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Kakuta K, Kasahara R, Sato K, Wada T. Solid-phase synthesis of oligodeoxynucleotides using nucleobase N-unprotected oxazaphospholidine derivatives bearing a long alkyl chain. Org Biomol Chem 2023; 21:7580-7592. [PMID: 37674464 DOI: 10.1039/d3ob01255g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
In this study, we developed a new approach for the solid-phase synthesis of oligodeoxynucleotides (ODNs) using nucleobase-unprotected oxazaphospholidine derivatives. We tackled the problem of the difficult purification of N-unprotected monomers due to their high affinity to silica gel by introducing a tetrahydrogeranyl group into the oxazaphospholidine monomers, thereby enhancing the lipophilicity and facilitating the isolation. In addition, the cyclic structure of oxazaphospholidine enabled a hydroxy-group-selective condensation with sufficient efficiency. Unmodified and boranophosphate/phosphate chimeric ODNs were successfully synthesized using this strategy. This synthetic method can be expected to afford ODNs containing base-labile functional groups.
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Affiliation(s)
- Kiyoshi Kakuta
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| | - Ryouta Kasahara
- 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.
| | - 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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2
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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Skiba J, Kowalczyk A, Gorski A, Dutkiewicz N, Gapińska M, Stróżek J, Woźniak K, Trzybiński D, Kowalski K. Replacement of the phosphodiester backbone between canonical nucleosides with a dirhenium carbonyl "click" linker-a new class of luminescent organometallic dinucleoside phosphate mimics. Dalton Trans 2023; 52:1551-1567. [PMID: 36655722 DOI: 10.1039/d2dt03995h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The first-in-class luminescent dinucleoside phosphate analogs with a [Re2(μ-Cl)2(CO)6(μ-pyridazine)] "click" linker as a replacement for the natural phosphate group are reported together with the synthesis of luminescent adenosine and thymidine derivatives having the [Re2(μ-Cl)2(CO)6(μ-pyridazine)] entity attached to positions 5' and 3', respectively. These compounds were synthesized by applying inverse-electron-demand Diels-Alder and copper(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition reactions in three or four steps. The obtained compounds exhibited orange emission (λPL ≈ 600 nm, ΦPL ≈ 0.10, and τ = 0.33-0.61 μs) and no toxicity (except for one nucleoside) to human HeLa cervical epithelioid and Ishikawa endometrial adenocarcinoma cancer cells in vitro. Furthermore, the compounds' ability to inhibit the growth of Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli bacterial strains was moderate and only observed at a high concentration of 100 μM. Confocal microscopy imaging revealed that the "dirhenium carbonyl" dinucleosides and nucleosides localized mainly in the membranous structures of HeLa cells and uniformly inside S. aureus and E. coli bacterial cells. An interesting finding was that some of the tested compounds were also found in the nuclei of HeLa cells.
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Affiliation(s)
- Joanna Skiba
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland.
| | - Aleksandra Kowalczyk
- Department of Molecular Microbiology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - Aleksander Gorski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, Poland
| | - Natalia Dutkiewicz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, Poland
| | - Magdalena Gapińska
- Faculty of Biology and Environmental Protection, Laboratory of Microscopic Imaging and Specialized Biological Techniques, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - Józef Stróżek
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland.
| | - Krzysztof Woźniak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Damian Trzybiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Konrad Kowalski
- Faculty of Chemistry, Department of Organic Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland.
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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] [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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Masaki Y, Maruyama A, Yoshida K, Tomori T, Kishimura T, Seio K. Oligodeoxynucleotides Modified with 2'- O-(Cysteinylaminobutyl)carbamoylethylribothymidine Residues for Native Chemical Ligation with Peptide at Internal Positions. Bioconjug Chem 2022; 33:272-278. [PMID: 35129971 DOI: 10.1021/acs.bioconjchem.1c00575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We used native chemical ligation (NCL) to synthesize a 2'-O-{N-[N-(S-tert-butylthiocysteinyl)aminobutyl]carbamoylethyl} (CysBCE) ribothymidine-derived oligonucleotide to expand the variety of peptide conjugation sites, allowing the incorporation of peptides at the 2'-hydroxy group when the oligonucleotide forms a duplex with the complementary strand. The NCL reaction with a peptide thioester and the modified oligonucleotide proceeded smoothly even when the CysBCE modification was in the middle of the oligonucleotide sequence. In addition, we incorporated two CysBCEs into an oligonucleotide to conjugate two peptides to one oligonucleotide. The results indicated that the tandem NCL reactions proceeded efficiently when the oligonucleotide hybridized to the complementary strand to avoid intramolecular disulfide formation between the two CysBCE groups. This method could be useful for peptide conjugation on the 2'-position.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan.,Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Atsuya Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Keita Yoshida
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Takahito Tomori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Tomohiro Kishimura
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa 226-8501, Japan
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Numan A, Brichacek M. Asymmetric Synthesis of Stereogenic Phosphorus P(V) Centers Using Chiral Nucleophilic Catalysis. Molecules 2021; 26:3661. [PMID: 34203996 PMCID: PMC8232703 DOI: 10.3390/molecules26123661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 11/21/2022] Open
Abstract
Organophosphates have been widely used in agrochemistry, as reagents for organic synthesis, and in biochemistry. Phosphate mimics possessing four unique substituents, and thereby a chirality center, are useful in transition metal catalysis and as nucleotide therapeutics. The catalytic, stereocontrolled synthesis of phosphorus-stereogenic centers is challenging and traditionally depends on a resolution or use of stochiometric auxiliaries. Herein, enantioenriched phosphorus centers have been synthesized using chiral nucleophilic catalysis. Racemic H-phosphinate species were coupled with nucleophilic alcohols under halogenating conditions. Chiral phosphonate products were synthesized in acceptable yields (33-95%) and modest enantioselectivity (up to 62% ee) was observed after identification of an appropriate chiral catalyst and optimization of the solvent, base, and temperature. Nucleophilic catalysis has a tremendous potential to produce enantioenriched phosphate mimics that could be used as prodrugs or chemical biology probes.
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Featherston AL, Kwon Y, Pompeo MM, Engl OD, Leahy DK, Miller SJ. Catalytic asymmetric and stereodivergent oligonucleotide synthesis. Science 2021; 371:702-707. [PMID: 33574208 DOI: 10.1126/science.abf4359] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022]
Abstract
We report the catalytic stereocontrolled synthesis of dinucleotides. We have demonstrated, for the first time to our knowledge, that chiral phosphoric acid (CPA) catalysts control the formation of stereogenic phosphorous centers during phosphoramidite transfer. Unprecedented levels of diastereodivergence have also been demonstrated, enabling access to either phosphite diastereomer. Two different CPA scaffolds have proven to be essential for achieving stereodivergence: peptide-embedded phosphothreonine-derived CPAs, which reinforce and amplify the inherent substrate preference, and C2-symmetric BINOL-derived CPAs, which completely overturn this stereochemical preference. The presently reported catalytic method does not require stoichiometric activators or chiral auxiliaries and enables asymmetric catalysis with readily available phosphoramidites. The method was applied to the stereocontrolled synthesis of diastereomeric dinucleotides as well as cyclic dinucleotides, which are of broad interest in immuno-oncology as agonists of the stimulator of interferon genes (STING) pathway.
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Affiliation(s)
| | - Yongseok Kwon
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Matthew M Pompeo
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Oliver D Engl
- Process Chemistry Development, Takeda Pharmaceuticals International Co., Cambridge, MA 02139, USA
| | - David K Leahy
- Process Chemistry Development, Takeda Pharmaceuticals International Co., Cambridge, MA 02139, USA.
| | - Scott J Miller
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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Crooke ST, Seth PP, Vickers TA, Liang XH. The Interaction of Phosphorothioate-Containing RNA Targeted Drugs with Proteins Is a Critical Determinant of the Therapeutic Effects of These Agents. J Am Chem Soc 2020; 142:14754-14771. [PMID: 32786803 DOI: 10.1021/jacs.0c04928] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent progress in understanding phosphorothioate antisense oligonucleotide (PS-ASO) interactions with proteins has revealed that proteins play deterministic roles in the absorption, distribution, cellular uptake, subcellular distribution, molecular mechanisms of action, and toxicity of PS-ASOs. Similarly, such interactions can alter the fates of many intracellular proteins. These and other advances have opened new avenues for the medicinal chemistry of PS-ASOs and research on all elements of the molecular pharmacology of these molecules. These advances have recently been reviewed. In this Perspective article, we summarize some of those learnings, the general principles that have emerged, and a few of the exciting new questions that can now be addressed.
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Affiliation(s)
- Stanley T Crooke
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Timothy A Vickers
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Xue-Hai Liang
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
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12
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Sato K, Wada T. Development of Efficient Synthetic Methods of Boranophosphate Oligonucleotides. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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13
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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] [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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