Faculty Profiles - ABE Hiroshi

Papers - ABE Hiroshi

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Design of Synthetic mRNAs for Highly Efficient Translation Reviewed

Masahito Inagaki, Mizuki Tada, Hiroshi Abe

Vol. 37 ( 3 ) page： 196 - 208 2022.7

Complete Chemical Synthesis of Minimal Messenger RNA by Efficient Chemical Capping Reaction Reviewed International journal

Naoko Abe, Akihiro Imaeda, Masahito Inagaki, Zhenmin Li, Daisuke Kawaguchi, Kaoru Onda, Yuko Nakashima, Satoshi Uchida, Fumitaka Hashiya, Yasuaki Kimura, Hiroshi Abe

ACS Chemical Biology Vol. 17 ( 6 ) page： 1308 - 1314 2022.5

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)

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

Development of Fluorophosphoramidate as a Biocompatibly Transformable Functional Group and its Application as a Phosphate Prodrug for Nucleoside Analogs. Reviewed International journal

Yuki Yoshida, Ti Zheng, Wataru Tanabe, Fumiaki Tomoike, Fumitaka Hashiya, Tetsuro Suzuki, Shuto Hirota, Yuriko Saiki, Akira Horii, Akiyoshi Hirayama, Tomoyosi Soga, Yasuaki Kimura, Hiroshi Abe

ChemMedChem Vol. 17 ( 17 ) page： e202200188 2022.4

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal)

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

Ligandability Assessment of Human Glutathione Transferase M1-1 Using Pesticides as Chemical Probes. Reviewed International journal

Charoutioun S Bodourian, Nirmal Poudel, Anastassios C Papageorgiou, Mariana Antoniadi, Nikolaos D Georgakis, Hiroshi Abe, Nikolaos E Labrou

International journal of molecular sciences Vol. 23 ( 7 ) 2022.3

Language：English Publishing type：Research paper (scientific journal)

Glutathione transferases (GSTs; EC 2.5.1.18) form a group of multifunctional enzymes that are involved in phase II of the cellular detoxification mechanism and are associated with increased susceptibility to cancer development and resistance to anticancer drugs. The present study aims to evaluate the ligandability of the human GSTM1-1 isoenzyme (hGSTM1-1) using a broad range of structurally diverse pesticides as probes. The results revealed that hGSTM1-1, compared to other classes of GSTs, displays limited ligandability and ligand-binding promiscuity, as revealed by kinetic inhibition studies. Among all tested pesticides, the carbamate insecticide pirimicarb was identified as the strongest inhibitor towards hGSTM1-1. Kinetic inhibition analysis showed that pirimicarb behaved as a mixed-type inhibitor toward glutathione (GSH) and 1-chloro-2,4-dinitrobenzene (CDNB). To shine a light on the restricted hGSTM1-1 ligand-binding promiscuity, the ligand-free crystal structure of hGSTM1-1 was determined by X-ray crystallography at 1.59 Å-resolution. Comparative analysis of ligand-free structure with the available ligand-bound structures allowed for the study of the enzyme's plasticity and the induced-fit mechanism operated by hGSTM1-1. The results revealed important structural features of the H-site that contribute to xenobiotic-ligand binding and specificity. It was concluded that hGSTM1-1 interacts preferentially with one-ring aromatic compounds that bind at a discrete site which partially overlaps with the xenobiotic substrate binding site (H-site). The results of the study form a basis for the rational design of new drugs targeting hGSTM1-1.

DOI： 10.3390/ijms23073606

Design of Synthetic mRNAs for Highly Ef ficient Translation Invited Reviewed Open Access

Inagaki M., Tada M., Abe H.

Drug Delivery System Vol. 37 ( 3 ) page： 196 - 208 2022

Authorship：Last author,　Corresponding author Language：Japanese Publishing type：Research paper (conference, symposium, etc.) Publisher：Drug Delivery System

Recently messenger RNA （mRNA）therapeutics is received much attention as one of the vaccination therapies to compete against the coronavirus disease 2019（COVID-19）pandemic. DDS mRNA therapeutics are generally produced by in vitro transcription utilizing RNA polymerase mediated elongation. However, its purity, stability, and protein synthesis ability, are difficult to be precisely controlled, which is pointed out as drawbacks that must be overcome. To overcome these issues, the introduction of chemically modified nucleic acids is focusing attention. However, it is difficult to flexible molecular design due to the requirement of RNA polymerase recognition ability of chemically modified nucleic acids under in vitro transcription reaction. In the future, the development of a new mRNA design concept based on a flexible molecular design by the progress of chemically modified mRNA therapeutics synthesis method. Under the situation, the authors are focusing on the translation mechanism of mRNA and proposing a new mRNA molecular design to accelerate the translation reaction cycle. In this paper, we introduce an update on therapeutic mRNA design.

DOI： 10.2745/dds.37.196

Open Access

Scopus

Complete chemical synthesis of long DNA transcriptable in human cells

Kazuki Yamaoka, Ryota Oikawa, Naoko Abe, Kosuke Nakamoto, Fumiaki Tomoike, Fumitaka Hashiya, Yasuaki Kimura, Hiroshi Abe

ChemBioChem Vol. 22 ( 23 ) page： 3273 - 3276 2021.12

Antisense Oligonucleotide Modified with Disulfide Units Induces Efficient Exon Skipping in <i>mdx</i> Myotubes through Enhanced Membrane Permeability and Nucleus Internalization Reviewed

Haruka Hiraoka, Zhaoma Shu, Bao Tri Le, Keiko Masuda, Kosuke Nakamoto, Lyu Fangjie, Naoko Abe, Fumitaka Hashiya, Yasuaki Kimura, Yoshihiro Shimizu, Rakesh N. Veedu, Hiroshi Abe

ChemBioChem Vol. 22 ( 24 ) page： 3437 - 3442 2021.10

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Wiley

DOI： 10.1002/cbic.202100413

Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/cbic.202100413

Variety of nucleotide polymerase mutants aiming to synthesize modified RNA Reviewed International journal

Sana Ohashi, Fumitaka Hashiya, Hiroshi Abe

ChemBioChem Vol. 22 ( 14 ) page： 2398 - 2406 2021.4

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Wiley

Significant efforts have been made to develop therapeutic RNA aptamers that exploit synthetic RNA to capture target molecules. However, ensuring RNA aptamers are resistant against intrinsic nucleases remains an issue and restricts their use as therapeutics. Introduction of chemical modifications to the 2' sugar moiety of RNA improves their stability effectively and can be achieved by chemical synthesis using modified phosphoramidites; however, this approach is not suitable for preparing long RNA molecules. Although recombinant nucleotide polymerases can transcribe RNA, these polymerases cannot synthesize modified RNA because they do not recognize 2' modified nucleoside triphosphates. In this review, we focus on several polymerase mutants that tolerate substrates containing modifications of the 2' sugar moiety to synthesize RNA, and the problems that must be overcome to prepare chemically modified RNA with high efficacy by in vitro transcription.

DOI： 10.1002/cbic.202100004

Structure, Synthesis and Inhibition Mechanism of Nucleoside Analogues as HIV‐1 Reverse Transcriptase Inhibitors (NRTIs) Reviewed International journal

Yuki Yoshida, Masakazu Honma, Yasuaki Kimura, Hiroshi Abe

ChemMedChem Vol. 16 ( 5 ) page： 743 - 766 2021.3

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Wiley

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

Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/cmdc.202000695

Chemical Synthesis of Circular RNAs with Phosphoramidate Linkages for Rolling‐Circle Translation

Kosuke Nakamoto, Hiroshi Abe

Current Protocols Vol. 1 ( 3 ) page： e43 2021.3

化学修飾核酸の合成と核酸医薬への応用

野村浩平, 村瀬裕貴, 中本航介, 木村康明, 阿部奈保子, 安成鎮, 小林芳明, 程久美子, 阿部洋

日本薬学会年会要旨集 Vol. 141年会 page： 27V05 - pm02S 2021.3

Phosphorothioate Modification of mRNA Accelerates Rate of Translation Initiation Providing More Efficient Protein Synthesis Reviewed

Hiroshi Abe, Daisuke Kawaguchi, Ayumi Kodama, Naoko Abe, Kei Takebuchi, Fumitaka Hashiya, Fumiaki Tomoike, Kousuke Nakamoto, Yasuaki Kimura, Yoshihiro Shimizu

Angewandte Chemie International Edition Vol. 59 ( 40 ) page： 17403 - 17407 2020.9

Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters

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

Journal of Chemical Theory and Computation Vol. 16 ( 9 ) page： 5923 - 5935 2020.9

Developments in siRNA Modification and Ligand Conjugated Delivery To Enhance RNA Interference Ability. International journal

Ander Maguregui, Hiroshi Abe

Chembiochem : a European journal of chemical biology Vol. 21 ( 13 ) page： 1808 - 1815 2020.7

Language：English Publishing type：Research paper (scientific journal)

There is great potential for siRNA in the treatment of diseases through the reduction of damaging protein translation by RNA interference. However, the delivery and cell uptake of siRNA pose a serious problem in its therapeutic application. Methods to overcome this issue include chemical modification of the siRNA duplex to improve pharmacokinetics, stability and efficacy, and conjugation to small ligand molecules to enable membrane penetration, targetability and potency. In this review, the most common modifications of siRNA will be discussed, along with ligand conjugates that are believed to be the most promising in advancing the field of targeted siRNA delivery.

DOI： 10.1002/cbic.202000009

Chemically synthesized circular RNAs with phosphoramidate linkages enable rolling circle translation Reviewed

Kosuke Nakamoto, Naoko Abe, Genichiro Tsuji, Yasuaki Kimura, Fumiaki Tomoike, Yoshihiro Shimizu, Hiroshi Abe

Chemical Communications Vol. 56 ( 46 ) page： 6217 - 6220 2020.6

Quantification of native mRNA dynamics in living neurons using fluorescence correlation spectroscopy and reduction-triggered fluorescent probes Reviewed

Fujita Hirotaka, Oikawa Ryota, Hayakawa Mayu, Tomoike Fumiaki, Kimura Yasuaki, Okuno Hiroyuki, Hatashita Yoshiki, Fiallos Oliveros Carolina, Bito Haruhiko, Ohshima Toshio, Tsuneda Satoshi, Abe Hiroshi, Inoue Takafumi

JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 295 ( 23 ) page： 7923 - 7940 2020.6

Disulfide-unit Conjugation Enables Ultrafast Cytosolic Internalization of Antisense DNA and siRNA Reviewed

Nakamoto Kosuke, Shu Zhaoma, Abe Hiroshi

JOURNAL OF SYNTHETIC ORGANIC CHEMISTRY JAPAN Vol. 78 ( 5 ) page： 456 - 464 2020.5

Translational control by secondary-structure formation in mRNA in a eukaryotic system

Kawaguchi Daisuke, Shimizu Saaya, Abe Naoko, Hashiya Fumitaka, Tomoike Fumiaki, Kimura Yasuaki, Abe Hiroshi

NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS Vol. 39 ( 1-3 ) page： 195 - 203 2020.2

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

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

HETEROCYCLES Vol. 100 ( 2 ) page： 253 - 266 2020.2

A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs Reviewed

Tian Shen, Terai Goro, Kobayashi Yoshiaki, Kimura Yasuaki, Abe Hiroshi, Asai Kiyoshi, Ui-Tei Kumiko

RNA BIOLOGY Vol. 17 ( 2 ) page： 264 - 280 2020.2

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Papers - ABE Hiroshi