Minneapolis MN 55455 USA
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3
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Thioether-linked dihydropyrrol-2-one analogues as PqsR antagonists against antibiotic resistant Pseudomonas aeruginosa. Bioorg Med Chem 2021; 31:115967. [PMID: 33434766 DOI: 10.1016/j.bmc.2020.115967] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023]
Abstract
The Pseudomonas quinolone system (pqs) is one of the key quorum sensing systems in antibiotic-resistant P. aeruginosa and is responsible for the production of virulence factors and biofilm formation. Thus, synthetic small molecules that can target the PqsR (MvfR) receptor can be utilized as quorum sensing inhibitors to treat P. aeruginosa infections. In this study, we report the synthesis of novel thioether-linked dihydropyrrol-2-one (DHP) analogues as PqsR antagonists. Compound 7g containing a 2-mercaptopyridyl linkage effectively inhibited the pqs system with an IC50 of 32 µM in P. aeruginosa PAO1. Additionally, these inhibitors significantly reduced bacterial aggregation and biofilm formation without affecting planktonic growth. The molecular docking study suggest that these inhibitors bind with the ligand binding domain of the MvfR as a competitive antagonist.
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4
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Beck KM, Krogh MB, Hornum M, Ludford PT, Tor Y, Nielsen P. Double-headed nucleotides as xeno nucleic acids: information storage and polymerase recognition. Org Biomol Chem 2020; 18:7213-7223. [PMID: 32909574 PMCID: PMC7517788 DOI: 10.1039/d0ob01426e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Xeno nucleic acids (XNAs) are artificial genetic systems based on sugar-modified nucleotides. Herein, we investigate double-headed nucleotides as a new XNA. A new monomer, AT, is presented, and together with previous double-headed nucleotide monomers, new nucleic acid motifs consisting of up to five consecutive A·T base pairs have been obtained. Sections composed entirely of double-headed nucleotides are well-tolerated within a DNA duplex and can condense the genetic information. For instance, a 13-mer duplex is condensed to an 11-mer modified duplex containing four double-headed nucleotides while simultaneously improving duplex thermal stability with +14.0 °C. Also, the transfer of information from double-headed to natural nucleotides by DNA polymerases has been examined. The first double-headed nucleoside triphosphate was prepared but could not be recognized and incorporated by the tested DNA polymerases. On the other hand, it proved possible for Therminator DNA polymerase to transfer the information of a double-headed nucleotide in a template sequence to natural DNA under controlled conditions.
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Affiliation(s)
- Kasper M Beck
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
| | - Marie B Krogh
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
| | - Mick Hornum
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
| | - Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
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5
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Sabir S, Subramoni S, Das T, Black DS, Rice SA, Kumar N. Design, Synthesis and Biological Evaluation of Novel Anthraniloyl-AMP Mimics as PQS Biosynthesis Inhibitors Against Pseudomonas aeruginosa Resistance. Molecules 2020; 25:molecules25133103. [PMID: 32646050 PMCID: PMC7412332 DOI: 10.3390/molecules25133103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 01/10/2023] Open
Abstract
The Pseudomonas quinolone system (PQS) is one of the three major interconnected quorum sensing signaling systems in Pseudomonas aeruginosa. The virulence factors PQS and HHQ activate the transcription regulator PqsR (MvfR), which controls several activities in bacteria, including biofilm formation and upregulation of PQS biosynthesis. The enzyme anthraniloyl-CoA synthetase (PqsA) catalyzes the first and critical step in the biosynthesis of quinolones; therefore, it is an attractive target for the development of anti-virulence therapeutics against Pseudomonas resistance. Herein, we report the design and synthesis of novel triazole nucleoside-based anthraniloyl- adenosine monophosphate (AMP) mimics. These analogues had a major impact on the morphology of bacterial biofilms and caused significant reduction in bacterial aggregation and population density. However, the compounds showed only limited inhibition of PQS and did not exhibit any effect on pyocyanin production.
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Affiliation(s)
- Shekh Sabir
- School of Chemistry, Faculty of Science, The University of New South Wales, Sydney, NSW 2052, Australia; (S.S.); (D.S.B.)
| | - Sujatha Subramoni
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore; (S.S.); (S.A.R.)
| | - Theerthankar Das
- Department of Infectious Diseases and Immunology, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
| | - David StC. Black
- School of Chemistry, Faculty of Science, The University of New South Wales, Sydney, NSW 2052, Australia; (S.S.); (D.S.B.)
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore; (S.S.); (S.A.R.)
| | - Naresh Kumar
- School of Chemistry, Faculty of Science, The University of New South Wales, Sydney, NSW 2052, Australia; (S.S.); (D.S.B.)
- Correspondence: ; Tel.: +61-2-9385-4698; Fax: +61-2-9385-6141
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6
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Woodroofe CC, Ivanic J, Monti S, Levine RL, Swenson RE. Repurposing the Pummerer Rearrangement: Determination of Methionine Sulfoxides in Peptides. Chembiochem 2020; 21:508-516. [PMID: 31365170 PMCID: PMC7065062 DOI: 10.1002/cbic.201900463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 12/29/2022]
Abstract
The reversible oxidation of methionine residues in proteins has emerged as a biologically important post-translational modification. However, detection and quantitation of methionine sulfoxide in proteins is difficult. Our aim is to develop a method for specifically derivatizing methionine sulfoxide residues. We report a Pummerer rearrangement of methionine sulfoxide treated sequentially with trimethylsilyl chloride and then 2-mercaptoimidazole or pyridine-2-thiol to produce a dithioacetal product. This derivative is stable to standard mass spectrometry conditions, and its formation identified oxidized methionine residues. The scope and requirements of dithioacetal formation are reported for methionine sulfoxide and model substrates. The reaction intermediates have been investigated by computational techniques and by 13 C NMR spectroscopy. These provide evidence for an α-chlorinated intermediate. The derivatization allows for detection and quantitation of methionine sulfoxide in proteins by mass spectrometry and potentially by immunochemical methods.
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Affiliation(s)
- Carolyn C. Woodroofe
- Imaging Probe Development CenterNational Heart, Lung and Blood InstituteNational Institutes of Health9800 Medical Center DriveRockvilleMD20850USA
| | - Joseph Ivanic
- Advanced Biomedical Computational Sciences GroupFrederick National Laboratory for Cancer Research operated byLeidos Biomedical Research, Inc.1011 Beasley DriveFrederickMD21701USA
| | - Sarah Monti
- Laboratory of Biochemistry, National Heart, Lung, and Blood InstituteNational Institutes of Health50 South DriveBethesdaMD20892USA
| | - Rodney L. Levine
- Laboratory of Biochemistry, National Heart, Lung, and Blood InstituteNational Institutes of Health50 South DriveBethesdaMD20892USA
| | - Rolf E. Swenson
- Imaging Probe Development CenterNational Heart, Lung and Blood InstituteNational Institutes of Health9800 Medical Center DriveRockvilleMD20850USA
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7
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Ager CR, Zhang H, Wei Z, Jones P, Curran MA, Di Francesco ME. Discovery of IACS-8803 and IACS-8779, potent agonists of stimulator of interferon genes (STING) with robust systemic antitumor efficacy. Bioorg Med Chem Lett 2019; 29:126640. [PMID: 31500996 PMCID: PMC6993876 DOI: 10.1016/j.bmcl.2019.126640] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/22/2019] [Accepted: 08/24/2019] [Indexed: 01/16/2023]
Abstract
Activation of the stimulator of interferon genes (STING) pathway by both exogenous and endogenous cytosolic DNA results in the production of interferon beta (IFN-β) and is required for the generation of cytotoxic T-cell priming against tumor antigens. In the clinical setting, pharmacological stimulation of the STING pathway has the potential to synergize with immunotherapy antibodies by boosting anti-tumor immune responses. We report the discovery of two highly potent cyclic dinucleotide STING agonists, IACS-8803 and IACS-8779, which show robust activation of the STING pathway in vitro and a superior systemic anti-tumor response in the B16 murine model of melanoma when compared to one of the clinical benchmark compounds.
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Affiliation(s)
- Casey R Ager
- Department of Immunology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blv., Houston 77030, TX, USA; The University of Texas MD Anderson UTHealth Graduate School of Biochemical Sciences, Immunology Program, 1515 Holcombe Blv., Houston 77030, TX, USA
| | - Huaping Zhang
- WuXi AppTec (Wuhan) Co., Ltd., 666 Gaoxin Road, Wuhan East Lake High-tech Development Zone, Hubei 430075, China
| | - Zhanlei Wei
- WuXi AppTec (Wuhan) Co., Ltd., 666 Gaoxin Road, Wuhan East Lake High-tech Development Zone, Hubei 430075, China
| | - Philip Jones
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blv., Houston 77030, TX, USA
| | - Michael A Curran
- Department of Immunology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blv., Houston 77030, TX, USA; The University of Texas MD Anderson UTHealth Graduate School of Biochemical Sciences, Immunology Program, 1515 Holcombe Blv., Houston 77030, TX, USA
| | - M Emilia Di Francesco
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blv., Houston 77030, TX, USA.
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8
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Kicsák M, Mándi A, Varga S, Herczeg M, Batta G, Bényei A, Borbás A, Herczegh P. Tricyclanos: conformationally constrained nucleoside analogues with a new heterotricycle obtained from a d-ribofuranose unit. Org Biomol Chem 2019; 16:393-401. [PMID: 29090729 DOI: 10.1039/c7ob02296d] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A novel type of nucleoside analogue in which the sugar part is replaced by a new tricycle, 3,7,10-trioxa-11-azatricyclo[5.3.1.05,11]undecane has been prepared by substrate-controlled asymmetric synthesis. 1,5-Dialdehydes obtained from properly protected or unprotected uridine, ribothymidine, cytidine, inosine, adenosine and guanosine by metaperiodate oxidation reacted readily with tris(hydroxymethyl)aminomethane to provide the corresponding tricyclic derivatives with three new stereogenic centers. Through a double cyclisation cascade process the tricyclic compounds were obtained in good to high yields, with very high diastereoselectivity. Formation of one stereoisomer, out of the eight possible, was observed in all cases. The absolute configuration of the new stereotriad-containing tricyclic systems was aided by conventional NMR experiments followed by chemical shift calculations using an X-ray crystal structure as reference that was in good agreement with H-H distances obtained from a new ROESY NMR method. The synthesis was compatible with silyl, trityl and dimethoxytrityl protecting groups. A new reagent mixture containing ZnCl2, Et3SiH and hexafluoroisopropanol was developed for detritylation of the acid-sensitive tricyclano nucleosides.
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Affiliation(s)
- Máté Kicsák
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.
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9
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Utley LM, Maldonado J, Awad AM. A practical synthesis of xylo- and arabinofuranoside precursors by diastereoselective reduction using Corey-Bakshi-Shibata catalyst. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:20-34. [PMID: 29336673 DOI: 10.1080/15257770.2017.1414240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Corey-Bakshi-Shibata (CBS) catalyst provides an efficient mechanism to reduce ketones and achieve desired enantiopure alcohols. Herein, the diastereoselective reduction of C-2' and C-3'-keto ribofuranoside derivatives to the corresponding arabino- and xylofuranosides in greater than 95% diastereomeric excess is reported. The stereo-directed substitution with an azido group as well as the synthesis of prodrugs cytarabine and vidarabine are also described. The reported strategy offers superior diastereoselectivity, shorter reaction times, and obviates cooling required with comparable protocols involving achiral reductants.
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Affiliation(s)
- Lynn M Utley
- a Department of Chemistry , California State University Channel Islands , Camarillo , California , USA
| | - Jessica Maldonado
- a Department of Chemistry , California State University Channel Islands , Camarillo , California , USA
| | - Ahmed M Awad
- a Department of Chemistry , California State University Channel Islands , Camarillo , California , USA
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10
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Shirinfar B, Ahmed N. Chemical Glycosylations for the Synthesis of Building Units of Post-Translational Modifications. Helv Chim Acta 2017. [DOI: 10.1002/hlca.201700226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Bahareh Shirinfar
- School of Chemistry; University of Bristol; Bristol BS8 1TS United Kingdom
- Organic Chemistry Institute; University of Zürich; Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Nisar Ahmed
- School of Chemistry; University of Bristol; Bristol BS8 1TS United Kingdom
- Organic Chemistry Institute; University of Zürich; Winterthurerstrasse 190 8057 Zürich Switzerland
- School of Chemistry; Cardiff University; Cardiff CF10 3AT United Kingdom
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11
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Someya H, Itoh T, Aoki S. Synthesis of Disaccharide Nucleosides Utilizing the Temporary Protection of the 2',3'-cis-Diol of Ribonucleosides by a Boronic Ester. Molecules 2017; 22:E1650. [PMID: 28974027 PMCID: PMC6151833 DOI: 10.3390/molecules22101650] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 09/24/2017] [Accepted: 09/29/2017] [Indexed: 11/16/2022] Open
Abstract
Disaccharide nucleosides are an important class of natural compounds that have a variety of biological activities. In this study, we report on the synthesis of disaccharide nucleosides utilizing the temporary protection of the 2',3'-cis-diol of ribonucleosides, such as adenosine, guanosine, uridine, 5-metyluridine, 5-fluorouridine and cytidine, by a boronic ester. The temporary protection of the above ribonucleosides permits the regioselective O-glycosylation of the 5'-hydroxyl group with thioglycosides using a p-toluenesulfenyl chloride (p-TolSCl)/silver triflate (AgOTf) promoter system to afford the corresponding disaccharide nucleosides in fairly good chemical yields. The formation of a boronic ester prepared from uridine and 4-(trifluoromethyl)phenylboronic acid was examined by ¹H, 11B and 19F NMR spectroscopy.
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Affiliation(s)
- Hidehisa Someya
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| | - Taiki Itoh
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| | - Shin Aoki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
- Imaging Frontier Center, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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12
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Abstract
Oligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2'-, 3'-, and 5'-positions of the sugar moieties, and the internucleotide phospho-linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Geeta Meher
- Spring Bank Pharmaceuticals, Inc, Milford, Massachusetts
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13
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Soltani Rad MN, Behrouz S, Asrari Z, Khalafi-Nezhad A. A simple and regioselective one-pot procedure for the direct N-acylation of some purine and pyrimidine nucleobases via carboxylic acids using cyanuric chloride. MONATSHEFTE FUR CHEMIE 2014. [DOI: 10.1007/s00706-014-1270-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Pulido J, Sobczak AJ, Balzarini J, Wnuk SF. Synthesis and cytostatic evaluation of 4-N-alkanoyl and 4-N-alkyl gemcitabine analogues. J Med Chem 2013; 57:191-203. [PMID: 24341356 DOI: 10.1021/jm401586a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The coupling of gemcitabine with functionalized carboxylic acids (C9-C13) or reactions of 4-N-tosylgemcitabine with the corresponding alkyl amines afforded 4-N-alkanoyl and 4-N-alkyl gemcitabine derivatives. The analogues with a terminal hydroxyl group on the alkyl chain were efficiently fluorinated under conditions that are compatible with protocols for (18)F labeling. The 4-N-alkanoylgemcitabines showed potent cytostatic activities in the low nanomolar range against a panel of tumor cell lines, whereas cytotoxicity of the 4-N-alkylgemcitabines were in the low micromolar range. The cytotoxicity for the 4-N-alkanoylgemcitabine analogues was reduced approximately by 2 orders of magnitude in the 2'-deoxycytidine kinase (dCK)-deficient CEM/dCK(-) cell line, whereas cytotoxicity of the 4-N-alkylgemcitabines was only 2-5 times lower. None of the compounds acted as efficient substrates for cytosolic dCK; therefore, the 4-N-alkanoyl analogues need to be converted first to gemcitabine to display a significant cytostatic potential, whereas 4-N-alkyl derivatives attain modest activity without measurable conversion to gemcitabine.
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Affiliation(s)
- Jesse Pulido
- Department of Chemistry and Biochemistry, ‡Department of Environmental and Occupational Health, Florida International University , Miami, Florida 33199, United States
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15
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Samuels ER, McNary J, Aguilar M, Awad AM. Effective synthesis of 3'-deoxy-3'-azido nucleosides for antiviral and antisense ribonucleic guanidine (RNG) applications. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2013; 32:109-23. [PMID: 23473099 DOI: 10.1080/15257770.2013.766752] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Two synthetic routes to 3'-deoxy-3'-azido nucleosides are described, one toward the synthesis of 3'-deoxy-3'-azidouridine and a second toward 3'-deoxy-3'-azidocytidine. The target compounds may serve as precursors to provide building blocks for use in automated synthesis of guanidine-linked RNA analogs (RNG) or oligonucleotide N3'→P5' phosphoramidates. Moreover, the synthetic approaches are adaptable to the general synthesis of 3'-substituted 3'-deoxynucleosides for development of new antiviral drugs.
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Affiliation(s)
- Eric R Samuels
- Chemistry Program, California State University Channel Islands, Camarillo, CA 93012, USA
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16
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Kamei T, Fukaminato T, Tamaoki N. A photochromic ATP analogue driving a motor protein with reversible light-controlled motility: controlling velocity and binding manner of a kinesin-microtubule system in an in vitro motility assay. Chem Commun (Camb) 2012; 48:7625-7. [PMID: 22735457 DOI: 10.1039/c2cc33552b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We synthesized two photochromic ATP analogues (ATP-Azos) featuring azobenzene derivatives tethered at the 2' position of the ribose ring. In the presence of the ATP-Azo tethering p-tert-butylazobenzene, we observed reversible photo-control of the motility, velocity and binding manner, of a kinesin-microtubule system in an in vitro motility assay.
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Affiliation(s)
- Takashi Kamei
- Research Institute for Electronic Science, Hokkaido University, N20, W10, Kita-ku, Sapporo, Hokkaido, Japan
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17
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Takagi K, Sugimoto S, Yamakado R, Nobuke K. Self-Assembly of Oligothiophene Chromophores by m-Calix[3]amide Scaffold. J Org Chem 2011; 76:2471-8. [DOI: 10.1021/jo102160x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Koji Takagi
- Department of Materials Science and Engineering, Nagoya Institute of Technology Gokiso, Showa, Nagoya 466-8555, Japan
| | - Shinri Sugimoto
- Department of Materials Science and Engineering, Nagoya Institute of Technology Gokiso, Showa, Nagoya 466-8555, Japan
| | - Ryohei Yamakado
- Department of Materials Science and Engineering, Nagoya Institute of Technology Gokiso, Showa, Nagoya 466-8555, Japan
| | - Katsuya Nobuke
- Department of Materials Science and Engineering, Nagoya Institute of Technology Gokiso, Showa, Nagoya 466-8555, Japan
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18
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Sobkowski M. A convenient protection for 4-oxopyrimidine moieties in nucleosides by the pivaloyl group. ACTA ACUST UNITED AC 2010. [DOI: 10.1135/cccc2009084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Application of the pivaloyl group as a protection for the N3 position of thymidine and uridine was investigated. Pivaloylation of thymidine is a very rapid reaction proceeding under mild conditions with excellent regioselectivity for sugar or thymine moiety, depending on the amines used. Several pivaloylated thymidine derivatives were obtained by treatment of unprotected thymidine with pivaloyl chloride under various experimental conditions. Stability of the N3-pivaloyl protecting group under basic and acidic conditions was evaluated and the conditions for its selective removal were found.
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Rigoli JW, Østergaard ME, Canady KM, Guenther DC, Hrdlicka PJ. Selective deacylation of peracylated ribonucleosides. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.01.147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Gupta P, Maity J, Shakya G, Prasad AK, Parmar VS, Wengel J. Synthesis and hybridization studies of α-configured arabino nucleic acids. Org Biomol Chem 2009; 7:2389-401. [DOI: 10.1039/b905019c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Odadzic D, Engels JW. Different strategies for the synthesis of 2'-O-aminoethyl adenosine building blocks. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:873-7. [PMID: 18058499 DOI: 10.1080/15257770701505295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The chemical modification of the 2'-O-position of nucleosides proved to be of great importance for the RNA stability. Greater stability of RNA duplexes allows a longer half life in the cell and, therefore, a better effect of RNA Interference. Here we investigated the synthesis of 2'-O-aminoethyl adenosine as a cationic modified building block.
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Affiliation(s)
- Dalibor Odadzic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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22
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Prasad AK, Kumar V, Maity J, Wang Z, Ravikumar VT, Sanghvi YS, Parmar VS. Benzoyl Cyanide: A Mild and Efficient Reagent for Benzoylation of Nucleosides. SYNTHETIC COMMUN 2006. [DOI: 10.1081/scc-200051693] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ashok K. Prasad
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi, India
| | - Vineet Kumar
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi, India
| | - Jyotirmoy Maity
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi, India
| | - Zhiwei Wang
- b ISIS Pharmaceuticals Inc. , Carlsbad, California, USA
| | | | - Yogesh S. Sanghvi
- b ISIS Pharmaceuticals Inc. , Carlsbad, California, USA
- c Rasayan Inc. , 2802 Crystal Ridge Road, Encinitas, CA, 92024, USA
| | - Virinder S. Parmar
- a Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi, India
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