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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: 3] [Impact Index Per Article: 1.0] [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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Yanachkov I, Zavizion B, Metelev V, Stevens LJ, Tabatadze Y, Yanachkova M, Wright G, Krichevsky AM, Tabatadze DR. Self-neutralizing oligonucleotides with enhanced cellular uptake. Org Biomol Chem 2018; 15:1363-1380. [PMID: 28074950 DOI: 10.1039/c6ob02576e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
There is tremendous potential for oligonucleotide (ON) therapeutics, but low cellular penetration due to their polyanionic nature is a major obstacle. We addressed this problem by developing a new approach for ON charge neutralization in which multiple branched charge-neutralizing sleeves (BCNSs) are attached to the internucleoside phosphates of ON by phosphotriester bonds. The BCNSs are terminated with positively charged amino groups, and are optimized to form ion pairs with the neighboring phosphate groups. The new modified ONs can be prepared by standard automated phosphoramidite chemistry in good yield and purity. They possess good solubility and hybridization properties, are not involved in non-standard intramolecular aggregation, have low cytotoxicity, adequate chemical stability, improved serum stability, and above all, display significantly enhanced cellular uptake. Thus, the new ON derivatives exhibit properties that make them promising candidates for the development of novel therapeutics or research tools for modulation of the expression of target genes.
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Affiliation(s)
- Ivan Yanachkov
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA. and GLSynthesis, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - Boris Zavizion
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA.
| | - Valeri Metelev
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA. and Department of Chemistry, Moscow State University, Leninskye gory1/40, Moscow 119991, Russian Federation
| | - Laura J Stevens
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA.
| | | | - Milka Yanachkova
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA. and GLSynthesis, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - George Wright
- GLSynthesis, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, USA
| | - David R Tabatadze
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA.
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Polyamine-oligonucleotide conjugates: a promising direction for nucleic acid tools and therapeutics. Future Med Chem 2015; 7:1733-49. [PMID: 26424049 DOI: 10.4155/fmc.15.90] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Chemical modification and/or the conjugation of small functional molecules to oligonucleotides have significantly improved their biological and biophysical properties, addressing issues such as poor cell penetration, stability to nucleases and low affinity for their targets. Here, the authors review the literature reporting on the biophysical, biochemical and biological properties of one particular class of modification - polyamine-oligonucleotide conjugates. Naturally derived and synthetic polyamines have been grafted onto a variety of oligonucleotide formats, including antisense oligonucleotides and siRNAs. In many cases this has had beneficial effects on their properties such as target hybridization, nuclease resistance, cellular uptake and activity. Polyamine-oligonucleotide conjugation, therefore, represents a promising direction for the further development of oligonucleotide-based therapeutics and tools.
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Brzezinska J, Gdaniec Z, Popenda L, Markiewicz WT. Polyaminooligonucleotide: NMR structure of duplex DNA containing a nucleoside with spermine residue, N-[4,9,13-triazatridecan-1-yl]-2'-deoxycytidine. Biochim Biophys Acta Gen Subj 2013; 1840:1163-70. [PMID: 24361616 DOI: 10.1016/j.bbagen.2013.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/26/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
Abstract
BACKGROUND The nature of the polyamine-DNA interactions at a molecular level is not clearly understood. METHODS In order to shed light on the binding preferences of polyamine with nucleic acids, the NMR solution structure of the DNA duplex containing covalently bound spermine was determined. RESULTS The structure of 4-N-[4,9,13-triazatridecan-1-yl]-2'-deoxycytidine (dCSp) modified duplex was compared to the structure of the reference duplex. Both duplexes are regular right-handed helices with all attributes of the B-DNA form. The spermine chain which is located in a major groove and points toward the 3' end of the modified strand does not perturb the DNA structure. CONCLUSION In our study the charged polyamine alkyl chain was found to interact with the DNA surface. In the majority of converged structures we identified the presumed hydrogen bonding interactions between O6 and N7 atoms of G4 and the first internal -NH2(+)- amino group. Additional interaction was found between the second internal -NH2(+)- amino group and the oxygen atom of the phosphate of C3 residue. GENERAL SIGNIFICANCE The knowledge of the location and nature of a structure-specific binding site for spermine in DNA should be valuable in understanding gene expression and in the design of new therapeutic drugs.
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Affiliation(s)
- Jolanta Brzezinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, PL-61704 Poznan, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, PL-61704 Poznan, Poland.
| | - Lukasz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, PL-61704 Poznan, Poland
| | - Wojciech T Markiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, PL-61704 Poznan, Poland.
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Müller S, Appel B, Krellenberg T, Petkovic S. The many faces of the hairpin ribozyme: Structural and functional variants of a small catalytic rna. IUBMB Life 2011; 64:36-47. [DOI: 10.1002/iub.575] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 08/18/2011] [Indexed: 12/15/2022]
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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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Levina AS, Mikhaleva EA, Repkova MN, Zarytova VF. [Synthesis of polyamine-containing oligonucleotides]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2008; 34:89-95. [PMID: 18365743 DOI: 10.1134/s1068162008010111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A simple and efficient method of synthesis of polyamine-oligonucleotide conjugates in high yields (up to 95%) was suggested. The terminal phosphate group of deprotected oligonucleotides was selectively activated with the redox pair triphenylphosphine-dipyridyl disulfide in the presence of a nucleophilic catalyst, and the activated oligonucleotide derivative was subjected to the reaction with a polyamine.
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Keniry MA, Owen EA. An investigation of the dynamics of spermine bound to duplex and quadruplex DNA by (13)C NMR spectroscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:637-46. [PMID: 17598053 DOI: 10.1007/s00249-007-0136-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 01/14/2007] [Accepted: 01/17/2007] [Indexed: 11/30/2022]
Abstract
A detailed analysis of the (13)C relaxation of (13)C-labelled spermine bound to duplex and quadruplex DNA is presented. T(1), T(2) and heteronuclear NOE data were collected at four (13)C frequencies (75.4, 125.7, 150.9 and 201.2 MHz). The data were analyzed in terms of a frequency-dependent order parameter, S (2)(omega), to estimate the generalized order parameter and the contributions to the relaxation from different motional frequencies in the picosecond-nanosecond timescale and from any exchange processes that may be occurring on the microsecond-millisecond timescale. The relaxation data was surprisingly similar for spermine bound to two different duplexes and a linear parallel quadruplex. Analysis of the relaxation data from these complexes confirmed the conclusions of previous studies that the dominant motion of spermine is independent of the macroscopic tumbling of the DNA and has an effective correlation time of approximately 50 ps. In contrast, spermine bound to a folded antiparallel quadruplex had faster relaxation rates, especially R (2). As with the other complexes, a fast internal motion of the order of 50 ps makes a substantial contribution to the relaxation. The generalized order parameter for spermine bound to duplex DNA and the linear quadruplex is small but is larger for spermine bound to the folded quadruplex. In the latter case, there is evidence for exchange between at least two populations of spermine occurring on the microsecond-millisecond timescale.
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Affiliation(s)
- Max A Keniry
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia.
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Pons B, Kotera M, Zuber G, Behr JP. Online synthesis of diblock cationic oligonucleotides for enhanced hybridization to their complementary sequence. Chembiochem 2006; 7:1173-6. [PMID: 16874748 DOI: 10.1002/cbic.200600178] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Bénédicte Pons
- Laboratoire de Chimie Génétique associé au C.N.R.S. Université Louis Pasteur de Strasbourg, Faculté de Pharmacie, B.P. 24, 67401 Illkirch, France
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Cooke LA, Frauendorf C, Gîlea MA, Holmes SC, Vyle JS. Solid-phase synthesis of terminal oligonucleotide–phosphoramidate conjugates. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2005.11.098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kovacheva YS, Tzokov SB, Murray IA, Grasby JA. The role of phosphate groups in the VS ribozyme-substrate interaction. Nucleic Acids Res 2004; 32:6240-50. [PMID: 15576350 PMCID: PMC535666 DOI: 10.1093/nar/gkh957] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The VS ribozyme trans-cleavage substrate interacts with the catalytic RNA via tertiary interactions. To study the role of phosphate groups in the ribozyme-substrate interaction, 18 modified substrates were synthesized, where an epimeric phosphorothioate replaces one of the phosphate diester linkages. Sites in the stem-loop substrate where phosphorothioate substitution impaired reaction cluster in two regions. The first site is the scissile phosphate diester linkage and nucleotides downstream of this and the second site is within the loop region. The addition of manganese ions caused recovery of the rate of reaction for phosphorothioate substitutions between A621 and A622 and U631 and C632, suggesting that these two phosphate groups may serve as ligands for two metal ions. In contrast, significant manganese rescue was not observed for the scissile phosphate diester linkage implying that electrophilic catalysis by metal ions is unlikely to contribute to VS ribozyme catalysis. In addition, an increase in the reaction rate of the unmodified VS ribozyme was observed when a mixture of magnesium and manganese ions acted as the cofactor. One possible explanation for this effect is that the cleavage reaction of the VS ribozyme is rate limited by a metal dependent docking of the substrate on the ribozyme.
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Affiliation(s)
- Yana S Kovacheva
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK
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