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Rietmeyer L, Li De La Sierra-Gallay I, Schepers G, Dorchêne D, Iannazzo L, Patin D, Touzé T, van Tilbeurgh H, Herdewijn P, Ethève-Quelquejeu M, Fonvielle M. Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis. Nucleic Acids Res 2022; 50:11415-11425. [PMID: 36350642 PMCID: PMC9723616 DOI: 10.1093/nar/gkac1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
Xenobiotic nucleic acids (XNAs) offer tremendous potential for synthetic biology, biotechnology, and molecular medicine but their ability to mimic nucleic acids still needs to be explored. Here, to study the ability of XNA oligonucleotides to mimic tRNA, we synthesized three L-Ala-tXNAs analogs. These molecules were used in a non-ribosomal peptide synthesis involving a bacterial Fem transferase. We compared the ability of this enzyme to use amino-acyl tXNAs containing 1',5'-anhydrohexitol (HNA), 2'-fluoro ribose (2'F-RNA) and 2'-fluoro arabinose. L-Ala-tXNA containing HNA or 2'F-RNA were substrates of the Fem enzyme. The synthesis of peptidyl-XNA and the resolution of their structures in complex with the enzyme show the impact of the XNA on protein binding. For the first time we describe functional tXNA in an in vitro assay. These results invite to test tXNA also as substitute for tRNA in translation.
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Affiliation(s)
| | | | - Guy Schepers
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Delphine Dorchêne
- INSERM UMR-S 1138, Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, F-75006 Paris, France
| | - Laura Iannazzo
- Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006Paris, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Thierry Touzé
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Mélanie Ethève-Quelquejeu
- Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006Paris, France
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2
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Neel AJ, Turnbull BWH, Carson WP, Benkovics T, Chung CK, Johnson HC, Liu Z, Peng F, Rummelt SM, Song ZJ, Tan L, Wang L, Xu F. A Unified Strategy to Fluorinated Nucleoside Analogues Via an Electrophilic Manifold. Org Lett 2022; 24:7701-7706. [PMID: 36227065 DOI: 10.1021/acs.orglett.2c03367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, we present a strategy for the preparation of 3'-fluorinated nucleoside analogues via the aminocatalytic, electrophilic fluorination of readily accessible and bench-stable 2'-ketonucleosides. Initially developed to facilitate the manufacture of 3'-fluoroguanosine (3'-FG)─a substructure of anticancer therapeutic MK-1454─this strategy has been extended to the synthesis of a variety of 3'-fluoronucleosides. Finally, we demonstrate the utility of the 2'-ketonucleoside synthon as a platform for further diversification and suggest that this methodology should be broadly applicable to the discovery of novel nucleoside analogues.
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Affiliation(s)
- Andrew J Neel
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ben W H Turnbull
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - William P Carson
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Tamas Benkovics
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Cheol K Chung
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Heather C Johnson
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zhuqing Liu
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Feng Peng
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Stephan M Rummelt
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zhiguo Jake Song
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Lushi Tan
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Lu Wang
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Feng Xu
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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3
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Nguyen VH, Tichý M, Rožánková S, Pohl R, Downey AM, Doleželová E, Tloušťová E, Slapničková M, Zíková A, Hocek M. Synthesis and anti-trypanosomal activity of 3'-fluororibonucleosides derived from 7-deazapurine nucleosides. Bioorg Med Chem Lett 2021; 40:127957. [PMID: 33741462 DOI: 10.1016/j.bmcl.2021.127957] [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: 02/04/2021] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 10/21/2022]
Abstract
Trypanosoma brucei parasites cause Human African Trypanosomiasis and the current drugs for its treatment are often inefficient and toxic. This urges the need to development of new antitrypanosomal agents. We report the synthesis and biological profiling of 3'-deoxy-3'-fluororibonucleosides derived from 7-deazaadenine nucleosides bearing diverse substituents at position 7. They were synthesized through glycosylation of 6-chloro-7-bromo- or -7-iodo-7-deazapurine with protected 3'-fluororibose followed by cross-coupling reactions at position 7 and/or deprotection. Most of the title nucleosides displayed micromolar or submicromolar activity against Trypanosoma brucei brucei. The most active were the 7-bromo- and 7-iododerivatives which exerted double-digit nanomolar activity against T. b. brucei and T. b. gambiense and no cytotoxicity and thus represent promising candidates for further development.
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Affiliation(s)
- Van Hai Nguyen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Michal Tichý
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Samanta Rožánková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - A Michael Downey
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Eva Doleželová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Eva Tloušťová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Martina Slapničková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czech Republic.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic.
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4
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Iannazzo L, Fonvielle M, Braud E, Hřebabecký H, Procházková E, Nencka R, Mathé C, Arthur M, Etheve-Quelquejeu M. Synthesis of tRNA analogues containing a terminal ribose locked in the South conformation to study tRNA-dependent enzymes. Org Biomol Chem 2019; 16:1903-1911. [PMID: 29484333 DOI: 10.1039/c8ob00019k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the synthetic route of two constrained dinucleotides and the determination of the sugar puckering by NMR analyses of the starting nucleosides. Enzymatic ligation to microhelix-RNAs provide access to tRNA analogues containing a 3' terminal A76 locked in South conformation. Biological evaluation of our tRNA analogues has been performed using amino-acyl tRNA-dependent transferase FemXWv, which mediates non-ribosomal incorporation of amino acids into the bacterial cell wall. We have shown that our tRNA analogues inhibited the aminoacyl transfer reaction catalyzed by FemXWv with IC50s of 10 and 8 μM. These results indicate that FemXWv displays a moderate preference for tRNAs containing a terminal A76 locked in the South conformation and that a South to North switch in the conformation of the terminal ribose might contribute to the release of the uncharged tRNAAla product of the aminoacyl transfer reaction catalyzed by FemXwv.
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Affiliation(s)
- Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France
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5
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Guo F, Li Q, Zhou C. Synthesis and biological applications of fluoro-modified nucleic acids. Org Biomol Chem 2018; 15:9552-9565. [PMID: 29086791 DOI: 10.1039/c7ob02094e] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Owing to the unique physical properties of a fluorine atom, incorporating fluoro-modifications into nucleic acids offers striking biophysical and biochemical features, and thus significantly extends the breadth and depth of biological applications of nucleic acids. In this review, fluoro-modified nucleic acids that have been synthesized through either solid phase synthesis or the enzymatic approach are briefly summarised, followed by a section describing their biomedical applications in nucleic acid-based therapeutics, 18F PET imaging and mechanistic studies of DNA modifying enzymes. In the last part, the utility of 19F NMR and MRI for probing the structure, dynamics and molecular interactions of fluorinated nucleic acids is reviewed.
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Affiliation(s)
- Fengmin Guo
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
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