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Hatano A, Matsuzaka R, Shimane G, Wakana H, Suzuki K, Nishioka C, Kojima A, Kidowaki M. Introduction of pseudo-base benzimidazole derivatives into nucleosides via base exchange by a nucleoside metabolic enzyme. Bioorg Med Chem 2023; 91:117411. [PMID: 37451053 DOI: 10.1016/j.bmc.2023.117411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
In alternate organic synthesis, biocatalysis using enzymes provides a more stereoselective and cost-effective approach. Synthesis of unnatural nucleosides by nucleoside base exchange reactions using nucleoside-metabolizing enzymes has previously shown that the 5-position recognition of pyrimidine bases on nucleoside substrates is loose and can be used to introduce functional molecules into pyrimidine nucleosides. Here we explored the incorporation of purine pseudo bases into nucleosides by the base exchange reaction of pyrimidine nucleoside phosphorylase (PyNP), demonstrating that an imidazole five-membered ring is an essential structure for the reaction. In the case of benzimidazole, the base exchange proceeded to give the deoxyribose form in 96 % yield, and the ribose form in 23 % yield. The reaction also proceeded with 1H-imidazo[4,5-b]phenazine, a benzimidazole analogue with an additional ring, although the yield of nucleoside was only 31 %. Docking simulations between 1H and imidazo[4,5-b]phenazine nucleoside and the active site of PyNP (PDB 1BRW) supported our observation that 1H-imidazo[4,5-b]phenazine can be used as a substrate by PyNP. Thus, the enzymatic substitution reaction using PyNP can be used to incorporate many purine pseudo bases and benzimidazole derivatives with various functional groups into nucleoside structures, which have potential utility as diagnostic or therapeutic agents.
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Affiliation(s)
- Akihiko Hatano
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan.
| | - Riki Matsuzaka
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Genki Shimane
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Hiroyuki Wakana
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Kou Suzuki
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Chisato Nishioka
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Aoi Kojima
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Masatoshi Kidowaki
- Department of Applied Chemistry, Shibaura Institute of Technology, 3-7-5, Toyosu, Koto-ku, Tokyo 135-8548, Japan
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2
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Gong Y, Chen L, Zhang W, Salter R. Transglycosylation in the Modification and Isotope Labeling of Pyrimidine Nucleosides. Org Lett 2020; 22:5577-5581. [PMID: 32628494 DOI: 10.1021/acs.orglett.0c01941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transglycosylation of pyrimidine nucleosides is demonstrated in a one-pot synthesis of uridine derivatives under microwave irradiation. Inductive activation of 2',3',5'-tri-O-acetyl uridine with a 5-nitro group produces a more-reactive glycosyl donor. Under optimized Vorbrüggen conditions, the 5-nitrouridine facilitates a reversible nucleobase exchange with a series of 5-substituted uracils. The protocol is also exemplified in a gram-scale reaction under thermal heating. The strategy provides easy access to isotopically labeled uridine.
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Affiliation(s)
- Yong Gong
- Discovery Sciences, Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Lu Chen
- Discovery Sciences, Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Wei Zhang
- Discovery Sciences, Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Rhys Salter
- Discovery Sciences, Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
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3
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Wen Z, Tuttle PR, Howlader AH, Vasilyeva A, Gonzalez L, Tangar A, Lei R, Laverde EE, Liu Y, Miksovska J, Wnuk SF. Fluorescent 5-Pyrimidine and 8-Purine Nucleosides Modified with an N-Unsubstituted 1,2,3-Triazol-4-yl Moiety. J Org Chem 2019; 84:3624-3631. [PMID: 30806513 DOI: 10.1021/acs.joc.8b03135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Cu(I)- or Ag(I)-catalyzed cycloaddition between 8-ethynyladenine or guanine nucleosides and TMSN3 gave 8-(1- H-1,2,3-triazol-4-yl) nucleosides in good yields. On the other hand, reactions of 5-ethynyluracil or cytosine nucleosides with TMSN3 led to the chemoselective formation of triazoles via Cu(I)-catalyzed cycloaddition or vinyl azides via Ag(I)-catalyzed hydroazidation. These nucleosides with a minimalistic triazolyl modification showed excellent fluorescent properties with 8-(1- H-1,2,3-triazol-4-yl)-2'-deoxyadenosine (8-TrzdA), exhibiting a quantum yield of 44%. The 8-TrzdA 5'-triphosphate was incorporated into duplex DNA containing a one-nucleotide gap by DNA polymerase β.
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Affiliation(s)
- Zhiwei Wen
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Paloma R Tuttle
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - A Hasan Howlader
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Anna Vasilyeva
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Laura Gonzalez
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Antonija Tangar
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Ruipeng Lei
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Eduardo E Laverde
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Yuan Liu
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Stanislaw F Wnuk
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
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4
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Elgemeie GH, Alkhursani SA, Mohamed RA. New synthetic strategies for acyclic and cyclic pyrimidinethione nucleosides and their analogues. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:12-87. [PMID: 30729891 DOI: 10.1080/15257770.2018.1498511] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pyrimidinethione nucleosides are effective compounds and have significant and pivotal effects in several fields. New synthetic strategies for many pyrimidinethione nucleosides including acyclic and cyclic derivatives have been reported.
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Affiliation(s)
- Galal H Elgemeie
- a Chemistry Department, Faculty of Science , Helwan University , Helwan , Cairo , Egypt
| | - Sheikha A Alkhursani
- b Chemistry Department, Girls College of Science , Immam Abdulrahman Bin Faisal University , Dammam , Kingdom of Saudi Arabia
| | - Reham A Mohamed
- c Chemistry of Natural and Microbial Products Department, National Research Center , Dokki , Cairo , Egypt
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5
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Hatano A, Wakana H, Terado N, Kojima A, Nishioka C, Iizuka Y, Imaizumi T, Uehara S. Bio-catalytic synthesis of unnatural nucleosides possessing a large functional group such as a fluorescent molecule by purine nucleoside phosphorylase. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01063g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Unnatural nucleosides are attracting interest as potential diagnostic tools, medicines, and functional molecules.
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Affiliation(s)
- Akihiko Hatano
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Hiroyuki Wakana
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Nanae Terado
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Aoi Kojima
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Chisato Nishioka
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Yu Iizuka
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Takuya Imaizumi
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
| | - Sanae Uehara
- Department of Chemistry
- Shibaura Institute of Technology
- Saitama
- Japan
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6
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Ferraboschi P, Ciceri S, Grisenti P. Synthesis of Antitumor Fluorinated Pyrimidine Nucleosides. ORG PREP PROCED INT 2017. [DOI: 10.1080/00304948.2017.1290994] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Hatano A, Shiraishi M, Terado N, Tanabe A, Fukuda K. Enzymatic synthesis and RNA interference of nucleosides incorporating stable isotopes into a base moiety. Bioorg Med Chem 2015; 23:6683-8. [PMID: 26404411 DOI: 10.1016/j.bmc.2015.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 11/25/2022]
Abstract
Thymidine phosphorylase was used to catalyze the conversion of thymidine (or methyluridine) and uracil incorporating stable isotopes to deoxyuridine (or uridine) with the uracil base incorporating the stable isotope. These base-exchange reactions proceeded with high conversion rates (75-96%), and the isolated yields were also good (64-87%). The masses of all synthetic compounds incorporating stable isotopes were identical to the theoretical molecular weights via EIMS. (13)C NMR spectra showed spin-spin coupling between (13)C and (15)N in the synthetic compounds, and the signals were split, further proving incorporation of the isotopes into the compounds. The RNA interference effects of this siRNA with uridine incorporating stable isotopes were also investigated. A 25mer siRNA had a strong knockdown effect on the MARCKS protein. The insertion position and number of uridine moieties incorporating stable isotopes introduced into the siRNA had no influence on the silencing of the target protein. This incorporation of stable isotopes into RNA and DNA has the potential to function as a chemically benign tracer in cells.
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Affiliation(s)
- Akihiko Hatano
- Department of Chemistry, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan.
| | - Mitsuya Shiraishi
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Nanae Terado
- Department of Chemistry, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Atsuhiro Tanabe
- Department of Chemistry, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Kenji Fukuda
- Taiyo Nippon Sanso Corp., 10 Okubo, Tsukuba-shi, Ibaragi 300-2611, Japan
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