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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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Duschmalé J, Hansen HF, Duschmalé M, Koller E, Albaek N, Møller MR, Jensen K, Koch T, Wengel J, Bleicher K. In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3' and 5' thiophosphate linkages. Nucleic Acids Res 2020; 48:63-74. [PMID: 31754711 PMCID: PMC6943131 DOI: 10.1093/nar/gkz1099] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 11/12/2022] Open
Abstract
The introduction of non-bridging phosphorothioate (PS) linkages in oligonucleotides has been instrumental for the development of RNA therapeutics and antisense oligonucleotides. This modification offers significantly increased metabolic stability as well as improved pharmacokinetic properties. However, due to the chiral nature of the phosphorothioate, every PS group doubles the amount of possible stereoisomers. Thus PS oligonucleotides are generally obtained as an inseparable mixture of a multitude of diastereoisomeric compounds. Herein, we describe the introduction of non-chiral 3′ thiophosphate linkages into antisense oligonucleotides and report their in vitro as well as in vivo activity. The obtained results are carefully investigated for the individual parameters contributing to antisense activity of 3′ and 5′ thiophosphate modified oligonucleotides (target binding, RNase H recruitment, nuclease stability). We conclude that nuclease stability is the major challenge for this approach. These results highlight the importance of selecting meaningful in vitro experiments particularly when examining hitherto unexplored chemical modifications.
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Affiliation(s)
- Jörg Duschmalé
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
- To whom correspondence should be addressed. Tel: +41 61 68 86081; Fax: +41 61 68 88714;
| | - Henrik Frydenlund Hansen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Martina Duschmalé
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Erich Koller
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Nanna Albaek
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Marianne Ravn Møller
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Klaus Jensen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Troels Koch
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Konrad Bleicher
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
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Horiba M, Yamaguchi T, Obika S. Synthesis and Properties of Oligonucleotides Having Ethynylphosphonate Linkages. J Org Chem 2020; 85:1794-1801. [PMID: 31867976 DOI: 10.1021/acs.joc.9b01318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ethynylphosphonate (EP)-linked thymidine dimers were synthesized via a palladium-catalyzed cross-coupling reaction and successfully incorporated into oligonucleotides. The oligonucleotides containing EP linkages appropriately formed a duplex with their complementary single-stranded RNA (ssRNA) and single-stranded DNA. The oligonucleotides containing both the EP linkages and 2'-O,4'-C-methylene-bridged nucleic acid/locked nucleic acid exhibited strong duplex-forming ability toward the complementary ssRNA. The EP-modified oligonucleotides exhibited higher exonuclease resistances than their natural counterparts. Moreover, one EP modification to a gapmer-type antisense oligonucleotide resulted in a switch of the cleavage site in the target ssRNA. Therefore, the EP modification can be applied for controlling the cleavage site in the RNase H-dependent mechanism.
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Affiliation(s)
- Masahiko Horiba
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , 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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Islam MA, Fujisaka A, Mori S, Ito KR, Yamaguchi T, Obika S. Synthesis and biophysical properties of 5'-thio-2',4'-BNA/LNA oligonucleotide. Bioorg Med Chem 2018; 26:3634-3638. [PMID: 29886084 DOI: 10.1016/j.bmc.2018.05.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 10/16/2022]
Abstract
Phosphorothioate modification of oligonucleotides is one of the most promising chemical modifications in nucleic acid therapeutics. Structurally similar 5'-thio or phosphorothiolate-modified nucleotides, in which the 5'-bridging oxygen atom is replaced with a sulfur atom, are attracting attention and gaining importance in oligonucleotide-based research. In our present study, we synthesized 5'-thio-2',4'-BNA/LNA monomers bearing thymine or 5-methylcytosine nucleobase. The 5'-thio-2',4'-BNA/LNA monomers were successfully incorporated into target oligonucleotides, and their nuclease stability and binding affinity with complementary strands were evaluated.
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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
| | - Shohei Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kosuke Ramon Ito
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, 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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