1
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Zhang L, Liu Y, Li CX, Zhu L, Xiong GY, Fan SL, Dai JJ, Xiao H. Phosphine-Promoted Tandem Intermolecular Diels-Alder Reactions with Pentadienyl 4-Nitrobenzoate as a Diene Precursor. Org Lett 2023; 25:6506-6510. [PMID: 37624728 DOI: 10.1021/acs.orglett.3c02209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
A phosphine-promoted tandem Diels-Alder reaction using pentadienyl 4-nitrobenzoate (α-vinyl MBH adduct) as a diene precursor with 3-olefinic oxindoles or CF3-activated ketones as dienophiles has been developed. The reaction proceeds through the formation of a pentadienyl phosphonium intermediate via SN2'' addition, which acts as both a D-A diene and a precursor for the exomethylene moiety. This method offers a metal-free and step-efficient approach for synthesizing exomethylene-bearing spirooxindoles and dihydropyrans, which are privileged structures found in natural products.
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Affiliation(s)
- Le Zhang
- School of Food and Biological Engineering, Hefei University of Technology, 485 Danxia Road, Hefei, 230601, P. R. China
| | - Ye Liu
- School of Food and Biological Engineering, Hefei University of Technology, 485 Danxia Road, Hefei, 230601, P. R. China
| | - Chao-Xu Li
- School of Food and Biological Engineering, Hefei University of Technology, 485 Danxia Road, Hefei, 230601, P. R. China
| | - Lei Zhu
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, School of Chemistry and Materials Science, Hubei Engineering University, Xiaogan, 432000, P. R. China
| | - Guo-Yin Xiong
- School of Food and Biological Engineering, Hefei University of Technology, 485 Danxia Road, Hefei, 230601, P. R. China
| | - Shi-Lu Fan
- School of Food and Biological Engineering, Hefei University of Technology, 485 Danxia Road, Hefei, 230601, P. R. China
| | - Jian-Jun Dai
- School of Food and Biological Engineering, Hefei University of Technology, 485 Danxia Road, Hefei, 230601, P. R. China
| | - Hua Xiao
- School of Food and Biological Engineering, Hefei University of Technology, 485 Danxia Road, Hefei, 230601, P. R. China
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, School of Chemistry and Materials Science, Hubei Engineering University, Xiaogan, 432000, P. R. China
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2
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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3
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Nietzold F, Rubner S, Labuzek B, Golik P, Surmiak E, Del Corte X, Kitel R, Protzel C, Reppich-Sacher R, Stichel J, Magiera-Mularz K, Holak TA, Berg T. Nutlin-3a-aa: Improving the Bioactivity of a p53/MDM2 Interaction Inhibitor by Introducing a Solvent-Exposed Methylene Group. Chembiochem 2023; 24:e202300006. [PMID: 36602436 DOI: 10.1002/cbic.202300006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/06/2023]
Abstract
Nutlin-3a is a reversible inhibitor of the p53/MDM2 interaction. We have synthesized the derivative Nutlin-3a-aa bearing an additional exocyclic methylene group in the piperazinone moiety. Nutlin-3a-aa is more active than Nutlin-3a against purified wild-type MDM2, and is more effective at increasing p53 levels and releasing transcription of p53 target genes from MDM2-induced repression. X-ray analysis of wild-type MDM2-bound Nutlin-3a-aa indicated that the orientation of its modified piperazinone ring was altered in comparison to the piperazinone ring of MDM2-bound Nutlin-3a, with the exocyclic methylene group of Nutlin-3a-aa pointing away from the protein surface. Our data point to the introduction of exocyclic methylene groups as a useful approach by which to tailor the conformation of bioactive molecules for improved biological activity.
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Affiliation(s)
- Florian Nietzold
- Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Stefan Rubner
- Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Beata Labuzek
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Przemysław Golik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Ewa Surmiak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Xabier Del Corte
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.,Present address: Departamento de Química Orgánica I, Centro de Investigación y Estudios Avanzados "Lucio Lascaray", Facultad de Farmacia, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Radoslaw Kitel
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Christoph Protzel
- Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Regina Reppich-Sacher
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Thorsten Berg
- Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
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4
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Das G, Harikrishna S, Gore KR. Influence of Sugar Modifications on the Nucleoside Conformation and Oligonucleotide Stability: A Critical Review. CHEM REC 2022; 22:e202200174. [PMID: 36048010 DOI: 10.1002/tcr.202200174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/16/2022] [Indexed: 12/15/2022]
Abstract
Ribofuranose sugar conformation plays an important role in the structure and dynamics of functional nucleic acids such as siRNAs, AONs, aptamers, miRNAs, etc. To improve their therapeutic potential, several chemical modifications have been introduced into the sugar moiety over the years. The stability of the oligonucleotide duplexes as well as the formation of stable and functional protein-oligonucleotide complexes are dictated by the conformation and dynamics of the sugar moiety. In this review, we systematically categorise various ribofuranose sugar modifications employed in DNAs and RNAs so far. We discuss different stereoelectronic effects imparted by different substituents on the sugar ring and how these effects control sugar puckering. Using this data, it would be possible to predict the precise use of chemical modifications and design novel sugar-modified nucleosides for therapeutic oligonucleotides that can improve their physicochemical properties.
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Affiliation(s)
- Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| | - S Harikrishna
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
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5
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Ito Y, Nishida K, Tsutsui N, Fuchi Y, Hari Y. Synthesis and Properties of Oligonucleotides Containing 2′‐
O
,4′‐
C
‐Ethylene‐Bridged 5‐Methyluridine with Exocyclic Methylene and Methyl Groups in the Bridge. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences Tokushima Bunri University Nishihama, Yamashiro-cho Tokushima 770-8514 Japan
| | - Kodai Nishida
- Faculty of Pharmaceutical Sciences Tokushima Bunri University Nishihama, Yamashiro-cho Tokushima 770-8514 Japan
| | - Norika Tsutsui
- Faculty of Pharmaceutical Sciences Tokushima Bunri University Nishihama, Yamashiro-cho Tokushima 770-8514 Japan
| | - Yasufumi Fuchi
- Faculty of Pharmaceutical Sciences Tokushima Bunri University Nishihama, Yamashiro-cho Tokushima 770-8514 Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences Tokushima Bunri University Nishihama, Yamashiro-cho Tokushima 770-8514 Japan
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6
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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7
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8
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9
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Osawa T, Kim H, Shoji M, Saijo M, Dohi M, Ito Y, Obika S, Hari Y. Synthesis of 2'- C,4'- C-Methyleneoxy-Bridged Thymidine Derivatives and Properties of Modified Oligonucleotides. J Org Chem 2019; 84:13336-13344. [PMID: 31565938 DOI: 10.1021/acs.joc.9b01496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
2',4'-Bridged nucleic acid (2',4'-BNA) analogues are used for therapeutic oligonucleotides, owing to their excellent hybridizing ability with complementary RNA and high resistance toward enzymatic degradation. We developed 2',4'-BNA analogues with oxygen atoms at 6'-positions (e.g., EoNA and EoDNAs) and demonstrated that the presence of 6'-oxygen atoms in the bridge structure could show positive effect on the properties of the modified oligonucleotides. Herein, we designed and synthesized 7'-methyl derivatives of methyleneoxy-bridged 2'-deoxyribonucleic acid (MoDNA), possessing a five-membered bridge with 6'-oxygen atom via radical cyclization for the bridge construction. The synthesized monomers were incorporated into the oligonucleotides by solid-phase oligonucleotide synthesis. The MoDNA-modified oligonucleotides showed high affinity toward single-stranded RNA and double-stranded DNA, as well as excellent resistance toward nuclease compared with the corresponding natural oligonucleotide.
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Affiliation(s)
- Takashi Osawa
- Faculty of Pharmaceutical Sciences , Tokushima Bunri University , Nishihama, Yamashiro-cho, Tokushima 770-8514 , Japan.,Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Han Kim
- Faculty of Pharmaceutical Sciences , Tokushima Bunri University , Nishihama, Yamashiro-cho, Tokushima 770-8514 , Japan
| | - Misa Shoji
- Faculty of Pharmaceutical Sciences , Tokushima Bunri University , Nishihama, Yamashiro-cho, Tokushima 770-8514 , Japan
| | - Miku Saijo
- Faculty of Pharmaceutical Sciences , Tokushima Bunri University , Nishihama, Yamashiro-cho, Tokushima 770-8514 , Japan
| | - Masakazu Dohi
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Yuta Ito
- Faculty of Pharmaceutical Sciences , Tokushima Bunri University , Nishihama, Yamashiro-cho, Tokushima 770-8514 , Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences , Tokushima Bunri University , Nishihama, Yamashiro-cho, Tokushima 770-8514 , Japan
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10
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Ito Y, Tsutsui N, Osawa T, Hari Y. Synthesis of the Methyl Analog of 2′-O,4′-C-Ethylene-Bridged 5-Methyluridine via Intramolecular Radical Cyclization and Properties of Modified Oligonucleotides. J Org Chem 2019; 84:9093-9100. [DOI: 10.1021/acs.joc.9b01035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Norika Tsutsui
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Takashi Osawa
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
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11
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Mangla P, Maity J, Rungta P, Verma V, Sanghvi YS, Prasad AK. Synthesis of 6′‐Methyl‐2′‐
O
,4′‐
C
‐methylene‐
α
‐L‐ ribofuranosyl‐pyrimidine Nucleosides. ChemistrySelect 2019. [DOI: 10.1002/slct.201900809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Priyanka Mangla
- Bioorganic Laboratory, Department of ChemistryUniversity of Delhi Delhi- 110 007 India
| | - Jyotirmoy Maity
- Bioorganic Laboratory, Department of ChemistryUniversity of Delhi Delhi- 110 007 India
| | - Pallavi Rungta
- Bioorganic Laboratory, Department of ChemistryUniversity of Delhi Delhi- 110 007 India
| | - Vineet Verma
- Bioorganic Laboratory, Department of ChemistryUniversity of Delhi Delhi- 110 007 India
| | | | - Ashok K. Prasad
- Bioorganic Laboratory, Department of ChemistryUniversity of Delhi Delhi- 110 007 India
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12
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Benizri S, Gissot A, Martin A, Vialet B, Grinstaff MW, Barthélémy P. Bioconjugated Oligonucleotides: Recent Developments and Therapeutic Applications. Bioconjug Chem 2019; 30:366-383. [PMID: 30608140 PMCID: PMC6766081 DOI: 10.1021/acs.bioconjchem.8b00761] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Oligonucleotide-based agents have the potential to treat or cure almost any disease, and are one of the key therapeutic drug classes of the future. Bioconjugated oligonucleotides, a subset of this class, are emerging from basic research and being successfully translated to the clinic. In this Review, we first briefly describe two approaches for inhibiting specific genes using oligonucleotides-antisense DNA (ASO) and RNA interference (RNAi)-followed by a discussion on delivery to cells. We then summarize and analyze recent developments in bioconjugated oligonucleotides including those possessing GalNAc, cell penetrating peptides, α-tocopherol, aptamers, antibodies, cholesterol, squalene, fatty acids, or nucleolipids. These novel conjugates provide a means to enhance tissue targeting, cell internalization, endosomal escape, target binding specificity, resistance to nucleases, and more. We next describe those bioconjugated oligonucleotides approved for patient use or in clinical trials. Finally, we summarize the state of the field, describe current limitations, and discuss future prospects. Bioconjugation chemistry is at the centerpiece of this therapeutic oligonucleotide revolution, and significant opportunities exist for development of new modification chemistries, for mechanistic studies at the chemical-biology interface, and for translating such agents to the clinic.
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Affiliation(s)
- Sebastien Benizri
- Inserm U1212, F-33076 Bordeaux, France
- CNRS 5320, F-33076 Bordeaux, France
- Universitéde Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux Cedex, France
| | - Arnaud Gissot
- Inserm U1212, F-33076 Bordeaux, France
- CNRS 5320, F-33076 Bordeaux, France
- Universitéde Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux Cedex, France
| | - Andrew Martin
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston, Massachusetts 02215, United States
| | - Brune Vialet
- Inserm U1212, F-33076 Bordeaux, France
- CNRS 5320, F-33076 Bordeaux, France
- Universitéde Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux Cedex, France
| | - Mark W. Grinstaff
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston, Massachusetts 02215, United States
| | - Philippe Barthélémy
- Inserm U1212, F-33076 Bordeaux, France
- CNRS 5320, F-33076 Bordeaux, France
- Universitéde Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux Cedex, France
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13
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Habuchi T, Yamaguchi T, Aoyama H, Horiba M, Ito KR, Obika S. Hybridization and Mismatch Discrimination Abilities of 2',4'-Bridged Nucleic Acids Bearing 2-Thiothymine or 2-Selenothymine Nucleobase. J Org Chem 2019; 84:1430-1439. [PMID: 30632750 DOI: 10.1021/acs.joc.8b02863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligonucleotides modified with 2'- O,4'- C-spirocyclopropylene-bridged nucleic acid (scpBNA) exhibit excellent duplex-forming ability with their complementary single-stranded RNA (ssRNA). Here, we demonstrate that scpBNA bearing a 2-thiothymine (scpBNA-S2T) or 2-selenothymine (scpBNA-Se2T) nucleobase provides robust mismatch discrimination capabilities to oligonucleotides without compromising their high binding affinities toward the full complementary ssRNA. X-ray crystallographic analysis of a self-assembling oligonucleotide featuring 2',4'-BNA/LNA-2-thiothymine (2',4'-BNA/LNA-S2T, where 2',4'-BNA and LNA stand for "2'- O,4'- C-methylene-bridged nucleic acid" and "locked nucleic acid", respectively), a prototype of scpBNA-S2T, revealed that the 2-thiocarbonyl moiety plays a crucial role in the destabilization of thymine-guanine mismatched wobble base pairs.
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Affiliation(s)
- Takaki Habuchi
- 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
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Masahiko Horiba
- 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
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
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14
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Kasuya T, Kugimiya A. Role of Computationally Evaluated Target Specificity in the Hepatotoxicity of Gapmer Antisense Oligonucleotides. Nucleic Acid Ther 2018; 28:312-317. [PMID: 30095329 DOI: 10.1089/nat.2018.0724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Gapmer antisense oligonucleotides (gapmers) sometimes cleave nontarget pre-mRNAs by recognizing target-like intronic/exonic portions. This off-target RNA cleavage could be a major cause of the hepatotoxicity that is induced by gapmers. In line with these findings, we hypothesized that gapmers with higher specificity have less hepatotoxicity, and that those with lower specificity have greater toxicity. To examine this concept, we investigated various Malat1-targeting gapmers with various computationally evaluated target specificities. We had expected that higher specificity gapmers would have lower hepatotoxicity, but these factors were not significantly related. In silico analysis of gapmer sequences does not always contribute to mitigating the risk of hepatotoxicity. Transcriptome analysis indicated that nontoxic gapmers do not cleave off-target RNAs, although they have many target-like RNA sequences. The present results shed light on the mechanism of the hepatotoxicity of gapmers.
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Affiliation(s)
- Takeshi Kasuya
- Discovery Research and Disease Research Laboratory, Shionogi & Co., Ltd. , Osaka, Japan
| | - Akira Kugimiya
- Discovery Research and Disease Research Laboratory, Shionogi & Co., Ltd. , Osaka, Japan
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15
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Osawa T, Sawamura M, Wada F, Yamamoto T, Obika S, Hari Y. Synthesis, duplex-forming ability, enzymatic stability, and in vitro antisense potency of oligonucleotides including 2'-C,4'-C-ethyleneoxy-bridged thymidine derivatives. Org Biomol Chem 2018; 15:3955-3963. [PMID: 28440828 DOI: 10.1039/c7ob00698e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We synthesized thymidine derivatives of 2'-C,4'-C-ethyleneoxy-bridged 2'-deoxyribonucleic acids with an 8'-methyl group ((R)-Me-EoDNA and (S)-Me-EoDNA) and without any substituent (EoDNA). Oligonucleotides including these EoDNAs showed high hybridization abilities with complementary RNA and excellent enzymatic stabilities compared with natural DNA. Moreover, the in vitro antisense potency of oligonucleotides with these EoDNAs and our recently reported methylene-EoDNAs was investigated and compared with that of LNA, which is a practical chemical modification for oligonucleotide-therapeutic agents. The results showed that EoDNAs and methylene-EoDNAs could be promising candidates for antisense technology.
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Affiliation(s)
- Takashi Osawa
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
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16
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Morihiro K, Kasahara Y, Obika S. Biological applications of xeno nucleic acids. MOLECULAR BIOSYSTEMS 2017; 13:235-245. [PMID: 27827481 DOI: 10.1039/c6mb00538a] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Xeno nucleic acids (XNAs) are a group of chemically modified nucleic acid analogues that have been applied to various biological technologies such as antisense oligonucleotides, siRNAs and aptamers.
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Affiliation(s)
- Kunihiko Morihiro
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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17
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Plashkevych O, Upadhayaya RS, Chattopadhyaya J. Carbocyclic C-C Bond Formation: Intramolecular Radical Ring Closure to Yield Diastereomerically Pure (7'S-Me- or 7'R-Me-) Carba-LNA Nucleotide Analogs. ACTA ACUST UNITED AC 2017. [PMID: 28628208 DOI: 10.1002/cpnc.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In light of the impressive gene-silencing properties of carba-LNA modified oligo DNA and RNA, both in antisense RNA and siRNA approaches, which have been confirmed as proof-of-concept for biochemical applications in post-transcriptional gene silencing, we envision the true potential of carba-LNA modifications to be revealed soon. Herein we provide detailed protocols for synthesis of carba-LNA-A, -G, -5-Me C, and -T nucleosides on a medium/large scale (gram scale), as well as important guidelines for incorporation of these modified carba-LNAs into DNA or RNA oligonucleotides. Creation of a stereoselective C-C bond during the 5-exo radical intramolecular cyclization involves trapping of a C2' radical intermediate intramolecularly by the vicinal double bond of a C4'-tethered ─CH2 -CH═CH2 group. All diastereomers of substituted carba-LNAs are now available in pure form. The present procedure allows carba-LNA to be commercialized for medicinal or biotechnological purposes. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Ram Shankar Upadhayaya
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Bioimics AB, Uppsala, Sweden
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18
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Mitsuoka Y, Yamamoto T, Kugimiya A, Waki R, Wada F, Tahara S, Sawamura M, Noda M, Fujimura Y, Kato Y, Hari Y, Obika S. Triazole- and Tetrazole-Bridged Nucleic Acids: Synthesis, Duplex Stability, Nuclease Resistance, and in Vitro and in Vivo Antisense Potency. J Org Chem 2016; 82:12-24. [PMID: 27936689 DOI: 10.1021/acs.joc.6b02417] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Antisense oligonucleotides are attractive therapeutic agents for several types of disease. One of the most promising modifications of antisense oligonucleotides is the introduction of bridged nucleic acids. As we report here, we designed novel bridged nucleic acids, triazole-bridged nucleic acid (TrNA), and tetrazole-bridged nucleic acid (TeNA), whose sugar conformations are restricted to N-type by heteroaromatic ring-bridged structures. We then successfully synthesized TrNA and TeNA and introduced these monomers into oligonucleotides. In UV-melting experiments, TrNA-modified oligonucleotides exhibited increased binding affinity toward complementary RNA and decreased binding affinity toward complementary DNA, although TeNA-modified oligonucleotides were decomposed under the annealing conditions. Enzymatic degradation experiments demonstrated that introduction of TrNA at the 3'-terminus rendered oligonucleotides resistant to nuclease digestion. Furthermore, we tested the silencing potencies of TrNA-modified antisense oligonucleotides using in vitro and in vivo assays. These experiments revealed that TrNA-modified antisense oligonucleotides induced potent downregulation of gene expression in liver. In addition, TrNA-modified antisense oligonucleotides showed a tendency for increased liver biodistribution. Taken together, our findings indicate that TrNA is a good candidate for practical application in antisense methodology.
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Affiliation(s)
- Yasunori Mitsuoka
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita Osaka 565-0871, Japan.,Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd. , 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita Osaka 565-0871, Japan
| | - Akira Kugimiya
- Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd. , 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Reiko Waki
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita Osaka 565-0871, Japan
| | - Fumito Wada
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita Osaka 565-0871, Japan
| | - Saori Tahara
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita Osaka 565-0871, Japan
| | - Motoki Sawamura
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita Osaka 565-0871, Japan
| | - Mio Noda
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita Osaka 565-0871, Japan
| | - Yuko Fujimura
- Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd. , 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yuki Kato
- Research Laboratory for Development, Shionogi & Co., Ltd. , 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita Osaka 565-0871, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University , Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita Osaka 565-0871, Japan
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19
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Ries A, Kumar R, Lou C, Kosbar T, Vengut-Climent E, Jørgensen PT, Morales JC, Wengel J. Synthesis and Biophysical Investigations of Oligonucleotides Containing Galactose-Modified DNA, LNA, and 2'-Amino-LNA Monomers. J Org Chem 2016; 81:10845-10856. [PMID: 27736097 DOI: 10.1021/acs.joc.6b01917] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Galactose-modified thymidine, LNA-T, and 2'-amino-LNA-T nucleosides were synthesized, converted into the corresponding phosphoramidite derivatives and introduced into short oligonucleotides. Compared to the unmodified control strands, the galactose-modified oligonucleotides in general, and the N2'-functionalized 2'-amino-LNA derivatives in particular, showed improved duplex thermal stability against DNA and RNA complements and increased ability to discriminate mismatches. In addition, the 2'-amino-LNA-T derivatives induced remarkable 3'-exonuclease resistance. These results were further investigated using molecular modeling studies.
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Affiliation(s)
- Annika Ries
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Rajesh Kumar
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Tamer Kosbar
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Empar Vengut-Climent
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark.,Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC Universidad de Sevilla , Americo Vespucio 49, 41092 Sevilla, Spain
| | - Per T Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Juan C Morales
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC Universidad de Sevilla , Americo Vespucio 49, 41092 Sevilla, Spain.,Department of Biochemistry and Molecular Pharmacology, Institute of Parasitology and Biomedicine López Neyra , CSIC Avenida del conocimiento 17, 18016 Granada, Spain
| | - 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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20
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Abstract
Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.
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Affiliation(s)
- W Brad Wan
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
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21
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Ribonuclease H1-dependent hepatotoxicity caused by locked nucleic acid-modified gapmer antisense oligonucleotides. Sci Rep 2016; 6:30377. [PMID: 27461380 PMCID: PMC4961955 DOI: 10.1038/srep30377] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/30/2016] [Indexed: 12/16/2022] Open
Abstract
Gapmer antisense oligonucleotides cleave target RNA effectively in vivo, and is considered as promising therapeutics. Especially, gapmers modified with locked nucleic acid (LNA) shows potent knockdown activity; however, they also cause hepatotoxic side effects. For developing safe and effective gapmer drugs, a deeper understanding of the mechanisms of hepatotoxicity is required. Here, we investigated the cause of hepatotoxicity derived from LNA-modified gapmers. Chemical modification of gapmer’s gap region completely suppressed both knockdown activity and hepatotoxicity, indicating that the root cause of hepatotoxicity is related to intracellular gapmer activity. Gene silencing of hepatic ribonuclease H1 (RNaseH1), which catalyses gapmer-mediated RNA knockdown, strongly supressed hepatotoxic effects. Small interfering RNA (siRNA)-mediated knockdown of a target mRNA did not result in any hepatotoxic effects, while the gapmer targeting the same position on mRNA as does the siRNA showed acute toxicity. Microarray analysis revealed that several pre-mRNAs containing a sequence similar to the gapmer target were also knocked down. These results suggest that hepatotoxicity of LNA gapmer is caused by RNAseH1 activity, presumably because of off-target cleavage of RNAs inside nuclei.
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22
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Yamamoto T, Wada F, Harada-Shiba M. Development of Antisense Drugs for Dyslipidemia. J Atheroscler Thromb 2016; 23:1011-25. [PMID: 27466159 PMCID: PMC5090806 DOI: 10.5551/jat.rv16001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Abnormal elevation of low-density lipoprotein (LDL) and triglyceride-rich lipoproteins in plasma as well as dysfunction of anti-atherogenic high-density lipoprotein (HDL) have both been recognized as essential components of the pathogenesis of atherosclerosis and are classified as dyslipidemia. This review describes the arc of development of antisense oligonucleotides for the treatment of dyslipidemia. Chemically-armed antisense candidates can act on various kinds of transcripts, including mRNA and miRNA, via several different endogenous antisense mechanisms, and have exhibited potent systemic anti-dyslipidemic effects. Here, we present specific cutting-edge technologies have recently been brought into antisense strategies, and describe how they have improved the potency of antisense drugs in regard to pharmacokinetics and pharmacodynamics. In addition, we discuss perspectives for the use of armed antisense oligonucleotides as new clinical options for dyslipidemia, in the light of outcomes of recent clinical trials and safety concerns indicated by several clinical and preclinical studies.
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23
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Mitsuoka Y, Aoyama H, Kugimiya A, Fujimura Y, Yamamoto T, Waki R, Wada F, Tahara S, Sawamura M, Noda M, Hari Y, Obika S. Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure. Org Biomol Chem 2016; 14:6531-8. [PMID: 27296230 DOI: 10.1039/c6ob01051b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A sulfonamide-bridged nucleic acid without an N-substituent (SuNA[NH]) was successfully synthesized. A comparison of the SuNA[NMe]- and SuNA[NH]-modified oligonucleotides revealed that the duplex-forming abilities of the SuNA[NMe]-modified oligonucleotides with complementary DNA and RNA were higher than those of the SuNA[NH]-modified oligonucleotides. The crystal structures of DNA duplexes containing a SuNA[NR] revealed that the helical structures of the two duplexes and hydration patterns around the bridge moiety were different. These results provide insights into hydration patterns and rationale for the high RNA affinity of SuNA-modified oligonucleotides.
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Affiliation(s)
- Yasunori Mitsuoka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. and Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Akira Kugimiya
- Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yuko Fujimura
- Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Reiko Waki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Fumito Wada
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Saori Tahara
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Motoki Sawamura
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Mio Noda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. and Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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24
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Yamaguchi T, Horiba M, Obika S. Synthesis and properties of 2'-O,4'-C-spirocyclopropylene bridged nucleic acid (scpBNA), an analogue of 2',4'-BNA/LNA bearing a cyclopropane ring. Chem Commun (Camb) 2016; 51:9737-40. [PMID: 25985928 DOI: 10.1039/c5cc02024g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
2'-O,4'-C-Spirocyclopropylene bridged nucleic acid (scpBNA), an analogue of 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA/LNA) bearing a cyclopropane ring at the 6'-position, was synthesized and successfully incorporated into oligonucleotides. The scpBNA-modified oligonucleotides showed excellent duplex-forming ability with complementary single-stranded RNA and exhibited increased enzymatic stability as compared to the corresponding natural and 2',4'-BNA/LNA-modified oligonucleotides. Our results demonstrate the potential of scpBNA for gene therapeutics, such as antisense technology.
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Affiliation(s)
- Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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25
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Dai W, Zhang X, Zhang J, Lin Y, Cao S. Synthesis of Exocyclic Trisubstituted Alkenes
via
Nickel‐ Catalyzed Kumada‐Type Cross‐Coupling Reaction of
gem
‐ Difluoroalkenes with Di‐Grignard Reagents. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201500889] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Wenpeng Dai
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology (ECUST), Shanghai 200237, People's Republic of China, Fax: (+86)‐21‐64252603; phone: (+86)‐21‐64253452
| | - Xuxue Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology (ECUST), Shanghai 200237, People's Republic of China, Fax: (+86)‐21‐64252603; phone: (+86)‐21‐64253452
| | - Juan Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology (ECUST), Shanghai 200237, People's Republic of China, Fax: (+86)‐21‐64252603; phone: (+86)‐21‐64253452
| | - Yingyin Lin
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology (ECUST), Shanghai 200237, People's Republic of China, Fax: (+86)‐21‐64252603; phone: (+86)‐21‐64253452
| | - Song Cao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology (ECUST), Shanghai 200237, People's Republic of China, Fax: (+86)‐21‐64252603; phone: (+86)‐21‐64253452
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26
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Osawa T, Obika S, Hari Y. Synthesis and properties of novel 2′-C,4′-C-ethyleneoxy-bridged 2′-deoxyribonucleic acids with exocyclic methylene groups. Org Biomol Chem 2016; 14:9481-9484. [DOI: 10.1039/c6ob01960a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Three methylene-EoDNAs were synthesized from 5-methyluridine and their modified oligonucleotides showed strong binding affinity with ssRNA and high nuclease resistance.
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Affiliation(s)
- Takashi Osawa
- Faculty of Pharmaceutical Sciences
- Tokushima Bunri University
- Tokushima 770-8514
- Japan
- Graduate School of Pharmaceutical Sciences
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Osaka 565-0871
- Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences
- Tokushima Bunri University
- Tokushima 770-8514
- Japan
- Graduate School of Pharmaceutical Sciences
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27
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Yamamoto T, Yahara A, Waki R, Yasuhara H, Wada F, Harada-Shiba M, Obika S. Amido-bridged nucleic acids with small hydrophobic residues enhance hepatic tropism of antisense oligonucleotides in vivo. Org Biomol Chem 2015; 13:3757-65. [PMID: 25690587 DOI: 10.1039/c5ob00242g] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High scalability of a novel bicyclic nucleoside building block, amido-bridged nucleic acid (AmNA), to diversify pharmacokinetic properties of therapeutic antisense oligonucleotides is described. N2'-functionalization of AmNA with a variety of hydrophobic groups is straightforward. Combinations of these modules display similar antisense knockdown effects and improve cellular uptake, relative to sequence-matched conventional 2',4'-bridged nucleic acid (2',4'-BNA) in vivo.
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Affiliation(s)
- Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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28
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Osawa T, Hari Y, Dohi M, Matsuda Y, Obika S. Synthesis and Properties of the 5-Methyluridine Derivative of 3,4-Dihydro-2H-pyran-Bridged Nucleic Acid (DpNA). J Org Chem 2015; 80:10474-81. [PMID: 26431393 DOI: 10.1021/acs.joc.5b01425] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A novel 2'-O,4'-C-bridged nucleic acid, 3,4-dihydro-2H-pyran bridge moiety (DpNA), with a dioxabicyclo[3.2.1]oct-3-ene ring was designed. Construction of the dihydropyran bridge was achieved by dehydration of a six-membered hemiacetal ring, and the DpNA monomer was synthesized in 10 steps from 5-methyluridine (total yield 9%). The synthesized DpNA monomer was incorporated into oligonucleotides to examine the properties of the modified oligonucleotides. The DpNA-modified oligonucleotides possessed high affinity toward ssRNA and were more resistant to nucleases compared to the corresponding natural oligonucleotide.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST) , 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University , Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Masakazu Dohi
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuya Matsuda
- 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.,Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST) , 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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29
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Prakash TP, Lima WF, Murray HM, Li W, Kinberger GA, Chappell AE, Gaus H, Seth PP, Bhat B, Crooke ST, Swayze EE. Identification of metabolically stable 5'-phosphate analogs that support single-stranded siRNA activity. Nucleic Acids Res 2015; 43:2993-3011. [PMID: 25753666 PMCID: PMC4381071 DOI: 10.1093/nar/gkv162] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 12/23/2022] Open
Abstract
The ss-siRNA activity in vivo requires a metabolically stable 5'-phosphate analog. In this report we used crystal structure of the 5'-phosphate binding pocket of Ago-2 bound with guide strand to design and synthesize ss-siRNAs containing various 5'-phosphate analogs. Our results indicate that the electronic and spatial orientation of the 5'-phosphate analog was critical for ss-siRNA activity. Chemically modified ss-siRNA targeting human apoC III mRNA demonstrated good potency for inhibiting ApoC III mRNA and protein in transgenic mice. Moreover, ApoC III ss-siRNAs were able to reduce the triglyceride and LDL cholesterol in transgenic mice demonstrating pharmacological effect of ss-siRNA. Our study provides guidance to develop surrogate phosphate analog for ss-siRNA and demonstrates that ss-siRNA provides an alternative strategy for therapeutic gene silencing.
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Affiliation(s)
- Thazha P Prakash
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Walt F Lima
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Heather M Murray
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Wenyu Li
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | | | | | - Hans Gaus
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Balkrishen Bhat
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Isis Pharmaceuticals Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
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30
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Šála M, Dejmek M, Procházková E, Hřebabecký H, Rybáček J, Dračínský M, Novák P, Rosenbergová Š, Fukal J, Sychrovský V, Rosenberg I, Nencka R. Synthesis of locked cyclohexene and cyclohexane nucleic acids (LCeNA and LCNA) with modified adenosine units. Org Biomol Chem 2015; 13:2703-15. [DOI: 10.1039/c4ob02193b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We designed novel conformationally locked cyclohexene nucleic acid and studied their properties.
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31
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Rigo F, Seth PP, Bennett CF. Antisense oligonucleotide-based therapies for diseases caused by pre-mRNA processing defects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:303-52. [PMID: 25201110 DOI: 10.1007/978-1-4939-1221-6_9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Before a messenger RNA (mRNA) is translated into a protein in the cytoplasm, its pre-mRNA precursor is extensively processed through capping, splicing and polyadenylation in the nucleus. Defects in the processing of pre-mRNAs due to mutations in RNA sequences often cause disease. Traditional small molecules or protein-based therapeutics are not well suited for correcting processing defects by targeting RNA. However, antisense oligonucleotides (ASOs) designed to bind RNA by Watson-Crick base pairing can target most RNA transcripts and have emerged as the ideal therapeutic agents for diseases that are caused by pre-mRNA processing defects. Here we review the diverse ASO-based mechanisms that can be exploited to modulate the expression of RNA. We also discuss how advancements in medicinal chemistry and a deeper understanding of the pharmacokinetic and toxicological properties of ASOs have enabled their use as therapeutic agents. We end by describing how ASOs have been used successfully to treat various pre-mRNA processing diseases in animal models.
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Affiliation(s)
- Frank Rigo
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA, USA,
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32
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Mori K, Kodama T, Obika S. Synthesis and hybridization property of a boat-shaped pyranosyl nucleic acid containing an exocyclic methylene group in the sugar moiety. Bioorg Med Chem 2014; 23:33-7. [PMID: 25496806 DOI: 10.1016/j.bmc.2014.11.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 12/29/2022]
Abstract
A boat-shaped pyranosyl nucleic acid (BsNA) having an exocyclic methylene group in the sugar moiety was synthesized to investigate the possibility that the axial H3' of original BsNA is the cause of its duplex destabilization. The synthesized BsNA analog was chemically stable against various nucleophiles. From the thermal stability of duplex oligonucleotides including the BsNA analog, it was found that the duplex-forming ability can be sensitive to the size of functional groups at the 3'-position.
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Affiliation(s)
- Kazuto Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Kodama
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Mitsuoka Y, Fujimura Y, Waki R, Kugimiya A, Yamamoto T, Hari Y, Obika S. Sulfonamide-bridged nucleic acid: synthesis, high RNA selective hybridization, and high nuclease resistance. Org Lett 2014; 16:5640-3. [PMID: 25341881 DOI: 10.1021/ol503029v] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
2'-N,4'-C-(N-methylamino)sulfonylmethylene-bridged thymidine (SuNA), which has a six-membered linkage including a sulfonamide moiety, was synthesized and introduced into oligonucleotides. The oligonucleotides containing SuNA exhibited excellent nuclease resistance, a high affinity toward single-stranded RNA, and a low affinity toward single-stranded DNA compared to the natural oligonucleotide.
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Affiliation(s)
- Yasunori Mitsuoka
- Graduate School of Pharmaceutical Sciences, Osaka University , 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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Yildirim I, Kierzek E, Kierzek R, Schatz GC. Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results. J Phys Chem B 2014; 118:14177-87. [PMID: 25268896 DOI: 10.1021/jp506703g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
When used in nucleic acid duplexes, locked nucleic acid (LNA) and 2'-O-methyl RNA residues enhance the duplex stabilities, and this makes it possible to create much better RNA aptamers to target specific molecules in cells. Thus, LNA and 2'-O-methyl RNA residues are finding increasingly widespread use in RNA-based therapeutics. Herein, we utilize molecular dynamics (MD) simulations and UV melting experiments to investigate the structural and thermodynamic properties of 13 nucleic acid duplexes, including full DNA, RNA, LNA, and 2'-O-methyl RNA duplexes as well as hybrid systems such as LNA:RNA, 2'-O-methyl RNA:RNA, LNA/2'-O-methyl RNA:RNA, and RNA/2'-O-methyl RNA:RNA duplexes. The MD simulations are based on a version of the Amber force field revised specifically for RNA and LNA residues. Our results indicate that LNA and 2'-O-methyl RNA residues have two different hybridization mechanisms when included in hybrid duplexes with RNA wherein the former underwinds while the latter overwinds the duplexes. These computational predictions are supported by X-ray structures of LNA and 2'-O-methyl RNA duplexes that were recently presented by different groups, and there is also good agreement with the measured thermal stabilities of the duplexes. We find out that the "underwinding" phenomenon seen in LNA and LNA:RNA hybrid duplexes happens due to expansion of the major groove widths (Mgw) of the duplexes that is associated with decrease in the slide and twist values in base-pair steps. In contrast, 2'-O-methyl RNA residues in RNA duplexes slightly overwind the duplexes while the backbone is forced to stay in C3'-endo. Moreover, base-pair stacking in the LNA and LNA:RNA hybrid systems is gradually reduced with the inclusion of LNA residues in the duplexes while no such effect is seen in the 2'-O-methyl RNA systems. Our results show how competition between base stacking and structural rigidity in these RNA hybrid systems influences structures and stabilities. Even though both LNA and 2'-O-methyl RNA residues have C3'-endo sugar puckering, structurally LNA residues have a frozen sugar backbone which provides entropic enhancement of stabilities while the 2'-O-methyl RNA residues are more flexible and maintain base stacking that is almost untouched compared to RNA. Thus, enhancement of the structural stabilities of RNA duplexes by 2'-O-methyl RNA modifications is smaller than for the corresponding LNA modifications. Indeed, our experimental measurements show that on average each 2'-O-methyl RNA and LNA substitution in a RNA duplex enhances duplex stability by 0.2 and 1.4 kcal/mol, respectively. Our computational binding free energy predictions are qualitatively in line with these results. The only exception is for the full 2'-O-methyl RNA duplex, which is overstabilized, implying that further force field revisions are needed. Collectively, the results presented in this paper explain the atomistic details of the structural and thermodynamic roles of LNA and 2'-O-methyl RNA residues in RNA hybrid duplexes, shedding light on the mechanism behind targeting endogenous micro RNA (miRNA) in order to regulate mRNA activity and inhibit gene expression in the cell.
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Affiliation(s)
- Ilyas Yildirim
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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35
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Karimiahmadabadi M, Erfan S, Földesi A, Chattopadhyaya J. Distal Two-Bond versus Three-Bond Electronegative Oxo-Substituent Effect Controls the Kinetics and Thermodynamics of the Conversion of a C-Nitroso Function to the Corresponding Oxime in the Conformationally Locked Pentofuranose (Bicyclo[2.2.1]heptane) System. J Org Chem 2014; 79:7266-76. [DOI: 10.1021/jo500266k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Mansoureh Karimiahmadabadi
- Program of Chemical Biology,
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sayeh Erfan
- Program of Chemical Biology,
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
| | - Andras Földesi
- Program of Chemical Biology,
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jyoti Chattopadhyaya
- Program of Chemical Biology,
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
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36
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Martínez-Montero S, Deleavey GF, Kulkarni A, Martín-Pintado N, Lindovska P, Thomson M, González C, Götte M, Damha MJ. Rigid 2',4'-difluororibonucleosides: synthesis, conformational analysis, and incorporation into nascent RNA by HCV polymerase. J Org Chem 2014; 79:5627-35. [PMID: 24873952 DOI: 10.1021/jo500794v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report on the synthesis and conformational properties of 2'-deoxy-2',4'-difluorouridine (2',4'-diF-rU) and cytidine (2',4'-diF-rC) nucleosides. NMR analysis and quantum mechanical calculations show that the strong stereoelectronic effects induced by the two fluorines essentially "lock" the conformation of the sugar in the North region of the pseudorotational cycle. Our studies also demonstrate that NS5B HCV RNA polymerase was able to accommodate 2',4'-diF-rU 5'-triphosphate (2',4'-diF-rUTP) and to link the monophosphate to the RNA primer strand. 2',4'-diF-rUTP inhibited RNA synthesis in dinucleotide-primed reactions, although with relatively high half-maximal inhibitory concentrations (IC50 > 50 μM). 2',4'-diF-rU/C represents rare examples of "locked" ribonucleoside mimics that lack a bicyclic ring structure.
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Affiliation(s)
- Saúl Martínez-Montero
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC Canada H3A 0B8
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37
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Seth PP, Swayze EE. Unnatural Nucleoside Analogs for Antisense Therapy. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1002/9783527676545.ch12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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38
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39
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Hari Y, Morikawa T, Osawa T, Obika S. Synthesis and properties of 2'-O,4'-C-ethyleneoxy bridged 5-methyluridine. Org Lett 2013; 15:3702-5. [PMID: 23815244 DOI: 10.1021/ol401566r] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
2'-O,4'-C-Ethyleneoxy bridged 5-methyluridine (EoNA-T), possessing a seven-membered linkage and an anomeric 4'-carbon, was synthesized and introduced into oligonucleotides by using an automated DNA synthesizer. The EoNA-modified oligonucleotides significantly stabilized the duplexes with single-stranded RNA and triplexes with double-stranded DNA relative to the natural oligonucleotide and oligonucleotides modified by another seven-membered bridged 5-methyluridine, 2',4'-BNA(COC)-T. In addition, EoNA-T showed excellent nuclease resistance.
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Affiliation(s)
- Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan.
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40
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Morihiro K, Kodama T, Kentefu, Moai Y, Veedu RN, Obika S. Selenomethylene Locked Nucleic Acid Enables Reversible Hybridization in Response to Redox Changes. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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Morihiro K, Kodama T, Kentefu, Moai Y, Veedu RN, Obika S. Selenomethylene locked nucleic acid enables reversible hybridization in response to redox changes. Angew Chem Int Ed Engl 2013; 52:5074-8. [PMID: 23580244 DOI: 10.1002/anie.201300555] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Indexed: 12/27/2022]
Affiliation(s)
- Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan
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42
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Deleavey GF, Damha MJ. Designing chemically modified oligonucleotides for targeted gene silencing. ACTA ACUST UNITED AC 2012; 19:937-54. [PMID: 22921062 DOI: 10.1016/j.chembiol.2012.07.011] [Citation(s) in RCA: 423] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/28/2012] [Accepted: 07/02/2012] [Indexed: 02/07/2023]
Abstract
Oligonucleotides (ONs), and their chemically modified mimics, are now routinely used in the laboratory as a means to control the expression of fundamentally interesting or therapeutically relevant genes. ONs are also under active investigation in the clinic, with many expressing cautious optimism that at least some ON-based therapies will succeed in the coming years. In this review, we will discuss several classes of ONs used for controlling gene expression, with an emphasis on antisense ONs (AONs), small interfering RNAs (siRNAs), and microRNA-targeting ONs (anti-miRNAs). This review provides a current and detailed account of ON chemical modification strategies for the optimization of biological activity and therapeutic application, while clarifying the biological pathways, chemical properties, benefits, and limitations of oligonucleotide analogs used in nucleic acids research.
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Affiliation(s)
- Glen F Deleavey
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC H3A 0B8, Canada.
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43
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Seth PP, Pallan PS, Swayze EE, Egli M. Synthesis, duplex stabilization and structural properties of a fluorinated carbocyclic LNA analogue. Chembiochem 2012. [PMID: 23193103 DOI: 10.1002/cbic.201200669] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA oligonucleotides modified with nucleoside monomers which have an electron withdrawing group (EWG) at the 2'-position of the furanose ring form more stable duplexes with complementary RNA as compared to unmodified DNA. Here we show that an anti-periplanar orientation of the nucleobase and the 2'-EWG is important for optimal duplex stabilization even for nucleic acid analogues with conformationally locked furanose rings.
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Affiliation(s)
- Punit P Seth
- Department of Medicinal Chemistry, Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA.
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44
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Karimiahmadabadi M, Földesi A, Chattopadhyaya J. Unusual strain-releasing nucleophilic rearrangement of a bicyclo[2.2.1]heptane system to a cyclohexenyl derivative. J Org Chem 2012; 77:9747-55. [PMID: 23062056 DOI: 10.1021/jo301871d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report an unusual strain-releasing reaction of 1-mesyloxy-8,7-dimethylbicyclo[2.2.1]heptane (3) by a base-promoted substitution at the chiral C3 followed by spontaneous concerted ring opening involving the most strained C2-C3-C4 bonds (with bond angle 94°) and the C2 bridgehead leading to anti-endo elimination of the C1-mesyloxy group by the conjugate base of adenine or thymine to give two diastereomeric C3'(S) and C3'(R) derivatives of 1-thyminyl and 9-adeninyl cyclohexene: 3 → T-4a + T-4b and 3 → A-5a + A-5b. These products have been unambiguously characterized by detailed 1D and 2D NMR (J-coupling constants and nOe analysis), mass, and UV spectroscopy. Evidence has been presented suggesting that the origin of these diastereomeric C3'(S) and C3'(R) derivatives of 1-thyminyl and 9-adeninyl cyclohexene from 3 is most probably a rearrangement mechanism of a trigonal bipyramidal intermediate formed in the S(N)2 displacement-ring-opening reaction.
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Affiliation(s)
- Mansoureh Karimiahmadabadi
- Program of Chemical Biology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
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45
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Superior Silencing by 2',4'-BNA(NC)-Based Short Antisense Oligonucleotides Compared to 2',4'-BNA/LNA-Based Apolipoprotein B Antisense Inhibitors. J Nucleic Acids 2012; 2012:707323. [PMID: 23056920 PMCID: PMC3463943 DOI: 10.1155/2012/707323] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/17/2012] [Accepted: 08/18/2012] [Indexed: 01/02/2023] Open
Abstract
The duplex stability with target mRNA and the gene silencing potential of a novel bridged nucleic acid analogue are described. The analogue, 2′,4′-BNANC antisense oligonucleotides (AONs) ranging from 10- to 20-nt-long, targeted apolipoprotein B. 2′,4′-BNANC was directly compared to its conventional bridged (or locked) nucleic acid (2′,4′-BNA/LNA)-based counterparts. Melting temperatures of duplexes formed between 2′,4′-BNANC-based antisense oligonucleotides and the target mRNA surpassed those of 2′,4′-BNA/LNA-based counterparts at all lengths. An in vitro transfection study revealed that when compared to the identical length 2′,4′-BNA/LNA-based counterpart, the corresponding 2′,4′-BNANC-based antisense oligonucleotide showed significantly stronger inhibitory activity. This inhibitory activity was more pronounced in shorter (13-, 14-, and 16-mer) oligonucleotides. On the other hand, the 2′,4′-BNANC-based 20-mer AON exhibited the highest affinity but the worst IC50 value, indicating that very high affinity may undermine antisense potency. These results suggest that the potency of AONs requires a balance between reward term and penalty term. Balance of these two parameters would depend on affinity, length, and the specific chemistry of the AON, and fine-tuning of this balance could lead to improved potency. We demonstrate that 2′,4′-BNANC may be a better alternative to conventional 2′,4′-BNA/LNA, even for “short” antisense oligonucleotides, which are attractive in terms of drug-likeness and cost-effective bulk production.
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Seth PP, Jazayeri A, Yu J, Allerson CR, Bhat B, Swayze EE. Structure Activity Relationships of α-L-LNA Modified Phosphorothioate Gapmer Antisense Oligonucleotides in Animals. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e47. [PMID: 23344239 PMCID: PMC3499693 DOI: 10.1038/mtna.2012.34] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the structure activity relationships of short 14-mer phosphorothioate gapmer antisense oligonucleotides (ASOs) modified with α-L-locked nucleic acid (LNA) and related modifications targeting phosphatase and tensin homologue (PTEN) messenger RNA in mice. α-L-LNA represents the α-anomer of enantio-LNA and modified oligonucleotides show LNA like binding affinity for complementary RNA. In contrast to sequence matched LNA gapmer ASOs which showed elevations in plasma alanine aminotransferase (ALT) levels indicative of hepatotoxicity, gapmer ASOs modified with α-L-LNA and related analogs in the flanks showed potent downregulation of PTEN messenger RNA in liver tissue without producing elevations in plasma ALT levels. However, the α-L-LNA ASO showed a moderate dose-dependent increase in liver and spleen weights suggesting a higher propensity for immune stimulation. Interestingly, replacing α-L-LNA nucleotides in the 3′- and 5′-flanks with R-5′-Me-α-L-LNA but not R-6′-Me- or 3′-Me-α-L-LNA nucleotides, reversed the drug induced increase in organ weights. Examination of structural models of dinucleotide units suggested that the 5′-Me group increases steric bulk in close proximity to the phosphorothioate backbone or produces subtle changes in the backbone conformation which could interfere with recognition of the ASO by putative immune receptors. Our data suggests that introducing steric bulk at the 5′-position of the sugar-phosphate backbone could be a general strategy to mitigate the immunostimulatory profile of oligonucleotide drugs. In a clinical setting, proinflammatory effects manifest themselves as injection site reactions and flu-like symptoms. Thus, a mitigation of these effects could increase patient comfort and compliance when treated with ASOs.
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47
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Hanessian S, Schroeder BR, Giacometti RD, Merner BL, Ostergaard M, Swayze EE, Seth PP. Structure-based design of a highly constrained nucleic acid analogue: improved duplex stabilization by restricting sugar pucker and torsion angle γ. Angew Chem Int Ed Engl 2012; 51:11242-5. [PMID: 22915274 DOI: 10.1002/anie.201203680] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/06/2012] [Indexed: 12/22/2022]
Abstract
Dual conformational restriction: a new, highly constrained modification of the α-L-locked nucleic acid (α-L-LNA) scaffold that locks the sugar furanose ring in an N-type configuration and also restricts rotation around torsion angle γ was synthesized. This new modification increases the thermostability of an oligonucleotide duplex compared to using a single mode of constraint alone.
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48
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Hanessian S, Schroeder BR, Giacometti RD, Merner BL, Østergaard M, Swayze EE, Seth PP. Structure-Based Design of a Highly Constrained Nucleic Acid Analogue: Improved Duplex Stabilization by Restricting Sugar Pucker and Torsion Angleγ. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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49
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Karimiahmadabadi M, Erfan S, Földesi A, Chattopadhyaya J. Steric Effects in the Tuning of the Diastereoselectivity of the Intramolecular Free-Radical Cyclization to an Olefin As Exemplified through the Synthesis of a Carba-Pentofuranose Scaffold. J Org Chem 2012; 77:6855-72. [DOI: 10.1021/jo300936g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mansoureh Karimiahmadabadi
- Program of
Chemical Biology, Department of Cell and
Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sayeh Erfan
- Program of
Chemical Biology, Department of Cell and
Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
| | - Andras Földesi
- Program of
Chemical Biology, Department of Cell and
Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jyoti Chattopadhyaya
- Program of
Chemical Biology, Department of Cell and
Molecular Biology, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden
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50
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Seth PP, Yu J, Jazayeri A, Pallan PS, Allerson CR, Østergaard ME, Liu F, Herdewijn P, Egli M, Swayze EE. Synthesis and antisense properties of fluoro cyclohexenyl nucleic acid (F-CeNA), a nuclease stable mimic of 2'-fluoro RNA. J Org Chem 2012; 77:5074-85. [PMID: 22591005 DOI: 10.1021/jo300594b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report the design and synthesis of 2'-fluoro cyclohexenyl nucleic acid (F-CeNA) pyrimidine phosphoramidites and the synthesis and biophysical, structural, and biological evaluation of modified oligonucleotides. The synthesis of the nucleoside phosphoramidites was accomplished in multigram quantities starting from commercially available methyl-D-mannose pyranoside. Installation of the fluorine atom was accomplished using nonafluorobutanesulfonyl fluoride, and the cyclohexenyl ring system was assembled by means of a palladium-catalyzed Ferrier rearrangement. Installation of the nucleobase was carried out under Mitsunobu conditions followed by standard protecting group manipulations to provide the desired pyrimidine phosphoramidites. Biophysical evaluation indicated that F-CeNA shows behavior similar to that of a 2'-modified nucleotide, and duplexes with RNA showed slightly lower duplex thermostability as compared to that of the more rigid 3'-fluoro hexitol nucleic acid (FHNA). However, F-CeNA modified oligonucleotides were significantly more stable against digestion by snake venom phosphodiesterases (SVPD) as compared to unmodified DNA, 2'-fluoro RNA (FRNA), 2'-methoxyethyl RNA (MOE), and FHNA modified oligonucleotides. Examination of crystal structures of a modified DNA heptamer duplex d(GCG)-T*-d(GCG):d(CGCACGC) by X-ray crystallography indicated that the cyclohexenyl ring system exhibits both the (3)H(2) and (2)H(3) conformations, similar to the C3'-endo/C2'-endo conformation equilibrium seen in natural furanose nucleosides. In the (2)H(3) conformation, the equatorial fluorine engages in a relatively close contact with C8 (2.94 Å) of the 3'-adjacent dG nucleotide that may represent a pseudo hydrogen bond. In contrast, the cyclohexenyl ring of F-CeNA was found to exist exclusively in the (3)H(2) (C3'-endo like) conformation in the crystal structure of the modified A-form DNA decamer duplex [d(GCGTA)-T*-d(ACGC)](2.) In an animal experiment, a 16-mer F-CeNA gapmer ASO showed similar RNA affinity but significantly improved activity compared to that of a sequence matched MOE ASO, thus establishing F-CeNA as a useful modification for antisense applications.
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Affiliation(s)
- Punit P Seth
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States.
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