1
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Novikova D, Sagaidak A, Vorona S, Tribulovich V. A Visual Compendium of Principal Modifications within the Nucleic Acid Sugar Phosphate Backbone. Molecules 2024; 29:3025. [PMID: 38998973 PMCID: PMC11243533 DOI: 10.3390/molecules29133025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Nucleic acid chemistry is a huge research area that has received new impetus due to the recent explosive success of oligonucleotide therapy. In order for an oligonucleotide to become clinically effective, its monomeric parts are subjected to modifications. Although a large number of redesigned natural nucleic acids have been proposed in recent years, the vast majority of them are combinations of simple modifications proposed over the past 50 years. This review is devoted to the main modifications of the sugar phosphate backbone of natural nucleic acids known to date. Here, we propose a systematization of existing knowledge about modifications of nucleic acid monomers and an acceptable classification from the point of view of chemical logic. The visual representation is intended to inspire researchers to create a new type of modification or an original combination of known modifications that will produce unique oligonucleotides with valuable characteristics.
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Affiliation(s)
- Daria Novikova
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Aleksandra Sagaidak
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Svetlana Vorona
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Vyacheslav Tribulovich
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
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2
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Shi Y, Zhen X, Zhang Y, Li Y, Koo S, Saiding Q, Kong N, Liu G, Chen W, Tao W. Chemically Modified Platforms for Better RNA Therapeutics. Chem Rev 2024; 124:929-1033. [PMID: 38284616 DOI: 10.1021/acs.chemrev.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
RNA-based therapies have catalyzed a revolutionary transformation in the biomedical landscape, offering unprecedented potential in disease prevention and treatment. However, despite their remarkable achievements, these therapies encounter substantial challenges including low stability, susceptibility to degradation by nucleases, and a prominent negative charge, thereby hindering further development. Chemically modified platforms have emerged as a strategic innovation, focusing on precise alterations either on the RNA moieties or their associated delivery vectors. This comprehensive review delves into these platforms, underscoring their significance in augmenting the performance and translational prospects of RNA-based therapeutics. It encompasses an in-depth analysis of various chemically modified delivery platforms that have been instrumental in propelling RNA therapeutics toward clinical utility. Moreover, the review scrutinizes the rationale behind diverse chemical modification techniques aiming at optimizing the therapeutic efficacy of RNA molecules, thereby facilitating robust disease management. Recent empirical studies corroborating the efficacy enhancement of RNA therapeutics through chemical modifications are highlighted. Conclusively, we offer profound insights into the transformative impact of chemical modifications on RNA drugs and delineates prospective trajectories for their future development and clinical integration.
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Affiliation(s)
- Yesi Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xueyan Zhen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yiming Zhang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yongjiang Li
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Seyoung Koo
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qimanguli Saiding
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Gang Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Wei Chen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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3
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Mazarei M, Shahabi Rabori V, Ghasemi N, Salehi M, Rayatpisheh N, Jahangiri N, Saberiyan M. LncRNA MALAT1 signaling pathway and clinical applications in overcome on cancers metastasis. Clin Exp Med 2023; 23:4457-4472. [PMID: 37695391 DOI: 10.1007/s10238-023-01179-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023]
Abstract
In spite of its high mortality rate and difficulty in finding a cure, scientific advancements have contributed to a reduction in cancer-related fatalities. Aberrant gene expression during carcinogenesis emphasizes the importance of targeting the signaling networks that control gene expression in cancer treatment. Long noncoding RNAs (lncRNAs), which are transcribed RNA molecules that play a role in gene expression regulation, are a recent innovative therapeutic approach for diagnosing and treating malignancies. MALAT1, a well-known lncRNA, functions in gene expression, RNA processing, and epigenetic control. High expression levels of MALAT1 are associated with several human disorders, including metastasis, invasion, autophagy, and proliferation of cancer cells. MALAT1 affects various signaling pathways and microRNAs (miRNAs), and this study aims to outline its functional roles in cancer metastasis and its interactions with cellular signaling pathways. Moreover, MALAT1 and its interactions with signaling pathways can be promising target for cancer treatment.
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Affiliation(s)
- Madineh Mazarei
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Nazila Ghasemi
- Department of Biology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Mehrnaz Salehi
- School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Najmeh Rayatpisheh
- School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Negin Jahangiri
- Department of Biology, Faculty of Basic Sciences and Engineering, Gonbad Kavous University, Gonbad-e Kavus, Iran
| | - Mohammadreza Saberiyan
- Department of Medical Genetics, Faculty of Medicine, School of Medical Sciences, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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4
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Yamaguchi T, Horie N, Aoyama H, Kumagai S, Obika S. Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids. Nucleic Acids Res 2023; 51:7749-7761. [PMID: 37462081 PMCID: PMC10450189 DOI: 10.1093/nar/gkad608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/28/2023] [Accepted: 07/09/2023] [Indexed: 08/26/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are becoming a promising class of drugs for treating various diseases. Over the past few decades, many modified nucleic acids have been developed for application to ASOs, aiming to enhance their duplex-forming ability toward cognate mRNA and improve their stability against enzymatic degradations. Modulating the sugar conformation of nucleic acids by substituting an electron-withdrawing group at the 2'-position or incorporating a 2',4'-bridging structure is a common approach for enhancing duplex-forming ability. Here, we report on incorporating an N-tert-butylguanidinium group at the 2',4'-bridging structure, which greatly enhances duplex-forming ability because of its interactions with the minor groove. Our results indicated that hydrophobic substituents fitting the grooves of duplexes also have great potential to increase duplex-forming ability.
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Affiliation(s)
- Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naohiro Horie
- 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
| | - Shinji Kumagai
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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5
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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: 6] [Impact Index Per Article: 6.0] [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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6
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Akita T, Tomita-Sudo E, Itoh S, Sakimoto N, Masuda T, Nakamura A, Onishi Y, Koizumi M, Kawakami J. Not all 2',4'-bridged modifications stabilize DNA/RNA duplexes. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:57-64. [PMID: 37424260 DOI: 10.1080/15257770.2023.2232414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 07/11/2023]
Abstract
2',4'-Bridged modifications such as 2'-O,4'-C-methylene-bridged nucleotides (LNAs) and 2'-O,4'-C-ethylene-bridged nucleotides (ENAs) provide high binding affinity for duplex formation. Stabilization by the introduction of the bridged nucleic acids is considered to be due to pre-organization. In this study, we found that the introduction of 2',4'-C-bridged 2'-deoxynucleotides (CRNs; Conformationally Restricted Nucleotides) into DNA/RNA duplexes leads to destabilization, as opposed to the previously accepted notion that 2',4'-bridged modifications always lead to stabilization.
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Affiliation(s)
- Tomoka Akita
- Faculty of Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
- Konan Laboratory for Oligonucleotide Therapeutics, Konan University, Kobe, Japan
| | - Elisa Tomita-Sudo
- Konan Laboratory for Oligonucleotide Therapeutics, Konan University, Kobe, Japan
| | - Shin Itoh
- Faculty of Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
| | - Nae Sakimoto
- Konan Laboratory for Oligonucleotide Therapeutics, Konan University, Kobe, Japan
| | - Takeshi Masuda
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd, Shinagawa, Tokyo, Japan
| | - Akifumi Nakamura
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd, Shinagawa, Tokyo, Japan
| | - Yoshiyuki Onishi
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd, Shinagawa, Tokyo, Japan
| | - Makoto Koizumi
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd, Shinagawa, Tokyo, Japan
| | - Junji Kawakami
- Faculty of Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Japan
- Konan Laboratory for Oligonucleotide Therapeutics, Konan University, Kobe, Japan
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7
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Dowerah D, V. N. Uppuladinne M, Sarma PJ, Biswakarma N, Sonavane UB, Joshi RR, Ray SK, Namsa ND, Deka RC. Design of LNA Analogues Using a Combined Density Functional Theory and Molecular Dynamics Approach for RNA Therapeutics. ACS OMEGA 2023; 8:22382-22405. [PMID: 37396274 PMCID: PMC10308574 DOI: 10.1021/acsomega.2c07860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/17/2023] [Indexed: 07/04/2023]
Abstract
Antisense therapeutics treat a wide spectrum of diseases, many of which cannot be addressed with the current drug technologies. In the quest to design better antisense oligonucleotide drugs, we propose five novel LNA analogues (A1-A5) for modifying antisense oligonucleotides and establishing each with the five standard nucleic acids: adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U). Monomer nucleotides of these modifications were considered for a detailed Density Functional Theory (DFT)-based quantum chemical analysis to determine their molecular-level structural and electronic properties. A detailed MD simulation study was done on a 14-mer ASO (5'-CTTAGCACTGGCCT-3') containing these modifications targeting PTEN mRNA. Results from both molecular- and oligomer-level analysis clearly depicted LNA-level stability of the modifications, the ASO/RNA duplexes maintaining stable Watson-Crick base pairing preferring RNA-mimicking A-form duplexes. Notably, monomer MO isosurfaces for both purines and pyrimidines were majorly distributed on the nucleobase region in modifications A1 and A2 and in the bridging unit in modifications A3, A4, and A5, suggesting that A3/RNA, A4/RNA, and A5/RNA duplexes interact more with the RNase H and solvent environment. Accordingly, solvation of A3/RNA, A4/RNA, and A5/RNA duplexes was higher compared to that of LNA/RNA, A1/RNA, and A2/RNA duplexes. This study has resulted in a successful archetype for creating advantageous nucleic acid modifications tailored for particular needs, fulfilling a useful purpose of designing novel antisense modifications, which may overcome the drawbacks and improve the pharmacokinetics of existing LNA antisense modifications.
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Affiliation(s)
- Dikshita Dowerah
- CMML—Catalysis
and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784 028, India
| | - Mallikarjunachari V. N. Uppuladinne
- HPC—Medical
& Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune 411008, India
| | - Plaban J. Sarma
- CMML—Catalysis
and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784 028, India
- Department
of Chemistry, Gargaon College, Sivasagar, Assam 785685, India
| | - Nishant Biswakarma
- CMML—Catalysis
and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784 028, India
| | - Uddhavesh B. Sonavane
- HPC—Medical
& Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune 411008, India
| | - Rajendra R. Joshi
- HPC—Medical
& Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune 411008, India
| | - Suvendra K. Ray
- Department
of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, Assam 784028, India
- Center
for Multidisciplinary Research, Tezpur University, Napaam, Sonitpur, Assam 784028, India
| | - Nima D. Namsa
- Department
of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, Assam 784028, India
- Center
for Multidisciplinary Research, Tezpur University, Napaam, Sonitpur, Assam 784028, India
| | - Ramesh Ch. Deka
- CMML—Catalysis
and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784 028, India
- Center
for Multidisciplinary Research, Tezpur University, Napaam, Sonitpur, Assam 784028, India
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8
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Goswami A, Prasad AK, Maity J, Khaneja N. Synthesis and applications of bicyclic sugar modified locked nucleic acids: A review. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:503-529. [PMID: 35319343 DOI: 10.1080/15257770.2022.2052316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 03/01/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
A large number of Locked Nucleic Acids (LNAs) with variety of modifications and restricted conformations have been developed in the last few decades. These modifications have significantly improved the biological properties of oligonucleotides, when LNAs moieties were incorporated into them. Herein, the synthesis and applications of these modified locked nucleic acids as antisense oligonucleotides are discussed.Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2022.2052316 .
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Affiliation(s)
- Arkaja Goswami
- Department of Chemistry, Shyam Lal College, University of Delhi, Delhi, India
| | - Ashok K Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Jyotirmoy Maity
- Department of Chemistry, St. Stephen's College, University of Delhi, Delhi, India
| | - Neerja Khaneja
- Department of Chemistry, Shyam Lal College, University of Delhi, Delhi, India
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9
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Takegawa-Araki T, Kumagai S, Yasukawa K, Kuroda M, Sasaki T, Obika S. Structure-Activity Relationships of Anti-microRNA Oligonucleotides Containing Cationic Guanidine-Modified Nucleic Acids. J Med Chem 2022; 65:2139-2148. [PMID: 35084859 DOI: 10.1021/acs.jmedchem.1c01680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anti-microRNA oligonucleotides (AMOs) are valuable tools for the treatment of diseases caused by the dysregulation of microRNA expression. However, the correlation between chemical modifications in AMO sequences and the microRNA-inhibitory activity has not been fully elucidated. In this study, we synthesized a series of AMOs containing cationic guanidine-bridged nucleic acids (GuNA) and evaluated their activities using a dual luciferase assay. We also optimized the site of GuNA substitution and found an effective design for the inhibition of microRNA-21, which was partially different from that of conventional nucleic acid derivatives. This study showed that GuNA-substituted AMOs are effective in inhibiting the function of microRNA.
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Affiliation(s)
- Tomo Takegawa-Araki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Shinji Kumagai
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Kai Yasukawa
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Masataka Kuroda
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Takashi Sasaki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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10
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Sasaki T, Hirakawa Y, Yamairi F, Kurita T, Murahashi K, Nishimura H, Iwazaki N, Yasuhara H, Tateoka T, Ohta T, Obika S, Kotera J. Altered Biodistribution and Hepatic Safety Profile of a Gapmer Antisense Oligonucleotide Bearing Guanidine-Bridged Nucleic Acids. Nucleic Acid Ther 2022; 32:177-184. [PMID: 35073217 DOI: 10.1089/nat.2021.0034] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Guanidine-bridged nucleic acid (GuNA) is a novel 2',4'-bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA) analog containing cations that exhibit strong affinity for target RNA and superior nuclease resistance. In this study, Malat1 antisense oligonucleotide (ASO) bearing GuNA was evaluated for target knockdown (KD) activity and tolerability. The GuNA ASO did not interfere with RNase H recruitment on the target RNA/ASO heteroduplex and did show potent target KD activity in a skeletal muscle-derived cell line equivalent to that of the LNA ASO under gymnotic conditions, whereas almost no KD activity was observed in a hepatocyte-derived cell line. The GuNA ASO exhibited potent KD activity in various tissues; the KD activity in the skeletal muscle was equivalent with that of the LNA ASO, but the KD activities in the liver and kidney were clearly lower compared with the LNA ASO. In addition, despite the higher accumulation of the GuNA ASO in the liver, levels of aspartate aminotransferase and alanine aminotransferase with the GuNA ASO administration were not elevated compared with those induced by the LNA ASO. Our data indicate that the GuNA ASO is tolerable and exhibits unique altered pharmacological activities in comparison with the LNA ASO in terms of the relative effect between liver and skeletal muscle.
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Affiliation(s)
- Takashi Sasaki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
| | - Yoko Hirakawa
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
| | - Fumiko Yamairi
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
| | - Takashi Kurita
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
| | - Karin Murahashi
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
| | - Hirokazu Nishimura
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
| | - Norihiko Iwazaki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
| | - Hidenori Yasuhara
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
| | - Takashi Tateoka
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
| | - Tetsuya Ohta
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Jun Kotera
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Fujisawa, Kanagawa, Japan
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11
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Debreczeni N, Bege M, Herczeg M, Bereczki I, Batta G, Herczegh P, Borbás A. Tightly linked morpholino-nucleoside chimeras: new, compact cationic oligonucleotide analogues. Org Biomol Chem 2021; 19:8711-8721. [PMID: 34586122 DOI: 10.1039/d1ob01174j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The polyanionic phosphodiester backbone of nucleic acids contributes to high nuclease sensitivity and low cellular uptake and is therefore a major obstacle to the biological application of native oligonucleotides. Backbone modifications, particularly charge alterations is a proven strategy to provide artificial oligonucleotides with improved properties. Here, we describe the synthesis of a new type of oligonucleotide analogues consisting of a morpholino and a ribo- or deoxyribonucleoside in which the 5'-amino group of the nucleoside unit provides the nitrogen of the morpholine ring. The synthetic protocol is compatible with trityl and dimethoxytrityl protecting groups and azido functionality, and was extended to the synthesis of higher oligomers. The chimeras are positively charged in aqueous medium, due to the N-alkylated tertiary amine structure of the morpholino unit.
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Affiliation(s)
- Nóra Debreczeni
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- Doctoral School of Chemistry, University of Debrecen, Hungary
- Institute of Healthcare Industry, University of Debrecen, H-4032, Debrecen, Nagyerdei körút 98, Hungary
| | - Miklós Bege
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- Institute of Healthcare Industry, University of Debrecen, H-4032, Debrecen, Nagyerdei körút 98, Hungary
- MTA-DE Molecular Recognition and Interaction Research Group, UD, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Mihály Herczeg
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- Research Group for Oligosaccharide Chemistry of HAS, UD, H-4032, Debrecen, Egyetem tér 1, Hungary
| | - Ilona Bereczki
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- National Virology Laboratory, Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - Gyula Batta
- Department of Organic Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
| | - Pál Herczegh
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- National Virology Laboratory, Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary
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12
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Shimo T, Nakatsuji Y, Tachibana K, Obika S. Design and In Vitro Evaluation of Splice-Switching Oligonucleotides Bearing Locked Nucleic Acids, Amido-Bridged Nucleic Acids, and Guanidine-Bridged Nucleic Acids. Int J Mol Sci 2021; 22:ijms22073526. [PMID: 33805378 PMCID: PMC8037388 DOI: 10.3390/ijms22073526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/20/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022] Open
Abstract
Our group previously developed a series of bridged nucleic acids (BNAs), including locked nucleic acids (LNAs), amido-bridged nucleic acids (AmNAs), and guanidine-bridged nucleic acids (GuNAs), to impart specific characteristics to oligonucleotides such as high-affinity binding and enhanced enzymatic resistance. In this study, we designed a series of LNA-, AmNA-, and GuNA-modified splice-switching oligonucleotides (SSOs) with different lengths and content modifications. We measured the melting temperature (Tm) of each designed SSO to investigate its binding affinity for RNA strands. We also investigated whether the single-stranded SSOs formed secondary structures using UV melting analysis without complementary RNA. As a result, the AmNA-modified SSOs showed almost the same Tm values as the LNA-modified SSOs, with decreased secondary structure formation in the former. In contrast, the GuNA-modified SSOs showed slightly lower Tm values than the LNA-modified SSOs, with no inhibition of secondary structures. We also evaluated the exon skipping activities of the BNAs in vitro at both the mRNA and protein expression levels. We found that both AmNA-modified SSOs and GuNA-modified SSOs showed higher exon skipping activities than LNA-modified SSOs but each class must be appropriately designed in terms of length and modification content.
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13
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Horie N, Yamaguchi T, Kumagai S, Obika S. Synthesis and properties of oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing adenine, guanine, or 5-methylcytosine nucleobases. Beilstein J Org Chem 2021; 17:622-629. [PMID: 33747234 PMCID: PMC7940814 DOI: 10.3762/bjoc.17.54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/18/2021] [Indexed: 11/23/2022] Open
Abstract
Chemical modifications have been extensively used for therapeutic oligonucleotides because they strongly enhance the stability against nucleases, binding affinity to the targets, and efficacy. We previously reported that oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing the thymine (T) nucleobase show excellent biophysical properties for applications in antisense technology. In this paper, we describe the synthesis of GuNA[Me] phosphoramidites bearing other typical nucleobases including adenine (A), guanine (G), and 5-methylcytosine (mC). The phosphoramidites were successfully incorporated into oligonucleotides following the method previously developed for the GuNA[Me]-T-modified oligonucleotides. The binding affinity of the oligonucleotides modified with GuNA[Me]-A, -G, or -mC toward the complementary single-stranded DNAs or RNAs was systematically evaluated. All of the GuNA[Me]-modified oligonucleotides were found to have a strong affinity for RNAs. These data indicate that GuNA[Me] could be a useful modification for therapeutic antisense oligonucleotides.
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Affiliation(s)
- Naohiro Horie
- 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
| | - Shinji Kumagai
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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14
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Danielsen MB, Christensen NJ, Jørgensen PT, Jensen KJ, Wengel J, Lou C. Polyamine-Functionalized 2'-Amino-LNA in Oligonucleotides: Facile Synthesis of New Monomers and High-Affinity Binding towards ssDNA and dsDNA. Chemistry 2020; 27:1416-1422. [PMID: 33073896 DOI: 10.1002/chem.202004495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/16/2020] [Indexed: 12/15/2022]
Abstract
Attachment of cationic moieties to oligonucleotides (ONs) promises not only to increase the binding affinity of antisense ONs by reducing charge repulsion between the two negatively charged strands of a duplex, but also to augment their in vivo stability against nucleases. In this study, polyamine functionality was introduced into ONs by means of 2'-amino-LNA scaffolds. The resulting ONs exhibited efficient binding towards ssDNA, ssRNA and dsDNA targets, and the 2'-amino-LNA analogue carrying a triaminated linker showed the most pronounced duplex- and triplex-stabilizing effect. Molecular modelling revealed that favourable conformational and electrostatic effects led to salt-bridge formation between positively charged polyamine moieties and the Watson-Hoogsteen groove of the dsDNA targets, resulting in the observed triplex stabilization. All the investigated monomers showed increased resistance against 3'-nucleolytic digestion relative to the non-functionalized controls.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Niels Johan Christensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Per T Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Knud J Jensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Jesper Wengel
- 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
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15
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Kumagai S, Sawamoto H, Takegawa-Araki T, Arai Y, Yamakoshi S, Yamada K, Ohta T, Kawanishi E, Horie N, Yamaguchi T, Obika S. Synthesis and properties of GuNA purine/pyrimidine nucleosides and oligonucleotides. Org Biomol Chem 2020; 18:9461-9472. [PMID: 33179694 DOI: 10.1039/d0ob01970d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We recently designed guanidine-bridged nucleic acids (GuNA), and GuNA bearing a thymine (T) nucleobase was synthesized and successfully incorporated into oligonucleotides. The GuNA-T-modified oligonucleotides possessed high duplex-forming ability towards their complementary single-stranded RNAs and were highly stable against 3'-exonuclease. Therefore, GuNA is a promissing artificial nucleic acid for therapeutic antisense oligonucleotides. We herein report the facile synthesis of GuNA phosphoramidites bearing adenine (A), guanine (G), and 5-methylcytosine (mC) nucleobases and a robust method for the preparation of GuNA-modified oligonucleotides, even with sequences having acid-sensitive purine nucleobases. Oligonucleotides modified with GuNA-A, -G, or -mC possessed high duplex-forming ability, similar to those modified with GuNA-T. Moreover, some of the GuNA-modified oligonucleotides were revealed to have high base discriminating ability compared with that of their natural counterparts. GuNA nucleosides exhibited no genotoxicity in bacterial reverse mutation assays. Thus, all GuNAs (GuNA-T, -A, -G, and -mC) are now available to be examined in therapeutic applications.
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Affiliation(s)
- Shinji Kumagai
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan; 1000 Kamoshida, Aoba-ku, Yokohama 227-0033, Japan
| | - Hiroaki Sawamoto
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan; 1000 Kamoshida, Aoba-ku, Yokohama 227-0033, Japan
| | - Tomo Takegawa-Araki
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan; 1000 Kamoshida, Aoba-ku, Yokohama 227-0033, Japan
| | - Yuuki Arai
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan; 1000 Kamoshida, Aoba-ku, Yokohama 227-0033, Japan
| | - Shuhei Yamakoshi
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan; 1000 Kamoshida, Aoba-ku, Yokohama 227-0033, Japan
| | - Katsuya Yamada
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan; 1000 Kamoshida, Aoba-ku, Yokohama 227-0033, Japan
| | - Tetsuya Ohta
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan; 1000 Kamoshida, Aoba-ku, Yokohama 227-0033, Japan
| | - Eiji Kawanishi
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan; 1000 Kamoshida, Aoba-ku, Yokohama 227-0033, Japan
| | - Naohiro Horie
- 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. and National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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16
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Komine H, Mori S, Morihiro K, Ishida K, Okuda T, Kasahara Y, Aoyama H, Yamaguchi T, Obika S. Synthesis and Evaluation of Artificial Nucleic Acid Bearing an Oxanorbornane Scaffold. Molecules 2020; 25:E1732. [PMID: 32283778 PMCID: PMC7180610 DOI: 10.3390/molecules25071732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 01/07/2023] Open
Abstract
Natural oligonucleotides have many rotatable single bonds, and thus their structures are inherently flexible. Structural flexibility leads to an entropic loss when unwound oligonucleotides form a duplex with single-stranded DNA or RNA. An effective approach to reduce such entropic loss in the duplex-formation is the conformational restriction of the flexible phosphodiester linkage and/or sugar moiety. We here report the synthesis and biophysical properties of a novel artificial nucleic acid bearing an oxanorbornane scaffold (OxNorNA), where the adamant oxanorbornane was expected to rigidify the structures of both the linkage and sugar parts of nucleic acid. OxNorNA phosphoramidite with a uracil (U) nucleobase was successfully synthesized over 15 steps from a known sugar-derived cyclopentene. Thereafter, the given phosphoramidite was incorporated into the designed oligonucleotides. Thermal denaturation experiments revealed that oligonucleotides modified with the conformationally restricted OxNorNA-U properly form a duplex with the complementally DNA or RNA strands, although the Tm values of OxNorNA-U-modified oligonucleotides were lower than those of the corresponding natural oligonucleotides. As we had designed, entropic loss during the duplex-formation was reduced by the OxNorNA modification. Moreover, the OxNorNA-U-modified oligonucleotide was confirmed to have extremely high stability against 3'-exonuclease activity, and its stability was even higher than those of the phosphorothioate-modified counterparts (Sp and Rp). With the overall biophysical properties of OxNorNA-U, we expect that OxNorNA could be used for specialized applications, such as conformational fixation and/or bio-stability enhancement of therapeutic oligonucleotides (e.g., aptamers).
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Affiliation(s)
- Hibiki Komine
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Shohei Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kenta Ishida
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (H.K.); (S.M.); (K.I.); (T.O.); (Y.K.); (H.A.)
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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17
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Matsubara M, Honda K, Ozaki K, Kajino R, Kakisawa Y, Maeda Y, Ueno Y. Synthesis of siRNAs incorporated with cationic peptides R8G7 and R8A7 and the effect of the modifications on siRNA properties. RSC Adv 2020; 10:34815-34824. [PMID: 35514421 PMCID: PMC9056854 DOI: 10.1039/d0ra05919f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
Small interfering RNA (siRNA) can be used as an innovative next-generation drug. However, there are several challenges in the therapeutic application of siRNAs, including their low cell membrane permeability. In this study, we designed and synthesized siRNAs, incorporating the cationic peptides R8G7 and R8A7 to improve cell membrane permeability of siRNAs. Thermal denaturation studies revealed that R8G7 and R8A7 modifications increased the thermal stability of the siRNA duplexes. Incorporating these peptides at the 3′-ends of the siRNA passenger strands increased the stability of the siRNAs in a buffer containing bovine serum. Further, we found that the peptide–siRNA conjugates did not show sufficient RNA interference (RNAi) activity in the absence of the transfection reagent; however, when the transfection reagent was used, the peptide–siRNA conjugates preserved their RNAi activity. Small interfering RNA (siRNA) can be used as an innovative next-generation drug.![]()
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Affiliation(s)
- Miho Matsubara
- Course of Applied Life Science
- Faculty of Applied Biological Sciences
- Gifu University
- Gifu
- Japan
| | - Kenji Honda
- Course of Applied Life Science
- Faculty of Applied Biological Sciences
- Gifu University
- Gifu
- Japan
| | - Koki Ozaki
- Course of Applied Life Science
- Faculty of Applied Biological Sciences
- Gifu University
- Gifu
- Japan
| | - Ryohei Kajino
- United Graduate School of Agricultural Science
- Gifu University
- Gifu
- Japan
| | - Yuri Kakisawa
- Course of Applied Life Science
- Faculty of Applied Biological Sciences
- Gifu University
- Gifu
- Japan
| | - Yusuke Maeda
- Course of Applied Life Science
- Faculty of Applied Biological Sciences
- Gifu University
- Gifu
- Japan
| | - Yoshihito Ueno
- Course of Applied Life Science
- Faculty of Applied Biological Sciences
- Gifu University
- Gifu
- Japan
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18
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Moai Y, Hiroaki H, Obika S, Kodama T. Synthesis of selenomethylene-locked nucleic acids (SeLNA) nucleoside unit bearing an adenine base. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:131-140. [PMID: 31608780 DOI: 10.1080/15257770.2019.1675169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Synthesis of selenomethylene-locked nucleic acids nucleoside bearing an adenine base (SeLNA-A) was investigated. We first examined the stereoinversion reaction at 2'-positions of a 5',3'-O-TIPDS-protected 4'-C-(hydroxymethyl)ribosyladenine derivative to give the corresponding arabinosyladenine. After triflation, treatment of the arabinosyladenine derivative with a mixture of selenium and sodium borohydride in ethanol managed to construct the desired SeLNA skeleton. Finally, removal of TIPDS by treating with fluoride gave the SeLNA-A nucleoside. In this study, we found the heat-labile property of SeLNA-A. It is necessary to know more precise characteristics of SeLNA to achieve its oligonucleotides synthesis.
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Affiliation(s)
- Yoshihiro Moai
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hidekazu Hiroaki
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Saoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Tetsuya Kodama
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
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19
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Yamaguchi T, Obika S. Derivative Synthesis toward Enhancement of the Biophysical Properties of 2′,4′-Bridged Nucleic Acids. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University
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20
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Uematsu A, Kajino R, Maeda Y, Ueno Y. Synthesis and characterization of 4'- C-guanidinomethyl-2'- O-methyl-modified RNA oligomers. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:280-291. [PMID: 31530080 DOI: 10.1080/15257770.2019.1666277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This study investigated the synthesis and properties of 4'-C-guanidinomethyl-2'-O-methyluridine and RNAs containing the analog. Thermal and thermodynamic stabilities of double-stranded RNAs (dsRNAs) containing the nucleoside analog were examined. It was found that although the analog decreased the thermal and thermodynamic stabilities of dsRNA, it had base-discrimination ability. The 4'-C-guanidinomethyl modification increased stability of RNAs in a buffer containing serum. Furthermore, small interference RNAs incorporating one analog at the passenger strand still preserved their RNA interference activities. It was suggested that the 4'-guanidinomethyl modification significantly improved cell membrane permeability of RNA. Thus, 4'-C-guanidinomethyl-2'-O-methyl analogs may be useful in improving the properties of therapeutic siRNA molecules.
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Affiliation(s)
- Azusa Uematsu
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Ryohei Kajino
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Yusuke Maeda
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Yoshihito Ueno
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan.,United Graduate School of Agricultural Science, Gifu University, Gifu, Japan.,Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu, Japan
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21
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Kishimoto Y, Fujii A, Nakagawa O, Nagata T, Yokota T, Hari Y, Obika S. Synthesis and thermal stabilities of oligonucleotides containing 2'-O,4'-C-methylene bridged nucleic acid with a phenoxazine base. Org Biomol Chem 2018; 15:8145-8152. [PMID: 28920119 DOI: 10.1039/c7ob01874f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We designed and synthesized a novel artificial 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA/LNA) with a phenoxazine nucleobase and named this compound BNAP. Oligodeoxynucleotide (ODN) containing BNAP showed higher binding affinities toward complementary DNA and RNA as compared to ODNs bearing 2',4'-BNA/LNA with 5-methylcytosine or 2'-deoxyribonucleoside with phenoxazine. Thermodynamic analysis revealed that BNAP exhibits properties associated with the phenoxazine moiety in DNA/DNA duplexes and characteristics associated with the 2',4'-BNA/LNA moiety in DNA/RNA duplexes.
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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22
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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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23
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Sawamoto H, Arai Y, Yamakoshi S, Obika S, Kawanishi E. Synthetic Method for 2′-Amino-LNA Bearing Any of the Four Nucleobases via a Transglycosylation Reaction. Org Lett 2018. [DOI: 10.1021/acs.orglett.8b00476] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroaki Sawamoto
- Research Unit/Innovative Medical Science, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Yuuki Arai
- Research Unit/Immunology & Inflammation, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Shuhei Yamakoshi
- Research Unit/Immunology & Inflammation, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiji Kawanishi
- Research Unit/Immunology & Inflammation, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
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24
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Horie N, Kumagai S, Kotobuki Y, Yamaguchi T, Obika S. Facile synthesis and fundamental properties of an N-methylguanidine-bridged nucleic acid (GuNA[NMe]). Org Biomol Chem 2018; 16:6531-6536. [DOI: 10.1039/c8ob01307a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The GuNA[NMe]-modified oligonucleotides exhibited excellent duplex-forming ability towards the complementary single-stranded DNA and RNA, and showed robust enzymatic stability.
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Affiliation(s)
- Naohiro Horie
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Osaka 565-0871
- Japan
| | - Shinji Kumagai
- Soyaku. Innovative Research Division
- Mitsubishi Tanabe Pharma Corporation
- Yokohama 227-0033
- Japan
| | - Yutaro Kotobuki
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Osaka 565-0871
- Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Osaka 565-0871
- Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences
- Osaka University
- Osaka 565-0871
- Japan
- National Institutes of Biomedical Innovation
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25
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Pansuwan H, Ditmangklo B, Vilaivan C, Jiangchareon B, Pan-In P, Wanichwecharungruang S, Palaga T, Nuanyai T, Suparpprom C, Vilaivan T. Hydrophilic and Cell-Penetrable Pyrrolidinyl Peptide Nucleic Acid via Post-synthetic Modification with Hydrophilic Side Chains. Bioconjug Chem 2017; 28:2284-2292. [PMID: 28704609 DOI: 10.1021/acs.bioconjchem.7b00308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Peptide nucleic acid (PNA) is a nucleic acid mimic in which the deoxyribose-phosphate was replaced by a peptide-like backbone. The absence of negative charge in the PNA backbone leads to several unique behaviors including a stronger binding and salt independency of the PNA-DNA duplex stability. However, PNA possesses poor aqueous solubility and cannot directly penetrate cell membranes. These are major obstacles that limit in vivo applications of PNA. In previous strategies, the PNA can be conjugated to macromolecular carriers or modified with positively charged side chains such as guanidinium groups to improve the aqueous solubility and cell permeability. In general, a preformed modified PNA monomer was required. In this study, a new approach for post-synthetic modification of PNA backbone with one or more hydrophilic groups was proposed. The PNA used in this study was the conformationally constrained pyrrolidinyl PNA with prolyl-2-aminocyclopentanecarboxylic acid dipeptide backbone (acpcPNA) that shows several advantages over the conventional PNA. The aldehyde modifiers carrying different linkers (alkylene and oligo(ethylene glycol)) and end groups (-OH, -NH2, and guanidinium) were synthesized and attached to the backbone of modified acpcPNA by reductive alkylation. The hybrids between the modified acpcPNAs and DNA exhibited comparable or superior thermal stability with base-pairing specificity similar to those of unmodified acpcPNA. Moreover, the modified apcPNAs also showed the improvement of aqueous solubility (10-20 folds compared to unmodified PNA) and readily penetrate cell membranes without requiring any special delivery agents. This study not only demonstrates the practicality of the proposed post-synthetic modification approach for PNA modification, which could be readily applied to other systems, but also opens up opportunities for using pyrrolidinyl PNA in various applications such as intracellular RNA sensing, specific gene detection, and antisense and antigene therapy.
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Affiliation(s)
- Haruthai Pansuwan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University , Ta-Po District, Muang, Phitsanulok 65000, Thailand
| | | | | | | | | | | | | | - Thanesuan Nuanyai
- Rajamankala University of Technology Rattanakosin , Wang Klai Kangwon Campus, Huahin, Prachuap Khiri Khan 77110, Thailand
| | - Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University , Ta-Po District, Muang, Phitsanulok 65000, Thailand
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26
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Lou C, Samuelsen SV, Christensen NJ, Vester B, Wengel J. Oligonucleotides Containing Aminated 2'-Amino-LNA Nucleotides: Synthesis and Strong Binding to Complementary DNA and RNA. Bioconjug Chem 2017; 28:1214-1220. [PMID: 28332825 DOI: 10.1021/acs.bioconjchem.7b00061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mono- and diaminated 2'-amino-LNA monomers were synthesized and introduced into oligonucleotides. Each modification imparts significant stabilization of nucleic acid duplexes and triplexes, excellent sequence selectivity, and significant nuclease resistance. Molecular modeling suggested that structural stabilization occurs via intrastrand electrostatic attraction between the protonated amino groups of the aminated 2'-amino-LNA monomers and the host oligonucleotide backbone.
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Affiliation(s)
| | | | - Niels Johan Christensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen , Thorvaldsensvej 40, Frederiksberg 1871, Denmark
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27
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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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28
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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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29
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Hari Y, Obika S. Synthesis and Properties of 2’,4’-Bridged Nucleic Acids Containing Multiple Heteroatoms in the Bridges. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University
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30
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Berlinck RGS, Romminger S. The chemistry and biology of guanidine natural products. Nat Prod Rep 2016; 33:456-90. [DOI: 10.1039/c5np00108k] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The present review discusses the isolation, structure determination, synthesis, biosynthesis and biological activities of secondary metabolites bearing a guanidine group.
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Affiliation(s)
| | - Stelamar Romminger
- Instituto de Química de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
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31
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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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32
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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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33
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Kaura M, Hrdlicka PJ. Locked nucleic acid (LNA) induced effect on the hybridization and fluorescence properties of oligodeoxyribonucleotides modified with nucleobase-functionalized DNA monomers. Org Biomol Chem 2015; 13:7236-47. [PMID: 26055658 DOI: 10.1039/c5ob00860c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
LNA and nucleobase-modified DNA monomers are two types of building blocks that are used extensively in oligonucleotide chemistry. However, there are only very few reports in which these two monomer families are used alongside each other. In the present study we set out to characterize the biophysical properties of oligodeoxyribonucleotides in which C5-modified 2'-deoxyuridine or C8-modified 2'-deoxyadenosine monomers are flanked by LNA nucleotides. We hypothesized that the LNA monomers would alter the sugar rings of the modified DNA monomers toward more RNA-like North-type conformations for maximal DNA/RNA affinity and specificity. Indeed, the incorporation of LNA monomers almost invariably results in increased target affinity and specificity relative to the corresponding LNA-free ONs, but the magnitude of the stabilization varies greatly. Introduction of LNA nucleotides as direct neighbors into C5-pyrene-functionalized pyrimidine DNA monomers yields oligonucleotide probes with more desirable photophysical properties as compared to the corresponding LNA-free probes, including more intense fluorescence emission upon target binding and improved discrimination of single nucleotide polymorphisms (SNPs). These hybrid oligonucleotides are therefore promising probes for diagnostic applications.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
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34
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Guenther DC, Kumar P, Anderson BA, Hrdlicka PJ. C5-amino acid functionalized LNA: positively poised for antisense applications. Chem Commun (Camb) 2015; 50:9007-9. [PMID: 24983883 DOI: 10.1039/c4cc03623a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Incorporation of positively charged C5-amino acid functionalized LNA uridines into oligodeoxyribonucleotides (ONs) results in extraordinary RNA affinity, binding specificity and stability towards 3'-exonucleases.
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Affiliation(s)
- Dale C Guenther
- Department of Chemistry, University of Idaho, 875 Perimeter Drive MS2343, Moscow, ID 83844-2343, USA.
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35
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Kaura M, Kumar P, Hrdlicka PJ. Synthesis, hybridization characteristics, and fluorescence properties of oligonucleotides modified with nucleobase-functionalized locked nucleic acid adenosine and cytidine monomers. J Org Chem 2014; 79:6256-68. [PMID: 24933409 DOI: 10.1021/jo500994c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Conformationally restricted nucleotides such as locked nucleic acid (LNA) are very popular as affinity-, specificity-, and stability-enhancing modifications in oligonucleotide chemistry to produce probes for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. Considerable efforts have been devoted in recent years to optimize the biophysical properties of LNA through additional modification of the sugar skeleton. We recently introduced C5-functionalization of LNA uridines as an alternative and synthetically more straightforward approach to improve the biophysical properties of LNA. In the present work, we set out to test the generality of this concept by studying the characteristics of oligonucleotides modified with four different C5-functionalized LNA cytidine and C8-functionalized LNA adenosine monomers. The results strongly suggest that C5-functionalization of LNA pyrimidines is indeed a viable approach for improving the binding affinity, target specificity, and/or enzymatic stability of LNA-modified ONs, whereas C8-functionalization of LNA adenosines is detrimental to binding affinity and specificity. These insights will impact the future design of conformationally restricted nucleotides for nucleic acid targeting applications.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho , Moscow, Idaho 83844-2343, United States
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36
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Kaura M, Guenther DC, Hrdlicka PJ. Carbohydrate-functionalized locked nucleic acids: oligonucleotides with extraordinary binding affinity, target specificity, and enzymatic stability. Org Lett 2014; 16:3308-11. [PMID: 24890872 DOI: 10.1021/ol501306u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Three different C5-carbohydrate-functionalized LNA uridine phosphoramidites were synthesized and incorporated into oligodeoxyribonucleotides. C5-Carbohydrate-functionalized LNA display higher affinity toward complementary DNA/RNA targets (ΔTm/modification up to +11.0 °C), more efficient discrimination of mismatched targets, and superior resistance against 3'-exonucleases compared to conventional LNA. These properties render C5-carbohydrate-functionalized LNAs as promising modifications in antisense technology and other nucleic acid targeting applications.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho , Moscow, Idaho 83844-2343, United States
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