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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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2
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Koutsopetras I, Mishra AK, Benazza R, Hernandez-Alba O, Cianférani S, Chaubet G, Nicolai S, Waser J. Cysteine-Cysteine Cross-Conjugation of both Peptides and Proteins with a Bifunctional Hypervalent Iodine-Electrophilic Reagent. Chemistry 2023; 29:e202302689. [PMID: 37712523 DOI: 10.1002/chem.202302689] [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: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
Peptide and protein bioconjugation sees ever-growing applications in the pharmaceutical sector. Novel strategies and reagents that can address the chemo- and regioselectivity issues inherent to these biomolecules, while delivering stable and functionalizable conjugates, are therefore needed. Herein, we introduce the crosslinking ethynylbenziodazolone (EBZ) reagent JW-AM-005 for the conjugation of peptides and proteins through the selective linkage of cysteine residues. This easily accessed compound gives access to peptide dimers or stapled peptides under mild and tuneable conditions. Applied to the antibody fragment of antigen binding (Fab) species, JW-AM-005 delivered rebridged proteins in a one-pot three-reaction process with high regioselectivity, outperforming the standard reagents commonly used for this transformation.
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Affiliation(s)
- Ilias Koutsopetras
- UMR 7199 CNRS-UdS, Chime Bio-Fonctionnelle, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch cedex, France
| | - Abhaya Kumar Mishra
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéralede de Lausanne, 1015, Lausanne, Switzerland
| | - Rania Benazza
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg CNRS, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI-FR2048, 67087, Strasbourg, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg CNRS, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI-FR2048, 67087, Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg CNRS, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI-FR2048, 67087, Strasbourg, France
| | - Guilhem Chaubet
- UMR 7199 CNRS-UdS, Chime Bio-Fonctionnelle, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch cedex, France
| | - Stefano Nicolai
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéralede de Lausanne, 1015, Lausanne, Switzerland
| | - Jérôme Waser
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéralede de Lausanne, 1015, Lausanne, Switzerland
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3
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Mangla P, Vicentini Q, Biscans A. Therapeutic Oligonucleotides: An Outlook on Chemical Strategies to Improve Endosomal Trafficking. Cells 2023; 12:2253. [PMID: 37759475 PMCID: PMC10527716 DOI: 10.3390/cells12182253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The potential of oligonucleotide therapeutics is undeniable as more than 15 drugs have been approved to treat various diseases in the liver, central nervous system (CNS), and muscles. However, achieving effective delivery of oligonucleotide therapeutics to specific tissues still remains a major challenge, limiting their widespread use. Chemical modifications play a crucial role to overcome biological barriers to enable efficient oligonucleotide delivery to the tissues/cells of interest. They provide oligonucleotide metabolic stability and confer favourable pharmacokinetic/pharmacodynamic properties. This review focuses on the various chemical approaches implicated in mitigating the delivery problem of oligonucleotides and their limitations. It highlights the importance of linkers in designing oligonucleotide conjugates and discusses their potential role in escaping the endosomal barrier, a bottleneck in the development of oligonucleotide therapeutics.
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Affiliation(s)
- Priyanka Mangla
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
| | - Quentin Vicentini
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
- Department of Laboratory Medicine, Clinical Research Centre, Karolinska Institute, 141 57 Stockholm, Sweden
| | - Annabelle Biscans
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
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4
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Hou X, Wang G, Gaffney BL, Jones RA. Preparation of DNA and RNA Fragments Containing Guanine N 2 -Thioalkyl Tethers. Curr Protoc 2023; 3:e710. [PMID: 36943108 DOI: 10.1002/cpz1.710] [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] [Indexed: 03/23/2023]
Abstract
This article describes procedures for preparation of deoxyguanosine and guanosine derivatives in which the guanine N2 contains a thiopropyl tether, protected as a tert-butyl disulfide. After incorporation into a DNA or RNA fragment, this tether allows site-specific cross-linking to a thiol of a protein or another nucleic acid. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of diisopropyl-1-(tert-butylthio)-1,2-hydrazinedicarboxylate (4) Basic Protocol 2: Preparation of the 2'-deoxyguanosine N2 -propyl-tert-butyl disulfide phosphoramidite (12) Basic Protocol 3: Preparation of the guanosine N2 -propyl-tert-butyl disulfide phosphoramidite (20) Basic Protocol 4: Preparation of DNA fragments containing N2 -propyl-tert-butyl disulfide guanine Alternate Protocol: Preparation of RNA fragments containing N2 -propyl-tert-butyl disulfide guanine Basic Protocol 5: Conversion of N2 -propyl-tert-butyl disulfide to the free thiol, disulfide 5-thio-2-nitrobenzoic acid disulfide, or ethylamine disulfide.
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Affiliation(s)
- Xiaorong Hou
- Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Gang Wang
- Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | | | - Roger A Jones
- Rutgers, The State University of New Jersey, Piscataway, New Jersey
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5
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Pontarelli A, Liu JT, Oh JK, Wilds CJ. Preparation of a Convertible Spacer Containing a Disulfide Group for Versatile Functionalization of Oligonucleotides. Curr Protoc 2023; 3:e691. [PMID: 36840706 DOI: 10.1002/cpz1.691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The protocols described in this article provide details regarding the synthesis and characterization of a disulfide containing linker phosphoramidite for terminal functionalization of synthetic oligonucleotides. The linker is first synthesized from 6-mercaptohexanol in two steps and is incorporated at the 5' end of short DNA oligonucleotides using automated solid-phase synthesis. The linker contains a terminal tosylate group which is post-synthetically displaced by altering the deprotection conditions to yield a variety of functional handles (N3 , NH2 , OMe, SH) or alternatively, the tosylate can be displaced directly with primary amines such as tert-butylamine. The linker system is also compatible with RNA oligonucleotides enabling the introduction of various functional handles (N3 , NH2 ). The protocol outlined in this procedure provides access to a versatile linker for the terminal functionalization of oligonucleotides containing a disulfide bond which may serve useful in the synthesis of reduction-responsive oligonucleotide conjugates. As a proof of concept, in this protocol the linker is used to modify a dT10 oligonucleotide and then conjugated by copper(I)-mediated azide-alkyne cycloaddition (CuAAC) to an alkyne-modified poly(ethylene glycol) which shows concentration dependent release of the oligonucleotide upon treatment with 1,4-dithiothreitol, a reducing agent. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of disulfide linker phosphoramidite 3 Basic Protocol 2: Synthesis, functionalization, and characterization of DNA oligonucleotides containing disulfide linker phosphoramidite 3 Basic Protocol 3: Displacement of terminal tosylate functionalized DNA with primary aliphatic amines Basic Protocol 4: Synthesis of oligonucleotide-PEG conjugate Support Protocol: Preparation of PEG-alkyne.
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Affiliation(s)
- Alexander Pontarelli
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Jiang Tian Liu
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Jung Kwon Oh
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
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6
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Kupihár Z, Ferenc G, Petrovicz VL, Fáy VR, Kovács L, Martinek TA, Hegedüs Z. Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates. Pharmaceutics 2023; 15:pharmaceutics15010248. [PMID: 36678876 PMCID: PMC9865093 DOI: 10.3390/pharmaceutics15010248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Oligonucleotide conjugates are versatile scaffolds that can be applied in DNA-based screening platforms and ligand display or as therapeutics. Several different chemical approaches are available for functionalizing oligonucleotides, which are often carried out on the 5' or 3' end. Modifying oligonucleotides in the middle of the sequence opens the possibility to ligate the conjugates and create DNA strands bearing multiple different ligands. Our goal was to establish a complete workflow that can be applied for such purposes from monomer synthesis to templated ligation. To achieve this, a monomer is required with an orthogonal functional group that can be incorporated internally into the oligonucleotide sequence. This is followed by conjugation with different molecules and ligation with the help of a complementary template. Here, we show the synthesis and the application of a thiol-modified thymidine nucleoside phosphoramidite to prepare ligatable oligonucleotide conjugates. The conjugations were performed both in solution and on solid phase, resulting in conjugates that can be assembled into multivalent oligonucleotides decorated with tissue-targeting peptides using templated ligation.
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Affiliation(s)
- Zoltán Kupihár
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Györgyi Ferenc
- Institute of Plant Biology, Biological Research Centre, Eötvös Lóránd Research Network, H-6726 Szeged, Hungary
| | - Vencel L. Petrovicz
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Viktória R. Fáy
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Lajos Kovács
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Tamás A. Martinek
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network, H-6720 Szeged, Hungary
- Correspondence: (T.A.M.); (Z.H.)
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
- Correspondence: (T.A.M.); (Z.H.)
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7
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Zhang Y, Xu H, Jiang L, Liu Z, Lian C, Ding X, Wan C, Liu N, Wang Y, Yu Z, Zhu L, Yin F, Li Z. Sulfonium-Driven Neoantigen-Released DNA Nanodevice as a Precise Vaccine for Tumor Immunotherapy and Prevention. ACS NANO 2022; 16:19509-19522. [PMID: 36318615 DOI: 10.1021/acsnano.2c09708] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Peptide-based neoantigen vaccines hold tremendous potential for personalized tumor immunotherapy. However, effective delivery and controllable release of antigen peptides remain major challenges in stimulating robust and sustained immune responses. Programmable DNA nanodevices provide accurate fixed positions for antigens, which are convenient for the calculation of clinical dosage, and hold great potential as precise carriers. Here, a peptide-nucleic acid conjugate was prepared, which was driven by a propargyl sulfonium-based efficient and reversible bio-orthogonal reaction under weakly alkaline conditions, and folded into regular DNA nanodevice vaccines. The well-defined nanoplatform not only exhibits outstanding stability in serum, satisfactory safety, and effective internalization by antigen-presenting cells (RAW264.7 and BMDCs) but also obviously enhances cytokine (TNF-α, IL-6, and IL-12) secretion for further immune response. In vivo, the nanovaccine cooperating with OVA model antigens and CpG adjuvants stimulated an antigen-specific CD8+T cell response, significantly preventing the lung metastases of melanoma. In the B16-OVA tumor-bearing model, the growth inhibition rate of melanoma reached up to 50%. Similarly, the DNA nanodevice with neoantigen induced up to a maximum degree of complete MC-38 tumor regression in 80% of mice, possibly owing to antigen peptide reversible release driven by sulfonium and further cross-presentation. In brief, this study demonstrates that DNA nanodevices with sulfonium centers can provide a precise, biocompatible, and effective co-delivery vaccine platform for tumor immunotherapy and prevention.
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Affiliation(s)
- Yaping Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, P.R. China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Hongkun Xu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Leying Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Zhaodi Liu
- Department of Radiation Oncology, The First Affiliated Hospital, Anhui Medical University, Hefei 230022, P.R. China
| | - Chenshan Lian
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, P.R. China
| | - Xiaofeng Ding
- Department of Radiation Oncology, The First Affiliated Hospital, Anhui Medical University, Hefei 230022, P.R. China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Na Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Zhiqiang Yu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, P.R. China
| | - Lizhi Zhu
- Department of Pharmacy, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), The First Affiliated Hospital of Shenzhen University, Shenzhen 518055, P.R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, P.R. China
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, P.R. China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
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8
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Pontarelli A, Liu JT, Movasat H, Ménard S, Oh JK, Wilds CJ. Synthesis of a Convertible Linker Containing a Disulfide Group for Oligonucleotide Functionalization. Org Lett 2022; 24:5579-5583. [PMID: 35863757 DOI: 10.1021/acs.orglett.2c02149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis and incorporation of a tosylated phosphoramidite linker containing a disulfide bond is described. Incorporation of the linker into short DNA and RNA oligomers proceeded efficiently using automated solid phase synthesis. Treatment of the support bound oligonucleotide followed by cleavage from the solid support provided a variety of common functional handles, expanding the strategies of bifunctional modification of synthetic oligonucleotides for conjugation applications.
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Affiliation(s)
- Alexander Pontarelli
- Department of Chemistry and Biochemistry, Faculty of Arts and Science, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, Québec H4B 1R6, Canada
| | - Jiang Tian Liu
- Department of Chemistry and Biochemistry, Faculty of Arts and Science, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, Québec H4B 1R6, Canada
| | - Hourieh Movasat
- Department of Chemistry and Biochemistry, Faculty of Arts and Science, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, Québec H4B 1R6, Canada
| | - Sarah Ménard
- Department of Chemistry and Biochemistry, Faculty of Arts and Science, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, Québec H4B 1R6, Canada
| | - Jung Kwon Oh
- Department of Chemistry and Biochemistry, Faculty of Arts and Science, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, Québec H4B 1R6, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Faculty of Arts and Science, Concordia University, 7141 Rue Sherbrooke Ouest, Montréal, Québec H4B 1R6, Canada
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9
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Xiong H, Liu L, Wang Y, Jiang H, Wang X. Engineered Aptamer-Organic Amphiphile Self-Assemblies for Biomedical Applications: Progress and Challenges. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104341. [PMID: 34622570 DOI: 10.1002/smll.202104341] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Currently, nucleic acid aptamers are exploited as robust targeting ligands in the biomedical field, due to their specific molecular recognition, little immunogenicity, low cost, ect. Thanks to the facile chemical modification and high hydrophilicity, aptamers can be site-specifically linked with hydrophobic moieties to prepare aptamer-organic amphiphiles (AOAs), which spontaneously assemble into aptamer-organic amphiphile self-assemblies (AOASs). These polyvalent self-assemblies feature with enhanced target-binding ability, increased resistance to nuclease, and efficient cargo-loading, making them powerful platforms for bioapplications, including targeted drug delivery, cell-based cancer therapy, biosensing, and bioimaging. Besides, the morphology of AOASs can be elaborately manipulated for smarter biomedical functions, by regulating the hydrophilicity/hydrophobicity ratio of AOAs. Benefiting from the boom in DNA synthesis technology and nanotechnology, various types of AOASs, including aptamer-polymer amphiphile self-assemblies, aptamer-lipid amphiphile self-assemblies, aptamer-cell self-assemblies, ect, have been constructed with great biomedical potential. Particularly, stimuli-responsive AOASs with transformable structure can realize site-specific drug release, enhanced tumor penetration, and specific target molecule detection. Herein, the general synthesis methods of oligonucleotide-organic amphiphiles are firstly summarized. Then recent progress in different types of AOASs for bioapplications and strategies for morphology control are systematically reviewed. The present challenges and future perspectives of this field are also discussed.
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Affiliation(s)
- Hongjie Xiong
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yihan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Hui Jiang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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10
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Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch. Molecules 2021; 26:molecules26195925. [PMID: 34641475 PMCID: PMC8512084 DOI: 10.3390/molecules26195925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5’-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson–Crick base-pairing. We show that 5’-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5’-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.
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11
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Dutta K, Das R, Medeiros J, Thayumanavan S. Disulfide Bridging Strategies in Viral and Nonviral Platforms for Nucleic Acid Delivery. Biochemistry 2021; 60:966-990. [PMID: 33428850 PMCID: PMC8753971 DOI: 10.1021/acs.biochem.0c00860] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Self-assembled nanostructures that are sensitive to environmental stimuli are promising nanomaterials for drug delivery. In this class, disulfide-containing redox-sensitive strategies have gained enormous attention because of their wide applicability and simplicity of nanoparticle design. In the context of nucleic acid delivery, numerous disulfide-based materials have been designed by relying on covalent or noncovalent interactions. In this review, we highlight major advances in the design of disulfide-containing materials for nucleic acid encapsulation, including covalent nucleic acid conjugates, viral vectors or virus-like particles, dendrimers, peptides, polymers, lipids, hydrogels, inorganic nanoparticles, and nucleic acid nanostructures. Our discussion will focus on the context of the design of materials and their impact on addressing the current shortcomings in the intracellular delivery of nucleic acids.
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Affiliation(s)
- Kingshuk Dutta
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Ritam Das
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- The Center for Bioactive Delivery- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Jewel Medeiros
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- The Center for Bioactive Delivery- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department of Biomedical Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003, United States
- The Center for Bioactive Delivery- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
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12
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Hyjek-Składanowska M, Stasińska AR, Napiórkowska-Gromadzka A, Bartłomiejczak A, Seth PP, Chmielewski MK, Nowotny M. Disulfide bridge cross-linking between protein and the RNA backbone as a tool to study RNase H1. Bioorg Med Chem 2020; 28:115741. [PMID: 32992250 DOI: 10.1016/j.bmc.2020.115741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
The chemical cross-linking of complexes of proteins with nucleic acids is often used in structural and mechanistic studies of these oftentimes unstable and transient complexes. To date, no method has been reported for the thiol-based conjugation of proteins with an RNA backbone, mainly because of instability of the modified ribonucleic acid that is functionalized at the phosphodiester and its rapid hydrolysis. Here, we report the site-specific synthesis of stable RNA oligonucleotides with a thiol-bearing linker that was attached to the phosphodiester backbone, where the ribonucleotide at the cross-linking site was either replaced with 2'-deoxy- or 2'-fluororibonucleotide. The utility of this approach was validated in cross-linking tests with RNase H1, a model protein for RNA/DNA binding and key effector in DNA-like antisense drug therapy. Furthermore, scale-up cross-linking and purification of the complexes confirmed that the method is useful for obtaining preparations of protein-RNA/DNA complexes with purity and stability that are suitable for further biochemical and structural studies. The present approach broadens the repertoire of disulfide-based cross-linking strategies and is a novel tool for the stabilization of protein-RNA complexes in which the interaction occurs via the RNA backbone. This methodology may be broadly applicable to studies of otherwise unstable or transient complexes of proteins with RNA and RNA/DNA.
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Affiliation(s)
- Malwina Hyjek-Składanowska
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland; Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland
| | - Anna R Stasińska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań 61-704, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, Poznań 61-612, Poland
| | - Agnieszka Napiórkowska-Gromadzka
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland; Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland
| | - Aneta Bartłomiejczak
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, United States
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań 61-704, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, Poznań 61-612, Poland.
| | - Marcin Nowotny
- Structural Biology Center, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland; Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., Warsaw 02-109, Poland.
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Abrosimova LA, Samsonova AR, Perevyazova TA, Yunusova AK, Artyukh RI, Romanova EA, Zheleznaya LA, Oretskaya TS, Kubareva EA. The Role of Cysteine Residues in the Interaction of Nicking Endonuclease BspD6I with DNA. Mol Biol 2020. [DOI: 10.1134/s0026893320040020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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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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