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Kennelly S, Sawyer JM, Payne AF, Ciota AT, Harki DA. Development of 3'-Deoxy-3',4'-didehydro-nucleoside Prodrug Inhibitors of West Nile and Zika Viruses. ACS Med Chem Lett 2024; 15:1334-1339. [PMID: 39140046 PMCID: PMC11318099 DOI: 10.1021/acsmedchemlett.4c00225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/16/2024] [Accepted: 06/26/2024] [Indexed: 08/15/2024] Open
Abstract
The antiviral enzyme viperin catalyzes the formation of 3'-deoxy-3',4'-didehydro-cytidine-5'-triphosphate (ddhCTP). ddhCTP is incorporated into viral genomes and terminates genomic replication to confer broad-spectrum antiviral effects. We have previously utilized phosphoramidate pronucleotide (ProTide) technology to enable metabolic production of ddhCTP in cells from an exogenously dosed 3'-deoxy-3',4'-didehydro-cytidine ProTide, which confers inhibitory activity against West Nile virus (WNV) and Zika virus (ZIKV). Herein, we synthesized 3'-deoxy-3',4'-didehydro-nucleosides containing all native nucleobases (thymine, uracil, adenine, guanine, and hypoxanthine), elaborated each to a ProTide, and measured their activity for controlling WNV and ZIKV infection. In comparison to the ddhC ProTide, we found that the ProTides of 3'-deoxy-3',4'-didehydro-guanosine and 3'-deoxy-3',4'-didehydro-adenosine possess 2- and 4-fold greater antiviral effects against ZIKV, respectively. Collectively, this work advances the development of 3'-deoxy-3',4'-didehydro nucleosides as promising compounds for further development into broad-spectrum antiviral agents.
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Affiliation(s)
- Samantha
A. Kennelly
- Department
of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - Jacob M. Sawyer
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Anne F. Payne
- Department
of Biomedical Sciences, State University
of New York at Albany School of Public Health, Albany, New York 12144, United States
- The
Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, New York 12201, United States
| | - Alexander T. Ciota
- Department
of Biomedical Sciences, State University
of New York at Albany School of Public Health, Albany, New York 12144, United States
- The
Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, New York 12201, United States
| | - Daniel A. Harki
- Department
of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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Verardo D, Adelizzi B, Rodriguez-Pinzon DA, Moghaddam N, Thomée E, Loman T, Godron X, Horgan A. Multiplex enzymatic synthesis of DNA with single-base resolution. SCIENCE ADVANCES 2023; 9:eadi0263. [PMID: 37418522 PMCID: PMC10328407 DOI: 10.1126/sciadv.adi0263] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
Enzymatic DNA synthesis (EDS) is a promising benchtop and user-friendly method of nucleic acid synthesis that, instead of solvents and phosphoramidites, uses mild aqueous conditions and enzymes. For applications such as protein engineering and spatial transcriptomics that require either oligo pools or arrays with high sequence diversity, the EDS method needs to be adapted and certain steps in the synthesis process spatially decoupled. Here, we have used a synthesis cycle comprising a first step of site-specific silicon microelectromechanical system inkjet dispensing of terminal deoxynucleotidyl transferase enzyme and 3' blocked nucleotide, and a second step of bulk slide washing to remove the 3' blocking group. By repeating the cycle on a substrate with an immobilized DNA primer, we show that microscale spatial control of nucleic acid sequence and length is possible, which, here, are assayed by hybridization and gel electrophoresis. This work is distinctive for enzymatically synthesizing DNA in a highly parallel manner with single base control.
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Affiliation(s)
| | | | | | | | | | - Tessa Loman
- DNA Script, 67 Avenue de Fontainebleau, 94270 Le Kremlin-Bicêtre, France
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Higashi SL, Shintani Y, Ikeda M. Installing Reduction Responsiveness into Biomolecules by Introducing Nitroaryl Groups. Chemistry 2022; 28:e202201103. [DOI: 10.1002/chem.202201103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Sayuri L. Higashi
- United Graduate School of Drug Discovery and Medical Information Sciences Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Present address: Institut für Physiologische Chemie und Pathobiochemie Universität Münster Waldeyerstraße 15 48149 Münster Germany
| | - Yuki Shintani
- Department of Life Science and Chemistry Graduate School of Natural Science and Technology Gifu University 1-1 Yanagido Gifu 501-1193 Japan
| | - Masato Ikeda
- United Graduate School of Drug Discovery and Medical Information Sciences Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Department of Life Science and Chemistry Graduate School of Natural Science and Technology Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Institute for Glyco-core Research (iGCORE) Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Institute of Nano-Life-Systems Institutes of Innovation for Future Society Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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Saneyoshi H, Nakamura K, Terasawa K, Ono A. A Bioreductive Protecting Group for RNA Synthesis. Curr Protoc 2021; 1:e240. [PMID: 34499818 DOI: 10.1002/cpz1.240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This protocol describes a method for the preparation of ribonucleoside phosphoramidite bearing a bioreductive protecting group on the 2'-OH group and its application in the synthesis of bioreduction-responsive oligonucleotides. The protecting group used in this method consists of the modified 4-nitrobenzyl skeleton, which has gem-dimethyl groups at benzylic positions to enable deprotection under physiological conditions. Applying the synthesized ribonucleoside phosphoramidite to solid-phase synthesis of oligonucleotides, a 2'-O-protected oligonucleotide was obtained without any undesirable cleavages under standard oligonucleotide synthesis conditions. The 2'-O-protected oligonucleotide was then treated with a combination of nitroreductase (Escherichia coli) and NADH as a bioreduction system for cleavage of the 2'-O-protecting group. After reduction of the nitro group, the protecting group was deprotected in a time-dependent manner. Thus, this protection technology is a potential new tool for production of reduction-responsive RNA-based materials that can be used in life and medical sciences. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of ribonucleoside phosphoramidite bearing a bioreductive protecting group Basic Protocol 2: Synthesis of 2'-O-protected oligonucleotides and their deprotection properties under bioreduction.
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Affiliation(s)
- Hisao Saneyoshi
- Department of Chemistry, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Kodai Nakamura
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, Yokohama, Japan
| | - Kazuma Terasawa
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, Yokohama, Japan
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, Yokohama, Japan
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