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Danielsen MB, Wengel J. Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides. Beilstein J Org Chem 2021; 17:1828-1848. [PMID: 34386102 PMCID: PMC8329367 DOI: 10.3762/bjoc.17.125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 12/20/2022] Open
Abstract
Antisense oligonucleotides (ASOs) have the ability of binding to endogenous nucleic acid targets, thereby inhibiting the gene expression. Although ASOs have great potential in the treatment of many diseases, the search for favorable toxicity profiles and distribution has been challenging and consequently impeded the widespread use of ASOs as conventional medicine. One strategy that has been employed to optimize the delivery profile of ASOs, is the functionalization of ASOs with cationic amine groups, either by direct conjugation onto the sugar, nucleobase or internucleotide linkage. The introduction of these positively charged groups has improved properties like nuclease resistance, increased binding to the nucleic acid target and improved cell uptake for oligonucleotides (ONs) and ASOs. The modifications highlighted in this review are some of the most prevalent cationic amine groups which have been attached as single modifications onto ONs/ASOs. The review has been separated into three sections, nucleobase, sugar and backbone modifications, highlighting what impact the cationic amine groups have on the ONs/ASOs physiochemical and biological properties. Finally, a concluding section has been added, summarizing the important knowledge from the three chapters, and examining the future design for ASOs.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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2
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Cho CA, Liang C, Perera J, Brimble MA, Swift S, Jin J. Guanidinylated Amphiphilic Polycarbonates with Enhanced Antimicrobial Activity by Extending the Length of the Spacer Arm and Micelle Self-Assembly. Macromol Biosci 2020; 20:e2000065. [PMID: 32459065 DOI: 10.1002/mabi.202000065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/01/2020] [Indexed: 01/23/2023]
Abstract
Nine guanidinylated amphiphilic polycarbonates are rationally designed and synthesized. Each polymer has the same biodegradable backbone but different side groups. The influence of the hydrophobic/hydrophilic effect on antimicrobial activities and cytotoxicity is systematically investigated. The results verify that tuning the length of the spacer arm between the cationic guanidine group and the polycarbonate backbone is an efficient design strategy to alter the hydrophobic/hydrophilic balance without changing the cationic charge density. A spacer arm of six methylene units (CH2 )6 shows the best antimicrobial activity (minimum inhibitory concentration, MIC = 40 µg mL-1 against Escherichia coli, MIC = 20 µg mL-1 against Staphylococcus aureus, MIC = 40 µg mL-1 against Candida albicans) with low hemolytic activity (HC50 > 2560 µg mL-1 ). Furthermore, the guanidinylated polycarbonates exhibit the ability to self-assemble and present micelle-like nanostructure due to their intrinsic amphiphilic macromolecular structure. Transmission electron microscopy and dynamic light scattering measurements confirm polymer micelle formation in aqueous solution with sizes ranging from 82 to 288 nm.
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Affiliation(s)
- Chloe A Cho
- School of Chemical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Chao Liang
- School of Chemical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Janesha Perera
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, 1142, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, 1142, New Zealand
| | - Jianyong Jin
- School of Chemical Sciences, University of Auckland, Auckland, 1142, New Zealand
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3
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Islam MA, Fujisaka A, Kawakami J, Yamaguchi T, Obika S. Different reactivity of Sp and Rp isomers of phosphorothioate-modified oligonucleotides in a duplex structure. Bioorg Med Chem Lett 2020; 30:127166. [PMID: 32527537 DOI: 10.1016/j.bmcl.2020.127166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 10/24/2022]
Abstract
The presence of a stereoisomeric center at the phosphorus atom in phosphorothioate-modified oligonucleotides (PS-ONs) has been recognized as an important feature since the early stages of their development. Therefore, several studies have been conducted on the chirality of PS-ONs. In this study, we evaluated the stereo-biased chemistry of PS-ON duplexes. Depending on their absolute configurations, PS-ON duplexes were found to have significantly different and stereospecific reactivities towards simple alkylating reagent.
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Affiliation(s)
- Md Ariful Islam
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali 3814, Bangladesh
| | - Aki Fujisaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Faculty of Pharmacy, Osaka Ohtani University, Nishikiori-Kita 3-11-1, Tondabayashi, Osaka 584-8540, Japan
| | - Junji Kawakami
- Faculty of Frontiers of Innovative Research in Science and Technology, Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Soboleva T, Esquer HJ, Anderson SN, Berreau LM, Benninghoff AD. Mitochondrial-Localized Versus Cytosolic Intracellular CO-Releasing Organic PhotoCORMs: Evaluation of CO Effects Using Bioenergetics. ACS Chem Biol 2018; 13:2220-2228. [PMID: 29932318 PMCID: PMC6117112 DOI: 10.1021/acschembio.8b00387] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
While interactions between carbon monoxide (CO) and mitochondria have been previously studied, the methods used to deliver CO (gas or CO-releasing metal carbonyl compounds) lack subcellular targeting and/or controlled delivery. Thus, the effective concentration needed to produce changes in mitochondrial bioenergetics is yet to be fully defined. To evaluate the influence of mitochondrial-targeted versus intracellularly released CO on mitochondrial oxygen consumption rates, we developed and characterized flavonol-based CO donor compounds that differ at their site of release. These molecules are metal-free, visible light triggered CO donors (photoCORMs) that quantitatively release CO and are trackable in cells via confocal microscopy. Our studies indicate that at a concentration of 10 μM, the mitochondrial-localized and cytosolic CO-releasing compounds are similarly effective in terms of decreasing ATP production, maximal respiration, and the reserve capacity of A549 cells. This concentration is the lowest to impart changes in mitochondrial bioenergetics for any CO-releasing molecule (CORM) reported to date. The results reported herein demonstrate the feasibility of using a structurally tunable organic photoCORM framework for comparative intracellular studies of the biological effects of carbon monoxide.
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Affiliation(s)
- Tatiana Soboleva
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Hector J. Esquer
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah 84322-4815, United States
| | - Stacey N. Anderson
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Lisa M. Berreau
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Abby D. Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah 84322-4815, United States
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5
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Meng M, Ducho C. Oligonucleotide analogues with cationic backbone linkages. Beilstein J Org Chem 2018; 14:1293-1308. [PMID: 29977397 PMCID: PMC6009206 DOI: 10.3762/bjoc.14.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/26/2018] [Indexed: 12/28/2022] Open
Abstract
Their unique ability to selectively bind specific nucleic acid sequences makes oligonucleotides promising bioactive agents. However, modifications of the nucleic acid structure are an essential prerequisite for their application in vivo or even in cellulo. The oligoanionic backbone structure of oligonucleotides mainly hampers their ability to penetrate biological barriers such as cellular membranes. Hence, particular attention has been given to structural modifications of oligonucleotides which reduce their overall number of negative charges. One such approach is the site-specific replacement of the negatively charged phosphate diester linkage with alternative structural motifs which are positively charged at physiological pH, thus resulting in zwitterionic or even oligocationic backbone structures. This review provides a general overview of this concept and summarizes research on four according artificial backbone linkages: aminoalkylated phosphoramidates (and related systems), guanidinium groups, S-methylthiourea motifs, and nucleosyl amino acid (NAA)-derived modifications. The synthesis and properties of the corresponding oligonucleotide analogues are described.
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Affiliation(s)
- Melissa Meng
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
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Álvarez Porebski PW, Lynen F. Offline comprehensive liquid chromatography in combination with a Deoxyribonuclease I immobilized enzymatic reactor for selective screening of oligonucleotide mixtures. J Chromatogr A 2016; 1451:164-168. [PMID: 27208984 DOI: 10.1016/j.chroma.2016.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/01/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
The development of a comprehensive ion-pair chromatography-immobilized enzyme reactor×ion-pair chromatography (IPC-IMER×IPC) methodology for the advanced characterization of DNA/RNA oligonucleotides (ONs) mixtures has been carried out. More in detail, a DNase I IMER has been coupled to IPC in the post column configuration, followed by the collection of the eluting fractions and reanalysis by IPC. The effect of the mobile phase over the IMER activity was qualitatively evaluated. The methodology proved to generate relevant ON degradation profiles that might be correlated with the ON stability towards nucleases. Moreover, this platform shows potential for its further implementation in selective analysis of ON mixtures and in mapping studies.
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Affiliation(s)
- Piotr Wiktor Álvarez Porebski
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
| | - Frederic Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
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Milton S, Honcharenko D, Rocha CSJ, Moreno PMD, Smith CIE, Strömberg R. Nuclease resistant oligonucleotides with cell penetrating properties. Chem Commun (Camb) 2015; 51:4044-7. [PMID: 25664358 DOI: 10.1039/c4cc08837a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
2'-O-AECM modified oligonucleotides provide an unusual combination of remarkable properties. This includes the combination of high resistance towards enzymatic degradation and the spontaneous cellular uptake of AECM oligonucleotides.
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Affiliation(s)
- Stefan Milton
- Karolinska Institutet, Department of Biosciences and Nutrition, Novum, Hälsovägen 7, SE-14183, Huddinge, Sweden.
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Álvarez Porebski PW, Gyssels E, Madder A, Lynen F. Hyphenation of a Deoxyribonuclease I immobilized enzyme reactor with liquid chromatography for the online stability evaluation of oligonucleotides. J Chromatogr A 2015; 1422:18-26. [PMID: 26515385 DOI: 10.1016/j.chroma.2015.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/05/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
The stability of antisense oligonucleotides (ONs) toward nucleases is a key aspect for their possible implementation as therapeutic agents. Typically, ON stability studies are performed off-line, where the ONs are incubated with nucleases in solution, followed by their analysis. The problematics of off-line processing render the detailed comparison of relative ON stability quite challenging. Therefore, the development of an online platform based on an immobilized enzyme reactor (IMER) coupled to liquid chromatography (LC) was developed as an alternative for improved ON stability testing. More in detail, Deoxyribonuclease I (DNase I) was immobilized on epoxy-silica particles of different pore sizes and packed into a column for the construction of an IMER. Subsequently, the hyphenation of the IMER with ion-pair chromatography (IPC) and ion-exchange chromatography (IEC) was evaluated, leading to the successful development of two online methodologies: IMER-IPC and IMER-IEC. More specifically, natural and modified DNA and RNA oligonucleotides were used for testing the performance of the methodologies. Both methodologies proved to be simple, automatable, fast and highly reproducible for the quantitative and qualitative evaluation of ON degradation. In addition, the extended IMER life time in combination with a more straightforward control of the reaction kinetics substantiate the applicability of the IMER-LC platform for ON stability tests and its implementation in routine and research laboratories.
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Affiliation(s)
- Piotr Wiktor Álvarez Porebski
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
| | - Ellen Gyssels
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
| | - Frederic Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
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Brzezinska J, Markiewicz WT. Non-Nucleosidic Analogues of Polyaminonucleosides and Their Influence on Thermodynamic Properties of Derived Oligonucleotides. Molecules 2015; 20:12652-69. [PMID: 26184145 PMCID: PMC6332422 DOI: 10.3390/molecules200712652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/08/2015] [Accepted: 07/09/2015] [Indexed: 11/22/2022] Open
Abstract
The rationale for the synthesis of cationic modified nucleosides is higher expected nuclease resistance and potentially better cellular uptake due to an overall reduced negative charge based on internal charge compensation. Due to the ideal distance between cationic groups, polyamines are perfect counterions for oligodeoxyribonucleotides. We have synthesized non-nucleosidic analogues built from units that carry different diol structures instead of sugar residues and functionalized with polyamines. The non-nucleosidic analogues were attached as internal or 5′-terminal modifications in oligodeoxyribonucleotide strands. The thermodynamic studies of these polyaminooligonucleotide analogues revealed stabilizing or destabilizing effects that depend on the linker or polyamine used.
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Affiliation(s)
- Jolanta Brzezinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
| | - Wojciech T Markiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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Sharma VK, Sharma RK, Singh SK. Antisense oligonucleotides: modifications and clinical trials. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00184b] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Sharma VK, Rungta P, Prasad AK. Nucleic acid therapeutics: basic concepts and recent developments. RSC Adv 2014. [DOI: 10.1039/c3ra47841f] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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