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Wariishi T, Kataoka Y, Nakamura T, Kasahara Y, Kuroda M, Obika S, Kuwahara M. Lantern-type G-quadruplex fluorescent sensors for detecting divalent metal ions. Anal Biochem 2024; 690:115525. [PMID: 38554995 DOI: 10.1016/j.ab.2024.115525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
Three thioflavin T (ThT) derivatives, namely ThT/ethylenediaminetetraacetic acid conjugates (E1T, E2T, and E1T1P), were designed and synthesized as sensing components for divalent metal ion detection. Furthermore, these ThT derivatives were used to design lantern-type G-quadruplex (G4) fluorescent sensors. The fluorescence intensities of the ThT derivatives decreased by 1.2- to 5.6-folds in the presence of Ni2+ and Cu2+, respectively, regardless of the topology of the utilized G4. Conversely, when Mn2+ and Zn2+ coexisted in antiparallel G4, the fluorescence intensities of E2T increased to approximately 3.3- and 2.3-folds, respectively, depending on the concentration of the divalent metal ion, allowing for quantitative analyses. The Job plot analysis revealed that the binding ratio of G4 and E2T changed from 2:1 to 1:2 with the increasing concentration of the divalent metal ions. These results indicated that the basic principle of such a lantern-type G4 sensor can be applied to the detection of divalent metal ions and other types of targets, such as proteins, and small molecules via ThT derivatization.
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Affiliation(s)
- Tomoko Wariishi
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo, 156-8550, Japan
| | - Yuka Kataoka
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo, 156-8550, Japan
| | - Tomoaki Nakamura
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo, 156-8550, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka, 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masataka Kuroda
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka, 567-0085, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka, 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo, 156-8550, Japan.
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2
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Matsubayashi T, Yoshioka K, Lei Mon SS, Katsuyama M, Jia C, Yamaguchi T, Hara RI, Nagata T, Nakagawa O, Obika S, Yokota T. Erratum: Favorable efficacy and reduced acute neurotoxicity by antisense oligonucleotides with 2',4' -BNA/LNA with 9-(aminoethoxy)phenoxazine. Mol Ther Nucleic Acids 2024; 35:102182. [PMID: 38590918 PMCID: PMC10999694 DOI: 10.1016/j.omtn.2024.102182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
[This corrects the article DOI: 10.1016/j.omtn.2024.102161.].
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3
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Togawa H, Okubo T, Horiuchi K, Yamaguchi T, Tomita-Sudo E, Akita T, Kawakami J, Obika S. Separation of the diastereomers of phosphorothioated siRNAs by anion-exchange chromatography under non-denaturing conditions. J Chromatogr A 2024; 1721:464847. [PMID: 38552370 DOI: 10.1016/j.chroma.2024.464847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
Abstract
In recent years, several small interfering RNA (siRNA) therapeutics have been approved, and most of them are phosphorothioate (PS)-modified for improving nuclease resistance. This chemical modification induces chirality in the phosphorus atom, leading to the formation of diastereomers. Recent studies have revealed that Sp and Rp configurations of PS modifications of siRNAs have different biological properties, such as nuclease resistance and RNA-induced silencing complex (RISC) loading. These results highlight the importance of determining diastereomeric distribution in quality control. Although various analytical approaches have been used to separate diastereomers (mainly single-stranded oligonucleotides), it becomes more difficult to separate all of them as the number of PS modifications increases. Despite siRNA exhibits efficacy in the double-stranded form, few reports have examined the separation of diastereomers in the double-stranded form. In this study, we investigated the applicability of non-denaturing anion-exchange chromatography (AEX) for the separation of PS-modified siRNA diastereomers. Separation of the four isomers of the two PS bonds tended to improve in the double-stranded form compared to the single-stranded form. In addition, the effects of the analytical conditions and PS-modified position on the separation were evaluated. Moreover, the elution order of the Sp and Rp configurations was confirmed, and the steric difference between them, i.e., the direction of the anionic sulfur atom, appeared to be important for the separation mechanism in non-denaturing AEX. Consequently, all 16 peak tops of the four PS modifications were detected in one sequence, and approximately 30 peak tops were detected out of 64 isomers of six PS bonds, indicating that non-denaturing AEX is a useful technique for the quality control of PS-modified siRNA therapeutics.
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Affiliation(s)
- Hiroyuki Togawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Takashi Okubo
- CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Kazuki Horiuchi
- CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Elisa Tomita-Sudo
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tomoka Akita
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Junji Kawakami
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Kohashi H, Nagata R, Tamenori Y, Amatani T, Ueda Y, Mori Y, Kasahara Y, Obika S, Shimojo M. A novel transient receptor potential C3/C6 selective activator induces the cellular uptake of antisense oligonucleotides. Nucleic Acids Res 2024:gkae245. [PMID: 38621757 DOI: 10.1093/nar/gkae245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
Antisense oligonucleotide (ASO) therapy is a novel therapeutic approach in which ASO specifically binds target mRNA, resulting in mRNA degradation; however, cellular uptake of ASOs remains critically low, warranting improvement. Transient receptor potential canonical (TRPC) channels regulate Ca2+ influx and are activated upon stimulation by phospholipase C-generated diacylglycerol. Herein, we report that a novel TRPC3/C6/C7 activator, L687, can induce cellular ASO uptake. L687-induced ASO uptake was enhanced in a dose- and incubation-time-dependent manner. L687 enhanced the knockdown activity of various ASOs both in vitro and in vivo. Notably, suppression of TRPC3/C6 by specific siRNAs reduced ASO uptake in A549 cells. Application of BAPTA-AM, a Ca2+ chelator, and SKF96365, a TRPC3/C6 inhibitor, suppressed Ca2+ influx via TRPC3/C6, resulting in reduced ASO uptake, thereby suggesting that Ca2+ influx via TRPC3/C6 is critical for L687-mediated increased ASO uptake. L687 also induced dextran uptake, indicating that L687 increased endocytosis. Adding ASO to L687 resulted in endosome accumulation; however, the endosomal membrane disruptor UNC7938 facilitated endosomal escape and enhanced knockdown activity. We discovered a new function for TRPC activators regarding ASO trafficking in target cells. Our findings provide an opportunity to formulate an innovative drug delivery system for the therapeutic development of ASO.
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Affiliation(s)
- Hiroto Kohashi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Ryu Nagata
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Yusuke Tamenori
- School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Tomorrow Amatani
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yoshifumi Ueda
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yasuo Mori
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka 565-0871, Japan
| | - Masahito Shimojo
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
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5
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Soter de Mariz e Miranda L, Schroeder Borges Gonçalves R, Uziel J, Obika S, Lubin-Germain N. Editorial: Nucleosides, nucleotides and nucleic acids: chemistry and biology. Front Chem 2024; 12:1401510. [PMID: 38660568 PMCID: PMC11040680 DOI: 10.3389/fchem.2024.1401510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Affiliation(s)
| | | | - Jacques Uziel
- CY Cergy-Paris Université, BioCIS, CNRS, Cergy, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Nadege Lubin-Germain
- CY Cergy-Paris Université, BioCIS, CNRS, Cergy, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
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Huo W, Miki K, Mu H, Osawa T, Yamaguma H, Kasahara Y, Obika S, Kawaguchi Y, Hirose H, Futaki S, Miyazaki Y, Shinoda W, Akai S, Ohe K. Light-controllable cell-membrane disturbance for intracellular delivery. J Mater Chem B 2024. [PMID: 38456552 DOI: 10.1039/d3tb02956e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Highly polar and charged molecules, such as oligonucleotides, face significant barriers in crossing the cell membrane to access the cytoplasm. To address this problem, we developed a light-triggered twistable tetraphenylethene (TPE) derivative, TPE-C-N, to facilitate the intracellular delivery of charged molecules through an endocytosis-independent pathway. The central double bond of TPE in TPE-C-N is planar in the ground state but becomes twisted in the excited state. Under light irradiation, this planar-to-twisted structural change induces continuous cell membrane disturbances. Such disturbance does not lead to permanent damage to the cell membrane. TPE-C-N significantly enhanced the intracellular delivery of negatively charged molecules under light irradiation when endocytosis was inhibited through low-temperature treatment, confirming the endocytosis-independent nature of this delivery method. We have successfully demonstrated that the TPE-C-N-mediated light-controllable method can efficiently promote the intracellular delivery of charged molecules, such as peptides and oligonucleotides, with molecular weights ranging from 1000 to 5000 Da.
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Affiliation(s)
- Wenting Huo
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan.
| | - Koji Miki
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan.
| | - Huiying Mu
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan.
| | - Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 565-0871, Japan
| | - Harumi Yamaguma
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Yuuya Kasahara
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, 565-0871, Japan
| | | | - Hisaaki Hirose
- Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
| | - Yusuke Miyazaki
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 565-0871, Japan
| | - Kouichi Ohe
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan.
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Yum J, Aulia F, Kamiya K, Hori M, Qiao N, Kim BS, Naito M, Ogura S, Nagata T, Yokota T, Uchida S, Obika S, Kim HJ, Miyata K. Hydrophobicity Tuning of Cationic Polyaspartamide Derivatives for Enhanced Antisense Oligonucleotide Delivery. Bioconjug Chem 2024; 35:125-131. [PMID: 38290165 DOI: 10.1021/acs.bioconjchem.3c00456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Various cationic polymers are used to deliver polyplex-mediated antisense oligonucleotides (ASOs). However, few studies have investigated the structural determinants of polyplex functionalities in polymers. This study focused on the polymer hydrophobicity. A series of amphiphilic polyaspartamide derivatives possessing various hydrophobic (R) moieties together with cationic diethylenetriamine (DET) moieties in the side chain (PAsp(DET/R)s) were synthesized to optimize the R moieties (or hydrophobicity) for locked nucleic acid (LNA) gapmer ASO delivery. The gene knockdown efficiencies of PAsp(DET/R) polyplexes were plotted against a hydrophobicity parameter, logD7.3, of PAsp(DET/R), revealing that the gene knockdown efficiency was substantially improved by PAsp(DET/R) with logD7.3 higher than -2.4. This was explained by the increased polyplex stability and improved cellular uptake of ASO payloads. After intratracheal administration, the polyplex samples with a higher logD7.3 than -2.4 induced a significantly higher gene knockdown in the lung tissue compared with counterparts with lower hydrophobicity and naked ASO. These results demonstrate that the hydrophobicity of PAsp(DET/R) is crucial for efficient ASO delivery in vitro and in vivo.
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Affiliation(s)
- Jongmin Yum
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Nucleotide and Peptide Drug Discovery Center (TIDE Center), Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Fadlina Aulia
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Keisuke Kamiya
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mao Hori
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Nan Qiao
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Beob Soo Kim
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mitsuru Naito
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satomi Ogura
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tetsuya Nagata
- Nucleotide and Peptide Drug Discovery Center (TIDE Center), Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Takanori Yokota
- Nucleotide and Peptide Drug Discovery Center (TIDE Center), Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Satoshi Uchida
- Department of Advanced Nanomedical Engineering, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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8
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Osawa T, Akino T, Obika S. Synthesis, Duplex-Forming Ability, and Enzymatic Stability of Oligonucleotides Modified with Amide-Linked Dinucleotides Containing a 3',4'-Tetrahydropyran-Bridged Nucleic Acid. J Org Chem 2024; 89:269-280. [PMID: 38064209 DOI: 10.1021/acs.joc.3c02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Replacement of a phosphodiester linkage with an amide linkage can improve the binding affinity of oligonucleotides to complementary RNA and their stability toward nucleases. In addition, restricting the conformation of the sugar moiety and the phosphate backbone in oligonucleotides effectively improves duplex stability. In this study, we designed amide-linked dinucleotides containing a 3',4'-tetrahydropyran-bridged nucleic acid (3',4'-tpBNA) with a constrained sugar conformation as well as a torsion angle ε. Phosphoramidites of the designed dinucleotides were synthesized and incorporated into oligonucleotides. Conformational analysis of the synthesized dinucleotides showed that the sugar conformation of the S-isomer of the amide-linked dinucleotide containing 3',4'-tpBNA was N-type, which has the same conformation as that of the RNA duplex, while that of another R-isomer was S-type. Tm analysis indicated that the oligonucleotides containing the synthesized S-isomer showed RNA-selective hybridizing ability, although their duplex-forming ability was slightly inferior to that of natural oligonucleotides. Interestingly, the stability of the oligonucleotides toward endonucleases was significantly improved by modification with the two types of amide-linked dinucleotides developed in this study.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Taiki Akino
- 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
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
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9
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Osawa T, Obika S. Synthesis of Coumarin-Conjugated Oligonucleotides via Knoevenagel Condensation to Prepare an Oligonucleotide Library. Chem Pharm Bull (Tokyo) 2024; 72:143-148. [PMID: 38296555 DOI: 10.1248/cpb.c23-00295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
DNA-encoded libraries (DELs) are attracting attention as a screening tool in the early stages of drug discovery. In the development of DELs, drug candidate compounds are chemically synthesized on barcode DNA. Therefore, it is important to perform the synthesis under mild conditions so as to not damage the DNA. On the other hand, coumarins are gaining increasing research focus not only because they possess excellent fluorescence properties, but also because many medicines contain a coumarin skeleton. Among the various reactions developed for the synthesis of coumarins thus far, Knoevenagel condensation followed by intramolecular cyclization under mild conditions can yield coumarins. In this study, we developed a new synthetic method for preparing a coumarin-conjugated oligonucleotide library via Knoevenagel condensation. The results showed that coumarins substituted at the 5-, 6-, 7-, or 8-positions could be constructed on DNA to afford a total of 26 coumarin-conjugated DNAs. Moreover, this method was compatible with enzymatic ligation, demonstrating its utility in DEL synthesis. The developed strategy for the construction of coumarin scaffolds based on Knoevenagel condensation may contribute to the use of DELs in drug discovery and medicinal chemistry.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University
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10
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Ishida K, Kasahara Y, Hoshino H, Okuda T, Obika S. Systematic Analysis of 2'- O-Alkyl Modified Analogs for Enzymatic Synthesis and Their Oligonucleotide Properties. Molecules 2023; 28:7911. [PMID: 38067640 PMCID: PMC10708256 DOI: 10.3390/molecules28237911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Enzymatic oligonucleotide synthesis is used for the development of functional oligonucleotides selected by in vitro selection. Expanding available sugar modifications for in vitro selection helps the functional oligonucleotides to be used as therapeutics reagents. We previously developed a KOD DNA polymerase mutant, KOD DGLNK, that enzymatically synthesized fully-LNA- or 2'-O-methyl-modified oligonucleotides. Here, we report a further expansion of the available 2'-O-alkyl-modified nucleotide for enzymatic synthesis by KOD DGLNK. We chemically synthesized five 2'-O-alkyl-5-methyluridine triphosphates and incorporated them into the oligonucleotides. We also enzymatically synthesized a 2'-O-alkyl-modified oligonucleotide with a random region (oligonucleotide libraries). The 2'-O-alkyl-modified oligonucleotide libraries showed high nuclease resistance and a wide range of hydrophobicity. Our synthesized 2'-O-alkyl-modified oligonucleotide libraries provide novel possibilities that can promote the development of functional molecules for therapeutic use.
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Affiliation(s)
- Kenta Ishida
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan; (K.I.); (H.H.)
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan; (K.I.); (H.H.)
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Hidekazu Hoshino
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan; (K.I.); (H.H.)
| | - Takumi Okuda
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan; (K.I.); (H.H.)
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan; (K.I.); (H.H.)
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan
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11
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Mikami A, Mori S, Osawa T, Obika S. Post-Synthetic Nucleobase Modification of Oligodeoxynucleotides by Sonogashira Coupling and Influence of Alkynyl Modifications on the Duplex-Forming Ability. Chemistry 2023; 29:e202301928. [PMID: 37635089 DOI: 10.1002/chem.202301928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
Recently, it was reported that the alkynyl modification of nucleobases mitigates the toxicity of antisense oligonucleotides (ASO) while maintaining the efficacy. However, the general effect of alkynyl modifications on the duplex-forming ability of oligonucleotides (ONs) is unclear. In this study, post-synthetic nucleobase modification by Sonogashira coupling in aqueous medium was carried out to efficiently evaluate the physiological properties of various ONs with alkynyl-modified nucleobases. Although several undesired reactions, including nucleobase cyclization, were observed, various types of alkynyl-modified ONs were successfully obtained via Sonogashira coupling of ONs containing iodinated nucleobases. Evaluation of the stability of the duplex formed by the synthesized alkynyl-modified ONs showed that the alkynyl modification of pyrimidine was less tolerated than that of purine, although both the modifications occurred in the major groove of the duplex. These results can be attributed to the bond angle of the alkyne on the pyrimidine and the close proximity of the alkynyl substituents to the phosphodiester backbone. The synthetic method developed in this study may contribute to the screening of the optimal chemical modification of ASO because various alkynyl-modified ONs that are effective in reducing the toxicity of ASO can be easily synthesized by this method.
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Affiliation(s)
- Atsushi Mikami
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shohei Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takashi Osawa
- 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
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
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12
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Hayashida M, Suzuki R, Horie S, Masuda J, Yamaguchi T, Obika S. Applicability of supercritical fluid chromatography for oligonucleotide analysis: A proof-of-concept study. J Chromatogr A 2023; 1708:464333. [PMID: 37660558 DOI: 10.1016/j.chroma.2023.464333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
We evaluated the suitability of supercritical fluid chromatography (SFC) for oligonucleotide analysis using 4-mer oligonucleotides with various phosphorothioate (PS) contents as model compounds. Column screening showed that the diol-modified column was able to separate sequences with different PS contents. Optimization of the column body and additives allowed us to analyze polar oligonucleotides using SFC. Various sequences were also analyzed using the optimized method. A good peak shape was obtained when the guanine plus cytosine content of the analyte was two or less in the 4-mer oligonucleotides. Furthermore, we found that the retention times of the selected sequences were positively correlated with polar surface areas, indicating that oligonucleotides interact with polar stationary phases. In contrast, more hydrophobic full PS sequences were retained more strongly in the diol column than the full phosphodiester (PO) sequences. This suggests that the diol column has unique selectivity for PO and PS linkages. These results indicate that SFC is potentially applicable to oligonucleotide analysis with a separation mechanism that is different from that of ion-pair reversed-phase liquid chromatography.
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Affiliation(s)
- Momoka Hayashida
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Shimadzu Analytical Innovation Research Laboratories, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Risa Suzuki
- Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shinnosuke Horie
- Shimadzu Analytical Innovation Research Laboratories, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan; Shimadzu Europa GmbH, Albert-Hahn-Strasse 6-10, Duisburg 47269, Federal Republic of Germany
| | - Junichi Masuda
- Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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13
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Horie S, Suzuki Y, Yamamoto T, Obika S, Mohri K, Kiyota C, Ren Q, Warashina S, Wada Y, Watanabe Y, Mukai H, Sato Y. Novel strategy of liver cancer treatment with modified antisense oligonucleotides targeting human vasohibin-2. Cancer Sci 2023; 114:3740-3749. [PMID: 37430466 PMCID: PMC10475766 DOI: 10.1111/cas.15897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/16/2023] [Accepted: 06/14/2023] [Indexed: 07/12/2023] Open
Abstract
Vasohihibin-2 (VASH2) is a homolog of vasohibin-1 (VASH1) and is overexpressed in various cancers. Vasohihibin-2 acts on both cancer cells and cancer microenvironmental cells. Previous analyses have shown that VASH2 promotes cancer progression and abrogation of VASH2 results in significant anticancer effects. We therefore propose VASH2 to be a practical molecular target for cancer treatment. Modifications of antisense oligonucleotide (ASO) such as bridged nucleic acids (BNA)-based modification increases the specificity and stability of ASO, and are now applied to the development of a number of oligonucleotide-based drugs. Here we designed human VASH2-ASOs, selected an optimal one, and developed 2',4'-BNA-based VASH2-ASO. When systemically administered, naked 2',4'-BNA-based VASH2-ASO accumulated in the liver and showed its gene-silencing activity. We then examined the effect of 2',4'-BNA-based VASH2-ASO in liver cancers. Intraperitoneal injection of naked 2',4'-BNA-based VASH2-ASO exerted a potent antitumor effect on orthotopically inoculated human hepatocellular carcinoma cells. The same manipulation also showed potent antitumor activity on the splenic inoculation of human colon cancer cells for liver metastasis. These results provide a novel strategy for the treatment of primary as well as metastatic liver cancers by using modified ASOs targeting VASH2.
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Affiliation(s)
- Sachiko Horie
- Department of Vascular BiologyInstitute of Development, Aging and Cancer, Tohoku UniversitySendaiJapan
| | - Yasuhiro Suzuki
- Department of Vascular BiologyInstitute of Development, Aging and Cancer, Tohoku UniversitySendaiJapan
- New Industry Creation Hatchery CenterTohoku UniversitySendaiJapan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical SciencesOsaka UniversityOsakaJapan
- Present address:
Department of Chemistry of Biofunctional Molecules, School of Pharmaceutical SciencesNagasaki UniversityNagasakiJapan
| | - Satoshi Obika
- Graduate School of Pharmaceutical SciencesOsaka UniversityOsakaJapan
| | - Kohta Mohri
- Laboratory for Molecular Delivery and Imaging TechnologyRIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Chizuru Kiyota
- Laboratory for Molecular Delivery and Imaging TechnologyRIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Qin Ren
- Laboratory for Molecular Delivery and Imaging TechnologyRIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Shota Warashina
- Laboratory for Molecular Delivery and Imaging TechnologyRIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Yasuhiro Wada
- Laboratory for Pathophysiological and Health ScienceRIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Yasuyoshi Watanabe
- Laboratory for Pathophysiological and Health ScienceRIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Hidefumi Mukai
- Laboratory for Molecular Delivery and Imaging TechnologyRIKEN Center for Biosystems Dynamics ResearchKobeJapan
- Department of Pharmaceutical Informatics, Graduate School of Biomedical SciencesNagasaki UniversityNagasakiJapan
| | - Yasufumi Sato
- Department of Vascular BiologyInstitute of Development, Aging and Cancer, Tohoku UniversitySendaiJapan
- New Industry Creation Hatchery CenterTohoku UniversitySendaiJapan
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Miyagawa S, Horie T, Nishino T, Koyama S, Watanabe T, Baba O, Yamasaki T, Sowa N, Otani C, Matsushita K, Kojima H, Kimura M, Nakashima Y, Obika S, Kasahara Y, Kotera J, Oka K, Fujita R, Sasaki T, Takemiya A, Hasegawa K, Kimura T, Ono K. Inhibition of microRNA-33b in humanized mice ameliorates nonalcoholic steatohepatitis. Life Sci Alliance 2023; 6:e202301902. [PMID: 37263777 PMCID: PMC10235800 DOI: 10.26508/lsa.202301902] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/03/2023] Open
Abstract
Nonalcoholic steatohepatitis (NASH) can lead to cirrhosis and hepatocellular carcinoma in their advanced stages; however, there are currently no approved therapies. Here, we show that microRNA (miR)-33b in hepatocytes is critical for the development of NASH. miR-33b is located in the intron of sterol regulatory element-binding transcription factor 1 and is abundantly expressed in humans, but absent in rodents. miR-33b knock-in (KI) mice, which have a miR-33b sequence in the same intron of sterol regulatory element-binding transcription factor 1 as humans and express miR-33b similar to humans, exhibit NASH under high-fat diet feeding. This condition is ameliorated by hepatocyte-specific miR-33b deficiency but unaffected by macrophage-specific miR-33b deficiency. Anti-miR-33b oligonucleotide improves the phenotype of NASH in miR-33b KI mice fed a Gubra Amylin NASH diet, which induces miR-33b and worsens NASH more than a high-fat diet. Anti-miR-33b treatment reduces hepatic free cholesterol and triglyceride accumulation through up-regulation of the lipid metabolism-related target genes. Furthermore, it decreases the expression of fibrosis marker genes in cultured hepatic stellate cells. Thus, inhibition of miR-33b using nucleic acid medicine is a promising treatment for NASH.
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Affiliation(s)
- Sawa Miyagawa
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahiro Horie
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Nishino
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Koyama
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshimitsu Watanabe
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Baba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Yamasaki
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoya Sowa
- Division of Translational Research, National Hospital Organization, Kyoto Medical Center, Kyoto, Japan
| | - Chiharu Otani
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuki Matsushita
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidenori Kojima
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Kimura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhiro Nakashima
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Jun Kotera
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, Fujisawa-shi, Japan
| | - Kozo Oka
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, Fujisawa-shi, Japan
| | - Ryo Fujita
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, Fujisawa-shi, Japan
| | - Takashi Sasaki
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, Fujisawa-shi, Japan
| | - Akihiro Takemiya
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, Fujisawa-shi, Japan
| | - Koji Hasegawa
- Division of Translational Research, National Hospital Organization, Kyoto Medical Center, Kyoto, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koh Ono
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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16
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Chiba K, Yamaguchi T, Obika S. Development of 8-17 XNAzymes that are functional in cells. Chem Sci 2023; 14:7620-7629. [PMID: 37476720 PMCID: PMC10355097 DOI: 10.1039/d3sc01928d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
DNA enzymes (DNAzymes), which cleave target RNA with high specificity, have been widely investigated as potential oligonucleotide-based therapeutics. Recently, xeno-nucleic acid (XNA)-modified DNAzymes (XNAzymes), exhibiting cleavage activity in cultured cells, have been developed. However, a versatile approach to modify XNAzymes that function in cells has not yet been established. Here, we report an X-ray crystal structure-based approach to modify 8-17 DNAzymes; this approach enables us to effectively locate suitable XNAs to modify. Our approach, combined with a modification strategy used in designing antisense oligonucleotides, rationally designed 8-17 XNAzyme ("X8-17") that achieved high potency in terms of RNA cleavage and biostability against nucleases. X8-17, modified with 2'-O-methyl RNA, locked nucleic acid and phosphorothioate, successfully induced endogenous MALAT-1 and SRB1 RNA knockdown in cells. This approach may help in developing XNAzyme-based novel therapeutic agents.
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Affiliation(s)
- Kosuke Chiba
- 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
- National Institutes of Biomedical Innovation, Health and Nutrition 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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17
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Sawamoto H, Sasaki T, Takegawa-Araki T, Utsugi M, Furukawa H, Hirakawa Y, Yamairi F, Kurita T, Murahashi K, Yamada K, Ohta T, Kumagai S, Takemiya A, Obika S, Kotera J. Synthesis and properties of a novel modified nucleic acid, 2'-N-methanesulfonyl-2'-amino-locked nucleic acid. Bioorg Med Chem Lett 2023; 88:129289. [PMID: 37068560 DOI: 10.1016/j.bmcl.2023.129289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
2'-Amino-locked nucleic acid has a functionalizable nitrogen atom at the 2'-position of its furanose ring that can provide desired properties to a nucleic acid as a scaffold. In this study, we synthesized a novel nucleic acid, 2'-N-methanesulfonyl-2'-amino-locked nucleic acid (ALNA[Ms]) and conducted comparative studies on the physical and pharmacological properties of the ALNA[Ms] and on conventional nucleic acids, such as 2'-methylamino-LNA (ALNA[Me]), which is a classical 2'-amino-LNA derivative, and also on 2',4'-BNA/LNA (LNA). ALNA[Ms] oligomers exhibited binding affinities for the complementary RNA strand that are similar to those of conventional nucleic acids. Four types of ALNA[Ms] nucleosides exhibited no genotoxicity in bacterial reverse mutation assays. The knockdown abilities of Malat1 RNA using the Matat1 antisense oligonucleotide (ASO) containing ALNA[Ms] were higher than those of ALNA[Me] and were closer to those of LNA. Furthermore, the ASO containing ALNA[Ms] showed different tissue tropism from that containing LNA. ALNA[Ms] exhibited biological activities that were distinct from conventional constrained nucleic acids, suggesting the possibility that ALNA[Ms] can serve as novel modified nucleic acids in oligonucleotide therapeutics.
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Affiliation(s)
- Hiroaki Sawamoto
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan.
| | - Takashi Sasaki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, 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
| | - Masayuki Utsugi
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Hiroyuki Furukawa
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Yoko Hirakawa
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Fumiko Yamairi
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Takashi Kurita
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Karin Murahashi
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, 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
| | - Tetsuya Ohta
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, 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
| | - Akihiro Takemiya
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jun Kotera
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
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18
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Tanaka Y, Tanioku Y, Nakayama T, Aso K, Yamaguchi T, Kamada H, Obika S. Synthesis of multivalent fatty acid-conjugated antisense oligonucleotides: Cell internalization, physical properties, and in vitro and in vivo activities. Bioorg Med Chem 2023; 81:117192. [PMID: 36780806 DOI: 10.1016/j.bmc.2023.117192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
Herein, we describe the design and synthesis of multi-conjugatable fatty acid monomer phosphoramidites and their conjugation to antisense oligonucleotides (ASOs). Multivalent long-chain fatty acid conjugation improved the cellular uptake of ASOs but decreased in vitro activity due to alterations in physical properties and cellular localization. In addition, multivalently fatty acid-conjugated ASOs showed different organ specificity compared with that of unconjugated ASO in in vivo experiment. Although optimization of the linker structure between the fatty acid moiety and the ASO may be required, divalent long-chain fatty acid conjugation provides a new approach to increase endocytosis, thereby potentially improving the activity of therapeutic ASOs.
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Affiliation(s)
- Yuya Tanaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yurika Tanioku
- School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Taisuke Nakayama
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kotomi Aso
- 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.
| | - Haruhiko Kamada
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, 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, 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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19
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Togawa H, Okubo T, Nonaka Y, Yamaguchi T, Obika S. Retention behavior of short double-stranded oligonucleotide and its potential impurities by anion-exchange chromatography under non-denaturing conditions. J Chromatogr A 2023; 1691:463808. [PMID: 36706652 DOI: 10.1016/j.chroma.2023.463808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
Small interfering RNA (siRNA), consisting of two complementary single-stranded RNAs with overhanging bases, is being adopted as a potent and specific inhibitor of target gene expression. However, non-duplexed single strands and undesired double strands composed of impurities (e.g., n-1 mer) could be produced in addition to the target double strand in the siRNA manufacturing process. Compared to the liquid chromatography analysis of single strands, the analysis of the duplexes under non-denaturing conditions is challenging, since restricted chromatographic conditions are required to maintain the Watson-Crick hydrogen bonds. This study reports the analysis of double-stranded oligomers having approximately 20 base pairs with some overhanging bases as non-denatured forms by anion-exchange chromatography (AEX). Optimization of the chromatographic conditions could potentially achieve the adequate separation of excess single strands from the double strand. Non-optimal duplexes, such as duplexes with long overhangs or bulge structures, were prepared by intentionally deleting terminal or middle nucleotide(s) of either the sense or the antisense strand, and these non-optimal duplexes were eluted at different retention times in most of the cases. Interestingly, under alkaline chromatographic conditions (pH 9.0), non-optimal duplexes containing a shortmer tended to exhibit a stronger retention than their parent duplexes, although they possessed a less negative charge. This study demonstrated some retention behavior of double strands with overhangs by AEX under non-denaturing conditions.
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Affiliation(s)
- Hiroyuki Togawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Takashi Okubo
- CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Yumi Nonaka
- CERI Kurume, Chemicals Evaluation and Research Institute, Japan, 3-2-7 Miyanojin, Kurume, Fukuoka 839-0801, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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20
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Takakusa H, Iwazaki N, Nishikawa M, Yoshida T, Obika S, Inoue T. Drug Metabolism and Pharmacokinetics of Antisense Oligonucleotide Therapeutics: Typical Profiles, Evaluation Approaches, and Points to Consider Compared with Small Molecule Drugs. Nucleic Acid Ther 2023; 33:83-94. [PMID: 36735616 PMCID: PMC10066781 DOI: 10.1089/nat.2022.0054] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Oligonucleotide therapeutics are attracting attention as a new treatment modality for a range of diseases that have been difficult to target using conventional approaches. Technical advances in chemical modification and drug delivery systems have led to the generation of compounds with excellent profiles as pharmaceuticals, and 16 oligonucleotide therapeutics have been marketed to date. There is a growing need to develop optimal and efficient approaches to evaluate drug metabolism and pharmacokinetics (DMPK) and drug-drug interactions (DDIs) of oligonucleotide therapeutics. The DMPK/DDI profiles of small molecule drugs are highly diverse depending on their structural and physicochemical characteristics, whereas oligonucleotide therapeutics share similar DMPK profiles within each chemistry type. Most importantly, the mechanisms and molecules involved in the distribution and metabolism of oligonucleotides differ from those of small molecules. In addition, there are considerations regarding experimental approaches in the evaluation of oligonucleotides, such as bioanalytical challenges, the use of radiolabeled tracers, materials for in vitro metabolism/DDI studies, and methods to study biodistribution. In this review, we attempt to summarize the DMPK characteristics of antisense oligonucleotide (ASO) therapeutics and discuss some of the issues regarding how to optimize the evaluation and prediction of the DMPK and DDI of ASOs.
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Affiliation(s)
- Hideo Takakusa
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Norihiko Iwazaki
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corp., Yokohama, Japan
| | - Makiya Nishikawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Tokuyuki Yoshida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
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21
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Yoshida M, Oda C, Mishima K, Tsuji I, Obika S, Shimojo M. An antisense amido-bridged nucleic acid gapmer oligonucleotide targeting SRRM4 alters REST splicing and exhibits anti-tumor effects in small cell lung cancer and prostate cancer cells. Cancer Cell Int 2023; 23:8. [PMID: 36650528 PMCID: PMC9847160 DOI: 10.1186/s12935-022-02842-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/27/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Antisense oligonucleotide (ASO) medicine for clinical applications has been becoming a reality. We previously developed a gapmer ASO targeting Ser/Arg repetitive matrix 4 (SRRM4) that is abnormally expressed in small cell lung cancer (SCLC). However the detailed mechanism of ASO through repressing SRRM4 has not been completely elucidated. Further, effectiveness of SRRM4 ASO to prostate cancer (PCa) cells expressing SRRM4 similar to SCLC remains to be elucidated. RE1-silencing transcription factor (REST) is a tumor suppressor, and its splicing isoform (sREST) is abnormally expressed by SRRM4 and causes carcinogenesis with neuroendocrine phenotype in SCLC. The present study aimed to understand the contribution of REST splicing by SRRM4 ASO administration. METHODS SRRM4 expression and REST splicing were analyzed by RT-qPCR and conventional RT-PCR after treating SRRM4 ASO, and cell viability was analyzed in vitro. Exogenous reconstitution of Flag-tagged REST plasmid in SCLC cells and the splice-switching oligonucleotide (SSO) specific for REST was analyzed for cell viability. Furthermore, we expanded the application of SRRM4 ASO in PCa cells abnormally expressing SRRM4 mRNA in vitro. RESULTS SRRM4 ASO successfully downregulated SRRM4 expression, followed by repressed cell viability of SCLC and PCa cells in a dose-dependent manner. Administration of SRRM4 ASO then modified the alternative splicing of REST, resulting reduced cell viability. REST SSO specifically modified REST splicing increased REST expression, resulting in reduced cell viability. CONCLUSIONS Our data demonstrate that a gapmer ASO targeting SRRM4 (SRRM4 ASO) reduces cell viability through splicing changes of REST, followed by affecting REST-controlled genes in recalcitrant tumors SCLC and PCa cells.
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Affiliation(s)
- Misa Yoshida
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Chihiro Oda
- grid.136593.b0000 0004 0373 3971School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Keishiro Mishima
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Itsuki Tsuji
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Satoshi Obika
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan ,grid.136593.b0000 0004 0373 3971School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, 565-0871 Japan ,grid.482562.fNational Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka 567-0085 Japan
| | - Masahito Shimojo
- grid.136593.b0000 0004 0373 3971Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
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22
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Rahman Chowdhury T, Taufiq T, Ishida K, Ariful Islam M, Kasahara Y, Osawa T, Obika S. Synthesis and biophysical properties of tetravalent PEG-conjugated antisense oligonucleotide. Bioorg Med Chem 2023; 78:117149. [PMID: 36587552 DOI: 10.1016/j.bmc.2022.117149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
This study was aimed at developing a novel platform for tetravalent conjugation of 4-arm polyethylene glycol (PEG) with an antisense oligonucleotide (ASO). The ASO technology has several limitations, such as low cellular uptake, poor nuclease stability, and short half-life. PEG-conjugated ASOs may result in an improvement in the pharmacokinetic behavior of the drug. Moreover, PEGylation can reduce enzymatic degradation and renal excretion of the conjugates, thereby, increasing its blood stability and retention time. In this study, we successfully synthesized PEG-ASO conjugate consisting of 4-arm-PEG and four molecules of ASO (4-arm-PEG-tetra ASO). Its hybridization ability with complementary RNA, enzymatic stability, and in vitro gene silencing ability were evaluated. No significant difference in hybridization ability was observed between 4-arm-PEG-tetra ASO and the parent ASO. In addition, gene silencing activity of the 4-arm-PEG-tetra ASO was observed in vitro. However, the in vitro activity of the 4-arm-PEG-tetra ASO was slightly reduced as that of the parent ASO. Moreover, the 4-arm-PEG-tetra ASO showed appreciable stability in cellular extract, suggesting that it hybridizes with mRNA in its intact form, without being cleaved in the cell, and exhibits ASO activity.
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Affiliation(s)
- Taslima Rahman Chowdhury
- 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
| | - Tahia Taufiq
- 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
| | - Kenta Ishida
- 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
| | - Md Ariful Islam
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuuya Kasahara
- 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
| | - Takashi Osawa
- 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; 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, Osaka University (OTRI), 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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23
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Sakurai Y, Yamaguchi T, Yoshida T, Horiba M, Inoue T, Obika S. Synthesis and Properties of Nucleobase-Sugar Dual Modified Nucleic Acids: 2 '-OMe-RNA and scpBNA Bearing a 5-Hydroxycytosine Nucleobase. J Org Chem 2023; 88:154-162. [PMID: 36520114 DOI: 10.1021/acs.joc.2c02038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Naturally occurring 5-hydroxycytosine (5-OHCyt), which is associated with DNA damage, was recently found to reduce the hepatotoxicity of antisense oligonucleotides (ASOs) without compromising its antisense activity when used as a replacement for cytosine (Cyt). Additionally, sugar-modified nucleic acids, such as 2'-O-methylribonucleic acid (2'-OMe-RNA) and 2'-O,4'-C-spirocyclopropylene-bridged nucleic acid (scpBNA), have emerged as useful antisense materials. Herein, we aimed to combine these two advantages by designing dual modified nucleic acids 2'-OMe-RNA-5-OHCyt and scpBNA-5-OHCyt bearing the 5-OHCyt nucleobase to develop efficient and safe ASOs. We describe the synthesis of 2'-OMe-RNA-5-OHCyt and scpBNA-5-OHCyt phosphoramidites and their incorporation into oligonucleotides (ONs). The duplex-forming ability and base discrimination properties of 2'-OMe-RNA-5-OHCyt- and scpBNA-5-OHCyt-modified ONs were similar to those of 2'-OMe-RNA-Cyt- and scpBNA-mCyt-modified ONs, respectively. We also synthesized two 2'-OMe-RNA-5-OHCyt-modified ASOs, and one of the two was found to exhibit reduced hepatotoxicity while retaining target mRNA knockdown activity in in vivo experiments.
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Affiliation(s)
- Yota Sakurai
- 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
| | - Tokuyuki Yoshida
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Masahiko Horiba
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, 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, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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24
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Takegawa-Araki T, Yasukawa K, Iwazaki N, Maruyama H, Furukawa H, Sawamoto H, Obika S. Parallel synthesis of oligonucleotides containing N-acyl amino-LNA and their therapeutic effects as anti-microRNAs. Org Biomol Chem 2022; 20:9351-9361. [PMID: 36383101 DOI: 10.1039/d2ob01809h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
2'-Amino-locked nucleic acid (ALNA), maintains excellent duplex stability, and the nitrogen at the 2'-position is an attractive scaffold for functionalization. Herein, a facile and efficient method for the synthesis of various 2'-N-acyl amino-LNA derivatives by direct acylation of the 2'-amino moiety contained in the synthesized oligonucleotides and its fundamental properties are described. The introduction of the acylated amino-LNA enhances the potency of the molecules as therapeutic anti-microRNA oligonucleotides.
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Affiliation(s)
- Tomo Takegawa-Araki
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Kai Yasukawa
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Norihiko Iwazaki
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hideto Maruyama
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroyuki Furukawa
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroaki Sawamoto
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 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.
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25
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Osawa T, Ren Q, Obika S. Development of Phosphoramidite Reagents for the Synthesis of Base-Labile Oligonucleotides Modified with a Linear Aminoalkyl and Amino-PEG Linker at the 3'-End. Molecules 2022; 27:molecules27238501. [PMID: 36500594 PMCID: PMC9736658 DOI: 10.3390/molecules27238501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
Oligonucleotides with an amino linker at the 3'-end are useful for the preparation of conjugated oligonucleotides. However, chemically modified nucleosides, which are unstable under basic conditions, cannot be incorporated into oligonucleotides using the conventional method entailing the preparation of oligonucleotides bearing a 3'-amino linker. Therefore, we designed Fmoc-protected phosphoramidites for the synthesis of base-labile oligonucleotides modified with a 3'-amino linker. The resultant phosphoramidites were then successfully incorporated into oligonucleotides bearing a 3'-amino linker. Various basic solutions were investigated for protecting group removal. All the protecting groups were removed by treating the oligonucleotides with 40% aqueous methylamine at room temperature for 2 h. Thus, the deprotection time and temperature were significantly reduced compared to the conventional conditions (28% NH3 aq., 55 °C, 17 h). In addition, the oligonucleotide protecting groups could be removed using a mild base (e.g., 50 mM potassium carbonate methanol solution). Furthermore, base-labile oligonucleotides bearing an amino linker at the 3'-end were successfully synthesized using the developed phosphoramidite reagents, highlighting the utility of our strategy.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Osaka 565-0871, Japan
| | - Qin Ren
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Osaka 565-0871, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Japan
- Correspondence: ; Tel.: +81-6-6879-8200
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26
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Yamaji R, Nakagawa O, Kishimoto Y, Fujii A, Matsumura T, Nakayama T, Kamada H, Osawa T, Yamaguchi T, Obika S. Synthesis and physical and biological properties of 1,3-diaza-2-oxophenoxazine-conjugated oligonucleotides. Bioorg Med Chem 2022; 72:116972. [DOI: 10.1016/j.bmc.2022.116972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022]
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27
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Yoshida T, Morihiro K, Naito Y, Mikami A, Kasahara Y, Inoue T, Obika S. Identification of nucleobase chemical modifications that reduce the hepatotoxicity of gapmer antisense oligonucleotides. Nucleic Acids Res 2022; 50:7224-7234. [PMID: 35801870 PMCID: PMC9303313 DOI: 10.1093/nar/gkac562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 12/26/2022] Open
Abstract
Currently, gapmer antisense oligonucleotide (ASO) therapeutics are under clinical development for the treatment of various diseases, including previously intractable human disorders; however, they have the potential to induce hepatotoxicity. Although several groups have reported the reduced hepatotoxicity of gapmer ASOs following chemical modifications of sugar residues or internucleotide linkages, only few studies have described nucleobase modifications to reduce hepatotoxicity. In this study, we introduced single or multiple combinations of 17 nucleobase derivatives, including four novel derivatives, into hepatotoxic locked nucleic acid gapmer ASOs and examined their effects on hepatotoxicity. The results demonstrated successful identification of chemical modifications that strongly reduced the hepatotoxicity of gapmer ASOs. This approach expands the ability to design gapmer ASOs with optimal therapeutic profiles.
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Affiliation(s)
- Tokuyuki Yoshida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Yuki Naito
- Database Center for Life Science (DBCLS), 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi Mikami
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
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28
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Omuro S, Yamaguchi T, Kawase T, Terasaki M, Hirose K, Obika S. Physicochemical property evaluation of modified oligonucleotides by traveling-wave ion mobility mass spectrometry. Rapid Commun Mass Spectrom 2022; 36:e9279. [PMID: 35203101 DOI: 10.1002/rcm.9279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/27/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
RATIONALE Therapeutic oligonucleotides have molecular weights of more than 6000 Da. They typically contain chemically modified structures such as phosphorothioate (PS) and a locked nucleic acid (LNA). To determine the effect of the length and chemical modification on the physicochemical properties, various nucleic acids with different lengths and modified structures were analyzed using traveling-wave ion mobility mass spectrometry (TWIMS). METHODS The physicochemical characteristics of the modified oligonucleotides were determined using IM-MS. Each oligonucleotide was evaluated by confirming the multivalent charge state drift times, collision cross-section (CCS) values, and CCS widths. RESULTS By plotting the m/z for oligonucleotides of different lengths and the CCS values at each charge state, a bottoming-out shape plot at one charge per 4.0-3.5 bases was confirmed. Moreover, significant differences were observed in the CCS values between the PS-modified and unmodified oligonucleotides. The PS-modified oligonucleotide showed a wider CCS range that was proportional to the PS modification ratio of the oligonucleotide sequence. CONCLUSIONS The TWIMS results showed a correlation between the length and modification of oligonucleotides and the CCS values. In addition, it suggested that each charge state of the oligonucleotide ion has different physicochemical properties.
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Affiliation(s)
- Shogo Omuro
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | | | | | | | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
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29
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Hussain F, Rahman FI, Saha P, Mikami A, Osawa T, Obika S, Rahman SMA. Synthesis of Sugar and Nucleoside Analogs and Evaluation of Their Anticancer and Analgesic Potentials. Molecules 2022; 27:molecules27113499. [PMID: 35684435 PMCID: PMC9182362 DOI: 10.3390/molecules27113499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/21/2022] [Accepted: 05/22/2022] [Indexed: 02/04/2023] Open
Abstract
Chemical modification of sugars and nucleosides has a long history of producing compounds with improved selectivity and efficacy. In this study, several modified sugars (2–3) and ribonucleoside analogs (4–8) have been synthesized from α-d-glucose in a total of 21 steps. The compounds were tested for peripheral anti-nociceptive characteristics in the acetic acid-induced writhing assay in mice, where compounds 2, 7, and 8 showed a significant reduction in the number of writhes by 56%, 62%, and 63%, respectively. The compounds were also tested for their cytotoxic potential against human HeLa cell line via trypan blue dye exclusion test followed by cell counting kit-8 (CCK-8) assay. Compound 6 demonstrated significant cytotoxic activity with an IC50 value of 54 µg/mL. Molecular docking simulations revealed that compounds 2, 7, and 8 had a comparable binding affinity to cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) enzymes. Additionally, the bridged nucleoside analogs 7 and 8 potently inhibited adenosine kinase enzyme as well, which indicates an alternate mechanistic pathway behind their anti-nociceptive action. Cytotoxic compound 6 demonstrated strong docking with cancer drug targets human cytidine deaminase, proto-oncogene tyrosine-protein kinase Src, human thymidine kinase 1, human thymidylate synthase, and human adenosine deaminase 2. This is the first ever reporting of the synthesis and analgesic property of compound 8 and the cytotoxic potential of compound 6.
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Affiliation(s)
- Fahad Hussain
- Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh; (F.H.); (F.I.R.); (P.S.)
| | - Fahad Imtiaz Rahman
- Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh; (F.H.); (F.I.R.); (P.S.)
| | - Poushali Saha
- Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh; (F.H.); (F.I.R.); (P.S.)
| | - Atsushi Mikami
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Osaka 565-0871, Japan; (A.M.); (T.O.); (S.O.)
| | - Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Osaka 565-0871, Japan; (A.M.); (T.O.); (S.O.)
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Osaka 565-0871, Japan; (A.M.); (T.O.); (S.O.)
| | - S. M. Abdur Rahman
- Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh; (F.H.); (F.I.R.); (P.S.)
- Correspondence: ; Tel.: +880-1732477343
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30
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Ii H, Kasahara Y, Yamaguma H, Kageyama S, Kawauchi A, Obika S, Nakata S. Administration of Gapmer-type Antisense Oligonucleotides Targeting γ-Glutamylcyclotransferase Suppresses the Growth of A549 Lung Cancer Xenografts. Anticancer Res 2022; 42:1221-1227. [PMID: 35220212 DOI: 10.21873/anticanres.15589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM γ-Glutamyl cyclotransferase (GGCT) is up-regulated in various cancer types, including lung cancer. In this study, we evaluated efficacy of gapmer-type antisense oligonucleotides (ASOs) targeting GGCT in an A549 lung cancer xenograft mouse model and studied their mechanisms of action. MATERIALS AND METHODS GGCT was inhibited using GGCT-ASOs and cell proliferation was evaluated by dye exclusion test. Western blot analysis was conducted to measure expression of GGCT, p21, p16 and p27, phosphorylation of AMP-activated protein kinase, and caspase activation in A549 cells. Induction of apoptosis and up-regulation of reactive oxygen species were assessed by flow cytometry using annexin V staining and 2',7'-dichlorodihydrofluorescein diacetate dye, respectively. RESULTS GGCT-ASOs suppressed GGCT expression in A549 cells, inhibited proliferation, and induced apoptosis with activation of caspases. GGCT-ASOs also increased expression of cell-cycle regulating proteins, phospho-AMPK and ROS levels. Systemic administration of GGCT-ASOs to animals bearing A549 lung cancer xenografts showed significant antitumor effects without evident toxicity. CONCLUSION GGCT-ASOs appear to be promising as novel cancer therapeutic agents.
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Affiliation(s)
- Hiromi Ii
- Department of Clinical Oncology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Japan
| | - Harumi Yamaguma
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Japan
| | - Susumu Kageyama
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Akihiro Kawauchi
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan;
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Japan
| | - Susumu Nakata
- Department of Clinical Oncology, Kyoto Pharmaceutical University, Kyoto, Japan;
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31
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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32
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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Yasuhara H, Yoshida T, Sasaki K, Obika S, Inoue T. Reduction of Off-Target Effects of Gapmer Antisense Oligonucleotides by Oligonucleotide Extension. Mol Diagn Ther 2022; 26:117-127. [PMID: 34994962 PMCID: PMC8766371 DOI: 10.1007/s40291-021-00573-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2021] [Indexed: 12/03/2022]
Abstract
Aim Antisense oligonucleotide (ASO) has the potential to induce off-target effects by inadvertent binding of ASOs to unintended RNAs that have a sequence similar to the target RNA. In the present study, we focused on the association between oligonucleotide length and off-target effects. Oligonucleotide extension is assumed to have bilateral effects on hybridization-dependent changes in gene expression, i.e., one is the decrease of off-target effects based on the reduced number of off-target candidate genes with perfect matches, and the other is the increase of off-target effects based on the increased binding affinity between the ASO and the complementary RNAs that leads to better tolerability for mismatches. Methods To determine the effects of oligonucleotide extension of gapmer ASOs on off-target effects, an extensive microarray analysis was performed using human cells treated with a 14-mer gapmer ASO and the extended 18-mer derivatives with the same core 14-mer region. Results and Discussion Our data indicated that change in gene expression in the cells treated with 18-mer ASOs was significantly smaller than those with a 14-mer ASO, showing the decrease of off-target effects by oligonucleotide extension. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-021-00573-z.
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Affiliation(s)
- Hidenori Yasuhara
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Tokuyuki Yoshida
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kiyomi Sasaki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
| | - Takao Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.
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34
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Kita R, Osawa T, Obika S. Conjugation of oligonucleotides with activated carbamate reagents prepared by the Ugi reaction for oligonucleotide library synthesis. RSC Chem Biol 2022; 3:728-738. [PMID: 35755192 PMCID: PMC9175101 DOI: 10.1039/d1cb00240f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/15/2022] [Indexed: 11/23/2022] Open
Abstract
The DNA-encoded library (DEL) is a powerful tool for drug discovery. As a result, to obtain diverse DELs, many DNA-compatible chemical reactions have been developed over the past decade. Among the most commonly used reactions in medicinal chemistry, multicomponent reactions (MCRs) can lead to the generation of various compounds in a one-step reaction. In particular, the Ugi reaction can easily provide a peptoid library. Thus, we herein report a solution-phase DEL synthesis based on the Ugi reaction. Using 6-(4-nitrophenoxycarbonylamino)hexanoic acid and N-4-nitrophenoxycarbonylglycine as carboxylic acids, peptoids with activated carbamate moieties were obtained as the products of the Ugi reaction. These peptoids were then treated with oligonucleotides bearing a 5′- or 3′-terminal aminohexyl linker to give various oligonucleotide-tagged peptoids in good yields. Moreover, the obtained peptoids could be substituted by a Suzuki cross-coupling reaction and by hydrolysis of the carboxylate ester, followed by condensation with amines. These advances should therefore promote pharmaceutical and medicinal research using DELs. A solution-phase conjugation method based on the Ugi reaction is reported, which enables the synthesis of an oligonucleotide-tagged peptoid library.![]()
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Affiliation(s)
- Ryosuke Kita
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takashi Osawa
- 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
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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35
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Osawa T, Yano N, Aoyama H, Obika S. Synthesis, Duplex-Forming Ability, and Nuclease Resistance of Oligonucleotides Containing a Thymidine Derivative with a 1-Oxaspiro[4.5]decane Skeleton. Chem Pharm Bull (Tokyo) 2022; 70:699-706. [PMID: 36184452 DOI: 10.1248/cpb.c22-00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chemically modified nucleic acids are essential for the therapeutic application of oligonucleotides. In this study, 6'-C-spiro-thymidine exhibiting a fixed torsion angle γ was designed, synthesized, and incorporated into oligonucleotides. The conformational analysis of the 6'-C-spiro-thymidine monomer revealed that its torsion angle γ was in the +synclinal range (approx. 60°), which is similar to that in a natural RNA duplex, as expected. On the other hand, the sugar conformation of the RNA duplex is known to be predominantly an N-type, whereas that of the synthesized monomer was an S-type. The results of the UV melting analysis demonstrated that the duplex-forming ability of 6'-C-spiro-thymidine was inferior to that of natural DNA. Contrarily, 6'-C-spiro-thymidine could enhance the stability of oligonucleotides toward nucleases. Particularly, the incorporation of 6'-C-spiro-thymidine on the 3'-ends of the oligonucleotides significantly increased the nuclease resistance of the oligonucleotides.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Natsumi Yano
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University
- National Institutes of Biomedical Innovation, Health and Nutrition
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36
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Wada F, Yamamoto T, Kobayashi T, Tachibana K, Ito KR, Hamasaki M, Kayaba Y, Terada C, Yamayoshi A, Obika S, Harada-Shiba M. Drug discovery and development scheme for liver-targeting bridged nucleic acid antisense oligonucleotides. Mol Ther Nucleic Acids 2021; 26:957-969. [PMID: 34760338 PMCID: PMC8560717 DOI: 10.1016/j.omtn.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/15/2021] [Accepted: 10/06/2021] [Indexed: 11/21/2022]
Abstract
Antisense oligonucleotides (ASOs) containing bridged nucleic acids (BNAs) have been proven to be very powerful. However, ensuring a reliable discovery and translational development scheme for this class of ASOs with wider therapeutic windows remains a fundamental challenge. We here demonstrate the robustness of our scheme in the context of the selection of ASOs having two different BNA chemistries (2,′4′-BNA/locked nucleic acid [LNA] and amido-bridged nucleic acid [AmNA]) targeting human proprotein convertase subtilisin/kexin type 9 (PCSK9). The scheme features a two-step process, including (1) a unique and sensitive in vitro screening approach, called Ca2+ enrichment of medium (CEM) transfection, and (2) a ligand-targeted drug delivery approach to better reach target tissues, averting unintended accumulation of ASOs. Using CEM screening, we identified a candidate ASO that shows >70% cholesterol-lowering action in monkeys. An N-acetylgalactosamine (GalNAc) ligand then was appended to the candidate ASO to further broaden the therapeutic margin by altering the molecule’s pharmacokinetics. The GalNAc conjugate, HsPCSK9-1811-LNA, was found to be at least ten times more potent in non-human primates (compared with the unconjugated counterpart), with reduced nephrotoxicity in rats. Overall, we successfully showed that our drug development scheme is better suited for selecting clinically relevant BNA-based ASOs, especially for the treatment of liver-associated diseases.
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Affiliation(s)
- Fumito Wada
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Tadayuki Kobayashi
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keisuke Tachibana
- 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
| | - Mayumi Hamasaki
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Yukina Kayaba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Chisato Terada
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
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37
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Prakash M, Itoh Y, Fujiwara Y, Takahashi Y, Takada Y, Mellini P, Elboray EE, Terao M, Yamashita Y, Yamamoto C, Yamaguchi T, Kotoku M, Kitao Y, Singh R, Roy R, Obika S, Oba M, Wang DO, Suzuki T. Identification of Potent and Selective Inhibitors of Fat Mass Obesity-Associated Protein Using a Fragment-Merging Approach. J Med Chem 2021; 64:15810-15824. [PMID: 34727689 DOI: 10.1021/acs.jmedchem.1c01107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fat mass obesity-associated protein (FTO) is a DNA/RNA demethylase involved in the epigenetic regulation of various genes and is considered a therapeutic target for obesity, cancer, and neurological disorders. Here, we aimed to design novel FTO-selective inhibitors by merging fragments of previously reported FTO inhibitors. Among the synthesized analogues, compound 11b, which merges key fragments of Hz (3) and MA (4), inhibited FTO selectively over alkylation repair homologue 5 (ALKBH5), another DNA/RNA demethylase. Treatment of acute monocytic leukemia NOMO-1 cells with a prodrug of 11b decreased the viability of acute monocytic leukemia cells, increased the level of the FTO substrate N6-methyladenosine in mRNA, and induced upregulation of MYC and downregulation of RARA, which are FTO target genes. Thus, Hz (3)/MA (4) hybrid analogues represent an entry into a new class of FTO-selective inhibitors.
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Affiliation(s)
- Muthuraj Prakash
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukihiro Itoh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.,SANKEN, Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Yoshie Fujiwara
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukari Takahashi
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yuri Takada
- SANKEN, Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Paolo Mellini
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Elghareeb E Elboray
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.,Chemistry Department, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Mitsuhiro Terao
- SANKEN, Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | | | - Chika Yamamoto
- 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
| | - Masayuki Kotoku
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yuki Kitao
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Ritesh Singh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.,Department of Chemistry, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer 305817, Rajasthan, India
| | - Rohini Roy
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.,Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Makoto Oba
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Dan Ohtan Wang
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.,Center for Biosystems Dynamics Research, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.,SANKEN, Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan.,CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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38
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Kishimoto Y, Fujii A, Nakagawa O, Obika S. Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative. Org Biomol Chem 2021; 19:8063-8074. [PMID: 34494641 DOI: 10.1039/d1ob01462e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized an artificial nucleic acid, [3-(1,2-dihydro-2-oxobenzo[b][1,8]naphthyridine)]-2'-deoxy-D-ribofuranose (OBN), with a tricyclic structure in a nucleobase as a thymidine analog. Oligodeoxynucleotides (ODNs) containing consecutive OBN displayed improved duplex-forming ability with complementary single-stranded (ss) RNA and triplex-forming ability with double-stranded DNA in comparison with ODNs composed of natural thymidine. OBN-modified ODNs also displayed enhanced enzymatic resistance compared with ODNs with natural thymidine and phosphorothioate modification, respectively, due to the structural steric hindrance of the nucleobase. The fluorescence spectra of OBN-modified ODNs showed sufficient fluorescence intensity with ssDNA and ssRNA, which is an advantageous feature for fluorescence imaging techniques of nucleic acids with longer emission wavelengths than bicyclic thymine (bT).
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Affiliation(s)
- Yuki Kishimoto
- 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
| | - Akane Fujii
- 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
| | - Osamu Nakagawa
- 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.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima 770-8514, 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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Terada C, Wada F, Uchida M, Yasutomi Y, Oh K, Kawamoto S, Kayaba Y, Yamayoshi A, Harada-Shiba M, Obika S, Yamamoto T. Programmed Instability of Ligand Conjugation Manifold for Efficient Hepatocyte Delivery of Therapeutic Oligonucleotides. Nucleic Acid Ther 2021; 31:404-416. [PMID: 34468210 DOI: 10.1089/nat.2021.0036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ligand-targeted drug delivery (LTDD) has gained more attention in the field of nucleic acid therapeutics. To further elicit the potential of therapeutic oligonucleotides by means of LTDD, we newly developed (R)- and (S)-3-amino-1,2-propanediol (APD) manifold for ligand conjugation. N-acetylgalactosamine (GalNAc)/asialoglycoprotein receptor (ASGPr) system has been shown to be a powerful and robust paradigm of LTDD. Our novel APD-based GalNAc (GalNAcAPD) was shown to have intrinsic chemical instability that could play a role in better manipulation of active drug release. The APD manifold also enables facile production of conjugates through an on-support ligand cluster synthesis. We showed in a series of in vivo studies that while the knockdown activity of antisense oligonucleotides (ASOs) bearing 5'-GalNAcAPD was comparable to the conventional hydroxy-L-prolinol-linked GalNAc (GalNAcHP), 3'-GalNAcAPD elicited ASO activity by more than twice as much as the conventional 3'-GalNAcHP. This was ascribed partly to the GalNAcAPD's ideal susceptibility to nucleolytic digestion, which is expected to facilitate cytosolic internalization of ASO drugs. Moreover, an in vivo/ex vivo imaging study visualized the enhancement effect of monoantennary GalNAcAPD on liver localization of ASOs. This versatile manifold with chemical and biological instability would benefit therapeutic oligonucleotides that target both the liver and extrahepatic tissues.
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Affiliation(s)
- Chisato Terada
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Fumito Wada
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Mei Uchida
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yukari Yasutomi
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kaho Oh
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Seiya Kawamoto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Yukina Kayaba
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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40
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Yamaguchi T, Yamamoto C, Horiba M, Aoyama H, Obika S. Synthesis and duplex-forming ability of oligonucleotides modified with 4'-C,5'-C-methylene-bridged nucleic acid (4',5'-BNA). Bioorg Med Chem 2021; 46:116359. [PMID: 34391942 DOI: 10.1016/j.bmc.2021.116359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 01/16/2023]
Abstract
We describe herein the design and synthesis of 4'-C,5'-C-methylene-bridged nucleic acid (4',5'-BNA), a novel artificial nucleic acid with the torsion angle γ in a non-canonical +ac range. The 4',5'-BNA phosphoramidite bearing a thymine nucleobase was synthesized from a commercially available thymidine analog in 11 steps and successfully incorporated into oligonucleotides. The resulting oligonucleotides were evaluated for their duplex-forming ability toward single-stranded DNA and RNA.
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Affiliation(s)
- Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Chika Yamamoto
- 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
| | - Hiroshi Aoyama
- 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; National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.
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41
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Yamamoto T, Mukai Y, Wada F, Terada C, Kayaba Y, Oh K, Yamayoshi A, Obika S, Harada–Shiba M. Highly Potent GalNAc-Conjugated Tiny LNA Anti-miRNA-122 Antisense Oligonucleotides. Pharmaceutics 2021; 13:817. [PMID: 34072682 PMCID: PMC8228246 DOI: 10.3390/pharmaceutics13060817] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
The development of clinically relevant anti-microRNA antisense oligonucleotides (anti-miRNA ASOs) remains a major challenge. One promising configuration of anti-miRNA ASOs called "tiny LNA (tiny Locked Nucleic Acid)" is an unusually small (~8-mer), highly chemically modified anti-miRNA ASO with high activity and specificity. Within this platform, we achieved a great enhancement of the in vivo activity of miRNA-122-targeting tiny LNA by developing a series of N-acetylgalactosamine (GalNAc)-conjugated tiny LNAs. Specifically, the median effective dose (ED50) of the most potent construct, tL-5G3, was estimated to be ~12 nmol/kg, which is ~300-500 times more potent than the original unconjugated tiny LNA. Through in vivo/ex vivo imaging studies, we have confirmed that the major advantage of GalNAc over tiny LNAs can be ascribed to the improvement of their originally poor pharmacokinetics. We also showed that the GalNAc ligand should be introduced into its 5' terminus rather than its 3' end via a biolabile phosphodiester bond. This result suggests that tiny LNA can unexpectedly be recognized by endogenous nucleases and is required to be digested to liberate the parent tiny LNA at an appropriate time in the body. We believe that our strategy will pave the way for the clinical application of miRNA-targeting small ASO therapy.
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Affiliation(s)
- Tsuyoshi Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; (C.T.); (Y.K.); (K.O.); (A.Y.)
| | - Yahiro Mukai
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; (Y.M.); (F.W.); (S.O.)
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan;
| | - Fumito Wada
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; (Y.M.); (F.W.); (S.O.)
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan;
| | - Chisato Terada
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; (C.T.); (Y.K.); (K.O.); (A.Y.)
| | - Yukina Kayaba
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; (C.T.); (Y.K.); (K.O.); (A.Y.)
| | - Kaho Oh
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; (C.T.); (Y.K.); (K.O.); (A.Y.)
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; (C.T.); (Y.K.); (K.O.); (A.Y.)
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; (Y.M.); (F.W.); (S.O.)
| | - Mariko Harada–Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan;
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Nakae T, Obana M, Maeda T, Ikeda A, Miyazaki H, Tanaka S, Maeda M, Yamashita K, Terai K, Obika S, Fujio Y. Title: Gene transfer by pyro-drive jet injector is a novel therapeutic approach for muscle diseases. Gene 2021; 788:145664. [PMID: 33887371 DOI: 10.1016/j.gene.2021.145664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/19/2021] [Accepted: 04/15/2021] [Indexed: 01/23/2023]
Abstract
The angiogenic gene therapy is an attractive approach for the treatment of ischemic muscle diseases, including peripheral arterial disease and ischemic heart diseases. Although a variety of gene transfer methods have been developed, the efficiency of gene transfer is still limited. We have been developing the needleless high-energy bioinjector device, Pyro-drive Jet Injector (PJI), based on pyrotechnics using a combination of ignition powder and gunpowder, however, the utility of PJI in gene transfer into muscle tissues remains unclear. pcDNA3.1 plasmid containing Flag was injected to the thigh muscles of C57BL/6J mice using PJI or needle, as a control. Histological analysis demonstrated that the protein expression of Flag was observed in a wider range in PJI group than in needle group. To assess the validity of PJI for gene therapy, pcDNA3.1-human fibroblast growth factor 2 (FGF2), which has angiogenic activity and tissue protective properties, was injected into the ischemic thigh muscles with PJI or needle. ELISA assay revealed that the protein expression of FGF2 was increased in the thigh muscle tissues by PJI-mediated gene delivery. Significantly, histological analyses revealed that muscle fiber cross-sectional area and the number of endothelial marker CD31 (+) cells was increased in ischemic hind-limb tissues of the PJI-FGF2 group but not in those of needle-FGF2 group. To expand the applicability of the PJI-mediated gene transfer, pcDNA3.1-venus plasmid was injected into murine hearts with PJI or needle. PJI method was successful in gene transfer into murine hearts, especially into cardiomyocytes, with high efficiency when compared to needle method. Collectively, the non-needle, non-liposomal and non-viral gene transfer by PJI could be a novel therapeutic approach for muscle diseases.
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Affiliation(s)
- Takafumi Nakae
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - Masanori Obana
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical Sciences, Osaka University, Japan; Radioisotope Research Center, Institute for Radiation Sciences, Osaka University, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Japan; Global Center for Medical Engineering and Informatics (MEI), Osaka University, Japan.
| | - Takahiro Maeda
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - Akari Ikeda
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - Hiroshi Miyazaki
- Medical Device Research, Industry Business Unit, Daicel Corporation, Japan
| | - Shota Tanaka
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - Makiko Maeda
- Laboratory of Clinical Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, Japan.
| | - Kunihiko Yamashita
- Medical Device Research, Industry Business Unit, Daicel Corporation, Japan; Department of Device Application for Molecular Therapeutics, Graduate School of Medicine, Osaka University, Japan
| | - Kazuhiro Terai
- Medical Device Research, Industry Business Unit, Daicel Corporation, Japan
| | - Satoshi Obika
- Laboratory of Bioorganic Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - Yasushi Fujio
- Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical Sciences, Osaka University, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Japan; Laboratory of Clinical Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University, Japan.
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43
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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44
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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45
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Wada F, Hori SI, Obika S, Yamamoto T. Calcium-Mediated In Vitro Transfection Technique of Oligonucleotides with Broad Chemical Modification Compatibility. Methods Mol Biol 2021; 2176:141-154. [PMID: 32865788 DOI: 10.1007/978-1-0716-0771-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Oligonucleotide drugs (ODs) have gained increasing attention owing to their promising therapeutic potential. One major obstacle that ODs have been facing is the lack of appropriate in vitro validation systems that can predict in vivo activity and toxicity. We have devised a transfection method called CEM (Ca2+-enrichment method), where the simple enrichment of calcium ion with calcium chloride in culture medium potentiates the activity of various types of naked oligonucleotides including gapmers, siRNA, and phosphorodiamidate morpholino antisense oligonucleotides (PMO) in many cultured cell lines with limited cytotoxicity. We here describe a precise procedure of the method. Besides the benefit of the CEM's predictive power to accurately estimate in vivo activity of ODs of your interest in drug discovery and development settings, this cost-efficient, easy-to-access method can be a robust laboratory technique to modulate gene expressions with ODs with a variety of mechanisms of action.
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Affiliation(s)
- Fumito Wada
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Shin-Ichiro Hori
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Medicinal Chemistry Research Laboratory for Medium Molecular Drug Discovery, Shionogi & Co., Ltd., Osaka, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan. .,Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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46
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Nakagawa O, Aoyama H, Fujii A, Kishimoto Y, Obika S. Crystallographic Structure of Novel Types of Ag I -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids. Chemistry 2021; 27:3842-3848. [PMID: 33274789 DOI: 10.1002/chem.202004819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Indexed: 11/08/2022]
Abstract
Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2'-O,4'-C-methylene bridged nucleic acid in the presence of AgI ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of AgI -mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing AgI -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of AgI -mediated base pairs in the central region. The bent duplex structure induced by the addition of AgI ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.
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Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- 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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47
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Kishimoto Y, Nakagawa O, Fujii A, Yoshioka K, Nagata T, Yokota T, Hari Y, Obika S. 2',4'-BNA/LNA with 9-(2-Aminoethoxy)-1,3-diaza-2-oxophenoxazine Efficiently Forms Duplexes and Has Enhanced Enzymatic Resistance*. Chemistry 2021; 27:2427-2438. [PMID: 33280173 PMCID: PMC7898338 DOI: 10.1002/chem.202003982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 11/28/2022]
Abstract
Artificial nucleic acids are widely used in various technologies, such as nucleic acid therapeutics and DNA nanotechnologies requiring excellent duplex-forming abilities and enhanced nuclease resistance. 2'-O,4'-C-Methylene-bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA) with 1,3-diaza-2-oxophenoxazine (BNAP (BH )) was previously reported. Herein, a novel BH analogue, 2',4'-BNA/LNA with 9-(2-aminoethoxy)-1,3-diaza-2-oxophenoxazine (G-clamp), named BNAP-AEO (BAEO ), was designed. The BAEO nucleoside was successfully synthesized and incorporated into oligodeoxynucleotides (ODNs). ODNs containing BAEO possessed up to 104 -, 152-, and 11-fold higher binding affinities for complementary (c) RNA than those of ODNs containing 2'-deoxycytidine (C), 2',4'-BNA/LNA with 5-methylcytosine (L), or 2'-deoxyribonucleoside with G-clamp (PAEO ), respectively. Moreover, duplexes formed by ODN bearing BAEO with cDNA and cRNA were thermally stable, even under molecular crowding conditions induced by the addition of polyethylene glycol. Furthermore, ODN bearing BAEO was more resistant to 3'-exonuclease than ODNs with phosphorothioate linkages.
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Faculty of Pharmaceutical SciencesTokushima Bunri University180 Nishihamahoji, Yamashiro-choTokushima770-8514Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
| | - Kotaro Yoshioka
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Tetsuya Nagata
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Takanori Yokota
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical SciencesTokushima Bunri University180 Nishihamahoji, Yamashiro-choTokushima770-8514Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
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48
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Hirabayashi Y, Maki K, Kinoshita K, Nakazawa T, Obika S, Naota M, Watanabe K, Suzuki M, Arato T, Fujisaka A, Fueki O, Ito K, Onodera H. Considerations of the Japanese Research Working Group for the ICH S6 & Related Issues Regarding Nonclinical Safety Assessments of Oligonucleotide Therapeutics: Comparison with Those of Biopharmaceuticals. Nucleic Acid Ther 2021; 31:114-125. [PMID: 33470890 PMCID: PMC7997717 DOI: 10.1089/nat.2020.0879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This white paper summarizes the current consensus of the Japanese Research Working Group for the ICH S6 & Related Issues (WGS6) on strategies for the nonclinical safety assessment of oligonucleotide-based therapeutics (ONTs), specifically focused on the similarities and differences to biotechnology-derived pharmaceuticals (biopharmaceuticals). ONTs, like biopharmaceuticals, have high species and target specificities. However, ONTs have characteristic off-target effects that clearly differ from those of biopharmaceuticals. The product characteristics of ONTs necessitate specific considerations when planning nonclinical studies. Some ONTs have been approved for human use and many are currently undergoing nonclinical and/or clinical development. However, as ONTs are a rapidly evolving class of drugs, there is still much to learn to achieve optimal strategies for the development of ONTs. There are no formal specific guidelines, so safety assessments of ONTs are principally conducted by referring to published white papers and conventional guidelines for biopharmaceuticals and new chemical entities, and each ONT is assessed on a case-by-case basis. The WGS6 expects that this report will be useful in considering nonclinical safety assessments and developing appropriate guidelines specific for ONTs.
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Affiliation(s)
| | - Kazushige Maki
- Pharmaceuticals and Medical Devices Agency (PMDA), Chiyoda-ku, Japan
| | - Kiyoshi Kinoshita
- The Japan Pharmaceutical Manufacturers Association (JPMA), Chuo-ku, Japan
| | | | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Misaki Naota
- Pharmaceuticals and Medical Devices Agency (PMDA), Chiyoda-ku, Japan
| | - Kazuto Watanabe
- The Japan Pharmaceutical Manufacturers Association (JPMA), Chuo-ku, Japan
| | - Mutsumi Suzuki
- The Japan Pharmaceutical Manufacturers Association (JPMA), Chuo-ku, Japan
| | - Teruyo Arato
- Clinical Research and Medical Innovation Center, Hokkaido University Hospital, Sapporo, Japan
| | - Aki Fujisaka
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan.,Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi, Japan
| | - Osamu Fueki
- Pharmaceuticals and Medical Devices Agency (PMDA), Chiyoda-ku, Japan
| | - Kosuke Ito
- Pharmaceuticals and Medical Devices Agency (PMDA), Chiyoda-ku, Japan
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49
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Fukusumi H, Togo K, Sumida M, Nakamori M, Obika S, Baba K, Shofuda T, Ito D, Okano H, Mochizuki H, Kanemura Y. Alpha-synuclein dynamics in induced pluripotent stem cell-derived dopaminergic neurons from a Parkinson's disease patient (PARK4) with SNCA triplication. FEBS Open Bio 2021; 11:354-366. [PMID: 33301617 PMCID: PMC7876504 DOI: 10.1002/2211-5463.13060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/06/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder caused by the selective loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNc). Lewy bodies (LBs), another histological hallmark of PD, are observed in patients with familial or sporadic PD. The therapeutic potential of reducing the accumulation of α‐synuclein, a major LB component, has been investigated, but it remains unknown whether the formation of LBs results in the loss of DA neurons. PARK4 patients exhibit multiplication of the α‐synuclein gene (SNCA) without any pathological mutations, but their symptoms develop relatively early. Therefore, study of PARK4 might help elucidate the mechanism of α‐synuclein aggregation. In this study, we investigated the dynamics of α‐synuclein during the early stage of immature DA neurons, which were differentiated from human‐induced pluripotent stem cells (hiPSCs) derived from either a PARK4 patient with SNCA triplication or a healthy donor. We observed increased α‐synuclein accumulation in PARK4 hiPSC‐derived DA neurons relative to those derived from healthy donor hiPSCs. Interestingly, α‐synuclein accumulation disappeared over time in the PARK4 patient‐derived DA neurons. Moreover, an SNCA‐specific antisense oligonucleotide could reduce α‐synuclein levels during the accumulation stage. These observations may help reveal the mechanisms that regulate α‐synuclein levels, which may consequently be useful in the development of new therapies for patients with sporadic or familial PD.
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Affiliation(s)
- Hayato Fukusumi
- Division of Stem Cell Research, Department of Biomedical Research and Innovation, Institute for Clinical Research, National Hospital Organization Osaka National Hospital, Japan
| | - Kazuyuki Togo
- Department of Neurology, Graduate School of Medicine, Osaka University, Japan
| | - Miho Sumida
- Division of Regenerative Medicine, Department of Biomedical Research and Innovation, Institute for Clinical Research, National Hospital Organization Osaka National Hospital, Japan
| | - Masayuki Nakamori
- Department of Neurology, Graduate School of Medicine, Osaka University, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - Kousuke Baba
- Department of Neurology, Graduate School of Medicine, Osaka University, Japan
| | - Tomoko Shofuda
- Division of Stem Cell Research, Department of Biomedical Research and Innovation, Institute for Clinical Research, National Hospital Organization Osaka National Hospital, Japan
| | - Daisuke Ito
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Japan
| | - Yonehiro Kanemura
- Division of Regenerative Medicine, Department of Biomedical Research and Innovation, Institute for Clinical Research, National Hospital Organization Osaka National Hospital, Japan.,Department of Neurosurgery, National Hospital Organization Osaka National Hospital, Japan
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50
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Hoshino H, Kasahara Y, Kuwahara M, Obika S. DNA Polymerase Variants with High Processivity and Accuracy for Encoding and Decoding Locked Nucleic Acid Sequences. J Am Chem Soc 2020; 142:21530-21537. [PMID: 33306372 DOI: 10.1021/jacs.0c10902] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Xenobiotic nucleic acids (XNAs) are chemically modified nucleic acid analogues with potential applications in nucleic acid-based therapeutics including nucleic acid aptamers, ribozymes, small interfering RNAs, and antisense oligonucleotides. We have developed a promising XNA for therapeutic uses, 2',4'-bridged nucleic acid (2',4'-BNA), also known as locked nucleic acid (LNA). Unlike the rational design of small interfering and antisense oligonucleotides, the development of LNA aptamers and catalysts requires genetically engineered polymerases that enable the synthesis of LNA from DNA and the converse reverse transcription. However, no LNA decoders or encoders with sufficient performance have been developed. In this study, we developed variants of KOD DNA polymerase, a family B DNA polymerase derived from Thermococcus kodakarensis KOD1, which are effective LNA decoders and encoders, via structural analyses. KOD DGLNK (KOD: N210D/Y409G/A485L/D614N/E664K) enabled LNA synthesis from DNA (DNA → LNA), and KOD DLK (KOD: N210D/A485L/E664K) enabled LNA reverse transcription to DNA (LNA → DNA). Both variants exhibited greatly improved efficiency and accuracy. Notably, we synthesized LNAs longer than one kilobase using KOD DGLNK. We also showed that these variants can accept 2'-O-methyl (2'-OMe), a common modification for therapeutic uses. Here, we also show that LNA and 2'-OMe mix aptamer can be practically obtained via SELEX. The variants can be used as powerful tools for creating XNA aptamers and catalysts to completely eliminate the natural species, DNA and RNA.
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Affiliation(s)
- Hidekazu Hoshino
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,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, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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