1
|
Gong Y, Zhang W, Chen L, Lin R, Zhou R, Salter R. Nitro-Activated Nucleobase Exchange in the Synthesis of 2'-Fluoro-2'-Deoxyribonucleosides. J Org Chem 2022; 87:9330-9342. [PMID: 35759615 DOI: 10.1021/acs.joc.2c01093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Functionalized nucleosides bearing pyrimidine or purine bases can be prepared by activation of accessible pyrimidine nucleosides and subsequent transglycosylation. Nitration of lumicitabine, a 2'-fluoro-2'-deoxycytidine class antiviral agent, and its 2'-fluoro-2'-deoxyuridine precursor produce the same 5-nitro-2'-fluoro-2'-deoxyuridine. Under Vorbrüggen conditions, 5-nitrouracil serves as the leaving nucleobase and enables exchange with pyrimidine and purine nucleobases to anomeric 2'-fluoro-2'-deoxyribonucleosides in favor of β-anomers generally. The strategy is also applied in the isotopic labeling of 2'-fluoro-2'-deoxyuridines.
Collapse
Affiliation(s)
- Yong Gong
- Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Wei Zhang
- Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Lu Chen
- Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Ronghui Lin
- Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Ronghui Zhou
- Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Rhys Salter
- Janssen Research & Development, Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| |
Collapse
|
2
|
Horie N, Yamaguchi T, Kumagai S, Obika S. Synthesis and properties of oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing adenine, guanine, or 5-methylcytosine nucleobases. Beilstein J Org Chem 2021; 17:622-629. [PMID: 33747234 PMCID: PMC7940814 DOI: 10.3762/bjoc.17.54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/18/2021] [Indexed: 11/23/2022] Open
Abstract
Chemical modifications have been extensively used for therapeutic oligonucleotides because they strongly enhance the stability against nucleases, binding affinity to the targets, and efficacy. We previously reported that oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing the thymine (T) nucleobase show excellent biophysical properties for applications in antisense technology. In this paper, we describe the synthesis of GuNA[Me] phosphoramidites bearing other typical nucleobases including adenine (A), guanine (G), and 5-methylcytosine (mC). The phosphoramidites were successfully incorporated into oligonucleotides following the method previously developed for the GuNA[Me]-T-modified oligonucleotides. The binding affinity of the oligonucleotides modified with GuNA[Me]-A, -G, or -mC toward the complementary single-stranded DNAs or RNAs was systematically evaluated. All of the GuNA[Me]-modified oligonucleotides were found to have a strong affinity for RNAs. These data indicate that GuNA[Me] could be a useful modification for therapeutic antisense oligonucleotides.
Collapse
Affiliation(s)
- Naohiro Horie
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shinji Kumagai
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Fujisaka A, Hari Y, Takuma H, Rahman SMA, Yoshikawa H, Pang J, Imanishi T, Obika S. Effective syntheses of 2',4'-BNA NC monomers bearing adenine, guanine, thymine, and 5-methylcytosine, and the properties of oligonucleotides fully modified with 2',4'-BNA NC. Bioorg Med Chem 2019; 27:1728-1741. [PMID: 30862430 DOI: 10.1016/j.bmc.2019.02.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 12/11/2022]
Abstract
We efficiently synthesized 2'-O,4'-C-aminomethylene-bridged nucleic acid (2',4'-BNANC) monomers bearing the four nucleobases, guanine, adenine, thymine, and 5-methylcytosine and incorporated these monomers into oligonucleotides. Initially, we carried out the transglycosylation reaction on several 2'-O-substituted 5-methyluridines to evaluate the effects of 2'-substitutions on this reaction. Under the optimized conditions, purine nucleobases were successfully introduced, and 2',4'-BNANC monomers bearing adenine or guanine were obtained over several steps. In addition, the improved synthesis of the 2',4'-BNANC monomers bearing thymine or 5-methylcytosine was also achieved. The obtained 2',4'-BNANC monomers were subsequently incorporated into oligonucleotides and the duplex-forming abilities of the modified oligonucleotides were investigated. Duplexes containing 2',4'-BNANC monomers in both or either strands were found to possess excellent thermal stabilities.
Collapse
Affiliation(s)
- Aki Fujisaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Faculty of Pharmacy, Osaka Ohtani University, Nishikiori-Kita 3-11-1, Tondabayashi, Osaka 584-8540, Japan
| | - Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Hiroko Takuma
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - S M Abdur Rahman
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Clinical Pharmacy & Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - Haruhisa Yoshikawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; BNA Inc, 7-7-20 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Juanjuan Pang
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Imanishi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; BNA Inc, 7-7-20 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
5
|
Sawamoto H, Arai Y, Yamakoshi S, Obika S, Kawanishi E. Synthetic Method for 2′-Amino-LNA Bearing Any of the Four Nucleobases via a Transglycosylation Reaction. Org Lett 2018. [DOI: 10.1021/acs.orglett.8b00476] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroaki Sawamoto
- Research Unit/Innovative Medical Science, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Yuuki Arai
- Research Unit/Immunology & Inflammation, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Shuhei Yamakoshi
- Research Unit/Immunology & Inflammation, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiji Kawanishi
- Research Unit/Immunology & Inflammation, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000, Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| |
Collapse
|