1
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Yasuda T, Ueura D, Nakagomi M, Hanashima S, Peter Slotte J, Murata M. Design, synthesis of ceramide 1-phosphate analogs and their affinity for cytosolic phospholipase A 2 as evidenced by surface plasmon resonance. Bioorg Med Chem Lett 2024; 107:129792. [PMID: 38734389 DOI: 10.1016/j.bmcl.2024.129792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Ceramide 1-phosphate (C1P) is a lipid mediator that specifically binds and activates cytosolic phospholipase A2α (cPLA2α). To elucidate the structure-activity relationship of the affinity of C1P for cPLA2α in lipid environments, we prepared a series of C1P analogs containing structural modifications in the hydrophilic parts and subjected them to surface plasmon resonance (SPR). The results suggested the presence of a specific binding site for cPLA2α on the amide, 3-OH and phosphate groups in C1P structure. Especially, dihydro-C1P exhibited enhanced affinity for cPLA2α, suggesting the hydrogen bonding ability of 3-hydroxy group is important for interactions with cPLA2α. This study helps to understand the influence of specific structural moieties of C1P on the interaction with cPLA2α at the atomistic level and may lead to the design of drugs that regulate cPLA2α activation.
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Affiliation(s)
- Tomokazu Yasuda
- Research Foundation ITSUU Laboratory, C1232, Kanagawa Science Park R&D Building, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| | - Daiki Ueura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Madoka Nakagomi
- Research Foundation ITSUU Laboratory, C1232, Kanagawa Science Park R&D Building, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6A, FIN-20520 Turku, Finland
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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2
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Oka N, Hirabayashi H, Kumada K, Ando K. Synthesis of xanthosine 2-phosphate diesters via phosphitylation of the carbonyl group. Bioorg Med Chem Lett 2021; 54:128439. [PMID: 34748937 DOI: 10.1016/j.bmcl.2021.128439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
O2-Phosphodiesterification of xanthosine has been achieved by a one-pot procedure consisting of the phosphitylation of the 2-carbonyl group of appropriately protected xanthosine derivatives using phosphoramidites and N-(cyanomethyl)dimethylammonium triflate (CMMT), oxidation of the resulting xanthosine 2-phosphite triesters, and deprotection. In addition, a study on the hydrolytic stability of a fully deprotected xanthosine 2-phosphate diester has revealed that it is more stable at higher pH.
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Affiliation(s)
- Natsuhisa Oka
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Japan; Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Japan; Institute for Glyco-core Research (iGCORE), Gifu University 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Hiroki Hirabayashi
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Japan
| | - Kota Kumada
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Japan
| | - Kaori Ando
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Japan.
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3
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Radzikowska E, Kaczmarek R, Korczyński D, Krakowiak A, Mikołajczyk B, Baraniak J, Guga P, Wheeler KA, Pawlak T, Nawrot B. P-stereocontrolled synthesis of oligo(nucleoside N3'→O5' phosphoramidothioate)s - opportunities and limitations. RSC Adv 2020; 10:35185-35197. [PMID: 35515667 PMCID: PMC9056831 DOI: 10.1039/d0ra04987e] [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: 06/05/2020] [Accepted: 09/15/2020] [Indexed: 12/29/2022] Open
Abstract
3'-N-(2-Thio-1,3,2-oxathiaphospholane) derivatives of 5'-O-DMT-3'-amino-2',3'-dideoxy-ribonucleosides (NOTP-N), that bear a 4,4-unsubstituted, 4,4-dimethyl, or 4,4-pentamethylene substituted oxathiaphospholane ring, were synthesized. Within these three series, NOTP-N differed by canonical nucleobases (i.e., AdeBz, CytBz, GuaiBu, or Thy). The monomers were chromatographically separated into P-diastereomers, which were further used to prepare NNPSN' dinucleotides (3), as well as short P-stereodefined oligo(deoxyribonucleoside N3'→O5' phosphoramidothioate)s (NPS-) and chimeric NPS/PO- and NPS/PS-oligomers. The condensation reaction for NOTP-N monomers was found to be 5-6 times slower than the analogous OTP derivatives. When the 5'-end nucleoside of a growing oligomer adopts a C3'-endo conformation, a conformational 'clash' with the incoming NOTP-N monomer takes place, which is a main factor decreasing the repetitive yield of chain elongation. Although both isomers of NNPSN' were digested by the HINT1 phosphoramidase enzyme, the isomers hydrolyzed at a faster rate were tentatively assigned the R P absolute configuration. This assignment is supported by X-ray analysis of the protected dinucleotide DMTdGiBu NPSMeTOAc, which is P-stereoequivalent to the hydrolyzed faster P-diastereomer of dGNPST.
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Affiliation(s)
- Ewa Radzikowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Dariusz Korczyński
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Agnieszka Krakowiak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Barbara Mikołajczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Janina Baraniak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Kraig A Wheeler
- Whitworth University, Department of Chemistry 300 W. Hawthorne Rd. Spokane WA 99251 USA
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 90-363 Łódź Poland
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4
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Seio K, Shiozawa T, Sugiyama D, Ohno K, Tomori T, Masaki Y. 31P NMR Study on the Reactions of Amino Acids and Sugar Derivatives with Pyrophosphorous Acid as a Possible Prebiotic Phosphonylating Agent. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Takashi Shiozawa
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Daiki Sugiyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Kentaro Ohno
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Takahito Tomori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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5
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Hara RI, Yaoita A, Takeda K, Ueki H, Ishii A, Imoto H, Kobayashi S, Sano M, Noro M, Sato K, Wada T. Solid-Phase Synthesis of Fluorinated Analogues of Glycosyl 1-Phosphate Repeating Structures from Leishmania using the Phosphoramidite Method. ChemistryOpen 2018; 7:439-446. [PMID: 29928567 PMCID: PMC5987806 DOI: 10.1002/open.201800030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 01/08/2023] Open
Abstract
Bacterial and protozoan sugar chains contain glycosyl 1-phosphate repeating structures; these repeating structures have been studied for vaccine development. The fluorinated analogues of [β-Gal-(1→4)-α-Man-(1→6)-P-] n , which are glycosyl 1-phosphate repeating structures found in Leishmania, were synthesised using the solid-phase phosphoramidite method. This method has been less extensively studied for the synthesis of glycosyl 1-phosphate units than H-phosphonate chemistry. A stepwise synthesis of a compound containing five such repeating units has been conducted using the phosphoramidite method herein, which is the longest glycosyl 1-phosphate structures to be chemically constructed in a stepwise manner.
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical SciencesTokyo University of Science2641 YamazakiNoda, Chiba278–8510Japan
| | - Aya Yaoita
- Faculty of Pharmaceutical SciencesTokyo University of Science2641 YamazakiNoda, Chiba278–8510Japan
| | - Katsuya Takeda
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Hiroaki Ueki
- Faculty of Pharmaceutical SciencesTokyo University of Science2641 YamazakiNoda, Chiba278–8510Japan
| | - Ayumu Ishii
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Hideyuki Imoto
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Satoshi Kobayashi
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Michi Sano
- Faculty of Pharmaceutical SciencesTokyo University of Science2641 YamazakiNoda, Chiba278–8510Japan
| | - Mihoko Noro
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Kazuki Sato
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical SciencesTokyo University of Science2641 YamazakiNoda, Chiba278–8510Japan
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6
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Hara RI, Kobayashi S, Noro M, Sato K, Wada T. Synthesis and properties of 2-deoxy-2-fluoromannosyl phosphate derivatives. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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van der Es D, Groenia NA, Laverde D, Overkleeft HS, Huebner J, van der Marel GA, Codée JDC. Synthesis of E. faecium wall teichoic acid fragments. Bioorg Med Chem 2016; 24:3893-3907. [PMID: 26993744 DOI: 10.1016/j.bmc.2016.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 10/22/2022]
Abstract
The first synthesis of different Enterococcus faecium wall teichoic acid (WTA) fragments is presented. The structure of these major cell wall components was elucidated recently and it was shown that these glycerolphosphate (GroP) based polymers are built up from -6-(GalNAc-α(1-3)-GalNAc-β(1-2)-GroP)- repeating units. We assembled WTA fragments up to three repeating units in length, in two series that differ in the stereochemistry of the glycerolphosphate moiety. The key GalNAc-GalNAc-GroP synthons, required for the synthesis, were generated from galactosazide building blocks that were employed in highly stereoselective glycosylation reactions to furnish both the α- and β-configured linkages. By comparing the NMR spectra of the synthesized fragments with the isolated material it appears that the hereto undefined stereochemistry of the glycerol phosphate moiety is sn-glycerol-3-phosphate. The generated fragments will be valuable tools to study their immunological activity at the molecular level.
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Affiliation(s)
- Daan van der Es
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Nadia A Groenia
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Diana Laverde
- Division of Pediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Johannes Huebner
- Division of Pediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| | | | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
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8
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Roux L, Canard B, Alvarez K. (R)-9-[2-(Hydroxyphosphinylmethoxy)propyl]adenine as the precursor molecule for antivirals. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.05.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Oka N, Morita Y, Itakura Y, Ando K. Synthesis of inosine 6-phosphate diesters via phosphitylation of the carbonyl oxygen. Chem Commun (Camb) 2014; 49:11503-5. [PMID: 24177564 DOI: 10.1039/c3cc46617e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inosine derivatives bearing a phosphodiester group at the O(6)-position of the nucleobase were synthesized via phosphitylation of the carbonyl oxygen using phosphoramidites activated by non-nucleophilic acidic activators.
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Affiliation(s)
- Natsuhisa Oka
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
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10
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Nakano SI, Uotani Y, Sato Y, Oka H, Fujii M, Sugimoto N. Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules. Nucleic Acids Res 2013; 41:8581-90. [PMID: 23873956 PMCID: PMC3794578 DOI: 10.1093/nar/gkt608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2′-deoxyadenosine and 2′-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO4 and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2′-deoxycytidine lesions form the base pair with guanine while the 2′-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides.
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Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan, Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan, Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1, Okamoto, Higashinada-ku, Kobe, 658-8501, Japan, Molecular Engineering Institute (MEI), Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka, 820-8555, Japan and Department of Environmental and Biological Chemistry, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka, 820-8555, Japan
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11
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Roy B, Lefebvre I, Puy JY, Périgaud C. A facile and effective synthesis of lamivudine 5′-diphosphate. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2010.12.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Crauste C, Périgaud C, Peyrottes S. Synthesis of 2′,3′-Dideoxynucleoside Phosphoesters Using H-Phosphonate Chemistry on Soluble Polymer Support. J Org Chem 2010; 76:997-1000. [DOI: 10.1021/jo1022958] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Céline Crauste
- UMR 5247 CNRS-UM1-UM2, IBMM, Nucleosides & Phosphorylated Effectors Team, University Montpellier 2, cc1705, place E. Bataillon, 34095 Montpellier, France
| | - Christian Périgaud
- UMR 5247 CNRS-UM1-UM2, IBMM, Nucleosides & Phosphorylated Effectors Team, University Montpellier 2, cc1705, place E. Bataillon, 34095 Montpellier, France
| | - Suzanne Peyrottes
- UMR 5247 CNRS-UM1-UM2, IBMM, Nucleosides & Phosphorylated Effectors Team, University Montpellier 2, cc1705, place E. Bataillon, 34095 Montpellier, France
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13
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Munavalli S, Rohrbaugh DK, Berg FJ, Longo FR, Durst HD. Microwave Catalyzed Reactions of H-Dimethylphosphonate with Oxiranes. PHOSPHORUS SULFUR 2010. [DOI: 10.1080/10426500210221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- S. Munavalli
- a Geo-Centers, Inc. , PO Box 68, Gunpowder Branch, APG, MD, 21010
| | - D. K. Rohrbaugh
- b U.S. Army Edgewood Chemical Biological Center , Aberdeen Proving Ground, MD, 21010
| | - F. J. Berg
- b U.S. Army Edgewood Chemical Biological Center , Aberdeen Proving Ground, MD, 21010
| | - F. R. Longo
- a Geo-Centers, Inc. , PO Box 68, Gunpowder Branch, APG, MD, 21010
| | - H. D. Durst
- b U.S. Army Edgewood Chemical Biological Center , Aberdeen Proving Ground, MD, 21010
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14
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Dai Q, Saikia M, Li NS, Pan T, Piccirilli JA. Efficient chemical synthesis of AppDNA by adenylation of immobilized DNA-5'-monophosphate. Org Lett 2010; 11:1067-70. [PMID: 19191584 DOI: 10.1021/ol802815g] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AppDNA is an intermediate in enzyme-catalyzed DNA ligation reactions, and its efficient enzymatic synthesis requires a donor-template duplex of at least 11 base pairs in length. An efficient chemical synthesis of AppDNA with the coupling of an adenosine 5'-phosphorimidazolidate to an immobilized DNA-5'-monophosphate as the key step is described. The adenylation efficiencies of DNA-5'-monophosphate were excellent for oligonucleotides containing less than 11 nucleotides and at least 50% for oligonucleotides containing 15-25 nucleotides.
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Affiliation(s)
- Qing Dai
- Department of Biochemistry & Molecular Biology, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, USA
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15
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Barral K, Priet S, De Michelis C, Sire J, Neyts J, Balzarini J, Canard B, Alvarez K. Synthesis and antiviral activity of boranophosphonate isosteres of AZT and d4T monophosphates. Eur J Med Chem 2010; 45:849-56. [DOI: 10.1016/j.ejmech.2009.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 10/28/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
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16
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Durst HD, Rohrbaugh DK, Munavalli S. Microwave-Assisted Reaction of Dimethyl H-Phosphonate with Cyclohexene and Alkene Oxides. PHOSPHORUS SULFUR 2009. [DOI: 10.1080/10426500802561419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- H. D. Durst
- a U.S. Army Edgewood Chemical Biological Center , Aberdeen Proving Ground, Maryland, USA
| | - D. K. Rohrbaugh
- a U.S. Army Edgewood Chemical Biological Center , Aberdeen Proving Ground, Maryland, USA
| | - S. Munavalli
- b SAIC , Gunpowder Branch, Aberdeen Proving Ground, Maryland, USA
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17
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Ito T, Hayashi A, Kondo A, Uchida T, Tanabe K, Yamada H, Nishimoto SI. DNA hairpins containing a diaminostilbene derivative as a photoinduced electron donor for probing the effects of single-base mismatches on excess electron transfer in DNA. Org Lett 2009; 11:927-30. [PMID: 19170616 DOI: 10.1021/ol802896y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
To investigate the effects of local structural disorder induced by a single-base mismatch on excess electron transfer (EET) in DNA, a novel hairpin DNA containing diaminostilbene (DAS) as a photoinducible electron donor has been developed. It was clearly demonstrated that EET efficiency depends on the electron injection modes from the electron donors and redox properties of the mismatched bases.
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Affiliation(s)
- Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.
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18
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Higashida R, Oka N, Kawanaka T, Wada T. Nucleoside H-boranophosphonates: a new class of boron-containing nucleotide analogues. Chem Commun (Camb) 2009:2466-8. [PMID: 19532858 DOI: 10.1039/b901045a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A study on the synthesis of nucleoside H-boranophosphonates, a new class of nucleotide analogues having a P-->BH(3) and a P-H group, via condensation of the corresponding nucleosides with H-boranophosphonate derivatives is described.
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Affiliation(s)
- Renpei Higashida
- Department of Medical Genome Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
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19
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Sun Q, Edathil JP, Wu R, Smidansky ED, Cameron CE, Peterson BR. One-pot synthesis of nucleoside 5'-triphosphates from nucleoside 5'-H-phosphonates. Org Lett 2008; 10:1703-6. [PMID: 18393512 PMCID: PMC3104733 DOI: 10.1021/ol8003029] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleoside 5'-triphosphates (NTPs) play key roles in biology and medicine. However, these compounds are notoriously difficult to synthesize. We describe a one-pot method to prepare NTPs from nucleoside 5'-H-phosphonate monoesters via pyridinium phosphoramidates, and we used this approach to synthesize ATP, UTP, GTP, CTP, ribavirin-TP, and 6-methylpurine ribonucleoside-TP (6MePTP). Poliovirus RNA-dependent RNA polymerase efficiently employed 6MePTP as a substrate, suggesting that the cognate nucleoside, a poorly understood antiviral agent, may damage viral RNA.
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Affiliation(s)
- Qi Sun
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jocelyn P. Edathil
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Runzhi Wu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Eric D. Smidansky
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Craig E. Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Blake R. Peterson
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045
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Abstract
In this review, a short account of H-phosphonate chemistry and its application to the synthesis of biologically important phosphates and their analogs is given.
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21
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1,1-Dihydroperoxycyclododecane as a new, crystalline non-hygroscopic oxidizer for the chemical synthesis of oligodeoxyribonucleotides. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.10.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Meyer A, Bouillon C, Vidal S, Vasseur JJ, Morvan F. A versatile reagent for the synthesis of 5′-phosphorylated, 5′-thiophosphorylated or 5′-phosphoramidate-conjugated oligonucleotides. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.10.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Dowden J, Brown RS, Moreau C, Galione A, Potter BVL. Chemical synthesis of the novel Ca2+ messenger NAADP. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:513-8. [PMID: 16247981 DOI: 10.1081/ncn-200061786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The first total chemical synthesis of nicotinamide adenine dinucleotide phosphate (beta-NADP, 2) as a single isomer was achieved. This was subsequently converted into the important second messenger nicotinic acid adenine dinucleotide phosphate (p-NAADP) 1 and the identity of this material confirmed by biological evaluation. This flexible synthetic route offers new opportunities for the generation of NAADP 1 analogues that cannot be generated directly from NADP 2 or mainly enzymatic methods.
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Affiliation(s)
- James Dowden
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
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24
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Monteil M, Guenin E, Migianu E, Lutomski D, Lecouvey M. Bisphosphonate prodrugs: synthesis of new aromatic and aliphatic 1-hydroxy-1,1-bisphosphonate partial esters. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.05.053] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Migianu E, Monteil M, Even P, Lecouvey M. Novel approach to nucleoside-5'-(1-hydroxymethylene-1, 1-bisphosphonates): synthesis of new AZT analogues. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:121-33. [PMID: 15822618 DOI: 10.1081/ncn-51890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An efficient synthetic method of nucleoside-5'-(1-hydroxymethylene-1,1-bisphosphonates) is reported here. The procedure was optimized with 3'-protected thymidine and then applied to synthesis of new AZT analogues.
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Affiliation(s)
- Evelyne Migianu
- Laboratoire de Chimie Structurale Biomoléculaire (UMR 7033-CNRS), UFR SMBH, Université Paris 13, Bobigny Cedex, France
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Uzagare MC, Padiya KJ, Salunkhe MM, Sanghvi YS. NBS-DMSO as a nonaqueous nonbasic oxidation reagent for the synthesis of oligonucleotides. Bioorg Med Chem Lett 2004; 13:3537-40. [PMID: 14505665 DOI: 10.1016/s0960-894x(03)00754-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new method for the oxidation of nucleoside phosphite triester into phosphate triester under nonbasic and nonaqueous conditions using NBS-DMSO in CH(3)CN has been developed. The utility of this method for solution- and solid-phase synthesis of oligonucleotide is demonstrated.
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Munavalli S, Rohrbaugh DK, Durst HD. An Unusual Reaction of Dimethyl Azodicarboxylate with H-Dimethylphosphonate. PHOSPHORUS SULFUR 2003. [DOI: 10.1080/10426500390220998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- S. Munavalli
- a Geo-Centers, Inc. , Aberdeen Proving Ground, Maryland
| | - D. K. Rohrbaugh
- b U. S. Army, Edgewood Chemical Biological Center , Aberdeen Proving Ground, Maryland
| | - H. D. Durst
- b U. S. Army, Edgewood Chemical Biological Center , Aberdeen Proving Ground, Maryland
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Munavalli S, Rohrbaugh DK, Durst HD. Unusual Reaction of H-Dimethylphosphonate. PHOSPHORUS SULFUR 2003. [DOI: 10.1080/10426500307815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- S. Munavalli
- a Geo-Centers, Inc. , Aberdeen Proving Ground, Maryland
| | - D. K. Rohrbaugh
- b Edgewood Chemical Biological Center , US Army , Aberdeen Proving Ground, Maryland
| | - H. D. Durst
- b Edgewood Chemical Biological Center , US Army , Aberdeen Proving Ground, Maryland
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29
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Hird GS, Grinstaff MW. Synthesis and characterization of a dianionic carbohydrate-based phospholipid. Chem Phys Lipids 2002; 120:1-7. [PMID: 12426071 DOI: 10.1016/s0009-3084(02)00073-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A novel carbohydrate-based phospholipid containing a phosphatidic acid head group, bis-(2,3-lauroyl)-1-methoxy-5-ribo-phosphatidic acid (DLRPA), was synthesized and characterized by 1H NMR, 13C NMR, and 31P NMR. This molecule is an analog of dilauroyl phosphatidic acid (DLPA). The T(m) of DLRPA decreases with increasing pH in a similar pattern to DLPA, as determined by MDSC. From this thermotropic behavior, the apparent pK(a)s of DLRPA are estimated to be 4 and 8.
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Affiliation(s)
- Geoffrey S Hird
- Department of Chemistry, Paul M. Gross Chemical Laboratory, Duke University and Duke University Medical Center, Durham, NC 27708, USA
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Hayakawa Y. Toward an Ideal Synthesis of Oligonucleotides: Development of a Novel Phosphoramidite Method with High Capability. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.1547] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Rohrbaugh DK, Munavalli S, Wagner GW, Longo FR, Durst HD. Microwave Catalyzed Reaction of H-Dimethylphosphonate with N-(2,3-Epoxypropyl)Phthmide. PHOSPHORUS SULFUR 2001. [DOI: 10.1080/10426500108055109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Rohrbaugh DK, Longo FR, Durst HD, Munavalli S. Microwave Induced and Photocatalyzed Hydrophosphorylation Reactions of Perfluoroolefins. PHOSPHORUS SULFUR 2001. [DOI: 10.1080/10426500108055119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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Manoharan M, Lu Y, Casper MD, Just G. Allyl group as a protecting group for internucleotide phosphate and thiophosphate linkages in oligonucleotide synthesis: facile oxidation and deprotection conditions. Org Lett 2000; 2:243-6. [PMID: 10814292 DOI: 10.1021/ol9910518] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] The allyl group, which serves as a protecting group for an internucleotide bond for both phosphates and phosphorothioates, can be easily removed by good nucleophiles under weakly basic or neutral conditions. For a practical synthesis on solid support, camphorsulfonyloxaziridine was used as the oxidizing agent for synthesizing DNA, while the Beaucage reagent was used for preparing phosphorothioate oligomers. Both types of oligonucleotides were easily deprotected by concentrated ammonium hydroxide containing 2% mercaptoethanol.
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Affiliation(s)
- M Manoharan
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Carlsbad, California 92008, USA.
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