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Klabenkova KV, Zhdanova PV, Burakova EA, Bizyaev SN, Fokina AA, Stetsenko DA. A Convenient Oligonucleotide Conjugation via Tandem Staudinger Reaction and Amide Bond Formation at the Internucleotidic Phosphate Position. Int J Mol Sci 2024; 25:2007. [PMID: 38396686 PMCID: PMC10889076 DOI: 10.3390/ijms25042007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Staudinger reaction on the solid phase between an electronodeficit organic azide, such as sulfonyl azide, and the phosphite triester formed upon phosphoramidite coupling is a convenient method for the chemical modification of oligonucleotides at the internucleotidic phosphate position. In this work, 4-carboxybenzenesulfonyl azide, either with a free carboxy group or in the form of an activated ester such as pentafluorophenyl, 4-nitrophenyl, or pentafluorobenzyl, was used to introduce a carboxylic acid function to the terminal or internal internucleotidic phosphate of an oligonucleotide via the Staudinger reaction. A subsequent treatment with excess primary alkyl amine followed by the usual work-up, after prior activation with a suitable peptide coupling agent such as a uronium salt/1-hydroxybenzotriazole in the case of a free carboxyl, afforded amide-linked oligonucleotide conjugates in good yields including multiple conjugations of up to the exhaustive modification at each phosphate position for a weakly activated pentafluorobenzyl ester, whereas more strongly activated and, thus, more reactive aryl esters provided only single conjugations at the 5'-end. The conjugates synthesized include those with di- and polyamines that introduce a positively charged side chain to potentially assist the intracellular delivery of the oligonucleotide.
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Affiliation(s)
- Kristina V. Klabenkova
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Polina V. Zhdanova
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia;
| | - Ekaterina A. Burakova
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Sergei N. Bizyaev
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Alesya A. Fokina
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Dmitry A. Stetsenko
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
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Lakshman MK. Base Modifications of Nucleosides via the Use of Peptide-Coupling Agents, and Beyond. CHEM REC 2023; 23:e202200182. [PMID: 36166699 DOI: 10.1002/tcr.202200182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/26/2022] [Indexed: 01/24/2023]
Abstract
Several naturally occurring purine and pyrimidine nucleosides contain an amide linkage as part of the heterocyclic aglycone. Enolization of the amide and conversion to leaving groups at the amide carbon atom permits base modification by addition-elimination types of processes. Although a number of methods have been developed over the years for accomplishing such conversions, the present Personal Account describes efforts from the Lakshman laboratories. Facile activation of the amido groups in nucleobases can be achieved with peptide-coupling agents. Subsequent reaction with nucleophiles then accomplishes the base modifications. In many cases, the activation and displacement steps can be done as two-step, one-pot processes, whereas in other cases, discrete storable activated nucleosides can be isolated for subsequent displacement reactions. Using such an approach a wide range of nucleoside base modifications is readily achievable. In many instances, mechanistic investigations have been conducted so as to understand the activation process.
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Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
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3
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Shaikh AY, Björkling F, Nielsen PE, Franzyk H. Optimized Synthesis of Fmoc/Boc‐Protected PNA Monomers and their Assembly into PNA Oligomers. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ashif Y. Shaikh
- Center for Peptide-based Antibiotics, Department of Drug Design and Pharmacology Faculty of Heath and Medical Sciences University of Copenhagen Jagtvej 162 2100 Copenhagen Denmark
| | - Fredrik Björkling
- Center for Peptide-based Antibiotics, Department of Drug Design and Pharmacology Faculty of Heath and Medical Sciences University of Copenhagen Jagtvej 162 2100 Copenhagen Denmark
| | - Peter E. Nielsen
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Heath and Medical Sciences University of Copenhagen Blegdamsvej 3 2200 Copenhagen Denmark
| | - Henrik Franzyk
- Center for Peptide-based Antibiotics, Department of Drug Design and Pharmacology Faculty of Heath and Medical Sciences University of Copenhagen Jagtvej 162 2100 Copenhagen Denmark
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Fmoc-Based Assembly of PNA Oligomers: Manual and Microwave-Assisted Automated Synthesis. Methods Mol Biol 2021; 2105:1-16. [PMID: 32088861 DOI: 10.1007/978-1-0716-0243-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Exploration of PNA-peptide conjugates as potential antisense antibiotics necessitates a fast and efficient synthesis protocols for amounts that facilitate determination of structure-activity relationships and in vivo studies in animal infection models. Fmoc/Boc-protected PNA monomers are here used for assembly of oligomers by optimized protocols involving either a manual synthesis method at room temperature or automated microwave-assisted coupling of monomers on a peptide synthesizer.
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Flory JD, Shinde S, Lin S, Liu Y, Yan H, Ghirlanda G, Fromme P. PNA-peptide assembly in a 3D DNA nanocage at room temperature. J Am Chem Soc 2013; 135:6985-93. [PMID: 23521013 DOI: 10.1021/ja400762c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins and peptides fold into dynamic structures that access a broad functional landscape; however, designing artificial polypeptide systems is still a great challenge. Conversely, DNA engineering is now routinely used to build a wide variety of 2D and 3D nanostructures from hybridization based rules, and their functional diversity can be significantly expanded through site specific incorporation of the appropriate guest molecules. Here we demonstrate a new approach to rationally design 3D nucleic acid-amino acid complexes using peptide nucleic acid (PNA) to assemble peptides inside a 3D DNA nanocage. The PNA-peptides were found to bind to the preassembled DNA nanocage in 5-10 min at room temperature, and assembly could be performed in a stepwise fashion. Biophysical characterization of the DNA-PNA-peptide complex was performed using gel electrophoresis as well as steady state and time-resolved fluorescence spectroscopy. Based on these results we have developed a model for the arrangement of the PNA-peptides inside the DNA nanocage. This work demonstrates a flexible new approach to leverage rationally designed nucleic acid (DNA-PNA) nanoscaffolds to guide polypeptide engineering.
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Affiliation(s)
- Justin D Flory
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, Arizona 85287, United States
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Kokatla HP, Lakshman MK. One-pot etherification of purine nucleosides and pyrimidines. Org Lett 2011; 12:4478-81. [PMID: 20845979 DOI: 10.1021/ol101655h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A one-pot synthesis of ethers derived from inosine, guanosine, 2'-deoxyguanosine, and pyrimidinones is described. Exposure of the heterocycle to 1H-benzotriazol-1-yloxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and Cs(2)CO(3) produces a reactive intermediate, which is converted to the desired ether by subsequent addition of an appropriate alcohol or phenol and Cs(2)CO(3). Although rapid formation of HMPA from BOP can occur in the presence of an alcohol and base, as demonstrated by the reaction with methanol, under appropriate conditions these heteroaryl ethers can be efficiently synthesized.
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Affiliation(s)
- Hari Prasad Kokatla
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031-9198, USA
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7
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van der Heden van Noort GJ, Overkleeft HS, van der Marel GA, Filippov DV. Synthesis of nucleotidylated poliovirus VPg proteins. J Org Chem 2010; 75:5733-6. [PMID: 20704445 DOI: 10.1021/jo100757t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Phosphitylation of the side chain hydroxyl function of Fmoc protected tyrosine with 5'-phosphoramidites of suitably protected cytidine, adenosine, and guanosine, followed by oxidation gave three novel nucleotidylated amino acid building blocks. After protective group manipulation, these building blocks were used in a solid phase peptide synthesis to afford the nucleotidylated poliovirus proteins VPgpC, VPgpA, and VPgpG.
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Pires VS, da Nascimento S, Sonnet P. Synthesis of 4-Thiouracil KPGEPGPK Analogues as Potential TIIICBP Identification Tools. Int J Pept Res Ther 2010. [DOI: 10.1007/s10989-010-9227-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Kang F, Sui Z, Murray WV. Phosphonium Coupling in the Direct Bond Formations of Tautomerizable Heterocycles via C–OH Bond Activation. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fu‐An Kang
- Johnson & Johnson Pharmaceutical Research and Development, LLC 665 Stockton Drive, Exton, PA 19341, USA, Fax: +1‐610‐458‐8249
| | - Zhihua Sui
- Johnson & Johnson Pharmaceutical Research and Development, LLC 665 Stockton Drive, Exton, PA 19341, USA, Fax: +1‐610‐458‐8249
| | - William V. Murray
- Johnson & Johnson Pharmaceutical Research and Development, LLC 665 Stockton Drive, Exton, PA 19341, USA, Fax: +1‐610‐458‐8249
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TANG C, LI L, PANG Z, YUAN Z. Synthesis of Small Peptides and Their Use as Bifunctional Chelating Agents in Diagnostic Radiopharmaceuticals. CHINESE J CHEM 2009. [DOI: 10.1002/cjoc.200990018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Kang FA, Sui Z, Murray WV. Pd-catalyzed direct arylation of tautomerizable heterocycles with aryl boronic acids via C-OH bond activation using phosphonium salts. J Am Chem Soc 2008; 130:11300-2. [PMID: 18665598 DOI: 10.1021/ja804804p] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The first direct arylation via C-OH bond activation of tautomerizable heterocycles has been achieved using phosphonium salts, on the basis of a combination of the phosphonium coupling and Suzuki-Miyaura cross-coupling conditions. Optimal reaction condition is obtained through screening of phosphonium salts, Pd catalysts, and bases. The direct arylation via C-OH bond activation tolerates a variety of tautomerizable heterocycles and aryl boronic acids. The mechanism of the Pd-catalyzed phosphonium coupling is proposed to proceed via a domino seven-step process including the unprecedented heterocycle-Pd(II)-phosphonium species. Application of the Pd-catalyzed direct arylation via C-OH bond activation using PyBroP leads to the most efficient synthesis of the biologically important 6-arylpurine ribonucleoside in a single step from unactivated and unprotected inosine.
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Affiliation(s)
- Fu-An Kang
- Johnson & Johnson Pharmaceutical Research and Development, LLC, 665 Stockton Drive, Exton, Pennsylvania 19341, USA.
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12
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Altenbrunn F, Seitz O. O-Allyl protection in the Fmoc-based synthesis of difficult PNA. Org Biomol Chem 2008; 6:2493-8. [PMID: 18600269 DOI: 10.1039/b805165h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of homothymine PNA-oligomers can be plagued by the occurrence of a significant amount of truncation products, probably because on-resin aggregation hinders access during the coupling reactions. The use of low resin loading and the addition of the chaotropic salt KSCN in DMF allowed a partial remedy by conferring enhancements to the coupling yields. However, protection of the imide group by using O-allyl-protected thymine Fmoc-t(All) provided the most significant improvements to the yields, even in cases where the use of non-protected thymine building blocks resulted in 70% truncation products. Deallylation occurs during the TFA cleavage step. Thus, O-allyl-protection can be applied in combination with standard protocols used in automated PNA synthesis.
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Affiliation(s)
- Frank Altenbrunn
- Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489, Berlin, Germany
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13
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Fabani MM, Ivanova GD, Gait MJ. Peptide–Peptide Nucleic Acid Conjugates for Modulation of Gene Expression. THERAPEUTIC OLIGONUCLEOTIDES 2008. [DOI: 10.1039/9781847558275-00080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Martin M. Fabani
- Medical Research Council Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK
| | - Gabriela D. Ivanova
- Medical Research Council Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK
| | - Michael J. Gait
- Medical Research Council Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK
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Bae S, Lakshman MK. O6-(benzotriazol-1-yl)inosine derivatives: easily synthesized, reactive nucleosides. J Am Chem Soc 2007; 129:782-9. [PMID: 17243813 DOI: 10.1021/ja064682n] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel class of O6-(benzotriazol-1-yl)inosine as well as the corresponding 2'-deoxy derivatives can be conveniently prepared by a reaction between sugar-protected or -unprotected inosine or 2'-deoxyinosine nucleosides and 1H-benzotriazol-1-yloxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP). The reaction appears to proceed via a nucleoside phosphonium salt, and in the absence of any additional nucleophile, the released 1-hydroxybenzotriazole undergoes reaction with the formed phosphonium salt leading to the requisite O6-(benzotriazol-1-yl)inosine or 2'-deoxyinosine derivatives. Isolation and characterization of the phosphonium salt as well as analysis by 31P{1H} NMR appear to be consistent with this reaction pathway. The resulting O6-(benzotriazol-1-yl)inosine derivatives are effective as electrophilic nucleosides, undergoing facile reactions with a variety of nucleophiles such as alcohols, phenols, amines, and a thiol. Unusual and challenging nucleoside derivatives such as an aryl-bridged dimer, a nucleoside-amino acid conjugate, and a nucleoside-nucleoside dimer have also been synthesized from the O6-(benzotriazol-1-yl)-2'-deoxyinosine derivative. Finally, a fully protected DNA building block, the O6-(benzotriazol-1-yl)-2'-deoxyinosine 5'-O-DMT 3'-O-phosphoramidite, has been prepared and a preliminary evaluation of its use for DNA modification has been performed. Results from these studies indicate several important facts: A single, simple methodological approach provides a class of stable, isolable ribo and 2'-deoxyribonucleoside derivatives that possess excellent reactivity for SNAr chemistry with a wide range of nucleophiles. Also, a benzotriazolyl nucleoside phosphoramidite appears to be a suitable reagent for incorporation into DNA for purposes of site-specific DNA modification.
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Affiliation(s)
- Suyeal Bae
- Department of Chemistry, The City College and The City University of New York, 138th Street at Convent Avenue, New York, New York 10031-9198, USA
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