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Shioi R, Xiao L, Kool ET. Aqueous Activation of RNA 2'-OH for Conjugation with Amines and Thiols. Bioconjug Chem 2024; 35:43-50. [PMID: 38150592 DOI: 10.1021/acs.bioconjchem.3c00370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Strategies for covalent modification of RNA are important for enabling biological studies of the biopolymer and for enhancing properties of therapeutic RNAs. While a number of electrophiles have been observed to react with RNA, few methods exist for reaction with nucleophiles. Here, we describe new reagents that enable efficient conjugation of amines and other nucleophiles to unmodified RNA postsynthetically via transient activation of 2'-OH groups. Reaction of single-stranded RNA in aqueous solution with phenolic imidazolecarbamates at room temperature results in stoichiometric and superstoichiometric yields of imidazolecarbonyl group adducts, and control experiments with DNA confirm the site of reaction in RNA as 2'-OH. Subsequent incubation of imidazolecarbonyl-activated RNAs with primary or selected secondary amines results in rapid, high-yield conversion to carbamate conjugates. The activation and subsequent nucleophile reaction can be carried out either stepwise or in a one-pot reaction. Thiols and phenol species react to yield (thio)carbonate adducts, and amino acid sidechains also react, suggesting possible future utility for protein conjugates and analysis of protein-RNA interactions. The activation method is found to be selective to unpaired regions of RNA, and can be directed to a specific location in a strand by use of a loop-inducing helper DNA. The results establish novel and efficient reagents and methods for modifying RNA postsynthetically with nucleophiles.
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Affiliation(s)
- Ryuta Shioi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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2
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Traoré D, Biecher E, Mallet M, Rouanet S, Vasseur JJ, Smietana M, Dupouy C. Synthesis and properties of RNA constrained by a 2'-O-disulfide bridge. ChemistryOpen 2024:e202300232. [PMID: 38200655 DOI: 10.1002/open.202300232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Indexed: 01/12/2024] Open
Abstract
We recently reported the properties of RNA hairpins constrained by a dimethylene (DME) disulfide (S-S) linker incorporated between two adjacent nucleosides in the loop and showed that this linker locked the hairpin conformation thus disturbing the duplex/hairpin equilibrium. We have now investigated the influence of the length of the linker and synthesized oligoribonucleotides containing diethylene (DEE) and dipropylene (DPE) S-S bridges. This was achieved via the preparation of building blocks, namely 2'-O-acetylthioethyl (2'-O-AcSE) and 2'-O-acetylthiopropyl (2'-O-AcSP) uridine phosphoramidites, which were successfully incorporated into RNA sequences. Thermal denaturation analysis revealed that the DEE and DPE disulfide bridges destabilize RNA duplexes but do not disrupt the hairpin conformation. Furthermore, our investigation of the duplex/hairpin equilibrium indicated that sequences modified with DME and DEE S-S linkers predominantly lock the hairpin form, whereas the DPE S-S linker provides flexibility. These findings highlight the potential of S-S linkers to study RNA interactions.
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Affiliation(s)
- Diallo Traoré
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Elisa Biecher
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Manon Mallet
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Sonia Rouanet
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | | | - Michael Smietana
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Christelle Dupouy
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
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3
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Moore JM, Crom AB, Feldblyum JI, Genna DT. Disulfide-Driven Pore Functionalization of Metal-Organic Frameworks. Chemistry 2023; 29:e202302144. [PMID: 37486291 DOI: 10.1002/chem.202302144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 07/25/2023]
Abstract
Post-synthetic modification (PSM) imparts additional functionality to metal-organic frameworks (MOFs) that is often difficult to access using solvothermal synthesis. As such, expanding the repertory of PSM reactions available to the practitioner is of increased importance for the generation of materials tailored for desired applications. Herein, a method is described for the protecting group-free installation of diverse functional groups within the pores of a MIL-53(Al) analogue via disulfide bond formation. The majority of the reactions proceed with thiol-to-disulfide conversions ranging from high to nearly quantitative. The disulfide bonds are stable in various solvents and can be cleaved in the presence of a reducing agent.
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Affiliation(s)
- Jennifer M Moore
- Department of Chemical and Biological Sciences, Youngstown State University, One University Plaza, Youngstown, OH 44555, USA
| | - Audrey B Crom
- Department of Chemistry, The University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Jeremy I Feldblyum
- Department of Chemistry, The University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Douglas T Genna
- Department of Chemical and Biological Sciences, Youngstown State University, One University Plaza, Youngstown, OH 44555, USA
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4
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Enríquez‐Cabrera A, Ridier K, Salmon L, Routaboul L, Bousseksou A. Complete and Versatile Post‐Synthetic Modification on Iron‐Triazole Spin Crossover Complexes: A Relevant Material Elaboration Method. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Alejandro Enríquez‐Cabrera
- CNRS Laboratoire de Chimie de Coordination (LCC) 205 route de Narbonne, BP44099 Toulouse Cedex 4 31077 France
| | - Karl Ridier
- CNRS Laboratoire de Chimie de Coordination (LCC) 205 route de Narbonne, BP44099 Toulouse Cedex 4 31077 France
| | - Lionel Salmon
- CNRS Laboratoire de Chimie de Coordination (LCC) 205 route de Narbonne, BP44099 Toulouse Cedex 4 31077 France
| | - Lucie Routaboul
- CNRS Laboratoire de Chimie de Coordination (LCC) 205 route de Narbonne, BP44099 Toulouse Cedex 4 31077 France
| | - Azzedine Bousseksou
- CNRS Laboratoire de Chimie de Coordination (LCC) 205 route de Narbonne, BP44099 Toulouse Cedex 4 31077 France
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5
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Saneyoshi H, Nakamura K, Terasawa K, Ono A. Development of Bioreduction Labile Protecting Groups for the 2'-Hydroxyl Group of RNA. Org Lett 2020; 22:6006-6009. [PMID: 32663406 DOI: 10.1021/acs.orglett.0c02086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protection and deprotection of the 2'-hydroxyl group of RNAs are critical for RNA-based drug discovery. This paper reports development of a bioreduction labile protecting group of the 2'-hydroxyl group in RNA. After the reduction of the nitro group in a chemical or enzymatic manner, the protecting groups were removed spontaneously. The attachment of electron-donating groups to the benzene ring or benzylic carbon enabled fast and controllable deprotection of the 2'-hydroxyl protecting group under physiological conditions.
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Affiliation(s)
- Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Kodai Nakamura
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Kazuma Terasawa
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
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6
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Krasheninina OA, Fishman VS, Lomzov AA, Ustinov AV, Venyaminova AG. Postsynthetic On-Column 2' Functionalization of RNA by Convenient Versatile Method. Int J Mol Sci 2020; 21:E5127. [PMID: 32698484 PMCID: PMC7404181 DOI: 10.3390/ijms21145127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
We report a universal straightforward strategy for the chemical synthesis of modified oligoribonucleotides containing functional groups of different structures at the 2' position of ribose. The on-column synthetic concept is based on the incorporation of two types of commercial nucleotide phosphoramidites containing orthogonal 2'-O-protecting groups, namely 2'-O-thiomorpholine-carbothioate (TC, as "permanent") and 2'-O-tert-butyl(dimethyl)silyl (tBDMS, as "temporary"), to RNA during solid-phase synthesis. Subsequently, the support-bound RNA undergoes selective deprotection and follows postsynthetic 2' functionalization of the naked hydroxyl group. This convenient method to tailor RNA, utilizing the advantages of solid phase approaches, gives an opportunity to introduce site-specifically a wide range of linkers and functional groups. By this strategy, a series of RNAs containing diverse 2' functionalities were synthesized and studied with respect to their physicochemical properties.
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Affiliation(s)
- Olga A. Krasheninina
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Veniamin S. Fishman
- Institute of Cytology and Genetics SB RAS Lavrentiev Ave. 10, 630090 Novosibirsk, Russia;
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
| | - Alexey V. Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia;
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
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7
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Gauthier F, Bertrand JR, Vasseur JJ, Dupouy C, Debart F. Conjugation of Doxorubicin to siRNA Through Disulfide-based Self-immolative Linkers. Molecules 2020; 25:molecules25112714. [PMID: 32545345 PMCID: PMC7321315 DOI: 10.3390/molecules25112714] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Co-delivery systems of siRNA and chemotherapeutic drugs have been developed as an attractive strategy to optimize the efficacy of chemotherapy towards cancer cells with multidrug resistance. In these typical systems, siRNAs are usually associated to drugs within a carrier but without covalent interactions with the risk of a premature release and degradation of the drugs inside the cells. To address this issue, we propose a covalent approach to co-deliver a siRNA-drug conjugate with a redox-responsive self-immolative linker prone to intracellular glutathione-mediated disulfide cleavage. Herein, we report the use of two disulfide bonds connected by a pentane spacer or a p-xylene spacer as self-immolative linker between the primary amine of the anticancer drug doxorubicin (Dox) and the 2′-position of one or two ribonucleotides in RNA. Five Dox-RNA conjugates were successfully synthesized using two successive thiol-disulfide exchange reactions. The Dox-RNA conjugates were annealed with their complementary strands and the duplexes were shown to form an A-helix sufficiently stable under physiological conditions. The enzymatic stability of Dox-siRNAs in human serum was enhanced compared to the unmodified siRNA, especially when two Dox are attached to siRNA. The release of native Dox and RNA from the bioconjugate was demonstrated under reducing conditions suggesting efficient linker disintegration. These results demonstrate the feasibility of making siRNA-drug conjugates via disulfide-based self-immolative linkers for potential therapeutic applications.
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Affiliation(s)
- Florian Gauthier
- IBMM, University of Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (F.G.); (F.D.)
| | - Jean-Rémi Bertrand
- METSY UMR 9018 CNRS, Université Paris-Sud, Gustave Roussy, University Paris-Saclay, 94800 Villejuif Cedex, France;
| | - Jean-Jacques Vasseur
- IBMM, University of Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (F.G.); (F.D.)
- Correspondence: (J.-J.V.); (C.D.)
| | - Christelle Dupouy
- IBMM, University of Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (F.G.); (F.D.)
- Correspondence: (J.-J.V.); (C.D.)
| | - Françoise Debart
- IBMM, University of Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (F.G.); (F.D.)
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8
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Stasińska AR, Putaj P, Chmielewski MK. Disulfide bridge as a linker in nucleic acids’ bioconjugation. Part I: An overview of synthetic strategies. Bioorg Chem 2019; 92:103223. [DOI: 10.1016/j.bioorg.2019.103223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/26/2019] [Accepted: 08/26/2019] [Indexed: 12/23/2022]
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9
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Gauthier F, Malher A, Vasseur JJ, Dupouy C, Debart F. Conjugation of Small Molecules to RNA Using a Reducible Disulfide Linker Attached at the 2′-OH Position through a Carbamate Function. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Florian Gauthier
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Astrid Malher
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Christelle Dupouy
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Françoise Debart
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
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10
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Gauthier F, Beltran F, Biscans A, Debart F, Dupouy C, Vasseur JJ. A 2',2'-disulfide-bridged dinucleotide conformationally locks RNA hairpins. Org Biomol Chem 2019; 16:3181-3188. [PMID: 29645048 DOI: 10.1039/c8ob00328a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The synthesis and the impact of a disulfide bridge between 2'-O-positions of two adjacent nucleotides in an RNA duplex and in the loop of RNA hairpins are reported. The incorporation of this 2',2'-disulfide (S-S) bridge enabled thermal and enzymatic stabilization of the hairpin depending on its position in the loop. The influence of the disulfide bridge on RNA folding was studied at the HIV Dimerization Initiation Site (DIS) as an RNA sequence model. We have shown that this S-S bridge locked the hairpin form, whereas the extended duplex form was generated after the reduction of the disulfide bond in the presence of tris(2-carboxyethyl)phosphine or glutathione. Thus, the S-S bridge can be useful for understanding RNA folding; an RNA molecular beacon locked by an S-S bridge was also investigated as a sensor for the detection of glutathione.
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Affiliation(s)
- Florian Gauthier
- IBMM, UMR 5247, Univ. Montpellier, CNRS, ENSCM, Montpellier, France.
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11
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Gymnotic delivery and gene silencing activity of reduction-responsive siRNAs bearing lipophilic disulfide-containing modifications at 2'-position. Bioorg Med Chem 2018; 26:4635-4643. [PMID: 30121212 DOI: 10.1016/j.bmc.2018.07.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/09/2018] [Accepted: 07/19/2018] [Indexed: 12/25/2022]
Abstract
Modified oligoribonucleotides used as siRNAs bearing biolabile disulfide-containing groups at some 2'-positions were synthesized following a post-synthesis transformation of solid-supported 2'-O-acetylthiomethyl RNA, previously described. Thus, the reduction-responsive and lipophilic benzyldithiomethyl (BnSSM) modification was introduced at different locations into siRNAs targeting the Ewing sarcoma EWS-Fli1 protein. Thermal stability, serum stability and response to glutathione treatment of modified siRNAs were thoroughly investigated. Among 17 modified siRNAs, significant gene silencing activities were demonstrated for the 8 most stable siRNAs in serum (half-life > 1 h) when using a transfection reagent. Of special interest, two naked 2'-O-BnSSM siRNAs transfection exhibited a remarkable gene silencing activity after 24 h incubation. These inhibitions are consistent with an efficient gymnotic delivery demonstrated by the presence of the corresponding fluorescent siRNAs within cells.
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12
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Debart F, Dupouy C, Vasseur JJ. Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing. Beilstein J Org Chem 2018; 14:436-469. [PMID: 29520308 PMCID: PMC5827813 DOI: 10.3762/bjoc.14.32] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
Oligonucleotides (ONs) have been envisaged for therapeutic applications for more than thirty years. However, their broad use requires overcoming several hurdles such as instability in biological fluids, low cell penetration, limited tissue distribution, and off-target effects. With this aim, many chemical modifications have been introduced into ONs definitively as a means of modifying and better improving their properties as gene silencing agents and some of them have been successful. Moreover, in the search for an alternative way to make efficient ON-based drugs, the general concept of prodrugs was applied to the oligonucleotide field. A prodrug is defined as a compound that undergoes transformations in vivo to yield the parent active drug under different stimuli. The interest in stimuli-responsive ONs for gene silencing functions has been notable in recent years. The ON prodrug strategies usually help to overcome limitations of natural ONs due to their low metabolic stability and poor delivery. Nevertheless, compared to permanent ON modifications, transient modifications in prodrugs offer the opportunity to regulate ON activity as a function of stimuli acting as switches. Generally, the ON prodrug is not active until it is triggered to release an unmodified ON. However, as it will be described in some examples, the opposite effect can be sought. This review examines ON modifications in response to various stimuli. These stimuli may be internal or external to the cell, chemical (glutathione), biochemical (enzymes), or physical (heat, light). For each stimulus, the discussion has been separated into sections corresponding to the site of the modification in the nucleotide: the internucleosidic phosphate, the nucleobase, the sugar or the extremities of ONs. Moreover, the review provides a current and detailed account of stimuli-responsive ONs with the main goal of gene silencing. However, for some stimuli-responsive ONs reported in this review, no application for controlling gene expression has been shown, but a certain potential in this field could be demonstrated. Additionally, other applications in different domains have been mentioned to extend the interest in such molecules.
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Affiliation(s)
- Françoise Debart
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
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13
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Fonvielle M, Sakkas N, Iannazzo L, Le Fournis C, Patin D, Mengin-Lecreulx D, El-Sagheer A, Braud E, Cardon S, Brown T, Arthur M, Etheve-Quelquejeu M. Electrophilic RNA for Peptidyl-RNA Synthesis and Site-Specific Cross-Linking with tRNA-Binding Enzymes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Matthieu Fonvielle
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Nicolas Sakkas
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
| | - Chloé Le Fournis
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Afaf El-Sagheer
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
- Chemistry Branch, Dept. of Science and Mathematics, Faculty of Petroleum and Mining Engineering; Suez Canal University; Suez 43721 Egypt
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
| | - Sébastien Cardon
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Tom Brown
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
| | - Michel Arthur
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Mélanie Etheve-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
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14
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Fonvielle M, Sakkas N, Iannazzo L, Le Fournis C, Patin D, Mengin-Lecreulx D, El-Sagheer A, Braud E, Cardon S, Brown T, Arthur M, Etheve-Quelquejeu M. Electrophilic RNA for Peptidyl-RNA Synthesis and Site-Specific Cross-Linking with tRNA-Binding Enzymes. Angew Chem Int Ed Engl 2016; 55:13553-13557. [PMID: 27667506 DOI: 10.1002/anie.201606843] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/03/2016] [Indexed: 12/12/2022]
Abstract
RNA functionalization is challenging due to the instability of RNA and the limited range of available enzymatic reactions. We developed a strategy based on solid phase synthesis and post-functionalization to introduce an electrophilic site at the 3' end of tRNA analogues. The squarate diester used as an electrophile enabled sequential amidation and provided asymmetric squaramides with high selectivity. The squaramate-RNAs specifically reacted with the lysine of UDP-MurNAc-pentapeptide, a peptidoglycan precursor used by the aminoacyl-transferase FemXWv for synthesis of the bacterial cell wall. The peptidyl-RNA obtained with squaramate-RNA and unprotected UDP-MurNAc-pentapeptide efficiently inhibited FemXWv . The squaramate unit also promoted specific cross-linking of RNA to the catalytic Lys of FemXWv but not to related transferases recognizing different aminoacyl-tRNAs. Thus, squaramate-RNAs provide specificity for cross-linking with defined groups in complex biomolecules due to its unique reactivity.
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Affiliation(s)
- Matthieu Fonvielle
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France
| | - Nicolas Sakkas
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Chloé Le Fournis
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Afaf El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Chemistry Branch, Dept. of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez Canal University, Suez, 43721, Egypt
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Sébastien Cardon
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Michel Arthur
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France.
| | - Mélanie Etheve-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France. .,CNRS UMR 8601, Paris, F-75006, France.
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