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Jia X, Kullik GA, Bufano M, Brancale A, Schols D, Meier C. Membrane-permeable tenofovir-di- and monophosphate analogues. Eur J Med Chem 2024; 264:116020. [PMID: 38086193 DOI: 10.1016/j.ejmech.2023.116020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023]
Abstract
The development of new antiviral agents such as nucleoside analogues or acyclic nucleotide analogues (ANPs) and prodrugs thereof is an ongoing task. We report on the synthesis of three types of lipophilic triphosphate analogues of (R)-PMPA and dialkylated diphosphate analogues of (R)-PMPA. A highly selective release of the different nucleotide analogues ((R)-PMPA-DP, (R)-PMPA-MP, and (R)-PMPA) from these compounds was achieved. All dialkylated (R)-PMPA-prodrugs proved to be very stable in PBS as well as in CEM/0 cell extracts and human plasma. In primer extension assays, both the monoalkylated and the dialkylated (R)-PMPA-DP derivatives acted as (R)-PMPA-DP as a substrate for HIV-RT. In contrast, no incorporation events were observed using human polymerase γ. The dialkylated (R)-PMPA-compounds exhibited significant anti-HIV efficacy in HIV-1/2 infected cells (CEM/0 and CEM/TK-). Remarkably, the dialkylated (R)-PMPA-MP derivative 9a showed a 326-fold improved activity as compared to (R)-PMPA in HIV-2 infected CEM/TK- cells as well as a very high SI of 14,000. We are convinced that this study may significantly contribute to advancing antiviral agents developed based on nucleotide analogues in the future.
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Affiliation(s)
- Xiao Jia
- Organic Chemistry, Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany
| | - Giuliano A Kullik
- Organic Chemistry, Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany
| | - Marianna Bufano
- Dipartimento Chimica e Tecnologie del Farmaco, Facoltà di Farmacia e Medicina, University of Rome "La Sapienza", Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Andrea Brancale
- Department of Organic Chemistry, Vysoká Škola Chemicko-Technologická v Praze, Technická 5, 16628, Prague, Czech Republic
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Chris Meier
- Organic Chemistry, Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany; Centre for Structural Systems Biology (CSSB), Hamburg, DESY Campus, Notkestrasse 85, D-22607, Hamburg, Germany.
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2
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Dhurbachandra Singh C, Morshed Alom K, Kumar Kannan D, Simander Singh T, Samantaray S, Siddappa Ravi Kumara G, Jun Seo Y. mRNA incorporation of C(5)-halogenated pyrimidine ribonucleotides and induced high expression of corresponding protein for the development of mRNA vaccine. Bioorg Chem 2023; 141:106897. [PMID: 37793265 DOI: 10.1016/j.bioorg.2023.106897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023]
Abstract
In this report, we present our studies on mRNA, which was modified by introducing various halogen substituents at the C(5) position of the pyrimidine base. Specifically, we synthesized C(5)-halogenated (F, Cl, Br, I) pyrimidine ribonucleoside triphosphates and incorporated them into mRNA during in-vitro transcription. The efficiency of the in-vitro transcription reaction of halogenated pyrimidine was observed to decrease as the size of the halogen substituent increased and the electronegativity thereof decreased (F > Cl > Br) except for iodine. Interestingly, we found that, among the C(5)-halogenated pyrimidine ribonucleotides, mRNA incorporating C(5)-halogenated cytidine (5-F rCTP and 5-Cl rCTP) exhibited more prominent protein expression than mRNA modified with C(5)-halogenated uridine and unmodified mRNA. In particular, in the case of mRNA to which fluorine (5-F rCTP) and chlorine (5-Cl rCTP) were introduced, the protein was dramatically expressed about 4 to 5 times more efficiently than the unmodified mRNA, which was similar to pseudouridine (ψ). More interestingly, when pseudouridine(ψ) and fluorocytidine nucleotides (5-F rCTP), were simultaneously introduced into mRNA for dual incorporation, the protein expression efficiency dramatically increased as much as tenfold. The efficiency of cap-dependent protein expression is much higher than the IRES-dependent (internal ribosome entry site) expression with mRNA incorporating C(5)-halogenated pyrimidine ribonucleotide. We expect these results to contribute meaningfully to the development of therapeutics based on modified mRNA.
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Affiliation(s)
| | - Kazi Morshed Alom
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea
| | - Dinesh Kumar Kannan
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea
| | | | | | | | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea.
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3
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Lášek T, Dobiáš J, Buděšínský M, Kozák J, Lapuníková B, Rosenberg I, Birkuš G, Páv O. Synthesis of phosphonate derivatives of 2'-deoxy-2'-fluorotetradialdose d-nucleosides and tetradialdose d-nucleosides. Tetrahedron 2021; 89:132159. [PMID: 33879930 PMCID: PMC8049856 DOI: 10.1016/j.tet.2021.132159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/02/2021] [Accepted: 04/09/2021] [Indexed: 11/24/2022]
Abstract
Analogs of nucleosides and nucleotides represent a promising pool of potential therapeutics. This work describes a new synthetic route leading to 2'-deoxy-2'-fluorotetradialdose D-nucleoside phosphonates. Moreover, a new universal synthetic route leading to tetradialdose d-nucleosides bearing purine nucleobases is also described. All new compounds were tested as triphosphate analogs for inhibitory potency against a variety of viral polymerases. The fluorinated nucleosides were transformed to phosphoramidate prodrugs and evaluated in cell cultures against various viruses including influenza and SARS-CoV-2.
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Affiliation(s)
- Tomáš Lášek
- IOCB Prague, Flemingovo Nám. 2, 160 00, Prague, Czech Republic.,UCT Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Juraj Dobiáš
- IOCB Prague, Flemingovo Nám. 2, 160 00, Prague, Czech Republic
| | | | - Jaroslav Kozák
- IOCB Prague, Flemingovo Nám. 2, 160 00, Prague, Czech Republic
| | | | - Ivan Rosenberg
- IOCB Prague, Flemingovo Nám. 2, 160 00, Prague, Czech Republic
| | - Gabriel Birkuš
- IOCB Prague, Flemingovo Nám. 2, 160 00, Prague, Czech Republic
| | - Ondřej Páv
- IOCB Prague, Flemingovo Nám. 2, 160 00, Prague, Czech Republic
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Iammarino M, Haouet N, Di Taranto A, Berardi G, Benedetti F, Di Bella S, Chiaravalle AE. The analytical determination of polyphosphates in food: A point-to-point comparison between direct ion chromatography and indirect photometry. Food Chem 2020; 325:126937. [PMID: 32387985 DOI: 10.1016/j.foodchem.2020.126937] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/25/2020] [Accepted: 04/26/2020] [Indexed: 10/24/2022]
Abstract
Being an indirect approach, the standard method for the determination of polyphosphates (PPs) in food maybe characterized by high variability which can lead to significant errors in the final measurement. In this study, this method was validated and then compared to the ion chromatography-based approach. Method trueness and measurement uncertainty resulted comparable, while the precision of ion chromatography approach was higher. No "false positive" responses were obtained from ion chromatography analysis, while indirect photometry may cause "false positive" results (5% of analyzed samples). Regarding "false negative" results, this possibility maybe verified for all food types tested and for seafood when using indirect photometry and ion chromatography, respectively. The percentages of "false negative" samples were equal to 23.3% for indirect photometry and 10% for ion chromatography. In conclusion, the indirect photometry is a reliable method especially as "screening technique", while ion chromatography maybe used as a confirmatory technique, successfully.
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Affiliation(s)
- Marco Iammarino
- Chemistry Department, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy.
| | - Naceur Haouet
- Food Control Laboratory, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Via G. Salvemini 1, 06126 Perugia, Italy.
| | - Aurelia Di Taranto
- Chemistry Department, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy.
| | - Giovanna Berardi
- Chemistry Department, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy.
| | - Ferdinando Benedetti
- Food Control Laboratory, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Via G. Salvemini 1, 06126 Perugia, Italy.
| | - Sara Di Bella
- Food Control Laboratory, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Via G. Salvemini 1, 06126 Perugia, Italy.
| | - Antonio Eugenio Chiaravalle
- Chemistry Department, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy.
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Luciano DJ, Belasco JG. Analysis of RNA 5' ends: Phosphate enumeration and cap characterization. Methods 2019; 155:3-9. [PMID: 30419334 DOI: 10.1016/j.ymeth.2018.10.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 12/21/2022] Open
Abstract
The function and fate of cellular RNAs are often governed by the phosphorylation state at the 5' end or the identity of whatever cap may be present there. Here we describe methods for examining these important 5'-terminal features on any cellular or synthetic RNA of interest that can be detected by Northern blotting. One such method, PABLO, is a splinted ligation assay that makes it possible to accurately quantify the percentage of 5' ends that are monophosphorylated. Another, PACO, is a capping assay that reveals the percentage of 5' ends that are diphosphorylated. A third, boronate gel electrophoresis in conjunction with deoxyribozyme-mediated cleavage, enables different types of caps (e.g., m7Gppp caps versus NAD caps) to be distinguished from one another and the percentage of each to be determined. After completing all three tests, the percentage of 5' ends that are triphosphorylated can be deduced by process of elimination. Together, this battery of assays allows the 5' terminus of an RNA to be profiled in unprecedented detail.
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6
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Teixeira B, Vieira H, Mendes R. Polyphosphates changes in dried salted cod ( Gadus morhua) during industrial and domestic processing. J Food Sci Technol 2018; 55:1922-1932. [PMID: 29666545 DOI: 10.1007/s13197-018-3110-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/25/2018] [Accepted: 03/05/2018] [Indexed: 10/17/2022]
Abstract
Changes in added polyphosphates throughout the processing of dried salted cod in industrial environment were evaluated. As consumers purchase both dried salted cod and desalted cod, domestic and industrial desalting processes were performed. After brining, total phosphates increased to 11.6 and 16.6 g P2O5/kg in cod processed with 3 and 6% of polyphosphates, respectively. During dry-salting, total phosphates decreased in both cases to ca. 5 g P2O5/kg, suggesting that most polyphosphates were drained with the water released. Cod with polyphosphates needed 85 h extra drying time to achieve regulatory moisture levels. After desalting, total phosphates values in dry weight indicate that phosphates were not removed during this processing step. Free phosphates, and in particular triphosphate contents, were higher in cods desalted following domestic procedures, in comparison with industrial desalting. This study demonstrates that the use of polyphosphates is not recommended for the production of Portuguese dried salted cod. These additives prevent water from being removed during the drying process, increasing the costs. Moreover, in contrast to what was assumed, part of polyphosphates is retained in the final product, even after the desalting process.
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Affiliation(s)
- Bárbara Teixeira
- Department of Sea and Marine Resources, Portuguese Institute for the Sea and Atmosphere, R. Alfredo Magalhães Ramalho, 6, 1495-006 Lisbon, Portugal.,2Research Unit of Organic Chemistry, Natural and Agro-food Products, Aveiro University, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.,3Interdisciplinary Center of Marine and Environmental Research (CIIMAR), University of Porto, Rua das Bragas 289, 4050-123 Porto, Portugal
| | - Helena Vieira
- Department of Sea and Marine Resources, Portuguese Institute for the Sea and Atmosphere, R. Alfredo Magalhães Ramalho, 6, 1495-006 Lisbon, Portugal
| | - Rogério Mendes
- Department of Sea and Marine Resources, Portuguese Institute for the Sea and Atmosphere, R. Alfredo Magalhães Ramalho, 6, 1495-006 Lisbon, Portugal.,3Interdisciplinary Center of Marine and Environmental Research (CIIMAR), University of Porto, Rua das Bragas 289, 4050-123 Porto, Portugal
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Li E, Wang Y, Yu W, Lv Z, Peng Y, Liu B, Li S, Ho W, Wang Q, Li H, Chang J. Synthesis and biological evaluation of a novel β-D-2'-deoxy-2'-α-fluoro-2'-β-C-(fluoromethyl)uridine phosphoramidate prodrug for the treatment of hepatitis C virus infection. Eur J Med Chem 2017; 143:107-113. [PMID: 29172078 DOI: 10.1016/j.ejmech.2017.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/01/2017] [Accepted: 11/08/2017] [Indexed: 12/15/2022]
Abstract
A novel β-D-2'-deoxy-2'-α-fluoro-2'-β-C-(fluoromethyl)uridine phosphoramidate prodrug (1) has been synthesized. This compound exhibits submicromolar-level antiviral activity in vitro against HCV genotypes 1b, 1a, 2a, and S282T replicons (EC50 = 0.18-1.13 μM) with low cytotoxicity (CC50 > 1000 μM). Administered orally, prodrug 1 is well tolerated at doses of up to 4 g/kg in mice, and produces a high level of the corresponding triphosphate in rat liver.
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Affiliation(s)
- Ertong Li
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Yafeng Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China; Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Wenquan Yu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Zhigang Lv
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Youmei Peng
- Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Bingjie Liu
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wenzhe Ho
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Qingduan Wang
- Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Junbiao Chang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China.
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8
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Kim DR, Kim TS, Kim E, Min SJ, Shin D, Ahn DR. Synthesis of 3'-O-fluorescently mono-modified reversible terminators and their uses in sequencing-by-synthesis. Bioorg Med Chem Lett 2013; 24:209-13. [PMID: 24332495 DOI: 10.1016/j.bmcl.2013.11.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/13/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022]
Abstract
Next-generation sequencing (NGS) technologies recently developed are now used for study of genomes from various organisms. Sequencing-by-synthesis (SBS) is a key strategy in the NGS. The SBS uses nucleotides so-called dual-modified reversible terminators (DRTs) in which bases are labeled with fluorophores and 3'-OH is protected with a reversibly cleavable chemical group, respectively. In this study, we examined the possibility of performing SBS with mono-modified reversible terminators (MRTs), in which the reversible blocking group on the 3'-OH plays a dual role as a fluorescent signal report as well as a chemical protection. We studied cyclic reversible termination by using two MRTs (dA and dT), wherein the modifications were two different fluorophores and cleavable to regenerate a free 3'-OH. We here demonstrated that SBS could be achieved with incorporation of MRTs by a DNA polymerase and correct base-calls based on the two different colors from the fluorophores.
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Affiliation(s)
- Da-Rae Kim
- Center for Theragnosis, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Taek-Soo Kim
- College of Pharmacy, Gachon University, 191 Hambakmoero, Yoensu-Gu, Incheon, Republic of Korea
| | - Eunsun Kim
- Center for Neuro-medicine, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Sun-Joon Min
- Center for Neuro-medicine, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Dongyun Shin
- College of Pharmacy, Gachon University, 191 Hambakmoero, Yoensu-Gu, Incheon, Republic of Korea.
| | - Dae-Ro Ahn
- Center for Theragnosis, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, University of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea.
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