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Panigrahi B, Singh RK, Suryakant U, Mishra S, Potnis AA, Jena AB, Kerry RG, Rajaram H, Ghosh SK, Mandal D. Cyclic peptides nanospheres: A '2-in-1' self-assembled delivery system for targeting nucleus and cytoplasm. Eur J Pharm Sci 2022; 171:106125. [PMID: 35033697 DOI: 10.1016/j.ejps.2022.106125] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 11/28/2022]
Abstract
Vascular endothelial growth factor (VEGF) is considered as one of the vital growth factors for angiogenesis, which is primarily responsible for the progress and maintenance of new vascular network in tumor. Numerous studies report that inhibition of VEGF-induced angiogenesis is a potent technique for cancer suppression. Recently, RNA interference, especially small interfering RNA (siRNA) signified a promising approach to suppress the gene expression. However, the clinical implementation of biological macromolecules such as siRNA is significantly limited because of stability and bioavailability issues. Herein, self-assembled peptide nanospheres have been generated from L,L-cyclic peptides using hydrophobic (Trp), positively charged (Arg) and cysteine (Cys) amino acid residues and demonstrated as vehicles for intracellular delivery of VEGF siRNA and VEGF antisense oligonucleotide. Formation of peptide nanostructures is confirmed by HR-TEM, AFM, SEM and DLS analysis. Possible mechanism of self-assembly of the cyclic peptides and their binding with macromolecules are demonstrated by in-silico analysis. Gel electrophoresis reveals that the newly generated peptide based organic materials exhibit strong binding affinity toward siRNAs / antisense oligonucleotides (ASOs) at optimum concentration. Flow cytometry and confocal microscopy results confirm the efficiency of the new biomaterials toward the intracellular delivery of fluorescent labeled siRNA / ASOs. Furthermore, VEGF expression evaluated by western blot and RT-PCR upon the delivery of functional VEGF siRNA/ASOs suggests that very low concentrations of VEGF siRNA/ASOs cause significant gene knockdown at protein and mRNA levels, respectively.
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Affiliation(s)
- Bijayananda Panigrahi
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Campus 11, Patia, Bhubaneswar, Odisha, India 751024; Biopioneer Private Limited, Patia, Bhubaneswar, Odisha, India
| | - Rohit Kumar Singh
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Campus 11, Patia, Bhubaneswar, Odisha, India 751024
| | - Uday Suryakant
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Campus 11, Patia, Bhubaneswar, Odisha, India 751024
| | - Sourav Mishra
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Campus 11, Patia, Bhubaneswar, Odisha, India 751024
| | - Akhilesh A Potnis
- Molecular Biology Division, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, India 400085
| | - Atala B Jena
- Centre Of Excellence In Integrated Omics and Computational Biology, Utkal University, Vani Vihar, Bhubaneswar, Odisha, 751004, India
| | - Rout George Kerry
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha, 751004, India
| | - Hema Rajaram
- Molecular Biology Division, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, India 400085; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India, 400094
| | - Sunil K Ghosh
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, India, 400094; Bio-Organic Division, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, India, 400085
| | - Dindyal Mandal
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Campus 11, Patia, Bhubaneswar, Odisha, India 751024.
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Aho A, Äärelä A, Korhonen H, Virta P. Expanding the Scope of the Cleavable N-(methoxy)oxazolidine Linker for the Synthesis of Oligonucleotide Conjugates. Molecules 2021; 26:490. [PMID: 33477693 PMCID: PMC7838870 DOI: 10.3390/molecules26020490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Oligonucleotides modified by a 2'-deoxy-2'-(N-methoxyamino) ribonucleotide react readily with aldehydes in slightly acidic conditions to yield the corresponding N-(methoxy)oxazolidine-linked oligonucleotide-conjugates. The reaction is reversible and dynamic in slightly acidic conditions, while the products are virtually stable above pH 7, where the reaction is in a ''switched off-state''. Small molecular examinations have demonstrated that aldehyde constituents affect the cleavage rate of the N-(methoxy)oxazolidine-linkage. This can be utilized to adjust the stability of this pH-responsive cleavable linker for drug delivery applications. In the present study, Fmoc-β-Ala-H was immobilized to a serine-modified ChemMatrix resin and used for the automated assembly of two peptidealdehydes and one aldehyde-modified peptide nucleic acid (PNA). In addition, a triantennary N-acetyl-d-galactosamine-cluster with a β-Ala-H unit has been synthesized. These aldehydes were conjugated via N-(methoxy)oxazolidine-linkage to therapeutically relevant oligonucleotide phosphorothioates and one DNA-aptamer in 19-47% isolated yields. The cleavage rates of the conjugates were studied in slightly acidic conditions. In addition to the diverse set of conjugates synthesized, these experiments and a comparison to published data demonstrate that the simple conversion of Gly-H to β-Ala-H residue resulted in a faster cleavage of the N-(methoxy)oxazolidine-linker at pH 5, being comparable (T0.5 ca 7 h) to hydrazone-based structures.
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Affiliation(s)
| | | | | | - Pasi Virta
- Department of Chemistry, University of Turku, 20014 Turku, Finland; (A.A.); (A.Ä.); (H.K.)
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Rajwar A, Morya V, Kharbanda S, Bhatia D. DNA Nanodevices to Probe and Program Membrane Organization, Dynamics, and Applications. J Membr Biol 2020; 253:577-587. [DOI: 10.1007/s00232-020-00154-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/07/2020] [Indexed: 12/18/2022]
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Shang W, Su SN, Shi R, Mou ZD, Yu GQ, Zhang X, Niu D. Generation of Glycosyl Radicals from Glycosyl Sulfoxides and Its Use in the Synthesis of C-linked Glycoconjugates. Angew Chem Int Ed Engl 2020; 60:385-390. [PMID: 32935426 DOI: 10.1002/anie.202009828] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/08/2020] [Indexed: 02/05/2023]
Abstract
We here report glycosyl sulfoxides appended with an aryl iodide moiety as readily available, air and moisture stable precursors to glycosyl radicals. These glycosyl sulfoxides could be converted to glycosyl radicals by way of a rapid and efficient intramolecular radical substitution event. The use of this type of precursors enabled the synthesis of various complex C-linked glycoconjugates under mild conditions. This reaction could be performed in aqueous media and is amenable to the synthesis of glycopeptidomimetics and carbohydrate-DNA conjugates.
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Affiliation(s)
- Weidong Shang
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
| | - Sheng-Nan Su
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
| | - Rong Shi
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
| | - Ze-Dong Mou
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
| | - Guo-Qiang Yu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, China
| | - Xia Zhang
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
| | - Dawen Niu
- Department of Emergency, State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering, Sichuan University, No. 17 Renmin Nan Road, Chengdu, 610041, China
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Shang W, Su S, Shi R, Mou Z, Yu G, Zhang X, Niu D. Generation of Glycosyl Radicals from Glycosyl Sulfoxides and Its Use in the Synthesis of
C
‐linked Glycoconjugates. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009828] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Weidong Shang
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
| | - Sheng‐Nan Su
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
| | - Rong Shi
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
| | - Ze‐Dong Mou
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
| | - Guo‐Qiang Yu
- Discovery Chemistry Unit HitGen Inc. Building 6, No. Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District Chengdu 610200 China
| | - Xia Zhang
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
| | - Dawen Niu
- Department of Emergency State Key Laboratory of Biotherapy, West China Hospital, and School of Chemical Engineering Sichuan University No. 17 Renmin Nan Road Chengdu 610041 China
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Abstract
Efficient intracellular delivery of small-interfering ribonucleic acid (siRNA) to the target organ or tissues in the body is assumed as the main hurdle for a widespread use of siRNAs in the clinics. Solid lipid-based nanoparticles (SLNs) and derivatives can potentially fit this purpose by enabling to overcome the extracellular and intracellular physiological barriers affecting the delivery. For that, rational formulations and rational process designs are needed. This chapter addresses a comprehensive description and critical appraisal of the main production methods of this particular type of lipid nanoparticles and the leading strategies to prompt a targeted delivery of siRNA.
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Affiliation(s)
- Andreia Jorge
- Department of Chemistry, Coimbra Chemistry Centre, University of Coimbra, Coimbra, Portugal.
| | - Alberto Pais
- Department of Chemistry, Coimbra Chemistry Centre, University of Coimbra, Coimbra, Portugal
| | - Carla Vitorino
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
- Center for Neurosciences and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.
- Department of Chemistry, Coimbra Chemistry Centre, University of Coimbra, Coimbra, Portugal.
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Meschaninova MI, Novopashina DS, Semikolenova OA, Silnikov VN, Venyaminova AG. Novel Convenient Approach to the Solid-Phase Synthesis of Oligonucleotide Conjugates. Molecules 2019; 24:E4266. [PMID: 31771111 PMCID: PMC6930482 DOI: 10.3390/molecules24234266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/03/2023] Open
Abstract
A novel and convenient approach for the solid-phase 5'-functionalization of oligonucleotides is proposed in this article. The approach is based on the activation of free 5'-hydroxyl of polymer support-bound protected oligonucleotides by N,N'-disuccinimidyl carbonate followed by interaction with amino-containing ligands. Novel amino-containing derivatives of closo-dodecaborate, estrone, cholesterol, and α-tocopherol were specially prepared. A wide range of oligonucleotide conjugates bearing closo-dodecaborate, short peptide, pyrene, lipophilic residues (cholesterol, α-tocopherol, folate, estrone), aliphatic diamines, and propargylamine were synthesized and characterized to demonstrate the versatility of the approach. The developed method is suitable for the conjugate synthesis of oligonucleotides of different types (ribo-, deoxyribo-, 2'-O-methylribo-, and others).
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Affiliation(s)
- Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Olga A. Semikolenova
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Vladimir N. Silnikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
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8
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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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9
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Grijalvo S, Alagia A, Jorge AF, Eritja R. Covalent Strategies for Targeting Messenger and Non-Coding RNAs: An Updated Review on siRNA, miRNA and antimiR Conjugates. Genes (Basel) 2018; 9:E74. [PMID: 29415514 PMCID: PMC5852570 DOI: 10.3390/genes9020074] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 12/11/2022] Open
Abstract
Oligonucleotide-based therapy has become an alternative to classical approaches in the search of novel therapeutics involving gene-related diseases. Several mechanisms have been described in which demonstrate the pivotal role of oligonucleotide for modulating gene expression. Antisense oligonucleotides (ASOs) and more recently siRNAs and miRNAs have made important contributions either in reducing aberrant protein levels by sequence-specific targeting messenger RNAs (mRNAs) or restoring the anomalous levels of non-coding RNAs (ncRNAs) that are involved in a good number of diseases including cancer. In addition to formulation approaches which have contributed to accelerate the presence of ASOs, siRNAs and miRNAs in clinical trials; the covalent linkage between non-viral vectors and nucleic acids has also added value and opened new perspectives to the development of promising nucleic acid-based therapeutics. This review article is mainly focused on the strategies carried out for covalently modifying siRNA and miRNA molecules. Examples involving cell-penetrating peptides (CPPs), carbohydrates, polymers, lipids and aptamers are discussed for the synthesis of siRNA conjugates whereas in the case of miRNA-based drugs, this review article makes special emphasis in using antagomiRs, locked nucleic acids (LNAs), peptide nucleic acids (PNAs) as well as nanoparticles. The biomedical applications of siRNA and miRNA conjugates are also discussed.
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Affiliation(s)
- Santiago Grijalvo
- Institute of Advanced Chemistry of Catalonia (IQAC, CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Adele Alagia
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Andreia F Jorge
- Coimbra Chemistry Centre, (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC, CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
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10
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Lee SH, Kang YY, Jang HE, Mok H. Current preclinical small interfering RNA (siRNA)-based conjugate systems for RNA therapeutics. Adv Drug Deliv Rev 2016; 104:78-92. [PMID: 26514375 DOI: 10.1016/j.addr.2015.10.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 09/01/2015] [Accepted: 10/12/2015] [Indexed: 01/01/2023]
Abstract
Recent promising clinical results of RNA therapeutics have drawn big attention of academia and industries to RNA therapeutics and their carrier systems. To improve their feasibility in clinics, systemic evaluations of currently available carrier systems under clinical trials and preclinical studies are needed. In this review, we focus on recent noticeable preclinical studies and clinical results regarding siRNA-based conjugates for clinical translations. Advantages and drawbacks of siRNA-based conjugates are discussed, compared to particle-based delivery systems. Then, representative siRNA-based conjugates with aptamers, peptides, carbohydrates, lipids, polymers, and nanostructured materials are introduced. To improve feasibility of siRNA conjugates in preclinical studies, several considerations for the rational design of siRNA conjugates in terms of cleavability, immune responses, multivalent conjugations, and mechanism of action are also presented. Lastly, we discuss lessons from previous preclinical and clinical studies related to siRNA conjugates and perspectives of their clinical applications.
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Affiliation(s)
- Soo Hyeon Lee
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology Zurich (ETHZ), Zurich, Switzerland
| | - Yoon Young Kang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Hyo-Eun Jang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Hyejung Mok
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea.
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11
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Hesser AR, Brandsen BM, Walsh SM, Wang P, Silverman SK. DNA-catalyzed glycosylation using aryl glycoside donors. Chem Commun (Camb) 2016; 52:9259-62. [PMID: 27355482 DOI: 10.1039/c6cc04329a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report the identification by in vitro selection of Zn(2+)/Mn(2+)-dependent deoxyribozymes that glycosylate the 3'-OH of a DNA oligonucleotide. Both β and α anomers of aryl glycosides can be used as the glycosyl donors. Individual deoxyribozymes are each specific for a particular donor anomer.
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Affiliation(s)
- Anthony R Hesser
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
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12
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A new approach to the synthesis of ligands of asialoglycoprotein receptor for targeted delivery of oligonucleotides to hepatocytes. Russ Chem Bull 2016. [DOI: 10.1007/s11172-015-1056-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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13
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Dávalos A, Chroni A. Antisense oligonucleotides, microRNAs, and antibodies. Handb Exp Pharmacol 2015; 224:649-89. [PMID: 25523006 DOI: 10.1007/978-3-319-09665-0_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The specificity of Watson-Crick base pairing and the development of several chemical modifications to oligonucleotides have enabled the development of novel drug classes for the treatment of different human diseases. This review focuses on promising results of recent preclinical or clinical studies on targeting HDL metabolism and function by antisense oligonucleotides and miRNA-based therapies. Although many hurdles regarding basic mechanism of action, delivery, specificity, and toxicity need to be overcome, promising results from recent clinical trials and recent approval of these types of therapy to treat dyslipidemia suggest that the treatment of HDL dysfunction will benefit from these unique clinical opportunities. Moreover, an overview of monoclonal antibodies (mAbs) developed for the treatment of dyslipidemia and cardiovascular disease and currently being tested in clinical studies is provided. Initial studies have shown that these compounds are generally safe and well tolerated, but ongoing large clinical studies will assess their long-term safety and efficacy.
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Affiliation(s)
- Alberto Dávalos
- Laboratory of Disorders of Lipid Metabolism and Molecular Nutrition, Madrid Institute for Advanced Studies (IMDEA)-Food, Ctra. de Cantoblanco 8, 28049, Madrid, Spain,
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14
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Reyes-Darias JA, Sánchez-Luque FJ, Morales JC, Pérez-Rentero S, Eritja R, Berzal-Herranz A. Glucose conjugation of anti-HIV-1 oligonucleotides containing unmethylated CpG motifs reduces their immunostimulatory activity. Chembiochem 2015; 16:584-91. [PMID: 25683851 DOI: 10.1002/cbic.201402574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 02/05/2023]
Abstract
Antisense oligodeoxynucleotides (ODNs) are short synthetic DNA polymers complementary to a target RNA sequence. They are commonly designed to halt a biological event, such as translation or splicing. ODNs are potentially useful therapeutic agents for the treatment of different human diseases. Carbohydrate-ODN conjugates have been reported to improve the cell-specific delivery of ODNs through receptor mediated endocytosis. We tested the anti-HIV activity and biochemical properties of the 5'-end glucose-conjugated GEM 91 ODN targeting the initiation codon of the gag gene of HIV-1 RNA in cell-based assays. The conjugation of a glucose residue significantly reduces the immunostimulatory effect without diminishing its potent anti-HIV-1 activity. No significant effects were observed in either ODN stability in serum, in vitro degradation of antisense DNA-RNA hybrids by RNase H, cell toxicity, cellular uptake and ability to interfere with genomic HIV-1 dimerisation.
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Affiliation(s)
- José A Reyes-Darias
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), Parque Tecnológico de Ciencias de la Salud, Avd. del Conocimiento s/n, Armilla, 18016 Granada (Spain); Present address: Estación Experimental del Zaidín, (EEZ-CSIC), C/ Prof. Albareda, 1, 18008 Granada, (Spain)
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15
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Teze D, Dion M, Daligault F, Tran V, André-Miral C, Tellier C. Alkoxyamino glycoside acceptors for the regioselective synthesis of oligosaccharides using glycosynthases and transglycosidases. Bioorg Med Chem Lett 2013; 23:448-51. [DOI: 10.1016/j.bmcl.2012.11.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/13/2012] [Accepted: 11/18/2012] [Indexed: 12/01/2022]
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16
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Spinelli N, Defrancq E, Morvan F. Glycoclusters on oligonucleotide and PNA scaffolds: synthesis and applications. Chem Soc Rev 2012; 42:4557-73. [PMID: 23254681 DOI: 10.1039/c2cs35406c] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Conjugation of oligonucleotides (ONs) to a variety of reporter groups has been the subject of intensive research during the last decade. Conjugation is indeed of great interest because it can be used not only to improve the existing ONs properties but also to impart new ones. In this context tremendous efforts have been made to conjugate carbohydrate moieties to ONs. Indeed carbohydrates play an important role in biological processes such as signal transduction and cell adhesion through the recognition with sugar-binding proteins (i.e. lectins) located on the surface of cells. For this reason, carbohydrate-oligonucleotide conjugates (COCs) have been first developed for improving the poor cellular uptake or tissue specific delivery of ONs through receptor-mediated endocytosis. Besides the targeted ONs delivery, carbohydrate-oligonucleotide conjugates (COCs) are also evaluated in the context of carbohydrate biochips in which surface coating with carbohydrates is achieved by using the DNA-directed immobilization strategy (DDI). Peptide nucleic acids (PNAs) have also been extensively investigated as a surrogate of DNA for diverse applications. Therefore attachment of carbohydrate moieties to this class of molecules has been studied. The aforementioned applications of COCs require mimicking of the natural processes, in which the weak individual protein-carbohydrate binding is overcome by using multivalent interactions. This tutorial review focuses on the recent advances in carbohydrate-oligonucleotide conjugates and describes the major synthetic approaches available. In addition, an overview of applications that have been developed using various scaffolds allowing multivalent interactions is provided. Finally recent results on the use of peptide nucleic acids as oligonucleotides surrogate are described.
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Affiliation(s)
- Nicolas Spinelli
- Département de Chimie Moléculaire UMR 5250, CNRS Université Joseph Fourier, BP 53-38041, Grenoble cedex 9, France
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17
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Patnaik S, Dash SK, Sethi D, Kumar A, Gupta KC, Kumar P. Engineered polymer-supported synthesis of 3'-carboxyalkyl-modified oligonucleotides and their applications in the construction of biochips for diagnosis of the diseases. Bioconjug Chem 2012; 23:664-70. [PMID: 22369664 DOI: 10.1021/bc200610u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An engineered polymer support 5 has been prepared for the solid-phase assembly of 3'-carboxyalkyl-modified oligonucleotides using commonly available reagents. A two-step deprotection procedure resulted in the quantitative cleavage of oligonucleotides from the support and removal of the protecting groups from phosphodiesters and exocyclic amino groups of the nucleic bases. The fully deprotected oligomers, obtained in high yield, were desalted and analyzed on RP-HPLC. After characterization by MALDI-TOF, these carboxyalkylated oligonucleotides were immobilized onto the epoxy-functionalized glass microslides to prepare biochips. The performance of these biochips was evaluated under different sets of conditions and then successfully validated by the detection of base mismatches and human infectious disease, bacterial meningitis, caused by N. meningitidis.
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Affiliation(s)
- Satyakam Patnaik
- CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, Mall Road, Delhi 110 007, India
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18
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Kedracki D, Safir I, Gour N, Ngo KX, Vebert-Nardin C. DNA–Polymer Conjugates: From Synthesis, Through Complex Formation and Self-assembly to Applications. BIO-SYNTHETIC POLYMER CONJUGATES 2012. [DOI: 10.1007/12_2012_181] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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19
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Schlegel MK, Hütter J, Eriksson M, Lepenies B, Seeberger PH. Defined presentation of carbohydrates on a duplex DNA scaffold. Chembiochem 2011; 12:2791-800. [PMID: 22052782 DOI: 10.1002/cbic.201100511] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Indexed: 01/15/2023]
Abstract
A new method for the spatially defined alignment of carbohydrates on a duplex DNA scaffold is presented. The use of an N-hydroxysuccinimide (NHS)-ester phosphoramidite along with carbohydrates containing an alkylamine linker allows for on-column labeling during solid-phase oligonucleotide synthesis. This modification method during solid-phase synthesis only requires the use of minimal amounts of complex carbohydrates. The covalently attached carbohydrates are presented in the major groove of the B-form duplex DNA as potential substrates for murine type II C-type lectin receptors mMGL1 and mMGL2. CD spectroscopy and thermal melting revealed only minimal disturbance of the overall helical structure. Surface plasmon resonance and cellular uptake studies with bone-marrow-derived dendritic cells were used to assess the capability of these carbohydrate-modified duplexes to bind to mMGL receptors.
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Affiliation(s)
- Mark K Schlegel
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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20
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Pourceau G, Meyer A, Vasseur JJ, Morvan F. Synthesis of a glycomimetic oligonucleotide conjugate by 1,3-dipolar cycloaddition. Methods Mol Biol 2011; 751:167-93. [PMID: 21674331 DOI: 10.1007/978-1-61779-151-2_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
A glycomimetic oligonucleotide conjugate bearing four galactose residues on a mannose core is -synthesized using oligonucleotide solid-phase synthesis and Cu(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC, or "click" chemistry). To achieve this purpose, new building blocks (including the solid support and phosphoramidites) are synthesized and used on a DNA synthesizer to generate a tetraalkyne oligonucleotide, which is then conjugated with a galactose azide derivative by click chemistry to afford the desired 3'-tetragalactosyl-mannose oligonucleotide conjugate. The procedures described in this chapter provide a general approach for the synthesis of novel glycoconjugates that can be immobilized to a DNA chip via DNA-directed immobilization to study, for example, their multivalent interactions with lectins in cellular targeting/uptake, etc.
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21
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Kiviniemi A, Virta P, Drenichev MS, Mikhailov SN, Lönnberg H. Solid-supported 2'-O-glycoconjugation of oligonucleotides by azidation and click reactions. Bioconjug Chem 2011; 22:1249-55. [PMID: 21539388 DOI: 10.1021/bc200097g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
2'-O-[(2-Bromoethoxy)methyl]cytidine and 2'-O-[(2-azidoethoxy)methyl]cytidine have been prepared and introduced as appropriately protected 3'-phosphoramidite (1) and 3'-(H-phosphonate) (2) building blocks, respectively, into 2'-O-methyl oligoribonucleotides. The support-bound oligonucleotides were subjected to two consecutive conjugations with alkynyl-functionalized monosaccharides. The first saccharide was introduced by a Cu(I) promoted click reaction with 2 and the second by azidation of the 2-bromoethoxy group of 1 followed by the click reaction. The influence of the 2'-glycoconjugations on hybridization with DNA and 2'-O-methyl RNA targets was studied. Two saccharide units within a 15-mer oligonucleotide had a barely noticeable effect on the duplex stability, while introduction of a third one moderately decreased the melting temperature.
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Affiliation(s)
- Anu Kiviniemi
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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22
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Kiviniemi A, Virta P, Lönnberg H. Solid-supported synthesis and click conjugation of 4'-C-alkyne functionalized oligodeoxyribonucleotides. Bioconjug Chem 2011; 21:1890-901. [PMID: 20828203 DOI: 10.1021/bc100268w] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
4'-C-[N,N-Di(4-pentyn-1-yl)aminomethyl]thymidine and 4'-C-[N-methyl-N-(4-pentyn-1-yl)aminomethyl]thymidine 3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidites (1, 2) were synthesized, and one or two such monomers were incorporated into a 15-mer oligodeoxyribonucleotide. After chain assembly, azido-functionalized ligands, including appropriate derivatives of 1,4-phenylenedimethaneamine, mannose, paromamine, and neomycin, were conjugated to the alkynyl groups by the click chemistry on a solid support. The influence of the 4'-modifications on the melting temperature with DNA and 2'-O-methyl RNA targets was studied. Oligonucleotides containing one to four mannose ligands in the central part of the chain (up to two 4'-C-[N,N-di(4-pentyn-1-yl)aminomethyl]thymidine units) form equally stable duplexes with complementary 2'-OMe RNA as the corresponding unmodified DNA sequence. At high salt content, the mannose conjugation is even stabilizing. On using a DNA target, a modest destabilization occurs. All the amino group bearing conjugates stabilized the duplexes, the DNA·DNA duplexes more than the DNA·2'-O-methyl RNA duplexes.
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Affiliation(s)
- Anu Kiviniemi
- Department of Chemistry, University of Turku, Turku, Finland
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23
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Aviñó A, Ocampo SM, Lucas R, Reina JJ, Morales JC, Perales JC, Eritja R. Synthesis and in vitro inhibition properties of siRNA conjugates carrying glucose and galactose with different presentations. Mol Divers 2011; 15:751-7. [PMID: 21267652 DOI: 10.1007/s11030-011-9305-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 01/05/2011] [Indexed: 10/18/2022]
Abstract
Oligoribonucleotide conjugates and the corresponding siRNA duplexes against tumor necrosis factor carrying one, two, or four glucose and galactose residues at the 5'-end have been prepared using phosphoramidite chemistry. Carbohydrate-modified siRNA duplexes have similar inhibitory properties than unmodified RNA duplexes in HeLa cells transfected with oligofectamine. When HeLa cells were treated with siRNA carrying one, two, or four glucose residues without oligofectamine, no inhibition was observed. The inhibitory properties of siRNA carrying galactose residues without transfecting agent were tested on HuH-7 cells that have abundant asialoglycoprotein receptors. In these cells siRNA carrying galactose residues have slight anti-TNF inhibitory properties (25% in the best case) that are eliminated if the receptors are blocked with a competitor. These results demonstrate receptor-mediated uptake of siRNA carrying galactose residues, although the efficacy of the process is not enough for efficient RNA interference experiments.
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Affiliation(s)
- Anna Aviñó
- Institute for Research in Biomedicine (IRB Barcelona), Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Baldiri Reixac 10, 08028 Barcelona, Spain
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24
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Ikeda Y, Kubota D, Nagasaki Y. Simple solid-phase synthesis and biological properties of carbohydrate-oligonucleotide conjugates modified at the 3'-terminus. Bioconjug Chem 2010; 21:1685-90. [PMID: 20704260 DOI: 10.1021/bc100205v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A novel synthesis method for oligonucleotides possessing a functional moiety at the 3'-terminus was established based on solid-phase synthesis. In order to install the functional group at the 3'-terminus of the oligonucleotide, a solid support possessing the functional group was prepared. A carbohydrate was employed in this study for the functionalization of the oligonucleotide. To prepare a glycosylated solid support, a novel glycosyl acceptor (2) was synthesized using 4,4-dihydroxymethyl-cyclopenta-1-ene as the starting compound. The glycosylation reaction proceeded smoothly (yield = 95%) to yield the suitable glycosylated compound (3). After 8 was immobilized on the solid support, it was subjected to solid-phase oligonucleotide synthesis by the standard phosphoramidite coupling method. An oligonucleotide possessing a sugar moiety at the 3'-terminus was obtained after the products were deprotected and cleaved from the solid support. The stability of the carbohydrate-modified oligonucleotide was greatly increased even in the serum buffer, indicating that the sugar moiety at the 3'-position improved the resistance against enzymatic degradation. This technique was also applied to RNA synthesis. Galactose-ended siRNA was prepared and was confirmed to possess enough ability, at a concentration of 10 nM, to regulate the expression of the target gene.
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Affiliation(s)
- Yutaka Ikeda
- Grauate School of Pure and Applied Science, Tsukuba Research Center for Interdisciplinary Materials Science, University of Tsukuba, CREST, Japan Science and Technology Agency
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25
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Karskela M, Helkearo M, Virta P, Lönnberg H. Synthesis of oligonucleotide glycoconjugates using sequential click and oximation ligations. Bioconjug Chem 2010; 21:748-55. [PMID: 20225822 DOI: 10.1021/bc900529g] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Oligodeoxyribonucleotide glycoconjugates bearing two trivalent glycoclusters have been synthesized by two alternative methods based on solid-supported oximation of aminooxy functionalized oligonucleotides with glycoclusters constructed by click chemistry. In more detail, the trivalent glycoclusters (5 and 6) bearing three sugar pendants were first assembled by treating a 4-[tri-O-propargylpentaerythrityloxy]benzaldehyde scaffold with methyl 6-azido-6-deoxyglycopyranoside under the click reaction conditions. Two phosphoramidite reagents containing a phthaloyl protected aminooxy function, viz., 2-cyanoethyl N,N-diisopropylphosphoramidites derived from 3-[3,5-bis(phthalimidoxymethyl)phenoxy]propanol (12) and 5-(4,4'-dimethoxytrityl)-1,2-dideoxy-1-C-(2-phthalimidoxyethyl)-beta-d-erythro-pentofuranose (16), were synthesized and incorporated as branching units in appropriate places of the oligonucleotide chains. On using 12, the phthaloyl protections of the branching unit were removed and two identical glycoclusters were attached via oxime linkage to the 5'-terminus of the support-bound oligonucleotide chain. With branching unit 16, the phosphoramidite coupling and the oximation were carried out alternately, allowing introduction of two dissimilar trivalent glycoclusters close to the 3'-end of the oligonucleotide chain. The products (20, 26) were released and deprotected by ammonolysis and purified by HPLC chromatography.
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Affiliation(s)
- Marika Karskela
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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26
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Ustinov AV, Stepanova IA, Dubnyakova VV, Zatsepin TS, Nozhevnikova EV, Korshun VA. Modification of nucleic acids using [3 + 2]-dipolar cycloaddition of azides and alkynes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:437-81. [DOI: 10.1134/s1068162010040011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Singh Y, Murat P, Defrancq E. Recent developments in oligonucleotide conjugation. Chem Soc Rev 2010; 39:2054-70. [PMID: 20393645 DOI: 10.1039/b911431a] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Synthetic oligonucleotides (ONs) are being investigated for various therapeutic and diagnostic applications. The interest in ONs arises because of their capability to cause selective inhibition of gene expression by binding to the target DNA/RNA sequences through mechanisms such as antigene, antisense, and RNA interference. ONs with catalytic activity (ribozymes and DNAzymes) against the target sequences, and ability to bind to the target molecules (aptamers), ranging from small molecules to proteins, are also known. Therefore ONs are considered potentially useful for the treatment of viral diseases and cancer. ONs also find use in the design of DNA microchips (a powerful bio-analytical tool) and novel materials in nanotechnology. However, the clinical success achieved so far with ONs has not been satisfactory, and the major impediments have been recognised as their instability against nucleases, lack of target specificity, and poor uptake and targeted delivery. Tremendous efforts have been made to improve the ON properties by either incorporating chemical modifications in the ON structure or covalently linking (conjugation) reporter groups, with biologically relevant properties, to ONs. Conjugation is of great interest because it can be used not only to improve the existing ON properties but also to impart entirely new properties. This tutorial review focuses on the recent developments in ON conjugation, and describes the key challenges in efficient ON conjugation and major synthetic approaches available for successful ON conjugate syntheses. In addition, an overview on major classes of ON conjugates along with their use in therapeutics, diagnostics and nanotechnology is provided.
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Affiliation(s)
- Yashveer Singh
- Départment of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
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28
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Pourceau G, Meyer A, Vasseur JJ, Morvan F. Azide solid support for 3'-conjugation of oligonucleotides and their circularization by click chemistry. J Org Chem 2009; 74:6837-42. [PMID: 19663415 DOI: 10.1021/jo9014563] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A solid support bearing an azido linker was used to synthesize a 3'-azido-alkyl-oligonucleotide by phosphoramidite chemistry. The resulting oligonucleotide was either conjugated by 1,3-dipolar cycloaddition on solid support or in solution with mannose-propargyl derivative and in solution with dansyl propargyl. Besides, after introduction of an alkyne function at the 5'-end, the resulting oligonucleotide bearing both 3'-azide and 5'-alkyne functions was circularized.
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Affiliation(s)
- Gwladys Pourceau
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université Montpellier 1, Université Montpellier 2, Place Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
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29
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Lönnberg H. Solid-phase synthesis of oligonucleotide conjugates useful for delivery and targeting of potential nucleic acid therapeutics. Bioconjug Chem 2009; 20:1065-94. [PMID: 19175328 DOI: 10.1021/bc800406a] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Olignucleotide-based drugs show promise as a novel form of chemotherapy. Among the hurdles that have to be overcome on the way of applicable nucleic acid therapeutics, inefficient cellular uptake and subsequent release from endosomes to cytoplasm appear to be the most severe ones. Covalent conjugation of oligonucleotides to molecules that expectedly facilitate the internalization, targets the conjugate to a specific cell-type or improves the parmacokinetics offers a possible way to combat against these shortcomings. Since workable chemistry is a prerequisite for biological studies, development of efficient and reproducible methods for preparation of various types of oligonucleotide conjugates has become a subject of considerable importance. The present review summarizes the advances made in the solid-supported synthesis of oligonucleotide conjugates aimed at facilitating the delivery and targeting of nucleic acid drugs.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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30
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Synthesis and characterization of mannosylated oligoribonucleotides. Carbohydr Res 2009; 344:2137-43. [PMID: 19765694 DOI: 10.1016/j.carres.2009.08.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 08/13/2009] [Accepted: 08/25/2009] [Indexed: 10/20/2022]
Abstract
Oligoribonucleotide (RNA)-carbohydrate conjugates bearing mono- and divalent mannosides were readily obtained using 3,4-diethoxy-3-cyclobutene-1,2-dione as the linking agent in the presence of trace amount of triethylamine. The glycoconjugates were purified by HPLC and characterized by electrospray mass spectroscopy.
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31
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Karskela M, Virta P, Malinen M, Urtti A, Lönnberg H. Synthesis and cellular uptake of fluorescently labeled multivalent hyaluronan disaccharide conjugates of oligonucleotide phosphorothioates. Bioconjug Chem 2009; 19:2549-58. [PMID: 19053300 DOI: 10.1021/bc800260y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Clustered hyaluronan disaccharides were studied as mediators of cellular delivery of antisense oligonucleotides through receptor-mediated endocytosis. For this purpose, a synthetic route for preparation of an appropriately protected hyaluronic acid dimer bearing an aldehyde tether (1) was devised. Up to three non-nucleosidic phosphoramidite building blocks (2), each bearing two phthaloyl protected aminooxy groups, were then inserted into the 3'-terminus of the desired phosphorothioate oligodeoxyribonucleotide, and 6-FAM phosphoramidite was introduced into the 5'-terminus. After completion of the chain assembly, the aldehyde-tethered sugar ligands were attached to the deprotected aminooxy functions by on-support oximation. Three fluorescein-labeled phosphorothioate oligonucleotide glycoconjugates (28-30) containing two, four, or six hyaluronan disaccharides were prepared. The influence of the hyaluronan moieties on the cellular uptake of the thioated oligonucleotides was tested in a cell line expressing the hyaluronan receptor CD44. Specific uptake was not detected with this combination of multiple hyaluronan disaccharides.
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Affiliation(s)
- Marika Karskela
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland.
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32
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Weisbrod SH, Marx A. Novel strategies for the site-specific covalent labelling of nucleic acids. Chem Commun (Camb) 2008:5675-85. [PMID: 19009049 DOI: 10.1039/b809528k] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To broaden the scope of applications in DNA nano- and biotechnology, material science, diagnostics and molecular recognition the functionalization of DNA is of utmost importance. In the last decade many new methods have been developed to achieve this goal. Apart from the direct chemical synthesis of modified DNA by automated phosphoramidite chemistry incorporation of labelled triphosphates and the post-synthetic labelling approach evolved as valuable methods. New bioorthogonal reactions as Diels-Alder, click and Staudinger ligations pushed forward the post-synthetic approach as new insights into DNA polymerase substrate specificity allowed generation and amplification of labelled DNA strands. These novel developments are summarized herein.
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Affiliation(s)
- Samuel H Weisbrod
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457, Konstanz, Germany
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33
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Ding H, Yang R, Song Y, Xiao Q, Wu J. A highly efficient and selective synthesis of 1,2,3-triazole linked saccharide nucleosides via "click chemistry". NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:368-75. [PMID: 18404571 DOI: 10.1080/15257770801944055] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A series of 1,2,3-triazole linked saccharide nucleosides were synthesized in high yield and selectivity via "click chemistry" of the 3'-azido-2'-deoxythymidine and the propargyl carbohydrates. [image omitted].
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Affiliation(s)
- Haixin Ding
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science & Technology Normal University, Jiangxi, PR China
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34
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Preparation of carbohydrate-oligonucleotide conjugates using the squarate spacer. Bioorg Med Chem Lett 2008; 17:6535-8. [PMID: 17935985 DOI: 10.1016/j.bmcl.2007.09.078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2007] [Accepted: 09/24/2007] [Indexed: 02/04/2023]
Abstract
Attachment of carbohydrates to oligonucleotides has proven to induce receptor-mediated endocytosis. A facile method for the formation of covalent linkages between glycans and oligonucleotides is herein described. Thus, use of 3,4-diethoxy-3-cyclobutene-1,2-dione as a linking reagent provides easy conjugation between carbohydrates bearing an amino group at the reducing end and oligonucleotides bearing an aminoalkyl modification.
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35
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D'Onofrio J, Petraccone L, Martino L, Di Fabio G, Iadonisi A, Balzarini J, Giancola C, Montesarchio D. Synthesis, biophysical characterization, and anti-HIV activity of glyco-conjugated G-quadruplex-forming oligonucleotides. Bioconjug Chem 2008; 19:607-16. [PMID: 18254584 DOI: 10.1021/bc7003395] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel hybrid oligonucleotides carrying the G-quadruplex-forming d(5'TGGGAG3') sequence, conjugated with mono- or disaccharides at the 3' or 5'-end through phosphodiester bonds, have been synthesized as potential anti-HIV agents, via a fully automated, online phosphoramidite-based solid-phase strategy. CD-monitored thermal denaturation studies on the resulting quadruplexes indicated the insertion of a single monosaccharide at the 3'-end as the optimal modification, conferring improved stability to the quadruplex complex. In addition, the 3'-conjugation with glucose or mannose converted the anti-HIV inactive unmodified oligomer into active compounds. On the contrary, the 5'-tethering with these monosaccharides, as well as the conjugation, either at the 5' or 3'-end, with sucrose, were in all cases detrimental to quadruplex stability and did not improve the biological activity. On the basis of the assumption that the kinetically and thermodynamically favored formation of the quadruplex complex is a prerequisite for efficient antiviral activity, a novel bis-conjugated oligonucleotide was designed. This combined a mannose residue at the 3'-phosphate end with bulky aromatic tert-butyldiphenylsilyl (TBDPS) group at the 5'-end, previously shown to markedly favor the formation of quadruplex complexes. The 5',3'-bis-conjugated 6-mer, for which a detailed biophysical characterization has been carried out, resulted in 3-fold greater antiviral activity against HIV-1 than the sole 3'-glyco-conjugated oligonucleotide.
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Affiliation(s)
- Jennifer D'Onofrio
- Dipartimento di Chimica Organica e Biochimica and Dipartimento di Chimica Paolo Corradini, Università degli Studi di Napoli Federico II, Via Cintia 4, I-80126 Napoli, Italy
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36
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Andreotti G, Trincone A, Giordano A. Convenient synthesis of β-galactosyl nucleosides using the marine β-galactosidase from Aplysia fasciata. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.molcatb.2007.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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37
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Yan H, Tram K. Glycotargeting to improve cellular delivery efficiency of nucleic acids. Glycoconj J 2007; 24:107-23. [PMID: 17268860 DOI: 10.1007/s10719-006-9023-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Revised: 11/07/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Abstract
Nucleic acids bearing glycans of various structures have been under vigorous investigation in the past decade. The carbohydrate moieties of such complexes can serve as recognition sites for carbohydrate-binding proteins-lectins-and initiate receptor-mediated endocytosis. Therefore, carbohydrates can enhance cell targeting and internalization of nucleic acids that are associated with them and thus improve the bioavailability of nucleic acids as therapeutic agents. This review summarizes nucleic acid glycosylation in nature and approaches for the preparation of both non-covalently associated and covalently-linked carbohydrate-nucleic acid complexes.
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Affiliation(s)
- Hongbin Yan
- Department of Chemistry, Brock University, 500 Glenridge Ave., St. Catharines, ON, Canada.
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38
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Singh Y, Spinelli N, Defrancq E, Dumy P. A novel heterobifunctional linker for facile access to bioconjugates. Org Biomol Chem 2006; 4:1413-9. [PMID: 16557331 DOI: 10.1039/b518151h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A convenient synthesis of a novel heterobifunctional linker molecule is described. The linker contains a thiol-reactive nitropyridyl disulfide group (Npys) and an aldehyde-reactive aminooxy group with a propensity to form disulfide and oxime linkages. The utility of the linker molecule to cross-link different biomolecules has been demonstrated by employing it in the efficient preparation of a peptide-oligonucleotide conjugate. The linker reported herein could be a useful tool for cross-coupling of different but appropriately functionalised biomolecules.
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Affiliation(s)
- Yashveer Singh
- LEDSS, UMR CNRS 5616, ICMG FR 2607, Université Joseph Fourier, 301 rue de la Chimie, BP 53, F 38041, Grenoble Cedex 9, France
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39
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Singh Y, Renaudet O, Defrancq E, Dumy P. Preparation of a multitopic glycopeptide-oligonucleotide conjugate. Org Lett 2006; 7:1359-62. [PMID: 15787506 DOI: 10.1021/ol050134n] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
[structure: see text] A novel strategy to prepare glycopeptide-oligonucleotide conjugates bearing a glycocluster is reported. The strategy utilizes a cyclodecapeptide scaffold as a key intermediate to anchor the carbohydrate cluster and the oligonucleotide through sequential oxime bond formation. The oligonucleotide glycocluster retains the binding affinity and recognition specificity for the target sequence. Furthermore, the conjugate shows enhanced binding to the specific lectins due to the cooperative effect produced by the carbohydrate cluster.
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Affiliation(s)
- Yashveer Singh
- LEDSS, UMR CNRS 5616, ICMG FR 2607, Université Joseph Fourier, BP 53, F 38041, Grenoble Cedex 9, France
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