1
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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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2
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Nishina K, Yoshioka K, Yokota T, Hara RI. Comparison of interaction between antimiR and microRNA versus HDO-antimiR and microRNA by molecular dynamics simulation. Nucleosides Nucleotides Nucleic Acids 2024:1-16. [PMID: 38205778 DOI: 10.1080/15257770.2024.2302526] [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] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
Recently, we found DNA/RNA heteroduplex oligonucleotide-based antimiR (HDO-antimiR) can more efficiently inhibit the target miRNA than conventional antimiR after its cellular uptake. But the mechanism of HDO-antimiR about the target-silencing is unknown. We here tried to elucidate the interaction mechanism of HDO-antimiR to miRNA using molecular dynamics (MD) simulation. When interaction of the conventional antimiR or HDO-antimiR and the target miRNA was simulated, they combined with each other in various forms. In the hydrogen bond analyses, base site of the antimiR formed hydrogen bond with miRNA. On the other hand, phosphate site of the HDO-antimiR formed hydrogen bond with miRNA. These results suggested that there were differences about the binding mechanisms between antimiR and HDO-antimiR to the target miRNA. In particular, there was a difference in the binding site between antimiR and HDO-antimiR. Additionally, it was found that guanine in the miRNA is mainly involved in the binding to the antimiR or HDO-antimiR. MD simulation method is useful in understanding the mechanism of oligonucleotide therapeutics.
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Affiliation(s)
- Kazutaka Nishina
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rintaro Iwata Hara
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
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3
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Takahashi Y, Kakuta K, Namioka Y, Igarashi A, Sakamoto T, Iwata Hara R, Sato K, Wada T. Synthesis of P-Modified DNA from Boranophosphate DNA as a Precursor via Acyl Phosphite Intermediates. J Org Chem 2023; 88:10617-10631. [PMID: 37462534 PMCID: PMC10407935 DOI: 10.1021/acs.joc.3c00659] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 08/05/2023]
Abstract
In this study, we successfully synthesized several kinds of P-modified nucleic acids from boranophosphate DNAs via an acyl phosphite intermediate in solution and on a solid support. In the solution-phase synthesis, phosphorothioate diester, phosphotriester, and phosphoramidate diester were synthesized in a one-pot reaction from boranophosphodiester via the conversion of an acyl phosphite as a key intermediate. In addition, doubly P-modified nucleic acid derivatives which were difficult to synthesize by the phosphoramidite and H-phosphonate methods were also obtained by the conversion reaction. In the solid-phase synthesis, a boranophosphate derivative was synthesized on a solid support using the H-boranophosphonate method. Then, an acyl phosphite intermediate was formed by treatment with pivaloyl chloride in pyridine, followed by appropriate transformations to obtain the P-modified derivatives such as phosphotriester and phosphorothioate diester. Notably, it was suggested that the conversion reaction of a boranophosphate to a phosphorothioate diester proceeded with retention of the stereochemistry of the phosphorous center. In addition, a phosphorothioate/phosphate chimeric dodecamer was successfully synthesized from a boranophosphate/phosphate chimeric dodecamer using the same strategy. Therefore, boranophosphate derivatives are versatile precursors for the synthesis of P-modified DNA, including chimeric derivatives.
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Affiliation(s)
- Yuhei Takahashi
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kiyoshi Kakuta
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yukichi Namioka
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ayumi Igarashi
- Department
of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Taiichi Sakamoto
- Department
of Life Science, Chiba Institute of Technology, Graduate School of Advanced Engineering, Chiba 275-0016, Japan
| | - Rintaro Iwata Hara
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department
of Neurology and Neurological Science, Graduate School of Medicinal
and Dental Sciences, Tokyo Medical and Dental
University, Tokyo 113-8519, Japan
| | - Kazuki Sato
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takeshi Wada
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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4
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Miura M, Sakaue F, Matsuno H, Morita K, Yoshida A, Hara RI, Nishimura R, Nishida Y, Yokogawa M, Osawa M, Yokota T. TDP-43 N-terminal domain dimerisation or spatial separation by RNA binding decreases its propensity to aggregate. FEBS Lett 2023. [PMID: 37177801 DOI: 10.1002/1873-3468.14635] [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: 11/21/2022] [Revised: 03/18/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Aggregation of the 43 kDa TAR DNA-binding protein (TDP-43) is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RNA binding and TDP-43 N-terminal domain dimerisation have been suggested to ameliorate TDP-43 aggregation. However, the relationship between these factors and solubility of TDP-43 is largely unknown. Therefore, we developed new oligonucleotides which can recruit two TDP-43 molecules and interfere with their intermolecular interactions via spatial separation. Using these oligonucleotides and TDP-43-preferable UG-repeats, we uncovered two distinct mechanisms for modulating TDP-43 solubility by RNA binding: one is N-terminal domain dimerisation and the other is spatial separation of two TDP-43 molecules. This study provides new molecular insights into the regulation of TDP-43 solubility.
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Affiliation(s)
- Motoki Miura
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
| | - Fumika Sakaue
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
| | - Hirokazu Matsuno
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
| | - Kento Morita
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
| | - Akiko Yoshida
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
| | - Rintaro Iwata Hara
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
- NucleoTIDE and PepTIDE Drug Discovery Center, Tokyo Medical and Dental University
| | - Ren Nishimura
- Graduate School of Pharmaceutical Sciences, Keio University
| | - Yurika Nishida
- Graduate School of Pharmaceutical Sciences, Keio University
| | | | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, Keio University
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
- NucleoTIDE and PepTIDE Drug Discovery Center, Tokyo Medical and Dental University
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5
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Shiraishi T, Sato K, Hara RI, Wada T. Properties of artificial cationic oligodiaminosaccharides and oligopeptides that bind to A-type oligonucleotide duplexes. Nucleosides Nucleotides Nucleic Acids 2023:1-18. [PMID: 36850058 DOI: 10.1080/15257770.2023.2182444] [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] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
A critical strategy to improve the properties of oligonucleotide therapeutics is using cationic molecules as carriers. We developed artificial cationic molecules that bind to A-type oligonucleotide duplexes, such as siRNAs, in a stoichiometric ratio. In this study, we investigated the properties of oligo 2,6-diamino-D-galactoses (ODAGals) and L-2,4-diaminobutanoic acid oligomers (Dabs) and revealed their thermal and biological stabilization effects on A-type duplexes and their chemical stability. As a result, ODAGal and Dab with the same number of amino groups had the commensurate ability for the biological stabilization effect, whereas Dab enhanced the thermal stability of A-type duplexes more effectively than ODAGal.
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Affiliation(s)
- Tomomi Shiraishi
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
| | - Rintaro Iwata Hara
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan.,Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-Ku, Tokyo, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
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6
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Sato K, Chiba A, Shiraishi T, Ogawa Y, Hara RI, Wada T. Solid-phase synthesis of N-trichloroacetyl mannosamine 1-phosphate repeating units Mimicking capsular polysaccharide derived from Neisseria meningitidis serotype A. Carbohydr Res 2022; 518:108585. [DOI: 10.1016/j.carres.2022.108585] [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: 12/16/2021] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/02/2022]
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7
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Nagata T, Dwyer CA, Yoshida-Tanaka K, Ihara K, Ohyagi M, Kaburagi H, Miyata H, Ebihara S, Yoshioka K, Ishii T, Miyata K, Miyata K, Powers B, Igari T, Yamamoto S, Arimura N, Hirabayashi H, Uchihara T, Hara RI, Wada T, Bennett CF, Seth PP, Rigo F, Yokota T. Cholesterol-functionalized DNA/RNA heteroduplexes cross the blood-brain barrier and knock down genes in the rodent CNS. Nat Biotechnol 2021; 39:1529-1536. [PMID: 34385691 DOI: 10.1038/s41587-021-00972-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 06/02/2021] [Indexed: 02/07/2023]
Abstract
Achieving regulation of endogenous gene expression in the central nervous system (CNS) with antisense oligonucleotides (ASOs) administered systemically would facilitate the development of ASO-based therapies for neurological diseases. We demonstrate that DNA/RNA heteroduplex oligonucleotides (HDOs) conjugated to cholesterol or α-tocopherol at the 5' end of the RNA strand reach the CNS after subcutaneous or intravenous administration in mice and rats. The HDOs distribute throughout the brain, spinal cord and peripheral tissues and suppress the expression of four target genes by up to 90% in the CNS, whereas single-stranded ASOs conjugated to cholesterol have limited activity. Gene knockdown was observed in major CNS cell types and was greatest in neurons and microglial cells. Side effects, such as thrombocytopenia and focal brain necrosis, were limited by using subcutaneous delivery or by dividing intravenous injections. By crossing the blood-brain barrier more effectively, cholesterol-conjugated HDOs may overcome the limited efficacy of ASOs targeting the CNS without requiring intrathecal administration.
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Affiliation(s)
- Tetsuya Nagata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Kie Yoshida-Tanaka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kensuke Ihara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaki Ohyagi
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hidetoshi Kaburagi
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Haruka Miyata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoe Ebihara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takashi Ishii
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Kenichi Miyata
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | | | - Tomoko Igari
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | | | - Naoto Arimura
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | | | - Toshiki Uchihara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rintaro Iwata Hara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | | | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. .,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan.
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8
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Matsuda H, Ito H, Nukaga Y, Uehara S, Sato K, Hara RI, Wada T. Solid-phase synthesis of oligouridine boranophosphates using the H-boranophosphonate method with 2′-O-(2-cyanoethoxymethyl) protection. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153526] [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] [Indexed: 10/19/2022]
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9
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Hara RI, Wada T. Inhibition of off-target cleavage by RNase H using an artificial cationic oligosaccharide. Org Biomol Chem 2021; 19:6865-6870. [PMID: 34323246 DOI: 10.1039/d1ob00983d] [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
Sequence-dependent off-target effects are a serious problem of antisense oligonucleotide-based drugs. Some of these side effects are induced by ribonuclease H (RNase H)-mediated cleavage of non-target RNAs with base sequences similar to that of the target RNA. We found that an artificial cationic oligosaccharide, ODAGal4, improved single-base discrimination for RNase H cleavage.
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Affiliation(s)
- Rintaro Iwata Hara
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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10
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Sato K, Hagio T, Sano M, Muramoto K, Yaoita A, Noro M, Hara RI, Wada T. Solid-Phase Stereocontrolled Synthesis of Oligomeric P-Modified Glycosyl Phosphate Derivatives Using the Oxazaphospholidine Method. ACS Omega 2021; 6:20026-20041. [PMID: 34368588 PMCID: PMC8340430 DOI: 10.1021/acsomega.1c03058] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/13/2021] [Indexed: 05/09/2023]
Abstract
Glycosyl phosphate repeating units can be found in the glycoconjugates of some bacteria and protozoa parasites. These structures and their P-modified analogs are attractive synthetic targets as antimicrobial, antiparasitic, and vaccine agents. However, P-modified glycosyl phosphates exist in different diastereomeric forms due to the chiral phosphorus atoms, whose configuration would highly affect their physiochemical and biochemical properties. In this study, a stereocontrolled method was developed for the synthesis of P-modified glycosyl phosphate repeating units derived from the lipophosphoglycan of Leishmania using the oxazaphospholidine approach. The solid-phase synthesis facilitated the elongation and purification of the glycosyl phosphate derivatives, while two P-modified glycosyl phosphates (boranophosphate and phosphorothioate) were successfully synthesized with up to three repeating units.
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Affiliation(s)
- Kazuki Sato
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Tomoya Hagio
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Michi Sano
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kazumasa Muramoto
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Aya Yaoita
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Mihoko Noro
- Department
of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Building, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Rintaro Iwata Hara
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department
of Neurology and Neurological Science, Graduate School of Medicinal
and Dental Sciences, Tokyo Medical and Dental
University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Takeshi Wada
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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11
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Hara RI, Sato K, Wada T. Synthesis of Glycosyl Phosphate Repeats and Their Analogues. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Takeshi Wada
- Faculty of Pharmaceutical Sciences, Tokyo University of Science
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12
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Liao W, Akahira S, Hara RI, Wada T, Kusamori K, Takakura Y, Nishikawa M. Enhanced Immunostimulatory Activity of CpG Oligodeoxynucleotide by the Combination of Mannose Modification and Incorporation into Nanostructured DNA. Biol Pharm Bull 2021; 43:1188-1195. [PMID: 32741939 DOI: 10.1248/bpb.b20-00052] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The immunostimulatory activity of unmethylated cytosine-phosphate-guanine oligodeoxynucleotide (CpG ODN) could be improved via delivery to immune cells expressing Toll-like receptor 9 (TLR9). Previously, we showed that the polypod-like structured nucleic acid (polypodna), a nanostructured DNA comprised of three or more ODNs, was an efficient system for the delivery of CpG ODNs to immune cells. Because some TLR9-positive immune cells express mannose receptors (MR), the uptake of polypodna by immune cells can be further increased by its modification with mannose. In this study, we selected the phosphodiester CpG ODN, ODN1668, which has a sequence identical to CpG1668, and a hexapodna, a polypodna with six pods, to design a hexapodna that harbored ODN1668 or the mannosylated CpG ODN (Man-ODN1668) synthesized via modification of the 5'-terminal of ODN1668 with a synthesized mannose motif. By mixing ODN1668 or Man-ODN1668 with the hexapodna, ODN1668/hexapodna and Man-ODN1668/hexapodna were successfully formed with high yields. However, Man-ODN1668/hexapodna was found to induce a greater tumor necrosis factor-α release from TLR9- and MR-positive mouse peritoneal macrophages and macrophage-like J774.1 cells than Man-ODN1668 or ODN1668/hexapodna. These results indicate that the combination of mannose modification and incorporation into nanostructured DNA is a useful approach for enhancing the immunostimulatory activity of CpG ODN.
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Affiliation(s)
- Wenqing Liao
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University.,Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science
| | - Sakiko Akahira
- Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science
| | - Rintaro Iwata Hara
- Laboratory of Organic Chemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science.,Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University
| | - Takeshi Wada
- Laboratory of Organic Chemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science
| | - Kosuke Kusamori
- Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Makiya Nishikawa
- Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science
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13
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Abstract
Heteroduplex oligonucleotides (HDOs) were a novel type of nucleic acid drugs based on an antisense oligonucleotide (ASO) strand and its complementary RNA (cRNA ) strand. HDOs were originally designed to improve the properties of RNase H-dependent ASOs and we reported in our first paper that HDOs conjugated with an α-tocopherol ligand (Toc-HDO ) based on a gapmer ASO showed 20 times higher silencing effect to liver apolipoprotein B (apoB) mRNA in vivo than the parent ASO. Thereafter the HDO strategy was found to be also effective for improving the properties of ASOs modulating blood-brain barrier function and ASO antimiRs which are RNase H-independent ASOs. Therefore, the HDO strategy has been shown to be versatile technology platform to develop effective nucleic acid drugs.
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Affiliation(s)
- Rintaro Iwata Hara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
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14
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Matsuda H, Yoshida E, Shinoda T, Sato K, Hara RI, Wada T. Solution-phase synthesis of oligodeoxyribonucleotides using the H-phosphonate method with N-unprotected 5′-phosphite monomers. RSC Adv 2021; 11:38094-38107. [PMID: 35498072 PMCID: PMC9044012 DOI: 10.1039/d1ra06619f] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/17/2021] [Indexed: 11/21/2022] Open
Abstract
A new strategy for a solution-phase synthesis of oligodeoxyribonucleotides with 5′-phosphite monomers synthesized in a single step from unprotected 2′-deoxyribonucleosides.
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Affiliation(s)
- Hiromasa Matsuda
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- CMC Production Technology Laboratories, MTPC Production Technology & Supply Chain Management Division, Mitsubishi Tanabe Pharma Corporation, 3-16-89 Kashima, Yodogawa-ku, Osaka 532-8505, Japan
| | - Erina Yoshida
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takaaki Shinoda
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Rintaro Iwata Hara
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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15
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Hara RI, Yoshino R, Nukaga Y, Maeda Y, Sato K, Wada T. Synthesis and properties of DNA oligomers containing stereopure phosphorothioate linkages and C-5 modified deoxyuridine derivatives. RSC Adv 2020; 10:34006-34013. [PMID: 35519073 PMCID: PMC9056737 DOI: 10.1039/d0ra06970a] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/03/2020] [Indexed: 12/25/2022] Open
Abstract
Phosphorothioate (PS) modification, where a non-bridging oxygen atom in a phosphodiester linkage is replaced by a sulfur atom, is widely used to improve the properties of nucleic acid drugs. Each PS linkage can be found in two stereoisomers, Rp and Sp. Since one non-bridging oxygen or sulfur atom in Sp-PS or Rp-PS, respectively, is located close to the C-5 substituent of uracil in a DNA/RNA hybrid duplex, the combination of the stereochemistry of the PS linkages and the type of the C-5 modification of uracil bases is expected to affect the properties of the hybrid duplexes. Herein, DNA oligomers containing both stereopure phosphorohioate linkages and C-5 modified deoxyuridine derivatives were synthesized. The thermodynamic stability of the DNA/RNA and DNA/DNA duplexes and RNase H activity of the DNA/RNA duplexes were evaluated. The combination of 5-propynyluracil and (Rp)-PS linkages in a DNA strand could significantly increase the thermal stability of a DNA/RNA hybrid duplex without reducing its RNase H activity. The combination of 5-propynyluracil and (Rp)-PS linkages in a DNA strand could significantly increase the thermal stability of a DNA/RNA hybrid duplex.![]()
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
- Department of Neurology and Neurological Science
| | - Reijiro Yoshino
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Yohei Nukaga
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Yusuke Maeda
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Kazuki Sato
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
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16
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Sato K, Imai H, Shuto T, Hara RI, Wada T. Solid-Phase Synthesis of Phosphate/Boranophosphate Chimeric DNAs Using the H-Phosphonate- H-Boranophosphonate Method. J Org Chem 2019; 84:15032-15041. [PMID: 31657569 DOI: 10.1021/acs.joc.9b01257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Boranophosphate (PB) DNAs are promising antisense oligonucleotide candidates because of their attractive features, such as high nuclease resistance and low toxicity. However, a full boranophosphate backbone modification to antisense DNAs causes reduced duplex formation with complementary RNAs and reduced antisense activity. In this study, an efficient solid-phase synthesis of phosphate/boranophosphate (PO/PB) chimeric DNA was achieved by the combination of the H-phosphonate and H-boranophosphonate methods. The physiological and biological properties of the synthesized PO/PB chimeric DNAs were also evaluated. The strategy employed herein can facilitate the design and synthesis of PO/PB chimeric DNAs containing site-specific boranophosphate modifications.
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Affiliation(s)
- Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Hiroki Imai
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Tomohito Shuto
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences , The University of Tokyo , Bioscience Building 702, 5-1-5 Kashiwanoha , Kashiwa , Chiba 277-8562 , Japan
| | - Rintaro Iwata Hara
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan.,Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University , 1-5-45 Yushima , Bunkyo-ku , Tokyo 113-8519 , Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
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17
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Yoshioka K, Kunieda T, Asami Y, Guo H, Miyata H, Yoshida-Tanaka K, Sujino Y, Piao W, Kuwahara H, Nishina K, Hara RI, Nagata T, Wada T, Obika S, Yokota T. Highly efficient silencing of microRNA by heteroduplex oligonucleotides. Nucleic Acids Res 2019; 47:7321-7332. [PMID: 31214713 PMCID: PMC6698647 DOI: 10.1093/nar/gkz492] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 12/11/2022] Open
Abstract
AntimiR is an antisense oligonucleotide that has been developed to silence microRNA (miRNA) for the treatment of intractable diseases. Enhancement of its in vivo efficacy and improvement of its toxicity are highly desirable but remain challenging. We here design heteroduplex oligonucleotide (HDO)-antimiR as a new technology comprising an antimiR and its complementary RNA. HDO-antimiR binds targeted miRNA in vivo more efficiently by 12-fold than the parent single-stranded antimiR. HDO-antimiR also produced enhanced phenotypic effects in mice with upregulated expression of miRNA-targeting messenger RNAs. In addition, we demonstrated that the enhanced potency of HDO-antimiR was not explained by its bio-stability or delivery to the targeted cell, but reflected an improved intracellular potency. Our findings provide new insights into biology of miRNA silencing by double-stranded oligonucleotides and support the in vivo potential of this technology based on a new class of for the treatment of miRNA-related diseases.
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Affiliation(s)
- Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Taiki Kunieda
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Yutaro Asami
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Huijia Guo
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Haruka Miyata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kie Yoshida-Tanaka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Yumiko Sujino
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Wenying Piao
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Hiroya Kuwahara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kazutaka Nishina
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Rintaro Iwata Hara
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Takeshi Wada
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Satoshi Obika
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
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18
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Hara RI, Saito T, Kogure T, Hamamura Y, Uchiyama N, Nukaga Y, Iwamoto N, Wada T. Stereocontrolled Synthesis of Boranophosphate DNA by an Oxazaphospholidine Approach and Evaluation of Its Properties. J Org Chem 2019; 84:7971-7983. [PMID: 31140804 DOI: 10.1021/acs.joc.9b00658] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this paper, we describe the first stereocontrolled synthesis and properties of boranophosphate DNA (PB-DNA), which contains all of the four nucleobases longer than 10mer. Synthesis was accomplished via an oxazaphospholidine approach combined with acid-labile protecting groups on nucleobases. It was demonstrated that there were significant differences between all-( Rp)- and all-( Sp)-PB-DNA in terms of the duplex-formation ability, nuclease resistance, and ribonuclease H (RNase H) activity. In particular, all-( Sp)-PB-DNA was demonstrated to show a duplex-formation ability with RNA and RNase H activity, both of which are necessary for antisense-type nucleic acid therapeutics.
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan.,Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University , 1-5-45 Yushima , Bunkyo-ku , Tokyo 113-8519 , Japan
| | - Tatsuya Saito
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Tomoki Kogure
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Yuka Hamamura
- Graduate School of Frontier Sciences , The University of Tokyo , 5-1-5 Kashiwanoha , Kashiwa , Chiba 277-8562 , Japan
| | - Naoki Uchiyama
- Graduate School of Frontier Sciences , The University of Tokyo , 5-1-5 Kashiwanoha , Kashiwa , Chiba 277-8562 , Japan
| | - Yohei Nukaga
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
| | - Naoki Iwamoto
- Graduate School of Frontier Sciences , The University of Tokyo , 5-1-5 Kashiwanoha , Kashiwa , Chiba 277-8562 , Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences , Tokyo University of Science , 2641 Yamazaki , Noda , Chiba 278-8510 , Japan
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19
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Maeda Y, Iwata Hara R, Nishina K, Yoshida-Tanaka K, Sakamoto T, Yokota T, Wada T. Artificial cationic peptides that increase nuclease resistance of siRNA without disturbing RNAi activity. Nucleosides Nucleotides Nucleic Acids 2019; 38:338-348. [PMID: 30663497 DOI: 10.1080/15257770.2018.1543890] [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] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Properties of cationic peptides bearing amino or guanidino groups with various side chain lengths that bind to double stranded RNAs (dsRNAs) were investigated. Peptides with shorter side chain lengths effectively bound to dsRNAs (12mers) increasing their thermal stability. NMR measurements suggested that the cationic peptide binds to the inner side of the major groove of dsRNA. These peptides also increased the thermal stability of siRNA and effectively protected from RNase A digestion. On the other hand, both peptides containing amino groups and guanidine groups did not disturb RNAi activity.
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Affiliation(s)
- Yusuke Maeda
- a Faculty of Pharmaceutical Sciences , Tokyo University of Science , Noda , Chiba , Japan
| | - Rintaro Iwata Hara
- a Faculty of Pharmaceutical Sciences , Tokyo University of Science , Noda , Chiba , Japan.,b Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University , Bunkyo-ku , Tokyo , Japan
| | - Kazutaka Nishina
- b Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University , Bunkyo-ku , Tokyo , Japan
| | - Kie Yoshida-Tanaka
- b Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University , Bunkyo-ku , Tokyo , Japan
| | - Taiichi Sakamoto
- c Faculty of Advanced Engineering , Chiba Institute of Technology , Narashino , Chiba , Japan
| | - Takanori Yokota
- b Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University , Bunkyo-ku , Tokyo , Japan
| | - Takeshi Wada
- a Faculty of Pharmaceutical Sciences , Tokyo University of Science , Noda , Chiba , Japan
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20
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Hara RI, Yaoita A, Takeda K, Ueki H, Ishii A, Imoto H, Kobayashi S, Sano M, Noro M, Sato K, Wada T. Cover Feature: Solid-Phase Synthesis of Fluorinated Analogues of Glycosyl 1-Phosphate Repeating Structures from Leishmania
using the Phosphoramidite Method (ChemistryOpen 6/2018). ChemistryOpen 2018. [PMCID: PMC5987814 DOI: 10.1002/open.201800067] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The Cover Feature shows the structure of the longest analogue of chemically synthesized glycosyl 1‐phosphate repeating structure from Leishmania. More information can be found in the Full Paper by R. Iwata Hara et al. on page 439 in Issue 6, 2018 (DOI: https://doi.org/10.1002/open.201800030).![]()
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences; Tokyo University of Science; 2641 Yamazaki Noda, Chiba 278-8510 Japan
| | - Aya Yaoita
- Faculty of Pharmaceutical Sciences; Tokyo University of Science; 2641 Yamazaki Noda, Chiba 278-8510 Japan
| | - Katsuya Takeda
- Graduate School of Frontier Sciences; The University of Tokyo; 5-1-5 Kashiwanoha Kashiwa, Chiba 277-8562 Japan
| | - Hiroaki Ueki
- Faculty of Pharmaceutical Sciences; Tokyo University of Science; 2641 Yamazaki Noda, Chiba 278-8510 Japan
| | - Ayumu Ishii
- Graduate School of Frontier Sciences; The University of Tokyo; 5-1-5 Kashiwanoha Kashiwa, Chiba 277-8562 Japan
| | - Hideyuki Imoto
- Graduate School of Frontier Sciences; The University of Tokyo; 5-1-5 Kashiwanoha Kashiwa, Chiba 277-8562 Japan
| | - Satoshi Kobayashi
- Graduate School of Frontier Sciences; The University of Tokyo; 5-1-5 Kashiwanoha Kashiwa, Chiba 277-8562 Japan
| | - Michi Sano
- Faculty of Pharmaceutical Sciences; Tokyo University of Science; 2641 Yamazaki Noda, Chiba 278-8510 Japan
| | - Mihoko Noro
- Graduate School of Frontier Sciences; The University of Tokyo; 5-1-5 Kashiwanoha Kashiwa, Chiba 277-8562 Japan
| | - Kazuki Sato
- Graduate School of Frontier Sciences; The University of Tokyo; 5-1-5 Kashiwanoha Kashiwa, Chiba 277-8562 Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences; Tokyo University of Science; 2641 Yamazaki Noda, Chiba 278-8510 Japan
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21
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Hara RI, Yaoita A, Takeda K, Ueki H, Ishii A, Imoto H, Kobayashi S, Sano M, Noro M, Sato K, Wada T. Solid-Phase Synthesis of Fluorinated Analogues of Glycosyl 1-Phosphate Repeating Structures from Leishmania using the Phosphoramidite Method. ChemistryOpen 2018; 7:439-446. [PMID: 29928567 PMCID: PMC5987806 DOI: 10.1002/open.201800030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 02/27/2018] [Indexed: 01/08/2023] Open
Abstract
Bacterial and protozoan sugar chains contain glycosyl 1-phosphate repeating structures; these repeating structures have been studied for vaccine development. The fluorinated analogues of [β-Gal-(1→4)-α-Man-(1→6)-P-] n , which are glycosyl 1-phosphate repeating structures found in Leishmania, were synthesised using the solid-phase phosphoramidite method. This method has been less extensively studied for the synthesis of glycosyl 1-phosphate units than H-phosphonate chemistry. A stepwise synthesis of a compound containing five such repeating units has been conducted using the phosphoramidite method herein, which is the longest glycosyl 1-phosphate structures to be chemically constructed in a stepwise manner.
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical SciencesTokyo University of Science2641 YamazakiNoda, Chiba278–8510Japan
| | - Aya Yaoita
- Faculty of Pharmaceutical SciencesTokyo University of Science2641 YamazakiNoda, Chiba278–8510Japan
| | - Katsuya Takeda
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Hiroaki Ueki
- Faculty of Pharmaceutical SciencesTokyo University of Science2641 YamazakiNoda, Chiba278–8510Japan
| | - Ayumu Ishii
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Hideyuki Imoto
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Satoshi Kobayashi
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Michi Sano
- Faculty of Pharmaceutical SciencesTokyo University of Science2641 YamazakiNoda, Chiba278–8510Japan
| | - Mihoko Noro
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Kazuki Sato
- Graduate School of Frontier SciencesThe University of Tokyo5-1-5 KashiwanohaKashiwa, Chiba277–8562Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical SciencesTokyo University of Science2641 YamazakiNoda, Chiba278–8510Japan
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22
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Hara RI, Mitsuhashi Y, Saito K, Maeda Y, Wada T. Solid-Phase Synthesis of Oligopeptides Containing Sterically Hindered Amino Acids on Nonswellable Resin Using 3-Nitro-1,2,4-triazol-1-yl-tris(pyrrolidin-1-yl)phosphonium Hexafluorophosphate (PyNTP) as the Condensing Reagent. ACS Comb Sci 2018; 20:132-136. [PMID: 29338200 DOI: 10.1021/acscombsci.7b00184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Peptides are still difficult to synthesize when they contain sterically hindered amino acids, such as α,α-disubstituted amino acids and N-substituted amino acids. In this study, solid-phase syntheses of oligopeptides containing multiple α-aminoisobutyric acid (Aib) residues were performed in high yields by using a nonswellable resin as the solid-support and 3-nitro-1,2,4-triazol-1-yl-tris(pyrrolidin-1-yl)phosphonium hexafluorophosphate (PyNTP) as the condensing reagent.
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yuta Mitsuhashi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Keita Saito
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Yusuke Maeda
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Hara RI, Maeda Y, Fujimaki H, Wada T. Correction: Enhancement in RNase H activity of a DNA/RNA hybrid duplex using artificial cationic oligopeptides. Chem Commun (Camb) 2018; 54:11499. [DOI: 10.1039/c8cc90436g] [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
Correction for ‘Enhancement in RNase H activity of a DNA/RNA hybrid duplex using artificial cationic oligopeptides’ by Rintaro Iwata Hara et al., Chem. Commun., 2018, 54, 8526–8529.
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
- Department of Neurology and Neurological Science
| | - Yusuke Maeda
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Haruna Fujimaki
- Graduate School of Frontier Sciences
- The University of Tokyo
- Kashiwa
- Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
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24
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Hara RI, Maeda Y, Fujimaki H, Wada T. Enhancement in RNase H activity of a DNA/RNA hybrid duplex using artificial cationic oligopeptides. Chem Commun (Camb) 2018; 54:8526-8529. [DOI: 10.1039/c8cc04082f] [Citation(s) in RCA: 3] [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: 01/13/2023]
Abstract
This study assessed the effects of artificial cationic oligopeptides on a DNA/RNA hybrid duplex.
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
- Department of Neurology and Neurological Science
| | - Yusuke Maeda
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Haruna Fujimaki
- Graduate School of Frontier Sciences
- The University of Tokyo
- Kashiwa
- Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
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25
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26
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Yuki Ogawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Mihoko Noro
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Building 702, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
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Hara RI, Maeda Y, Sakamoto T, Wada T. Double-stranded RNA-binding artificial cationic oligosaccharides stabilizing siRNAs with a low N/P ratio. Org Biomol Chem 2017; 15:1710-1717. [PMID: 28138666 DOI: 10.1039/c6ob02690g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Novel double-stranded RNA (dsRNA)-binding molecules were developed for the effective thermodynamic and biological stabilization of nucleic acids including short interfering RNAs (siRNAs). β-(1→4)-Linked-2,6-diamino-2,6-dideoxy-d-galactopyranose oligomers (ODAGals) were synthesized for this purpose, and their binding ability with dsRNAs was evaluated. Fluorescence anisotropy measurements showed the 3mer and 4mer of ODAGals to be strongly bound (Kd < 0.02 μM). The UV melting experiments demonstrated that the binding of ODAGals to dsRNAs proceeded with significant thermodynamic stabilization of the duplexes. Furthermore, the 4mer of ODAGal was clearly revealed to almost completely protect siRNAs with a low N/P ratio (i.e., N in the oligocationic molecule to P in the siRNA ratio) from cleavage by RNase A. On the basis of these results, ODAGals can serve as promising stabilizers or carriers of dsRNA-based drugs such as RNAi drugs.
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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Abstract
We synthesized 2′-O-monohaloethoxymethyl-modified RNAs and evaluated their duplex formation ability.
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Affiliation(s)
| | - Masayuki Kageyama
- Graduate School of Frontier Sciences
- The University of Tokyo
- Kashiwa
- Japan
| | - Koichiro Arai
- Graduate School of Frontier Sciences
- The University of Tokyo
- Kashiwa
- Japan
| | - Naoki Uchiyama
- Graduate School of Frontier Sciences
- The University of Tokyo
- Kashiwa
- Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
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