研究者詳細 - 木村　康明

論文 - 木村　康明

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Internal cap-initiated translation for efficient protein production from circular mRNA.

Fukuchi K, Nakashima Y, Abe N, Kimura S, Hashiya F, Shichino Y, Liu Y, Ogisu R, Sugiyama S, Kawaguchi D, Inagaki M, Meng Z, Kajihara S, Tada M, Uchida S, Li TT, Maity R, Kawasaki T, Kimura Y, Iwasaki S, Abe H

Nature biotechnology 2025年2月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nature Biotechnology

Circular mRNA faces challenges in enhancing its translation potential as an RNA therapeutic. Here we introduce two molecular designs that bolster circular mRNA translation through an internal cap-initiated mechanism. The first consists of a circular mRNA with a covalently attached N7-methylguanosine (m7G) cap through a branching structure (cap-circ mRNA). This modification allows circular mRNA to recruit translation machinery and produce proteins more efficiently than internal ribosome entry site (IRES)-containing circular mRNAs. Combining with an N1-methylpseudouridine (m1Ψ) modification, cap-circ mRNA exhibits a lower acute immunostimulatory effect, maintaining high translation in mice. The second design features the non-covalent attachment of an m7G cap to a circular mRNA through hybridization with an m7G cap-containing oligonucleotide, enhancing translation by more than 50-fold. This setup allows circular mRNAs to synthesize reporter proteins upon hybridizing with capped mRNAs or long non-coding RNAs and to undergo rolling circle-type translation. These advancements broaden the therapeutic applications of circular mRNAs by minimizing their molecular size, elevating translation efficiency and facilitating cell-type-selective translation.

DOI： 10.1038/s41587-025-02561-8

Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures 査読有り

Inagaki, M; Abe, N; Li, ZM; Nakashima, Y; Acharyya, S; Ogawa, K; Kawaguchi, D; Hiraoka, H; Banno, A; Meng, ZY; Tada, M; Ishida, T; Lyu, P; Kokubo, K; Murase, H; Hashiya, F; Kimura, Y; Uchida, S; Abe, H

NATURE COMMUNICATIONS 14 巻 ( 1 ) 頁： 2657 2023年5月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nature Communications

Starting with the clinical application of two vaccines in 2020, mRNA therapeutics are currently being investigated for a variety of applications. Removing immunogenic uncapped mRNA from transcribed mRNA is critical in mRNA research and clinical applications. Commonly used capping methods provide maximum capping efficiency of around 80–90% for widely used Cap-0- and Cap-1-type mRNAs. However, uncapped and capped mRNA possesses almost identical physicochemical properties, posing challenges to their physical separation. In this work, we develop hydrophobic photocaged tag-modified cap analogs, which separate capped mRNA from uncapped mRNA by reversed-phase high-performance liquid chromatography. Subsequent photo-irradiation recovers footprint-free native capped mRNA. This approach provides 100% capping efficiency even in Cap-2-type mRNA with versatility applicable to 650 nt and 4,247 nt mRNA. We find that the Cap-2-type mRNA shows up to 3- to 4-fold higher translation activity in cultured cells and animals than the Cap-1-type mRNA prepared by the standard capping method.

DOI： 10.1038/s41467-023-38244-8

mRNAの完全化学合成を可能とする化学的キャップ化法の開発

阿部洋, 小川和哉, 阿部奈保子, 木村康明

MEDCHEM NEWS 33 巻 ( 2 ) 頁： 75 - 78 2023年5月

記述言語：日本語掲載種別：研究論文（学術雑誌）出版者・発行元：公益社団法人日本薬学会

近年、新型コロナウイルス感染症においてmRNAワクチンが大きな成功を収めた。しかし、mRNAワクチンは、mRNAの生体内不安定性等による活性の低下が課題としてあげられる。そこで、安定性向上が見込まれる化学修飾をmRNAに導入することが効果的であるが、それを実現するための汎用的合成法は存在しない。本研究ではmRNAへの化学修飾の導入の障壁となる酵素法を回避したmRNAの完全化学合成法を開発した。本手法では、mRNAに対して位置特異的な化学修飾の導入が可能であり、適切な化学修飾パターンにより翻訳活性と安定性の最大化が可能となる。本稿では、完全化学合成法の開発経緯、完全化学合成法による化学修飾mRNAの構造活性相関および本手法で合成したmRNAがんワクチンの治療効果について解説する。

DOI： 10.14894/medchem.33.2_75

SYNTHESIS AND BIOLOGICAL EVALUATION OF NMDI14 DERIVATIVES AS ANTI-MESOTHELIOMA AGENTS 国際誌

Hong Nhung Nguyen, Suzuki Koya, Kimura Yasuaki, Hirokawa Takatsugu, Murakami-Tonami Yuko, Abe Hiroshi

HETEROCYCLES 100 巻 ( 2 ) 頁： 253 - 266 2020年2月

記述言語：日本語掲載種別：研究論文（学術雑誌）出版者・発行元：Heterocycles

Mesothelioma is a severe tumor formed in pleura and peritoneum, for which no useful molecular-targeting therapy is available. We synthesized several derivatives of NMDI14, which is a reported inhibitor for non-sense mediated mRNA decay, and evaluated the activity of the NMDI14 derivatives as potential anti-mesothelioma agents. Some of the synthesized compounds showed promising activity in terms of cytotoxicity toward mesothelioma model cells and promotion of GAS5 expression selectively in mesothelioma cells. These results indicate that the NMDI14 derivatives may be useful for further developing clinically effective anti-mesothelioma drugs.

DOI： 10.3987/COM-19-14191

Intracellular Delivery of Antisense DNA and siRNA with Amino Groups Masked with Disulfide Units 国際誌

Shu Zhaoma, Ota Azumi, Takayama Yukiya, Katsurada Yuri, Kusamori Kosuke, Abe Naoko, Nakamoto Kosuke, Tomoike Fumiaki, Tada Seiichi, Ito Yoshihiro, Nishikawa Makiya, Kimura Yasuaki, Abe Hiroshi

CHEMICAL & PHARMACEUTICAL BULLETIN 68 巻 ( 2 ) 頁： 129 - 132 2020年2月

Intracellular Delivery of Antisense DNA and siRNA with Amino Groups Masked with Disulfide Units. 国際誌

Shu Z, Ota A, Takayama Y, Katsurada Y, Kusamori K, Abe N, Nakamoto K, Tomoike F, Tada S, Ito Y, Nishikawa M, Kimura Y, Abe H

Chemical & pharmaceutical bulletin 68 巻 ( 2 ) 頁： 129 - 132 2020年

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Chemical & pharmaceutical bulletin

Efficient methods for delivery of antisense DNA or small interfering RNA (siRNA) are highly needed. Cationic materials, which are conventionally used for anionic oligonucleotide delivery, have several drawbacks, including aggregate formation, cytotoxicity and a low endosome escape efficiency. In this report a bio-reactive mask (i.e., disulfide unit) for cationic amino groups was introduced, and the mask was designed such that it was removed at the target cell surface. Insolubility and severe cellular toxicity caused by exposed cationic groups are avoided when using the mask. Moreover, the disulfide unit used to mask the cationic group enabled direct delivery of oligonucleotides to the cell cytosol. The molecular design reported is a promising approach for therapeutic applications.

DOI： 10.1248/cpb.c19-00811

Disulfide-Unit Conjugation Enables Ultrafast Cytosolic Internalization of Antisense DNA and siRNA. 国際誌

Shu Z, Tanaka I, Ota A, Fushihara D, Abe N, Kawaguchi S, Nakamoto K, Tomoike F, Tada S, Ito Y, Kimura Y, Abe H

Angewandte Chemie (International ed. in English) 58 巻 ( 20 ) 頁： 6611 - 6615 2019年5月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Angewandte Chemie - International Edition

Development of intracellular delivery methods for antisense DNA and siRNA is important. Previously reported methods using liposomes or receptor-ligands take several hours or more to deliver oligonucleotides to the cytoplasm due to their retention in endosomes. Oligonucleotides modified with low molecular weight disulfide units at a terminus reach the cytoplasm 10 minutes after administration to cultured cells. This rapid cytoplasmic internalization of disulfide-modified oligonucleotides suggests the existence of an uptake pathway other than endocytosis. Mechanistic analysis revealed that the modified oligonucleotides are efficiently internalized into the cytoplasm through disulfide exchange reactions with the thiol groups on the cellular surface. This approach solves several critical problems with the currently available methods for enhancing cellular uptake of oligonucleotides and may be an effective approach in the medicinal application of antisense DNA and siRNA.

DOI： 10.1002/anie.201900993

Nano structure design for RNA interference

Shu, Z; Abe, N; Tomoike, F; Kimura, Y; Ito, Y; Abe, H

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 255 巻頁： . 2018年3月

Concise Affinity-Based Purification of Ligated mRNA for Structure-Activity Relationship Studies of Nucleosugar Modification Patterns. 査読有り国際誌

Yamada H, Iwai H, Hashiya F, Kimura Y, Abe H, Yamamoto J

Chembiochem : a European journal of chemical biology 26 巻 ( 2 ) 頁： e202400711 2025年1月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ChemBioChem

Position-specific nucleoside sugar modifications have been shown to improve the translational activity and stability of chemically synthesized mRNA. For pharmaceutical applications of chemically modified mRNAs, a rapid purification methodology is imperative to identify the optimal modification pattern. However, while the chemical synthesis of mRNAs can be accomplished by splint ligation of oligonucleotide fragments, the current purification method for ligated mRNAs based on denaturing polyacrylamide gel electrophoresis tends to be time consuming. In this study, we developed a two-step affinity purification method for rapid sample preparation. In this method, ligated mRNA is captured by oligo dT magnetic beads and streptavidin magnetic beads with 3’-biotinylated oligo DNA, which are complementary to the 3’-poly(A) and 5’ terminal sequences of the target mRNA, respectively. Therefore, the target mRNA can be isolated from a complex mixture of splint ligations. Using this method, six sugar-modified mRNAs were simultaneously purified, and the translational activities of these mRNAs were evaluated immediately after purification. The results demonstrate that this methodology is suitable for the rapid preparation of various chemically synthesized mRNAs to identify their optimal modification patterns.

DOI： 10.1002/cbic.202400711

Position-Specific Nucleoside Sugar Modifications in mRNA ORF: Enhancing Translational Function through Complete Chemical Synthesis of mRNA

Hiroshi Abe, Yasuaki Kimura, Masakazu Honma, Kosuke Nakamoto, Keiichi Motosawa, Takayuki Atago, Kana Asano, Fumitaka Hashiya, Naoko Abe, Keiko Kobayashi, Ryoko Ogisu, Atsushi Hashimoto, Keiko Hiraishi, Seiji Saito, Junichiro Yamamoto, Hiroto Iwai

2024年12月

Development of hydrophobic tag purifying monophosphorylated RNA for chemical synthesis of capped mRNA and enzymatic synthesis of circular mRNA. 査読有り国際誌 Open Access

Ototake M, Inagaki M, Kimura S, Onda K, Tada M, Kawaguchi D, Murase H, Fukuchi K, Gao Y, Kokubo K, Acharyya S, Meng Z, Ishida T, Kawasaki T, Abe N, Hashiya F, Kimura Y, Abe H

Nucleic acids research 52 巻 ( 20 ) 頁： 12141 - 12157 2024年11月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nucleic Acids Research

We developed phosphorylation reagents with a nitrobenzyl hydrophobic tag and used them for 5′-phosphorylation of chemically or transcriptionally synthesized RNA. The capability of hydrophobic tags to synthesize 5′-monophosphorylated RNA was evaluated based on the yield of the desired oligonucleotides, stability of protecting groups during cleavage/deprotection, separation ability in reverse-phase HPLC (RP-HPLC), and deprotection efficiency after RP-HPLC purification. The results showed that a nitrobenzyl derivative with a tert-butyl group at the benzyl position was most suitable for RNA 5′-phosphorylation. Using the developed phosphorylation reagent, we chemically synthesized 5′-phosphorylated RNA and confirmed that it could be purified by RP-HPLC and the following deprotection. In addition, we demonstrated complete chemical synthesis of minimal mRNA by chemical capping of 5′-monophosphorylated RNA. Ribonucleoside 5′-monophosphates with hydrophobic protecting groups have also been developed and used as substrates to transcriptionally synthesize 5′-phosphorylated RNA with >1000 bases. From the mixture of the by-products and the desired RNA, only 5′-monophosphorylated RNA could be effectively isolated by RP-HPLC. Furthermore, monophosphorylated RNA can be converted into circular mRNA via RNA ligase-mediated cyclization. Circular mRNA expression of nanoluciferase in cultured cells and mice. These techniques are important for the production of chemically synthesized mRNA and circular mRNA.

DOI： 10.1093/nar/gkae847

Internal cap-initiated translation provides efficient protein production from circular mRNA

hiroshi abe, Kosuke Fukuchi, Yuko Nakashima, Naoko Abe, Seigo Kimura, Fumitaka Hashiya, Yuichi Shichino, Satomi Sugiyama, Daisuke Kawaguchi, Masahito Inagaki, Zheyu Meng, Shiryu Kajihara, Mizuki Tada, Satoshi Uchida, Ting-Ting Li, Yiwei Liu, Ramkrishna Maity, Yasuaki Kimura, Shintaro Iwasaki, Ryoko Ogisu, Tairin Kawasaki

2024年11月

記述言語：英語掲載種別：研究論文（学術雑誌）

<title>Abstract</title>
<p>Circular mRNA, emerging as a groundbreaking RNA therapeutic strategy, faces challenges in enhancing its translation potential. Here, we introduce two innovative molecular designs that bolster circular mRNA translation through an internal cap-initiated mechanism. The first design involved a circular mRNA with a covalently attached <italic>N</italic><sup>7</sup>-methylguanosine (m<sup>7</sup>G) cap through a branching structure (cap-circ mRNA). This modification allows circular mRNA to recruit translation machinery and produce proteins more efficiently than IRES-containing circular mRNAs. Combining <italic>N</italic><sup>1</sup>-methylpseudouridine (m<sup>1</sup>Ψ) modification, cap-circ mRNA exhibits a lower acute immunostimulatory effect, maintaining high translation ability, in mice. The second design features the non-covalent attachment of an m<sup>7</sup>G cap to a circular mRNA through hybridization with an m<sup>7</sup>G cap-containing oligonucleotide, significantly enhancing translation by more than 50-fold. This setup allows the design of circular mRNAs to synthesize reporter proteins upon hybridizing with capped mRNAs or long non-coding RNAs and to undergo rolling circle-type translation. These advancements have broadened the therapeutic applications of circular mRNA by minimizing their molecular size, elevating translation efficiency, and facilitating cell-type selective translation.</p>

DOI： 10.21203/rs.3.rs-4203658/v1

Intracellular Delivery of Antisense Oligonucleotides by Tri-Branched Cyclic Disulfide Units. 査読有り国際誌 Open Access

Lyu F, Hakariya H, Hiraoka H, Li Z, Matsubara N, Soo Y, Hashiya F, Abe N, Shu Z, Nakamoto K, Kimura Y, Abe H

ChemMedChem 19 巻 ( 20 ) 頁： e202400472 2024年10月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ChemMedChem

Therapeutic oligonucleotides, such as antisense DNA, show promise in treating previously untreatable diseases. However, their applications are still hindered by the poor membrane permeability of naked oligonucleotides. Therefore, it is necessary to develop efficient methods for intracellular oligonucleotide delivery. Previously, our group successfully developed disulfide-based Membrane Permeable Oligonucleotides (MPON), which achieved enhanced cellular uptake and gene silencing effects through an endocytosis-free uptake mechanism. Herein, we report a new molecular design for the next generation of MPON, called trimer MPON. The trimer MPON consists of a tri-branched backbone, three α-lipoic acid units, and a spacer linker between the oligonucleotides and tri-branched cyclic disulfide unit. We describe the design, synthesis, and functional evaluation of the trimer MPON, offering new insights into the molecular design for efficient oligonucleotide delivery.

DOI： 10.1002/cmdc.202400472

Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs. 査読有り Open Access

Nomura K, An S, Kobayashi Y, Kondo J, Shi T, Murase H, Nakamoto K, Kimura Y, Abe N, Ui-Tei K, Abe H

Nucleic acids research 52 巻 ( 18 ) 頁： 10754 - 10774 2024年10月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nucleic Acids Research

In this study, we report the synthesis of 2′-formamidonucleoside phosphoramidite derivatives and their incorporation into siRNA strands to reduce seed-based off-target effects of small interfering RNAs (siRNAs). Formamido derivatives of all four nucleosides (A, G, C and U) were synthesized in 5-11 steps from commercial compounds. Introducing these derivatives into double-stranded RNA slightly reduced its thermodynamic stability, but X-ray crystallography and CD spectrum analysis confirmed that the RNA maintained its natural A-form structure. Although the introduction of the 2′-formamidonucleoside derivative at the 2nd position in the guide strand of the siRNA led to a slight decrease in the on-target RNAi activity, the siRNAs with different sequences incorporating 2′-formamidonucleoside with four kinds of nucleobases into any position other than 2nd position in the seed region revealed a significant suppression of off-target activity while maintaining on-target RNAi activity. This indicates that 2′-formamidonucleosides represent a promising approach for mitigating off-target effects in siRNA therapeutics.

DOI： 10.1093/nar/gkae741

2'-β-Methylselenyl nucleos(t)ide analogs as reverse transcriptase inhibitors against diverse HIV mutants. 査読有り Open Access

Yoshida Y, Niimi Y, Fushihara D, Katakura H, Fukui R, Murase H, Tomoike F, Hashiya F, Murakami T, Kodama EN, Suzuki T, Yasukawa K, Kimura Y, Abe H

Bioorganic & medicinal chemistry 110 巻頁： 117813 - 117813 2024年8月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Bioorganic and Medicinal Chemistry

Nucleoside reverse transcriptase inhibitors (NRTIs) have been extensively studied as drugs targeting HIV RT. However, the practice or use of approved NRTIs lacking the 3ʹ-hydroxy group often promotes frequent HIV mutations and generates drug-resistance. Here, we describe a novel NRTI with 2′-β-methylselenyl modification. We found that this modification inhibited the DNA elongation reaction by HIV-1 RT despite having a 3′-hydroxy group. Moreover, the conformation of this nucleoside analog is controlled at C3′-endo, a conformation that resists excision from the elongating DNA by HIV RT. Accordingly, the designed analogs exhibited activity against both wild-type HIV and multidrug-resistant HIV mutants.

DOI： 10.1016/j.bmc.2024.117813

Development of PCR primers enabling the design of flexible sticky ends for efficient concatenation of long DNA fragments. 査読有り Open Access

Nomura K, Onda K, Murase H, Hashiya F, Ono Y, Terai G, Oka N, Asai K, Suzuki D, Takahashi N, Hiraoka H, Inagaki M, Kimura Y, Shimizu Y, Abe N, Abe H

RSC chemical biology 5 巻 ( 4 ) 頁： 360 - 371 2024年4月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：RSC Chemical Biology

We developed chemically modified PCR primers that allow the design of flexible sticky ends by introducing a photo-cleavable group at the phosphate moiety. Nucleic acid derivatives containing o-nitrobenzyl photo-cleavable groups with a tert-butyl group at the benzyl position were stable during strong base treatment for oligonucleotide synthesis and thermal cycling in PCR reactions. PCR using primers incorporating these nucleic acid derivatives confirmed that chain extension reactions completely stopped at position 1 before and after the site of the photo-cleavable group was introduced. DNA fragments of 2 and 3 kbp, with sticky ends of 50 bases, were successfully concatenated with a high yield of 77%. A plasmid was constructed using this method. Finally, we applied this approach to construct a 48.5 kbp lambda phage DNA, which is difficult to achieve using restriction enzyme-based methods. After 7 days, we were able to confirm the generation of DNA of the desired length. Although the efficiency is yet to be improved, the chemically modified PCR primer offers potential to complement enzymatic methods and serve as a DNA concatenation technique.

DOI： 10.1039/d3cb00212h

Development and Comparison of 4-Thiouridine to Cytidine Base Conversion Reaction. 査読有り Open Access

Ohashi S, Nakamura M, Acharyya S, Inagaki M, Abe N, Kimura Y, Hashiya F, Abe H

ACS omega 9 巻 ( 8 ) 頁： 9300 - 9308 2024年2月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ACS Omega

To study transcriptome dynamics without harming cells, it is essential to convert chemical bases. 4-Thiouridine (4sU) is a biocompatible uridine analogue that can be converted into a cytidine analogue. Although several reactions can convert 4sU into a cytidine analogue, few studies have compared the features of these reactions. In this study, we performed three reported base conversion reactions, including osmium tetroxide, iodoacetamide, and sodium periodate treatment, as well as a new reaction using 2,4-dinitrofluorobenzene. We compared the reaction time, conversion efficacy, and effects on reverse transcription. These reactions successfully converted 4sU into a cytidine analogue quantitatively using trinucleotides. However, the conversion efficacy and effect on reverse transcription vary depending on the reaction with the RNA transcript. OsO4 treatment followed by NH4Cl treatment showed the best base-conversion efficiency. Nevertheless, each reaction has its own advantages and disadvantages as a tool for studying the transcriptome. Therefore, it is crucial to select the appropriate reaction for the target of interest.

DOI： 10.1021/acsomega.3c08516

Topological capture of mRNA for silencing gene expression. 査読有り

Lyu F, Tomita T, Abe N, Hiraoka H, Hashiya F, Nakashima Y, Kajihara S, Tomoike F, Shu Z, Onizuka K, Kimura Y, Abe H

Chemical communications (Cambridge, England) 59 巻 ( 77 ) 頁： 11564 - 11567 2023年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Chemical Communications

We describe herein topological mRNA capture using branched oligodeoxynucleotides (ODNs) with multiple reactive functional groups. These fragmented ODNs efficiently formed topological complexes on template mRNA in vitro. In cell-based experiments targeting AcGFP mRNA, the bifurcated reactive ODNs showed a much larger gene silencing effect than the corresponding natural antisense ODN.

DOI： 10.1039/d2cc06189a

The Effect of γ Phosphate Modified Deoxynucleotide Substrates on PCR Activity and Fidelity. 査読有り国際誌 Open Access

Hashiya F, Murase H, Chandela A, Hiraoka H, Inagaki M, Nakashima Y, Abe N, Nakamura M, Terai G, Kimura Y, Ando K, Oka N, Asai K, Abe H

Chembiochem : a European journal of chemical biology 24 巻 ( 14 ) 頁： e202200572 2023年7月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ChemBioChem

Controlling PCR fidelity is an important issue for molecular biology and high-fidelity PCR is essential for gene cloning. In general, fidelity control is achieved by protein engineering of polymerases. In contrast, only a few studies have reported controlling fidelity using chemically modified nucleotide substrates. In this report, we synthesized nucleotide substrates possessing a modification on Pγ and evaluated the effect of this modification on PCR fidelity. One of the substrates, nucleotide tetraphosphate, caused a modest decrease in Taq DNA polymerase activity and the effect on PCR fidelity was dependent on the type of mutation. The use of deoxyadenosine tetraphosphate enhanced the A : T→G : C mutation dramatically, which is common when using Taq polymerase. Conversely, deoxyguanosine tetraphosphate (dG4P) suppressed this mutation but increased the G : C→A : T mutation during PCR. Using an excess amount of dG4P suppressed both mutations successfully and total fidelity was improved.

DOI： 10.1002/cbic.202200572

Synthesis of nucleoside oligophosphates by electrophilic activation of phosphorothioate. 査読有り

Hasegawa S, Inagaki M, Kato S, Li Z, Kimura Y, Abe H

Organic & biomolecular chemistry 21 巻 ( 19 ) 頁： 3997 - 4001 2023年5月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Organic and Biomolecular Chemistry

We herein report a new synthetic method for nucleoside oligophosphates based on electrophilic activation of 5′-phosphorothioate nucleotides. The treatment of phosphorothioate with 2,4-dinitrochlorobenzene (DNCB) efficiently afforded the key activated species, electrophilic thioester nucleotides (EPT-Ns), which were coupled with various phosphate reagents to afford the target nucleoside oligophosphates, including an mRNA cap analog.

DOI： 10.1039/d2ob02260e

A 2'-modified uridine analog, 2'-O-(methylthiomethoxy)methyl uridine, for siRNA applications. 査読有り Open Access

Lyu F, An S, Kobayashi Y, Nomura K, Baba R, Abe N, Hiraoka H, Hashiya F, Shu Z, Ui-Tei K, Kimura Y, Abe H

Bioorganic & medicinal chemistry letters 74 巻頁： 128939 - 128939 2022年10月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Bioorganic and Medicinal Chemistry Letters

The medicinal applications of siRNAs have been intensively examined but are still hindered by their low molecular stability under biological conditions and off-target effects, etc. The introduction of chemical modifications to the nucleoside is a promising strategy for solving these limitations. Herein, we describe the development of a new uridine analog, U*, that has a (methylthiomethoxy)methoxy group at the 2′ position. The phosphoramidite reagent corresponding to U* was easily synthesized and the RNA oligonucleotides containing U* were stably prepared using a standard protocol for oligonucleotide synthesis. The introduction of U* into the siRNA resulted in positive or negative effects on the targeted gene silencing in a position-dependent manner, and the positive effects were attributed to the improved stability under biological conditions. The thermodynamic analysis of the U*-modified RNAs revealed a slight destabilization of the dsRNA, based depending on which U was strategically utilized to restrain the off-target effects of the siRNA. This study describes a rare example of nucleoside analogs with a large substitution at the 2′-position in the context of an siRNA application and is informative for the development of other analogs to further improve the molecular properties of siRNAs for medicinal applications.

DOI： 10.1016/j.bmcl.2022.128939

Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures.

Masahito Inagaki, Naoko Abe, Zhenmin Li, Yuko Nakashima, Susit Acharyya, Kazuya Ogawa, Daisuke Kawaguchi, Haruka Hiraoka, Ayaka Banno, Zheyu Meng, Mizuki Tada, Tatsuma Ishida, Pingxue Lyu, Kengo Kokubo, Hirotaka Murase, Fumitaka Hashiya, Yasuaki Kimura, Satoshi Uchida, Hiroshi Abe

2022年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：American Chemical Society (ACS)

Removing immunogenic uncapped mRNA from in vitro transcribed mRNA is critical in mRNA research and clinical applications. Commonly used capping methods provide a maximum capping efficiency of around 80-90% for widely used Cap-0- and Cap-1-type mRNAs. However, uncapped and capped mRNA possesses almost identical physicochemical properties, posing challenges to their physical separation. Herein, we developed hydrophobic photocaged tag-modified cap analogs, which separated capped mRNA from uncapped mRNA by reversed-phase HPLC. Subsequent photo-irradiation recovers footprint-free native capped mRNA. This approach provided 100% capping efficiency even in Cap-2-type mRNA with versatility applicable to 650 nt and 4,247 nt mRNA. The Cap-2-type mRNA showed up to 3 to 4-fold higher translational activity in cultured cells and animals than mRNA prepared by the standard capping method. Notably, the purification process simultaneously removed immunogenic double-stranded mRNA, another major contaminant of in vitro transcribed mRNA, drastically reducing mRNA immunogenicity in cultured cells.

DOI： 10.26434/chemrxiv-2022-vfjt6

Development of Fluorophosphoramidate as a Biocompatibly Transformable Functional Group and its Application as a Phosphate Prodrug for Nucleoside Analogs. 査読有り国際誌

Yoshida Y, Zheng T, Tanabe W, Tomoike F, Hashiya F, Suzuki T, Hirota S, Saiki Y, Horii A, Hirayama A, Soga T, Kimura Y, Abe H

ChemMedChem 17 巻 ( 17 ) 頁： e202200188 2022年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ChemMedChem

Synthetic phosphate-derived functional groups are important for controlling the function of bioactive molecules in vivo. Herein we describe the development of a new type of biocompatible phosphate analog, a fluorophosphoramidate (FPA) functional group that has characteristic P−F and P−N bonds. We found that FPA with a primary amino group was relatively unstable in aqueous solution and was converted to a monophosphate, while FPA with a secondary amino group was stable. Furthermore, by improving the molecular design of FPA, we developed a reaction in which a secondary amino group is converted to a primary amino group in the intracellular environment and clarified that the FPA group functions as a phosphate prodrug of nucleoside. Various FPA-gemcitabine derivatives were synthesized and their toxicity to cancer cells were evaluated. One of the FPA-gemcitabine derivatives showed superior toxicity compared with gemcitabine and its ProTide prodrug, which methodology is widely used in various nucleoside analogs, including anti-cancer and anti-virus drugs.

DOI： 10.1002/cmdc.202200188

Complete Chemical Synthesis of Minimal Messenger RNA by Efficient Chemical Capping Reaction. 査読有り国際誌

Abe N, Imaeda A, Inagaki M, Li Z, Kawaguchi D, Onda K, Nakashima Y, Uchida S, Hashiya F, Kimura Y, Abe H

ACS chemical biology 17 巻 ( 6 ) 頁： 1308 - 1314 2022年6月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ACS Chemical Biology

Site-specific chemical modification of mRNA can improve its translational efficiency and stability. For this purpose, it is desirable to develop a complete chemical synthesis method for chemically modified mRNA. The key is a chemical reaction that introduces a cap structure into the chemically synthesized RNA. In this study, we developed a fast and quantitative chemical capping reaction between 5′-phosphorylated RNA and N7-methylated GDP imidazolide in the presence of 1-methylimidazole in the organic solvent dimethyl sulfoxide. It enabled quantitative preparation of capping RNA within 3 h. We prepared chemically modified 107-nucleotide mRNAs, including N6-methyladenosine, insertion of non-nucleotide linkers, and 2′-O-methylated nucleotides at the 5′ end and evaluated their effects on translational activity in cultured HeLa cells. The results showed that mRNAs with non-nucleotide linkers in the untranslated regions were sufficiently tolerant to translation and that mRNAs with the Cap_2 structure had higher translational activity than those with the Cap_0 structure.

DOI： 10.1021/acschembio.1c00996

Antisense Oligonucleotide Modified with Disulfide Units Induces Efficient Exon Skipping in mdx Myotubes through Enhanced Membrane Permeability and Nucleus Internalization. 査読有り国際誌

Hiraoka H, Shu Z, Tri Le B, Masuda K, Nakamoto K, Fangjie L, Abe N, Hashiya F, Kimura Y, Shimizu Y, Veedu RN, Abe H

Chembiochem : a European journal of chemical biology 22 巻 ( 24 ) 頁： 3437 - 3442 2021年12月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ChemBioChem

We have found that antisense oligonucleotides and siRNA molecules modified with repeat structures of disulfide units can be directly introduced into the cytoplasm and exhibit a suppressive effect on gene expression. In this study, we analyzed the mechanism of cellular uptake of these membrane-permeable oligonucleotides (MPONs). Time-course analysis by confocal microscopy showed that the uptake of MPONs from the plasma membrane to the cytoplasm reached 50 % of the total uptake in about 5 min. In addition, analysis of the plasma membrane proteins to which MPONs bind, identified several proteins, including voltage-dependent anion channel. Next, we analyzed the behavior of MPONs in the cell and found them to be abundant in the nucleus as early as 24 h after addition with the amount increasing further after 48 and 72 h. The amount of MPONs was 2.5-fold higher than that of unmodified oligonucleotides in the nucleus after 72 h. We also designed antisense oligonucleotides and evaluated the effect of MPONs on mRNA exon skipping using DMD model cells; MPONs caused exon skipping with 69 % efficiency after 72 h, which was three times higher than the rate of the control. In summary, the high capacity for intracytoplasmic and nuclear translocation of MPONs is expected to be useful for therapeutic strategies targeting exon skipping.

DOI： 10.1002/cbic.202100413

Completely Chemically Synthesized Long DNA Can be Transcribed in Human Cells.

Yamaoka K, Oikawa R, Abe N, Nakamoto K, Tomoike F, Hashiya F, Kimura Y, Abe H

Chembiochem : a European journal of chemical biology 22 巻 ( 23 ) 頁： 3273 - 3276 2021年12月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ChemBioChem

Chemical ligation reaction of DNA is useful for the construction of long functional DNA using oligonucleotide fragments that are prepared by solid phase chemical synthesis. However, the unnatural linkage structure formed by the ligation reaction generally impairs the biological function of the resulting ligated DNA. We achieved the complete chemical synthesis of 78 and 258 bp synthetic DNAs via multiple chemical ligation reactions with phosphorothioate and haloacyl-modified DNA fragments. The latter synthetic DNA, coding shRNA for luciferase genes with a designed truncated SV promoter sequence, successfully induced the expected gene silencing effect in HeLa cells.

DOI： 10.1002/cbic.202100312

Structure, Synthesis and Inhibition Mechanism of Nucleoside Analogues as HIV-1 Reverse Transcriptase Inhibitors (NRTIs). 査読有り国際誌

Yoshida Y, Honma M, Kimura Y, Abe H

ChemMedChem 16 巻 ( 5 ) 頁： 743 - 766 2021年3月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ChemMedChem

Acquired immunodeficiency syndrome (AIDS) is caused by infection with the human immunodeficiency virus (HIV). Although treatments against HIV infection are available, AIDS remains a serious disease that causes many deaths annually. Although a variety of anti-HIV drugs have been synthesized and marketed to treat HIV-infected patients, nucleoside analogue reverse transcriptase inhibitors (NRTIs), which mimic nucleosides, are used extensively and remain a subject of interest to medicinal chemists. However, HIV has acquired drug resistance against NRTIs, and thus the struggle to find novel therapies continues. In this review, we trace the trajectory of NRTIs, focusing on the synthesis, mechanisms of action and applications of NRTIs that have been developed.

DOI： 10.1002/cmdc.202000695

その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/cmdc.202000695

Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis. 査読有り国際誌 Open Access

Kawaguchi D, Kodama A, Abe N, Takebuchi K, Hashiya F, Tomoike F, Nakamoto K, Kimura Y, Shimizu Y, Abe H

Angewandte Chemie (International ed. in English) 59 巻 ( 40 ) 頁： 17403 - 17407 2020年9月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Angewandte Chemie - International Edition

Messenger RNAs (mRNAs) with phosphorothioate modification (PS-mRNA) to the phosphate site of A, G, C, and U with all 16 possible combinations were prepared, and the translation reaction was evaluated using an E. coli cell-free translation system. Protein synthesis from PS-mRNA increased in 12 of 15 patterns when compared with that of unmodified mRNA. The protein yield increased 22-fold when the phosphorothioate modification at A/C sites was introduced into the region from the 5′-end to the initiation codon. Single-turnover analysis of PS-mRNA translation showed that phosphorothioate modification increases the number of translating ribosomes, thus suggesting that the rate of translation initiation (rate of ribosome complex formation) is positively affected by the modification. The method provides a new strategy for improving translation by using non-natural mRNA.

DOI： 10.1002/anie.202007111

その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/anie.202007111

Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters 査読有り国際誌

Sakuraba Shun, Iwakiri Junichi, Hamada Michiaki, Kameda Tomoshi, Tsuji Genichiro, Kimura Yasuaki, Abe Hiroshi, Asai Kiyoshi

JOURNAL OF CHEMICAL THEORY AND COMPUTATION 16 巻 ( 9 ) 頁： 5923 - 5935 2020年9月

記述言語：日本語掲載種別：研究論文（学術雑誌）出版者・発行元：Journal of Chemical Theory and Computation

Can current simulations quantitatively predict the stability of ribonucleic acids (RNAs)? In this research, we apply a free-energy perturbation simulation of RNAs containing inosine, a modified ribonucleic base, to the derivation of RNA nearest-neighbor parameters. A parameter set derived solely from 30 simulations was used to predict the free-energy difference of the RNA duplex with a mean unbiased error of 0.70 kcal/mol, which is a level of accuracy comparable to that obtained with parameters derived from 25 experiments. We further show that the error can be lowered to 0.60 kcal/mol by combining the simulation-derived free-energy differences with experimentally measured differences. This protocol can be used as a versatile method for deriving nearest-neighbor parameters of RNAs with various modified bases.

DOI： 10.1021/acs.jctc.0c00270

Chemically synthesized circular RNAs with phosphoramidate linkages enable rolling circle translation. 査読有り国際誌

Nakamoto K, Abe N, Tsuji G, Kimura Y, Tomoike F, Shimizu Y, Abe H

Chemical communications (Cambridge, England) 56 巻 ( 46 ) 頁： 6217 - 6220 2020年6月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Chemical Communications

Circular RNA without a stop codon enables rolling circle translation. To produce circular RNAs, we carried out one-pot chemical synthesis of circular RNA from RNA fragments with the use of an EDC/HOBt-based chemical ligation reaction. The synthesized circular RNAs acted as translation templates, despite the presence of unnatural phosphoramidate linkages.

DOI： 10.1039/d0cc02140g

Quantification of native mRNA dynamics in living neurons using fluorescence correlation spectroscopy and reduction-triggered fluorescent probes. 査読有り国際誌 Open Access

Fujita H, Oikawa R, Hayakawa M, Tomoike F, Kimura Y, Okuno H, Hatashita Y, Fiallos Oliveros C, Bito H, Ohshima T, Tsuneda S, Abe H, Inoue T

The Journal of biological chemistry 295 巻 ( 23 ) 頁： 7923 - 7940 2020年6月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Journal of Biological Chemistry

RNA localization in subcellular compartments is essential for spatial and temporal regulation of protein expression in neurons. Several techniques have been developed to visualize mRNAs inside cells, but the study of the behavior of endogenous and nonengineered mRNAs in living neurons has just started. In this study, we combined reduction-triggered fluorescent (RETF) probes and fluorescence correlation spectroscopy (FCS) to investigate the diffusion properties of activity-regulated cytoskeleton-associated protein (Arc) and IP3 receptor isoform 1 (Ip3r1) mRNAs. This approach enabled us to discriminate between RNA-bound and unbound fluorescent probes and to quantify mRNA diffusion parameters and concentrations in living rat primary hippocampal neurons. Specifically, we detected the induction of Arc mRNA production after neuronal activation in real time. Results from computer simulations with mRNA diffusion coefficients obtained in these analyses supported the idea that free diffusion is incapable of transporting mRNA of sizes close to those of Arc or Ip3r1 to distal dendrites. In conclusion, the combined RETF–FCS approach reported here enables analyses of the dynamics of endogenous, unmodified mRNAs in living neurons, affording a glimpse into the intracellular dynamics of RNA in live cells.

DOI： 10.1074/jbc.RA119.010921

A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs. 査読有り国際誌 Open Access

Tian S, Terai G, Kobayashi Y, Kimura Y, Abe H, Asai K, Ui-Tei K

RNA biology 17 巻 ( 2 ) 頁： 264 - 280 2020年2月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：RNA Biology

MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in the regulation of gene function by a mechanism known as RNA silencing. In a previous study, we revealed that miRNA-mediated silencing efficacy is correlated with the combinatorial thermodynamic properties of the miRNA seed–target mRNA duplex and the 5´-terminus of the miRNA duplex, which can be predicted using ‘miScore’. In this study, a robust refined-miScore was developed by integrating the thermodynamic properties of various miRNA secondary structures and the latest thermodynamic parameters of wobble base-pairing, including newly established parameters for I:C base pairing. Through repeated random sampling and machine learning, refined-miScore models calculated with either melting temperature (Tm) or free energy change (ΔG) values were successfully built and validated in both wild-type and adenosine-to-inosine edited miRNAs. In addition to the previously reported contribution of the seed–target duplex and 5´-terminus region, the refined-miScore suggests that the central and 3´-terminus regions of the miRNA duplex also play a role in the thermodynamic regulation of miRNA-mediated silencing efficacy.

DOI： 10.1080/15476286.2019.1678364

Intracellular build-up RNAi with single-strand circular RNAs as siRNA precursors. 査読有り国際誌

Kimura Y, Shu Z, Ito M, Abe N, Nakamoto K, Tomoike F, Shuto S, Ito Y, Abe H

Chemical communications (Cambridge, England) 56 巻 ( 3 ) 頁： 466 - 469 2020年1月

担当区分：筆頭著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Royal Society of Chemistry ({RSC})

We herein report a new approach for RNA interference, so-called "build-up RNAi" approach, where single-strand circular RNAs with a photocleavable unit or disulfide moiety were used as siRNA precursors. The advantages of using these circular RNA formats for RNAi were presented in aspects of immunogenicity and cellular uptake.

DOI： 10.1039/c9cc04872c

SYNTHESIS AND BIOLOGICAL EVALUATION OF NMDI14 DERIVATIVES AS ANTI-MESOTHELIOMA AGENTS 査読有り国際誌

Hong Nhung Nguyen, Suzuki Koya, Kimura Yasuaki, Hirokawa Takatsugu, Murakami-Tonami Yuko, Abe Hiroshi

Heterocycles 100 巻 ( 2 ) 頁： 253 - 266 2020年1月

Translational control by secondary-structure formation in mRNA in a eukaryotic system. 査読有り国際誌 Open Access

Kawaguchi D, Shimizu S, Abe N, Hashiya F, Tomoike F, Kimura Y, Abe H

Nucleosides, nucleotides & nucleic acids 39 巻 ( 1-3 ) 頁： 195 - 203 2020年

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nucleosides, Nucleotides and Nucleic Acids

Eukaryotic mRNA has a cap structure at the 5′ end and a poly(A) tail at the 3′ end. The cap and poly(A) tail form a complex with multiple translation factors, and mRNA forms a circularized structure called a closed-loop model. This circularized structure reportedly not only stabilizes mRNA but also promotes ribosome recycling during translation, which improves translation efficiency. We designed an artificial mRNA that forms a circularized structure without a cap structure and poly(A) tail and found that its translational efficiency was improved compared with that of a sequence without the circularized structure in a eukaryotic translation system.

DOI： 10.1080/15257770.2019.1671593

Intracellular delivery of Antisense DNA and siRNA with amino groups masked with disulfide units 査読有り国際誌

Zhaoma Shu, Azumi Ota, Yukiya Takayama, Yuri Katsurada, Kosuke Kusamori, Naoko Abe, Kosuke Nakamoto, Fumiaki Tomoike, Seiichi Tada, Yoshihiro Ito, Makiya Nishikawa, Yasuaki Kimura, Hiroshi Abe

Chemical and Pharmaceutical Bulletins 68 巻 ( 2 ) 頁： 129 - 132 2019年12月

Disulfide‐Unit Conjugation Enables Ultrafast Cytosolic Internalization of Antisense DNA and siRNA 査読有り国際誌

Zhaoma Shu, Iku Tanaka, Azumi Ota, Daichi Fushihara, Naoko Abe, Saki Kawaguchi, Kosuke Nakamoto, Fumiaki Tomoike, Seiichi Tada, Yoshihiro Ito, Yasuaki Kimura, Hiroshi Abe

Angewandte Chemie 131 巻 ( 20 ) 頁： 6683 2019年5月

A Covalent Inhibitor for Glutathione S-Transferase Pi (GSTP(1-1) ) in Human Cells. 査読有り国際誌

Shishido Y, Tomoike F, Kuwata K, Fujikawa H, Sekido Y, Murakami-Tonami Y, Kameda T, Abe N, Kimura Y, Shuto S, Abe H

Chembiochem : a European journal of chemical biology 20 巻 ( 7 ) 頁： 900 - 905 2019年4月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：ChemBioChem

Glutathione S-transferase π (GSTP 1-1 ) is overexpressed in many types of cancer and is involved in drug resistance. Therefore, GSTP 1-1 is an important target in cancer therapy, and many GST inhibitors have been reported. We had previously developed an irreversible inhibitor, GS-ESF, as an effective GST inhibitor; however, its cellular permeability was too low for it to be used in inhibiting intracellular GST. We have now developed new irreversible inhibitors by introducing sulfonyl fluoride (SF) into chloronitrobenzene (CNB). The mechanism of action was revealed to be that CNBSF first reacts with glutathione (GSH) through an aromatic substitution in the cell, then the sulfonyl group on the GSH conjugate with CNBSF reacts with Tyr108 of GST to form a sulfonyl ester bond. Our new inhibitor irreversible inhibited GSTP 1-1 both in vitro and in cellulo with a long duration of action.

DOI： 10.1002/cbic.201800671

その他リンク： http://orcid.org/0000-0002-3609-602X

膜透過性を有するGST共有結合性阻害剤の開発

友池史明, 宍戸裕子, 藤川遥加, 木村康明, 桑田啓子, 村上優子, 福井健二, 関戸好孝, 矢野貴人, 亀田倫史, 周東智, 阿部洋

日本薬学会年会要旨集 139年会巻 ( 2 ) 頁： 80 - 80 2019年3月

N(6)-methyl adenosine in siRNA evades immune response without reducing RNAi activity. 査読有り国際誌

Imaeda A, Tomoike F, Hayakawa M, Nakamoto K, Kimura Y, Abe N, Abe H

Nucleosides, nucleotides & nucleic acids 38 巻 ( 12 ) 頁： 972 - 979 2019年

Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach 査読有り国際誌

Shun Sakuraba, Junichi Iwakiri, Michiaki Hamada, Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe, Kiyoshi Asai

2018年10月

Chemical ligation reaction for oligonucleotides based on electrophilic phosphorothioester

Kimura Yasuaki, Maruyama Hideto, Oikawa Ryota, Hayakawa Mayu, Abe Naoko, Tsuji Genichiro, Matsuda Akira, Shuto Satoshi, Ito Yoshihiro, Abe Hiroshi

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 255 巻頁： . 2018年3月

Development of glutathione S-transferase (GST) covalent inhibitor

Shishido, Y; Tomoike, F; Kimura, Y; Kuwata, K; Yano, T; Fukui, K; Fujikawa, H; Sekido, Y; Murakami-Tonami, Y; Kameda, T; Shuto, S; Abe, H

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 255 巻頁： . 2018年3月

Chemical ligation reaction for oligonucleotides based on electrophilic phosphorothioester 査読有り国際誌

Kimura Yasuaki, Maruyama Hideto, Oikawa Ryota, Hayakawa Mayu, Abe Naoko, Tsuji Genichiro, Matsuda Akira, Shuto Satoshi, Ito Yoshihiro, Abe Hiroshi

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 255 巻 2018年3月

Chemical Ligation Reactions of Oligonucleotides for Biological and Medicinal Applications

Abe Hiroshi, Kimura Yasuaki

CHEMICAL & PHARMACEUTICAL BULLETIN 66 巻 ( 2 ) 頁： 117-122 2018年2月

Chemical Ligation Reactions of Oligonucleotides for Biological and Medicinal Applications. 査読有り国際誌

Abe H, Kimura Y

Chemical & pharmaceutical bulletin 66 巻 ( 2 ) 頁： 117 - 122 2018年

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Chemical and Pharmaceutical Bulletin

Chemical ligation of oligonucleotides (ONs) is the key reaction for various ON-based technologies. We have tried to solve the problems of RNA interference (RNAi) technology by applying ON chemical ligation to RNAi. We designed a new RNAi system, called intracellular buildup RNAi (IBR-RNAi), where the RNA fragments are built up into active small-interference RNA (siRNA) in cells through a chemical ligation reaction. Using the phosphorothioate and iodoacetyl groups as reactive functional groups for the ligation, we achieved RNAi effects without inducing immune responses. Additionally, we developed a new chemical ligation for IBR-RNAi, which affords a more native-like structure in the ligated product. The new ligation method should be useful not only for IBR-RNAi but also for the chemical synthesis of biofunctional ONs.

DOI： 10.1248/cpb.c17-00615

A covalent G-site inhibitor for glutathione S-transferase Pi (GSTP(1-1)). 査読有り国際誌

Shishido Y, Tomoike F, Kimura Y, Kuwata K, Yano T, Fukui K, Fujikawa H, Sekido Y, Murakami-Tonami Y, Kameda T, Shuto S, Abe H

Chemical communications (Cambridge, England) 53 巻 ( 81 ) 頁： 11138 - 11141 2017年10月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Chemical Communications

We herein report the first covalent G-site-binding inhibitor for GST, GS-ESF (1), which irreversibly inhibited the GSTP1-1 function. LC-MS/MS and X-ray structure analyses of the covalently linked GST-inhibitor complex suggested that 1 reacted with Tyr108 of GSTP1-1. The mechanism of covalent bond formation was discussed based on MD simulation results.

DOI： 10.1039/c7cc05829b

Chemical ligation of oligonucleotides using an electrophilic phosphorothioester. 査読有り国際誌 Open Access

Maruyama H, Oikawa R, Hayakawa M, Takamori S, Kimura Y, Abe N, Tsuji G, Matsuda A, Shuto S, Ito Y, Abe H

Nucleic acids research 45 巻 ( 12 ) 頁： 7042 - 7048 2017年7月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nucleic Acids Research

We developed a new approach for chemical ligation of oligonucleotides using the electrophilic phosphorothioester (EPT) group. A nucleophilic phosphorothioate group on oligonucleotides was converted into the EPT group by treatment with Sanger's reagent (1-fluoro-2,4-dinitrobenzene). EPT oligonucleotides can be isolated, stored frozen, and used for the ligation reaction. The reaction of the EPT oligonucleotide and an amino-modified oligonucleotide took place without any extra reagents at pH 7.0-8.0 at room temperature, and resulted in a ligation product with a phosphoramidate bond with a 39-85% yield. Thismethod has potential uses in biotechnology and chemical biology.

DOI： 10.1093/nar/gkx459

Supramolecular Ligands for Histone Tails by Employing a Multivalent Display of Trisulfonated Calix[4]arenes. 査読有り

Kimura Y, Saito N, Hanada K, Liu J, Okabe T, Kawashima SA, Yamatsugu K, Kanai M

Chembiochem : a European journal of chemical biology 16 巻 ( 18 ) 頁： 2599 - 2604 2015年12月

Catalytic anomeric aminoalkynylation of unprotected aldoses. 査読有り

Kimura Y, Ito S, Shimizu Y, Kanai M

Organic letters 15 巻 ( 16 ) 頁： 4130 - 4133 2013年8月

Inhibition of MAO-A and stimulation of behavioural activities in mice by the inactive prodrug form of the anti-influenza agent oseltamivir. 査読有り

Hiasa M, Isoda Y, Kishimoto Y, Saitoh K, Kimura Y, Kanai M, Shibasaki M, Hatakeyama D, Kirino Y, Kuzuhara T

British journal of pharmacology 169 巻 ( 1 ) 頁： 115 - 129 2013年5月

Design and Synthesis of Resin-Conjugated Tamiflu Analogs for Affinity Chromatography 査読有り

Yasuaki Kimura, Kenzo Yamatsugu, Motomu Kanai, Noriko Echigo, Takashi Kuzuhara, Masakatsu Shibasaki

BULLETIN OF THE KOREAN CHEMICAL SOCIETY 31 巻 ( 3 ) 頁： 588 - 594 2010年3月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：KOREAN CHEMICAL SOC

Two types of resin-conjugated Tamiflu analogs were synthesized by modifying our original synthetic route of oseltamivir phosphate (Tamiflu). The prepared resins bound to influenza virus neuraminidase, the main target of Tamiflu. The resins will be useful for isolating and identifying presumed endogenous vertebrate proteins that interact with Tamiflu, which might relate to the rarely observed abnormal behavior exhibited by some influenza patients treated with Tamiflu.

DOI： 10.5012/bkcs.2010.31.03.588

Design and synthesis of immobilized Tamiflu analog on resin for affinity chromatography 査読有り

Yasuaki Kimura, Kenzo Yamatsugu, Motomu Kanai, Noriko Echigo, Takashi Kuzuhara, Masakatsu Shibasaki

TETRAHEDRON LETTERS 50 巻 ( 26 ) 頁： 3205 - 3208 2009年7月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：PERGAMON-ELSEVIER SCIENCE LTD

A resin linked with the Tamiflu core was synthesized by modifying our original synthetic route Of oseltamivir phosphate (Tamiflu). The prepared resin bound to the influenza virus enzyme neuraminidase, the main target of Tamiflu. The immobilized Tamiflu analog will be useful for isolating and identifying presumed endogenous vertebrate proteins that interact with Tamiflu, which might relate to the abnormal behavior exhibited by some influenza patients treated with Tamiflu. (C) 2009 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.tetlet.2009.01.142

A synthesis of Tamiflu by using a barium-catalyzed asymmetric Diels-Alder-type reaction. 査読有り

Yamatsugu K, Yin L, Kamijo S, Kimura Y, Kanai M, Shibasaki M

Angewandte Chemie (International ed. in English) 48 巻 ( 6 ) 頁： 1070 - 1076 2009年

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