1
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Domon K, Puripat M, Fujiyoshi K, Hatanaka M, Kawashima SA, Yamatsugu K, Kanai M. Catalytic Chemoselective O-Phosphorylation of Alcohols. ACS CENTRAL SCIENCE 2020; 6:283-292. [PMID: 32123747 PMCID: PMC7047436 DOI: 10.1021/acscentsci.9b01272] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Indexed: 05/16/2023]
Abstract
Phosphorylation of alcohols is a fundamentally important reaction in both life science and physical science. Product phosphate monoesters play key roles in living organisms, natural products, pharmaceuticals, and organic materials. Most of the chemical methods to date for synthesizing phosphate monoesters, however, require multistep sequences or are limited to specific types of substrates possibly due to harsh conditions. An alternative way to enable the simple production of phosphate monoesters from highly functionalized precursor alcohols is, thus, highly desired. We report herein a catalytic phosphorylation of alcohols with high functional group tolerance using tetrabutylammonium hydrogen sulfate (TBAHS) and phosphoenolpyruvic acid monopotassium salt (PEP-K) as the catalyst and phosphoryl donor, respectively. This method enables the direct introduction of a nonprotected phosphate group to the hydroxy group of a diverse menu of alcohol substrates, including functionalized small molecules, carbohydrates, and unprotected peptides. Nuclear magnetic resonance, mass spectrometric, and density functional theory analyses suggest that an unprecedented mixed anhydride species, generated from PEP-K and TBAHS, acts as an active phosphoryl donor in this reaction. This operationally simple and chemoselective catalytic phosphorylation allows for the efficient production of densely functionalized O-phosphorylated compounds, which are useful in diverse fields including biology and medicine.
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Affiliation(s)
- K. Domon
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. Puripat
- Institute
for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - K. Fujiyoshi
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. Hatanaka
- Institute
for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
- Graduate
School of Science and Technology, Data Science Center, NAIST, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - S. A. Kawashima
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - K. Yamatsugu
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. Kanai
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Lee D, Switzer C. DNA duplex stability of the thio-iso-guanine•methyl-iso-Cytosine base pair. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 34:424-32. [PMID: 25965331 DOI: 10.1080/15257770.2015.1013127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We report the synthesis, incorporation into oligonucleotides, and base-pairing properties of the 2-thio-variant of iso-guanine. Iso-guanine is the purine component of a nonstandard base pair with 5-methyl-iso-cytosine. The 2-thio-iso-guanine • 5-methyl-iso-cytosine base pair is found to have similar stability to an adenine • thymine pair.
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Affiliation(s)
- Dongkye Lee
- a Department of Chemistry , University of California , Riverside , Riverside , California
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3
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Clément B, Molin DG, Jérôme C, Lecomte P. Synthesis of polyphosphodiesters by ring-opening polymerization of cyclic phosphates bearing allyl phosphoester protecting groups. ACTA ACUST UNITED AC 2015. [DOI: 10.1002/pola.27732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Benoït Clément
- Center for Education and Research on Macromolecules (CERM); University of Liège; B6a, Sart-Tilman 4000 Liège Belgium
| | - Daniel G. Molin
- BioMIMedics; Interreg EMR IV-A Consortium; Lead Partner Maastricht University; Universiteitssingel 50 6229ER Maastricht The Netherlands
| | - Christine Jérôme
- Center for Education and Research on Macromolecules (CERM); University of Liège; B6a, Sart-Tilman 4000 Liège Belgium
| | - Philippe Lecomte
- Center for Education and Research on Macromolecules (CERM); University of Liège; B6a, Sart-Tilman 4000 Liège Belgium
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4
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Synthesis of new biocarrier–nucleotide systems for cellular delivery in bacterial auxotrophic strains. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.09.096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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6
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Hernández-Rodríguez M, Xie J, Osornio YM, Krishnamurthy R. Mapping the landscape of potentially primordial informational oligomers: (3'→2')-D-phosphoglyceric acid linked acyclic oligonucleotides tagged with 2,4-disubstituted 5-aminopyrimidines as recognition elements. Chem Asian J 2011; 6:1252-62. [PMID: 21387563 DOI: 10.1002/asia.201000828] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Indexed: 11/09/2022]
Abstract
The (3'→2')-phosphodiester glyceric acid backbone containing an acyclic oligomer tagged with 2,4-disubstituted pyrimidines as alternative recognition elements have been synthesized. Strong cross-pairing of a 2,4-dioxo-5-aminopyrimidine hexamer, rivaling locked nucleic acid (LNA) and peptide nucleic acid (PNA), with complementary adenine-containing DNA and RNA sequences was observed. The corresponding 2,4-diamino- and 2-amino-4-oxo-5-aminopyrimidine-tagged oligomers were synthesized, but difficulties in deprotection, purification, and isolation thwarted further investigations. The acyclic phosphate backbone structure of the protected oligomer seems to be prone to an eliminative degradation owing to the acidic hydrogen at the 2'-position--an arrangement that renders the oligomer vulnerable to the conditions used for the removal of the protecting groups on the heterocyclic recognition element. However, the free oligomers seem to be stable under the conditions investigated.
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Affiliation(s)
- Marcos Hernández-Rodríguez
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA-92037, USA
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7
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Cvetovich RJ. Hydrogen Peroxide Oxidation of Phosphite Triesters in Oligonucleotide Syntheses. Org Process Res Dev 2010. [DOI: 10.1021/op900044z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Raymond J. Cvetovich
- Department of Process Research, Merck Research Laboratories, Rahway, New Jersey 07065, U.S.A
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8
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Patrone JD, Yao J, Scott NE, Dotson GD. Selective inhibitors of bacterial phosphopantothenoylcysteine synthetase. J Am Chem Soc 2009; 131:16340-1. [PMID: 19902973 PMCID: PMC2787235 DOI: 10.1021/ja906537f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial phosphopantothenolycysteine synthetase (PPCS) catalyzes the formation of phosphopantothenoylcysteine (PPC) from (R)-phosphopantothenate, l-cysteine, and cytidine-5'-triphosphate (CTP) and has been shown to be essential for growth and survival. The reaction proceeds through a phosphopantothenoyl cytidylate, mixed anhydride intermediate. Both structural and kinetic characterization studies on PPCS have shown differences in the nucleobase binding site between the bacterial and human enzyme. We report for the first time the design and synthesis of mimics of the phosphopantothenoyl cytidylate, which proved to be potent inhibitors of PPCS. These compounds were evaluated in vitro against PPCS from human and several species of bacteria and showed marked selectivity (up to 1000-fold) toward the bacterial enzymes. A phosphodiester intermediate mimic was the most potent of the compounds synthesized and displayed slow-onset, tight-binding kinetics toward E. faecalis PPCS.
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Affiliation(s)
- James D. Patrone
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
| | - Jiangwei Yao
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
| | - Nicole E. Scott
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
| | - Garry D. Dotson
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065
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9
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Brady PB, Morris EM, Fenton OS, Sculimbrene BR. Efficient catalyst turnover in the phosphitylation of alcohols with phosphoramidites. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2008.12.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Utagawa E, Ohkubo A, Sekine M, Seio K. Synthesis of branched oligonucleotides with three different sequences using an oxidatively removable tritylthio group. J Org Chem 2007; 72:8259-66. [PMID: 17900140 DOI: 10.1021/jo071173a] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We synthesized a three-way branched oligodeoxynucleotide (ODN) 30-mer using a new branch unit with acid-labile DMTr and oxidatively cleavable TrS groups as orthogonal protecting groups. The branched ODN was successfully synthesized using 5-[3,5-bis(trifluoromethyl)phenyl]-1H-tetrazole and (2R,8aS)-(+)-(camphorylsulfonyl)oxaziridine as the activator of phosphoramidite units and the oxidizing reagent, respectively. We also found that the TrS group was orthogonal to the Lev, TBDMS, and Fmoc groups. These results indicate the possibility of the synthesis of more complex four- and five-way branched ODNs by the combined use of DMTr, TrS, Lev, TBDMS, and Fmoc groups.
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Affiliation(s)
- Eri Utagawa
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
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11
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Prakash TP, Püschl A, Manoharan M. N,N'-Bis-(2-(cyano)ethoxycarbonyl)-2-methyl-2-thiopseudourea: a guanylating reagent for synthesis of 2'-O-[2-(Guanidinium)ethyl]-modified oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:149-59. [PMID: 17365794 DOI: 10.1080/15257770601112705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A guanylating reagent, N,N'-bis-(2-(cyano)ethoxycarbonyl)-2-thiopseudourea, was synthesized and used for synthesis of 2'-O-[2-(guanidinium)ethyl] (2'-O-GE) modified oligonucleotides. A convenient deprotection method for the 2'-O-GE oligonucleotides was developed.
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Affiliation(s)
- Thazha P Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals Inc., Carlsbad, California 92008. USA
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12
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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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13
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Gasparutto D, Cognet S, Roussel S, Cadet J. Synthesis of a convenient thymidine glycol phosphoramidite monomer and its site-specific incorporation into DNA fragments. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 24:1831-42. [PMID: 16438051 DOI: 10.1080/15257770500267279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
An original phosphoramidite building block of the thymidine glycol lesion has been prepared taking into account the additional diol function and the high lability of this oxidatively induced nucleobase damage. Then the modified nucleoside was site-specifically inserted into DNA fragments by solid support assembling followed by a "one-step" mild final deprotection treatment.
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Affiliation(s)
- Didier Gasparutto
- Labratoire des Lésions des Acides Nucléiques, Service Chimie Inorganique Biologique, UMR-E3 CEA-UJF, DRFMC, CEA Grenoble, France.
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14
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Dahl BM, Henriksen U, Dahl O. Improved synthesis of oligonucleotides with an allylic backbone. Oligonucleotides containing acyclic, achiral nucleoside analogues: N-1 or N-9-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]nucleobases. Org Biomol Chem 2006; 4:1115-23. [PMID: 16525556 DOI: 10.1039/b517504f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An improved phosphoramidite method is described to prepare oligonucleotides modified with the acyclic, achiral monomers 1. Examination of dimers, prepared on solid support or in solution, showed that phosphortriester dimers containing the allylic unit 1 were unstable towards bases, whereas phosphordiester dimers were stable. Phosphordiester dimers were obtained by replacing cyanoethyl phosphoramidites 2 with phosphoramidites 3, which gave phosphordiesters directly upon oxidation. The phosphordiester dimers were found to be stable towards capping and oxidation, but were somewhat labile towards acids. By reducing the contact time to acids during detritylation it was possible to prepare oligonucleotides containing 4 or 8 modified A, G or T units. The modified oligonucleotides hybridized to complementary DNA and RNA, although with reduced affinity (DeltaT(m) per modification -1 to -5 degrees C).
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Affiliation(s)
- Britta M Dahl
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark
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15
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Nitromethane as a scavenger of acrylonitrile in the deprotection of synthetic oligonucleotides. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.04.066] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Prakash TP, Püschl A, Lesnik E, Mohan V, Tereshko V, Egli M, Manoharan M. 2'-O-[2-(guanidinium)ethyl]-modified oligonucleotides: stabilizing effect on duplex and triplex structures. Org Lett 2005; 6:1971-4. [PMID: 15176796 DOI: 10.1021/ol049470e] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] Oligonucleotides with a novel 2'-O-[2-(guanidinium)ethyl] (2'-O-GE) modification have been synthesized using a novel protecting group strategy for the guanidinium group. This modification enhances the binding affinity of oligonucleotides to RNA as well as duplex DNA (DeltaT(m) 3.2 degrees C per modification). The 2'-O-GE modified oligonucleotides exhibited exceptional resistance to nuclease degradation. The crystal structure of a palindromic duplex formed by a DNA oligonucleotide with a single 2'-O-GE modification was solved at 1.16 A resolution.
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Affiliation(s)
- Thazha P Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA
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17
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Kulesza A, Frank C, Aebi M, Vasella A. Synthesis of Stable Dolichylphosphomannose Analogues. Helv Chim Acta 2004. [DOI: 10.1002/hlca.200490278] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Tomar RS, Joseph TJ, Murthy ASR, Yadav DV, Subbaiah G, Krishna Reddy KVSR. Identification and characterization of major degradation products of risperidone in bulk drug and pharmaceutical dosage forms. J Pharm Biomed Anal 2004; 36:231-5. [PMID: 15351071 DOI: 10.1016/j.jpba.2004.05.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2004] [Revised: 05/19/2004] [Accepted: 05/25/2004] [Indexed: 11/24/2022]
Abstract
Acid, base and oxygen stability of risperidone, a novel anti-psychotic drug, has been evaluated storing the sample in solution phase. One of the major degradation products has been identified and characterized by using techniques namely IR, MS and NMR after isolation by preparative LC. The other major degradation product has been identified with help of MS/MS data and by co-eluting in analytical LC with the available standard. The effect of acid and base resulted in the formation of hydroxy risperidone and the effect of oxygen lead to the formation of N-oxide of risperidone. The two major degradation products in the dosage forms were also characterized as 9-hydroxy risperidone and N-oxide of risperidone, after enrichment through preparative LC, by LC-MS/MS and HPLC. Structural elucidation of degradation product leading to the formation of N-oxide of risperidone is discussed in detail.
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Affiliation(s)
- Rajesh Singh Tomar
- Analytical Development Laboratory, Torrent Research Center, Bhat, Gandhinagar, Gujarat 382428, India
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19
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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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20
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Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)01104-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Prhavc M, Prakash TP, Minasov G, Cook PD, Egli M, Manoharan M. 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modified oligonucleotides: symbiosis of charge interaction factors and stereoelectronic effects. Org Lett 2003; 5:2017-20. [PMID: 12790517 DOI: 10.1021/ol0340991] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] Oligonucleotides with a novel, 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] (2'-O-DMAEOE) modification have been synthesized. This modification, a cationic analogue of the 2'-O-(2-methoxyethyl) (2'-O-MOE) modification, exhibits high binding affinity to target RNA (but not to DNA) and exceptional resistance to nuclease degradation. Analysis of the crystal structure of a self-complementary oligonucleotide containing a single 2'-O-DMAEOE modification explains the importance of charge factors and gauche effects on the observed antisense properties. 2'-O-DMAEOE modified oligonucleotides are ideal candidates for antisense drugs.
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Affiliation(s)
- Marija Prhavc
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA
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22
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Boesen T, Pedersen DS, Nielsen BM, Petersen AB, Henriksen U, Dahl BM, Dahl O. Oligonucleotides containing a new type of acyclic, achiral nucleoside analogue: 1-[3-hydroxy-2-(hydroxymethyl)prop-1-enyl]thymine. Bioorg Med Chem Lett 2003; 13:847-50. [PMID: 12617905 DOI: 10.1016/s0960-894x(03)00008-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
An achiral, acyclic nucleoside analogue has been incorporated once or twice in oligodeoxyribonucleotides by the phosphoramidite method, and conditions found which allow deprotection of the oligonucleotides containing a sensitive modified allylic unit. The binding affinity of the modified oligonucleotides towards complementary DNA and RNA was reduced compared to unmodified DNA (DeltaT(m) -2 to -6.5 degrees C). An oligonucleotide with two modifications at the 3'-end showed considerable resistance towards cleavage with a 3'-exonuclease.
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Affiliation(s)
- Thomas Boesen
- Department of Chemistry, The H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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23
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Prakash TP, Kawasaki AM, Lesnik EA, Owens SR, Manoharan M. 2'-O-[2-(amino)-2-oxoethyl] oligonucleotides. Org Lett 2003; 5:403-6. [PMID: 12583729 DOI: 10.1021/ol027131k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text] Oligonucleotides with novel modifications, 2'-O-[2-(amino)-2-oxoethyl] (2'-O-NAc), 2'-O-[2-(methylamino)-2-oxoethyl] (2'-O-NMAc), 2'-O-[2-(dimethylamino)-2-oxoethyl] (2'-O-DMAc), and 2'-O-[2-[[2-(dimethylamino)ethyl]amino]-2-oxoethyl] (2'-O-DMAEAc), have been synthesized. These modified oligonucleotides exhibit high binding affinity to complementary RNA (and not to DNA) and considerably enhance the nuclease stability of oligonucleotides with t(1/2) > 24 h.
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Affiliation(s)
- Thazha P Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals Inc., 2292 Faraday Avenue, Carlsbad, California 92008, USA
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24
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Prakash TP, Kawasaki AM, Fraser AS, Vasquez G, Manoharan M. Synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] modified nucleosides and oligonucleotides. J Org Chem 2002; 67:357-69. [PMID: 11798305 DOI: 10.1021/jo0103975] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A versatile synthetic route has been developed for the synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] (abbreviated as 2'-O-DMAOE) modified purine and pyrimidine nucleosides and their corresponding nucleoside phosphoramidites and solid supports. To synthesize 2'-O-DMAOE purine nucleosides, the key intermediate B (Scheme 1) was obtained from the 2'-O-allyl purine nucleosides (13a and 15) via oxidative cleavage of the carbon-carbon bond to the corresponding aldehydes followed by reduction. To synthesize pyrimidine nucleosides, opening the 2,2'-anhydro-5-methyluridine 5 with the borate ester of ethylene glycol gave the key intermediate B. The 2'-O-(2-hydroxyethyl) nucleosides were converted, in excellent yield, by a regioselective Mitsunobu reaction, to the corresponding 2'-O-[2-[(1,3-dihydro-1,3-dioxo-2H-isoindol-2-yl)oxy]ethyl] nucleosides (18, 19, and 20). These compounds were subsequently deprotected and converted into the 2'-O-[2-[(methyleneamino)oxy]ethyl] derivatives (22, 23, and 24). Reduction and a second reductive amination with formaldehyde yielded the corresponding 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] nucleosides (25, 26, and 27). These nucleosides were converted to their 3'-O-phosphoramidites and controlled-pore glass solid supports in excellent overall yield. Using these monomers, modified oligonucleotides containing pyrimidine and purine bases were synthesized with phosphodiester, phosphorothioate, and both linkages (phosphorothioate and phosphodiester) present in the same oligonucleotide as a chimera in high yields. The oligonucleotides were characterized by HPLC, capillary gel electrophoresis, and ESMS. The effect of this modification on the affinity of the oligonucleotides for complementary RNA and on nuclease stability was evaluated. The 2'-O-DMAOE modification enhanced the binding affinity of the oligonucleotides for the complementary RNA (and not for DNA). The modified oligonucleotides that possessed the phosphodiester backbone demonstrated excellent resistance to nuclease with t(1/2) > 24 h.
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Affiliation(s)
- Thazha P Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals Inc., 2292 Faraday Avenue, Carlsbad, California 92008, USA
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25
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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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26
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Kataoka M, Hattori A, Okino S, Hyodo M, Asano M, Kawai R, Hayakawa Y. Ethyl(methyl)dioxirane as an efficient reagent for the oxidation of nucleoside phosphites into phosphates under nonbasic anhydrous conditions. Org Lett 2001; 3:815-8. [PMID: 11263889 DOI: 10.1021/ol000364w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A convenient method for the oxidation of nucleoside phosphites into phosphates under nonbasic and nonaqueous conditions using commercially available ethyl(methyl)dioxirane has been developed. This oxidation is effective with both N-protected and N-unprotected strategies.
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Affiliation(s)
- M Kataoka
- Laboratory of Bioorganic Chemistry, Graduate School of Human Informatics, Nagoya University, Chikusa, Nagoya 464-8601, Japan
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27
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Guzaev AP, Manoharan M. 2-Benzamidoethyl group--a novel type of phosphate protecting group for oligonucleotide synthesis. J Am Chem Soc 2001; 123:783-93. [PMID: 11456611 DOI: 10.1021/ja0016396] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A number of 5'-O-(4,4'-dimethoxytrityl)thymidine N,N-diisopropylamino phosphoramidites protected at P(III) with derivatives of 2-benzamidoethanol were synthesized and incorporated into synthetic oligonucleotides. Depending on substitution patterns at the alkyl chain, amido group, and phenyl ring, the time required for removal of these protecting groups using concentrated ammonium hydroxide varied from 48 h at 55 degrees C to 25 min at 25 degrees C. Of the 11 groups studied, 2-[N-isopropyl-N- (4-methoxybenzoyl)amino]ethyl- (H) and omega-(thionobenzoylamino)alkyl protections (I and K) were most easily removed. Derivatives of the 2-[N-methyl-N-benzoylamino]ethyl group (E-G) demonstrated moderate stability, but those of the 2-(N-benzoylamino)ethyl group (A-C) were the most stable. For the most reactive group, H, a phosphitylating reagent, bisamidite 60, was synthesized and used in the preparation of four deoxynucleoside phosphoramidites 28 and 65-67, plus the 2'-O-(2-methoxyethyl)-5-methyluridine phosphoramidite 68. All of these novel building blocks were successfully tested in the preparation of natural, 20-mer oligonucleotides and their phosphorothioate analogues. With the model phosphotriester 37, the mechanism of deprotection was studied and revealed, in the case of group H, a pH-independent formation of the 2-oxazolinium cation 47. Under aqueous conditions, 47 gave 54, which in turn was converted in the presence of ammonia to a number of identified products. It is important to note that none of the products formed was reactive toward the oligonucleotide backbone or nucleic bases. Thus, a general strategy for protection of internucleosidic phosphodiester groups is described, which may also find application in synthetic organic chemistry of phosphorus(III) and (V).
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Affiliation(s)
- A P Guzaev
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 2292 Faraday Ave., Carlsbad, California 92009, USA.
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28
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Sørensen AM, Nielsen P. Synthesis of conformationally restricted dinucleotides by ring-closing metathesis. Org Lett 2000; 2:4217-9. [PMID: 11150203 DOI: 10.1021/ol0067639] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction:see text] The ring-closing metathesis reaction has been used in the synthesis of conformationally restricted dinucleotides as well as a 3'-nucleotide analogue. From bis-allylic nucleoside phosphates obtained from simple nucleoside precursors, the synthesis of unsaturated cyclophosphates has been accomplished using either Grubbs' catalyst or an improved analogue. Hereby, the conformational freedom of the nucleic acid phosphordiester linkage has been efficiently constrained.
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Affiliation(s)
- A M Sørensen
- Department of Chemistry, University of Southern Denmark, Odense University, 5230 Odense M, Denmark
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29
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Prakash TP, Manoharan M, Kawasaki AM, Lesnik EA, Owens SR, Vasquez G. 2'-O-[2-[N,N-(dialkyl)aminooxy]ethyl]-modified antisense oligonucleotides. Org Lett 2000; 2:3995-8. [PMID: 11112626 DOI: 10.1021/ol006555g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure] Oligonucleotides with two novel modifications, 2'-O-¿2-[N, N-(dimethyl)aminooxy]ethyl¿ (2'-O-DMAOE) and 2'-O-¿2-[N, N-(diethyl)aminooxy]ethyl¿ (2'-O-DEAOE), have been synthesized. These modifications exhibit high binding affinity to target RNA (and not to DNA) and enhance the nuclease stability of oligonucleotides considerably with t(1/2) > 24 h as a phosphodiester.
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Affiliation(s)
- T P Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals Inc., 2292 Faraday Avenue, Carlsbad, California 92008, USA
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30
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A new approach for the synthesis of 3′-deoxy-3′-C-formyl-ribonucleosides and the synthesis of alternating methylene(methylimino) linked phosphodiester backbone oligonucleotides with 2′-OH and 2′-OMe groups. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)01814-1] [Citation(s) in RCA: 4] [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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31
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Prakash TP, Manoharan M, Fraser AS, Kawasaki AM, Lesnik EA, Owens SR. Zwitterionic oligonucleotides with 2′-O-[3-(N,N-dimethylamino)propyl]-RNA modification: synthesis and properties. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)00703-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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