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Grandas A, Marchán V, Debéthune L, Pedroso E. Stepwise solid-phase synthesis of nucleopeptides. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.22. [PMID: 18428976 DOI: 10.1002/0471142700.nc0422s31] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Phosphodiester-linked peptide-oligonucleotide conjugates (nucleopeptides) are obtained by stepwise solid-phase procedures. The peptide is first assembled on a suitably derivatized solid matrix and the oligonucleotide is subsequently elongated at the free hydroxyl group of the linking amino acid. Temporary acid-labile and permanent base-labile protecting groups are combined. Careful choice of the protection scheme is required to prevent and minimize side reactions that may degrade the target molecule.
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Affiliation(s)
- Anna Grandas
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
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Sauerbrei B, Kappes T, Waldmann H. Enzymatic synthesis of peptide conjugates — Tools for the study of biological signal transduction. Top Curr Chem (Cham) 2008. [DOI: 10.1007/bfb0119220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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Kriek NMAJ, Meeuwenoord NJ, van den Elst H, Heus HA, van der Marel GA, Filippov DV. Chemical synthesis of picornaviral protein primers of RNA replication. Org Biomol Chem 2006; 4:3576-86. [PMID: 16990933 DOI: 10.1039/b608544j] [Citation(s) in RCA: 10] [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
Naturally occurring nucleopeptidic replication primers (VPg-pUpU) of poliovirus and coxsackie virus were chemically synthesized. The synthesis was accomplished via block-coupling of two minimally protected fragments of the target structures: a short RNA-nucleopeptide and a longer peptide segment containing diverse side-chain functionalities. The synthetic VPg-pUpU of coxsackie virus was characterized by NMR spectroscopy.
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Affiliation(s)
- Nicole M A J Kriek
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300, RA Leiden, The Netherlands
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Grandas A, Marchán V, Debéthune L, Pedroso E. Stepwise Solid‐Phase Synthesis of Nucleopeptides. ACTA ACUST UNITED AC 2004. [DOI: 10.1002/0471142700.nc0422s16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Stepwise solid phase synthesis of uridylylated viral genome-linked peptides using uridylylated amino acid building blocks. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00042-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Debéthune L, Marchán V, Fàbregas G, Pedroso E, Grandas A. Towards nucleopeptides containing any trifunctional amino acid (II). Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00793-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Jeyaraj DA, Waldmann H. Synthesis of nucleopeptides by an enzyme labile urethane protecting group. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(00)02121-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Moriguchi T, Yanagi T, Kunimori M, Wada T, Sekine M. Synthesis and properties of aminoacylamido-AMP: chemical optimization for the construction of an N-acyl phosphoramidate linkage. J Org Chem 2000; 65:8229-38. [PMID: 11101378 DOI: 10.1021/jo0008338] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the design and synthesis of a new type of aminoacyl-adenylate analogue (aa-AMPN) having an N-acyl phosphoramidate linkage where the oxygen atom of the mixed anhydride bond of aminoacyl-adenylate (aa-AMP) is replaced by an amino group. This new type of aa-AMP analogue is expected to be useful as material for studies on the recognition mechanism of the aminoacylation of tRNA and other biochemical reactions. The condensation of phosphoramidite derivatives of carboxamides with nucleoside derivatives failed, because the activated phosphoramidite derivatives reacted with not only the hydroxyl groups but also another reactive species. An alternative approach was examined by the reaction of 5'-O-phosphoramidite adenosine derivatives with carboxamide derivatives. The TBTr and TSE groups were chosen for protection of the amino group of amino acid amides and the phosphate group, respectively. Detailed studies revealed that the use of 5-(3,5-dinitrophenyl)-1H-tetrazole as an activating catalyst of phosphoramidites resulted in rapid condensation within 10 min to give fully protected aa-AMPN derivatives. No side reaction occurred. Deprotection of these products via a two-step procedure gave aa-AMPN derivatives in good yields. It also turned out that aa-AMPNs thus obtained are stable under both acidic and basic conditions, such as 0.1 M HCl (pH 1.0) and 0.1 M NaOH (pH 13.0).
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Affiliation(s)
- T Moriguchi
- Faculty of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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Affiliation(s)
- S Dey
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, USA
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A Novel Synthesis of Oligonucleotide–Peptide Conjugates with a Base-Labile Phosphate Linker between the Two Components According to the Allyl-Protected Phosphoramidite Strategy. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00376-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Robles J, Beltrán M, Marchán V, Pérez Y, Travesset I, Pedroso E, Grandas A. Towards nucleopeptides containing any trifunctional amino acid. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00815-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Eisele F, Owen DJ, Waldmann H. Peptide conjugates as tools for the study of biological signal transduction. Bioorg Med Chem 1999; 7:193-224. [PMID: 10218812 DOI: 10.1016/s0968-0896(98)00204-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Today, many biological phenomena are being investigated and understood in molecular detail, and organic chemistry is increasingly being directed towards biological phenomena. This review is intended to highlight this interplay of organic chemistry and biology, using biological signal transduction as an example. Lipo-, glyco-, phospho- and nucleoproteins play key roles in the processes whereby chemical signals are passed across cell membranes and further to the cell nucleus. For the study of the biological phenomena associated with these protein conjugates, structurally well-defined peptides containing the characteristic linkage region of the peptide backbone with the lipid, the carbohydrate or the phosphoric acid ester can provide valuable tools. The multi-functionality and pronounced acid- and base-lability of such compounds renders their synthesis a formidable challenge to conventional organic synthesis. However, the recent development of enzymatic protecting groups, provides one of the central techniques which, when coupled with classic chemical synthesis, can provide access to these complex and sensitive biologically relevant peptide conjugates under particularly mild conditions and with high selectivity.
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Affiliation(s)
- F Eisele
- Universität Karlsruhe, Institut für Organische Chemie, Germany
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Filippov D, Kuyl-Yeheskiely E, van der Marel GA, Tesser GI, van Boom JH. Synthesis of a nucleopeptide fragment from poliovirus genome. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)00558-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Jungmann V, Waldmann H. An enzymatic protecting group strategy for the synthesis of nucleopeptides. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(97)10873-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kappes T, Waldmann H. Enzymatic Synthesis of Peptide Conjugates: Tools for the Study of Biological Signal Transduction. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/jlac.199719970504] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Guibourdenche C, Seebach D, Natt F. Use of theWolff Rearrangement of Diazo Ketones from Amino Acids as a synthetic method for the formation of oligonucleo-peptides: A novel approach to chimeric biomolecules. Helv Chim Acta 1997. [DOI: 10.1002/hlca.19970800102] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Bruick RK, Dawson PE, Kent SB, Usman N, Joyce GF. Template-directed ligation of peptides to oligonucleotides. CHEMISTRY & BIOLOGY 1996; 3:49-56. [PMID: 8807828 DOI: 10.1016/s1074-5521(96)90084-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Oligonucleotide-peptide conjugates have several applications, including their potential use as therapeutic agents. We developed a strategy for the chemical ligation of unprotected peptides to oligonucleotides in aqueous solution. The two compounds are joined via a stable amide bond in a template-directed reaction. RESULTS Peptides, ending in a carboxy-terminal thioester, were converted to thioester-linked oligonucleotide-peptide intermediates. The oligonucleotide portion of the intermediate binds to a complementary oligonucleotide template, placing the peptide in close proximity to an adjacent template-bound oligonucleotide that terminates in a 3' amine. The ensuing reaction results in the efficient formation of an amide-linked oligonucleotide-peptide conjugate. CONCLUSIONS An oligonucleotide template can be used to direct the ligation of peptides to oligonucleotides via a highly stable amide linkage. The ligation reaction is sequence-specific, allowing the simultaneous ligation of multiple oligonucleotide-peptide pairs.
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Affiliation(s)
- R K Bruick
- The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, CA 92037, USA
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Robles J, Pedroso E, Grandas A. Solid-phase synthesis of a nucleopeptide from the linking site of adenovirus-2 nucleoprotein, -Ser(p5'CATCAT)-Gly-Asp-. Convergent versus stepwise strategy. Nucleic Acids Res 1995; 23:4151-61. [PMID: 7479079 PMCID: PMC307357 DOI: 10.1093/nar/23.20.4151] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The synthesis of a nucleopeptide with the sequence -Ser(p5'CATCAT)-Gly-Asp- has been undertaken by either convergent or stepwise solid-phase strategies, both of which use base-labile permanent protecting groups. The coupling of phosphitylated protected peptides onto oligonucleotide-resins did not afford the desired nucleopeptide, which was nevertheless obtained after oligonucleotide elongation at the hydroxyl group of the resin-bound peptide and deprotection under mild basic conditions. A preliminary study on the stability of different nucleopeptides to bases is also reported.
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Affiliation(s)
- J Robles
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona, Barcelona, Spain
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Bergmann F, Bannwarth W. Solid phase synthesis of directly linked peptide-oligodeoxynucleotide hybrids using standard synthesis protocols. Tetrahedron Lett 1995. [DOI: 10.1016/0040-4039(95)00155-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Stepwise solid-phase synthesis of nucleopeptide Phac-Ser(p5′CATCAT)-Gly-Asp-OH from adenovirus-2 nucleoprotein. Tetrahedron Lett 1994. [DOI: 10.1016/s0040-4039(00)73381-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ueno Y, Saito R, Hata T. Studies on the synthesis of nucleotidyl-peptides. II. The preparation of a nucleotidyl-peptide having a 5'-nucleotidyl-(P-O)-serine phosphodiester bond. Nucleic Acids Res 1993; 21:4451-7. [PMID: 8233778 PMCID: PMC311175 DOI: 10.1093/nar/21.19.4451] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The preparation of a nucleotidyl-peptide having a thymidine-5'-yl-(P-O)-serine phosphodiester bond, [H-Ala-Ser(pTpT)-Phe-OH](24) is described. After condensation between the phosphorylated peptide component and an oligonucleotide component, all protecting groups could be removed under neutral conditions without beta-elimination of the pTpT from the serine moiety.
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Affiliation(s)
- Y Ueno
- Department of Life Chemistry, Tokyo Institute of Technology, Yokohama, Japan
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Beaucage SL, Iyer RP. The synthesis of specific ribonucleotides and unrelated phosphorylated biomolecules by the phosphoramidite method. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)81543-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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