1
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Dillenburg M, Smith J, Wagner CR. The Many Faces of Histidine Triad Nucleotide Binding Protein 1 (HINT1). ACS Pharmacol Transl Sci 2023; 6:1310-1322. [PMID: 37854629 PMCID: PMC10580397 DOI: 10.1021/acsptsci.3c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Indexed: 10/20/2023]
Abstract
The histidine triad nucleotide binding protein 1 (HINT1) is a nucleoside phosphoramidase that has garnered interest due to its widespread expression and participation in a broad range of biological processes. Herein, we discuss the role of HINT1 as a regulator of several CNS functions, tumor suppressor, and mast cell activator via its interactions with multiple G-protein-coupled receptors and transcription factors. Importantly, altered HINT1 expression and mutation are connected to the progression of multiple disease states, including several neuropsychiatric disorders, peripheral neuropathy, and tumorigenesis. Additionally, due to its involvement in the activation of several clinically used phosphoramidate prodrugs, tremendous efforts have been made to better understand the interactions behind nucleoside binding and phosphoramidate hydrolysis by HINT1. We detail the substrate specificity and catalytic mechanism of HINT1 hydrolysis, while highlighting the structural biology behind these efforts. The aim of this review is to summarize the multitude of biological and pharmacological functions in which HINT1 participates while addressing the areas of need for future research.
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Affiliation(s)
- Maxwell Dillenburg
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jacob Smith
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carston R Wagner
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Cheng F, Li D, Li J, Tang Y, Wu Y, Xu S. Synthesis of Phosphinic Amides from Chlorophosphines and Hydroxyl Amines via P(III) to P(V) Rearrangement. Org Lett 2023; 25:2555-2559. [PMID: 36876752 DOI: 10.1021/acs.orglett.3c00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Phosphoranyl radicals are essential mediators to bring about new radicals but often produce a stoichiometric amount of phosphine oxide/sulfide waste. Herein, we devised a phosphorus-containing species as a radical precursor, but without the generation of phosphorus waste. Accordingly, a catalyst-free synthesis of phosphinic amides from hydroxyl amines and chlorophosphines via P(III) to P(V) rearrangement is described. Mechanistically, it may involve the initial formation of a R2N-O-PR2 species that undergoes homolysis of N-O bonds and subsequent radical recombination.
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Affiliation(s)
- Fang Cheng
- School of Chemistry, and Engineering Research Center of Energy Storage Materials and Devices, Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Dongqiu Li
- School of Chemistry, and Engineering Research Center of Energy Storage Materials and Devices, Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Jing Li
- School of Chemistry, and Engineering Research Center of Energy Storage Materials and Devices, Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Yuhai Tang
- School of Chemistry, and Engineering Research Center of Energy Storage Materials and Devices, Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Yong Wu
- School of Chemistry, and Engineering Research Center of Energy Storage Materials and Devices, Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Silong Xu
- School of Chemistry, and Engineering Research Center of Energy Storage Materials and Devices, Ministry of Education, Xi'an Jiaotong University, Xi'an 710049, P.R. China
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3
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Roy B, Navarro V, Peyrottes S. Prodrugs of Nucleoside 5'-Monophosphate Analogues: Overview of the Recent Literature Concerning their Synthesis and Applications. Curr Med Chem 2023; 30:1256-1303. [PMID: 36093825 DOI: 10.2174/0929867329666220909122820] [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: 04/20/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 11/22/2022]
Abstract
Nucleoside analogues are widely used as anti-infectious and antitumoral agents. However, their clinical use may face limitations associated with their physicochemical properties, pharmacokinetic parameters, and/or their peculiar mechanisms of action. Indeed, once inside the cells, nucleoside analogues require to be metabolized into their corresponding (poly-)phosphorylated derivatives, mediated by cellular and/or viral kinases, in order to interfere with nucleic acid biosynthesis. Within this activation process, the first-phosphorylation step is often the limiting one and to overcome this limitation, numerous prodrug approaches have been proposed. Herein, we will focus on recent literature data (from 2015 and onwards) related to new prodrug strategies, the development of original synthetic approaches and novel applications of nucleotide prodrugs (namely pronucleotides) leading to the intracellular delivery of 5'-monophosphate nucleoside analogues.
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Affiliation(s)
- Béatrice Roy
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), University of Montpellier, Route de Mende, 34293 Montpellier, France
| | - Valentin Navarro
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), University of Montpellier, Route de Mende, 34293 Montpellier, France
| | - Suzanne Peyrottes
- Team Nucleosides & Phosphorylated Effectors, Institute for Biomolecules Max Mousseron (IBMM), University of Montpellier, Route de Mende, 34293 Montpellier, France
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4
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Heidari N, Tarahhomi A, van der Lee A. Structural and Molecular Packing study of Three New Amidophosphoric Acid Esters and Assessment of Their Inhibiting Activity Against SARS‐CoV‐2 by Molecular Docking. ChemistrySelect 2022; 7:e202201504. [PMID: 36247410 PMCID: PMC9538075 DOI: 10.1002/slct.202201504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/07/2022] [Indexed: 11/14/2022]
Abstract
Three new compounds of amidophosphoric acid esters with a [OCH2C(CH3)2CH2O]P(O)[X] segment (where X=cyclopentylamido (1), 2‐aminopyridinyl (2) and pyrrolidinyl (3)) were synthesized and studied using FT‐IR and 31P/13C/1H NMR spectroscopies and single‐crystal X‐ray diffraction analysis. The compounds crystallize in the triclinic space groups P1‾
for 1 and 3 and in the orthorhombic space group Pca21 for 2, where the asymmetric unit consists of three symmetrically‐independent molecules for 1 and one molecule for 2 and 3. The intermolecular interactions and supramolecular assemblies are assessed by Hirshfeld surface analysis and enrichment ratios. The results reveal that the substituent effect plays an important role in directing the supramolecular structures. The presence of the aromatic substituent aminopyridine in 2 providing the C−H…π interactions leads to a larger variety in interactions including H…H, H…O/O…H, H…C/C…H and H…N/N…H contacts, whereas the packings of the compounds 1 and 3 bearing aliphatic substituents only include H…H and H…O/O…H contacts. The enrichment ratios affirm the importance of O…H/H…O contacts reflecting the hydrogen bond N−H…O interactions to be the enriched contacts. Compounds 1–3 were also investigated along with five similar reported structures with a [OCH2C(CH3)2CH2O]P(O) segment for their inhibitory behavior against SARS‐CoV‐2. The molecular docking results illustrate that the presence of the aromatic amido substituent versus the aliphatic type provides a more favorable condition for their biological activities.
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Affiliation(s)
- Nafiseh Heidari
- Department of Chemistry Semnan University Semnan 35131-19111 Iran
| | - Atekeh Tarahhomi
- Department of Chemistry Semnan University Semnan 35131-19111 Iran
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5
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Zhu YY, Niu Y, Niu YN, Yang SD. Recent advances in the synthesis and applications of phosphoramides. Org Biomol Chem 2021; 19:10296-10313. [PMID: 34812834 DOI: 10.1039/d1ob01566d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Phosphoramide, as an important framework of many biologically active molecules, has attracted widespread attention in recent decades. It is not only widely used in pharmaceuticals because of its excellent biological activities, but it also shows good performance in organic dyes, flame retardants and extractors. Thus, it is of great significance to develop effective and convenient methods for the synthesis of phosphoramides. In this review, the recent advancements made in the synthesis routes and applications of phosphoramides are discussed. The synthetic strategies of phosphoramides can be separated into five categories: phosphorus halides as the substrate, phosphates as the substrate, phosphorus hydrogen as the substrate, azides as the substrate and other methods. The latest examples of these methods are provided and some representative mechanisms are also described.
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Affiliation(s)
- Yuan-Yuan Zhu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
| | - Yuan Niu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
| | - Yan-Ning Niu
- Department of Teaching and Research, Nanjing Forestry University, Huaian 223003, P. R. China
| | - Shang-Dong Yang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
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6
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Gu W, Martinez S, Nguyen H, Xu H, Herdewijn P, De Jonghe S, Das K. Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues. J Med Chem 2020; 64:782-796. [PMID: 33356231 DOI: 10.1021/acs.jmedchem.0c01747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nucleotide analogues are used for treating viral infections such as HIV, hepatitis B, hepatitis C, influenza, and SARS-CoV-2. To become polymerase substrates, a nucleotide analogue must be phosphorylated by cellular kinases which is rate-limiting. The goal of this study is to develop dNTP/NTP analogues directly from nucleotides. Tenofovir (TFV) analogues were synthesized by conjugating with amino acids. We demonstrate that some conjugates act as dNTP analogues and HIV-1 reverse transcriptase (RT) catalytically incorporates the TFV part as the chain terminator. X-ray structures in complex with HIV-1 RT/dsDNA showed binding of the conjugates at the polymerase active site, however, in different modes in the presence of Mg2+ versus Mn2+ ions. The adaptability of the compounds is seemingly essential for catalytic incorporation of TFV by RT. 4d with a carboxyl sidechain demonstrated the highest incorporation. 4e showed weak incorporation and rather behaved as a dNTP-competitive inhibitor. This result advocates the feasibility of designing NTP/dNTP analogues by chemical substitutions to nucleotide analogues.
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Affiliation(s)
- Weijie Gu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium.,KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Sergio Martinez
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Hoai Nguyen
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Hongtao Xu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Kalyan Das
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
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7
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Kraszewski A, Sobkowski M, Stawinski J. H-Phosphonate Chemistry in the Synthesis of Electrically Neutral and Charged Antiviral and Anticancer Pronucleotides. Front Chem 2020; 8:595738. [PMID: 33282839 PMCID: PMC7691650 DOI: 10.3389/fchem.2020.595738] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/14/2020] [Indexed: 11/13/2022] Open
Abstract
In this review a short account of our work on the synthesis and biological activity of electrically neutral and charged anti-HIV and anticancer pronucleotides, presented on the background of the contemporary research in this area, is given.
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Affiliation(s)
- Adam Kraszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Michal Sobkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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8
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Strom A, Tong CL, Wagner CR. Histidine triad nucleotide-binding proteins HINT1 and HINT2 share similar substrate specificities and little affinity for the signaling dinucleotide Ap4A. FEBS Lett 2020; 594:1497-1505. [PMID: 31990367 DOI: 10.1002/1873-3468.13745] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 11/07/2022]
Abstract
Human histidine triad nucleotide-binding protein 2 (hHINT2) is an important player in human mitochondrial bioenergetics, but little is known about its catalytic capabilities or its nucleotide phosphoramidate prodrug (proTide)-activating activity akin to the cytosolic isozyme hHINT1. Here, a similar substrate specificity profile (kcat /Km ) for model phosphoramidate substrates was found for hHINT2 but with higher kcat and Km values when compared with hHINT1. A broader pH range for maximum catalytic activity was determined for hHINT2 (pK1 = 6.76 ± 0.16, pK2 = 8.41 ± 0.07). In addition, the known hHINT1-microphthalmia-inducing transcription factor-regulating molecule Ap4 A was found to have no detectable binding to HINT1 nor HINT2 by isothermal titration calorimetry. These results demonstrate that despite differences in their sequence and localization, HINT1 and HINT2 have similar nucleotide substrate specificities, which should be considered in future proTide design and in studies of their natural function.
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Affiliation(s)
- Alexander Strom
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Cher Ling Tong
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Carston R Wagner
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
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9
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Romanowska J, Kolodziej K, Sobkowski M, Rachwalak M, Jakubowski T, Golebiewska J, Kraszewski A, Boryski J, Dabrowska A, Stawinski J. Aryl H-phosphonates. 19. New anti-HIV pronucleotide phosphoramidate diesters containing amino- and hydroxypyridine auxiliaries. Eur J Med Chem 2019; 164:47-58. [PMID: 30590257 DOI: 10.1016/j.ejmech.2018.12.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/19/2018] [Accepted: 12/15/2018] [Indexed: 10/27/2022]
Abstract
We have designed a new type of AZT and ddU phosphoramidate diesters containing various combinations of 2-, 3-, 4-aminopyridine and 2-, 3-, 4-hydroxypyridine moieties attached to the phosphorus center, as potential anti-HIV pronucleotides. Depending on the pKa values of the aminopyridines and the hydroxypyridines used, alternative synthetic strategies based on H-phosphonate chemistry were developed for their preparation. Synthetic aspects of these transformations and the biological activity of the synthesized compounds are discussed.
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Affiliation(s)
- Joanna Romanowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| | - Krystian Kolodziej
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Michal Sobkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Marta Rachwalak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Tomasz Jakubowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Justyna Golebiewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Adam Kraszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Jerzy Boryski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Aleksandra Dabrowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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10
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Mondal D, Koehn EM, Yao J, Wiemer DF, Kohen A. Chemo-enzymatic synthesis of the exocyclic olefin isomer of thymidine monophosphate. Bioorg Med Chem 2018; 26:2365-2371. [PMID: 29606487 DOI: 10.1016/j.bmc.2018.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 03/15/2018] [Accepted: 03/21/2018] [Indexed: 12/19/2022]
Abstract
Exocyclic olefin variants of thymidylate (dTMP) recently have been proposed as reaction intermediates for the thymidyl biosynthesis enzymes found in many pathogenic organisms, yet synthetic reports on these materials are lacking. Here we report two strategies to prepare the exocyclic olefin isomer of dTMP, which is a putative reaction intermediate in pathogenic thymidylate biosynthesis and a novel nucleotide analog. Our most effective strategy involves preserving the existing glyosidic bond of thymidine and manipulating the base to generate the exocyclic methylene moiety. We also report a successful enzymatic deoxyribosylation of a non-aromatic nucleobase isomer of thymine, which provides an additional strategy to access nucleotide analogs with disrupted ring conjugation or with reduced heterocyclic bases. The strategies reported here are straightforward and extendable towards the synthesis of various pyrimidine nucleotide analogs, which could lead to compounds of value in studies of enzyme reaction mechanisms or serve as templates for rational drug design.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - Eric M Koehn
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - Jiajun Yao
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - David F Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States.
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
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11
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Shah R, Zhou A, Wagner CR. Switch-on fluorescent/FRET probes to study human histidine triad nucleotide binding protein 1 (hHint1), a novel target for opioid tolerance and neuropathic pain. Org Biomol Chem 2018; 15:10230-10237. [PMID: 29177353 DOI: 10.1039/c7ob02472j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Histidine Triad Nucleotide Binding Protein 1 (Hint1) has emerged to be an important post-synaptic protein associated with a variety of central nervous system disorders such as pain, addiction, and schizophrenia. Recently, inhibition of histidine nucleotide binding protein 1 (Hint1) with a small nucleoside inhibitor has shown promise as a new therapeutic strategy for the treatment of neuropathic pain. Herein, we describe the first rationally designed small molecule switch-on probes with dual fluorescence and FRET properties to study Hint1. Two non-natural fluorescent nucleosides with a fluorescent lifetime of 20 and 25 ns were each coupled through a linker to the indole ring, i.e. probes 7 and 8. Both probes were found to be water soluble and quenched intramolecularly via photoinduced electron transfer (PET) resulting in minimal background fluorescence. Upon incubating with Hint1, compound 7 and 8 exhibited a 40- and 16-fold increase in the fluorescence intensity compared to the control. Compounds 7 and 8 bind Hint1 with a dissociation constant of 0.121 ± 0.02 and 2.2 ± 0.36 μM, respectively. We demonstrate that probe 8 exhibits a switch-on FRET property with an active site tryptophan residue (W123). We show the utility of probes in performing quantitative ligand displacement studies, as well as in selective detection of Hint1 in the cell lysates. These probes should be useful for studying the dynamics of the active site, as well as for the development of fluorescence lifetime based high throughput screening assay to identify novel inhibitors for Hint1 in future.
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Affiliation(s)
- Rachit Shah
- Department of Medicinal Chemistry University of Minnesota, USA.
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12
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Abstract
A facile covalent bio-conjugation of hydroxyapatite has been developed and employed for the conjugation of hydrophobic proteins.
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Affiliation(s)
- Minjeong Jeon
- Department of Chemistry
- Center for NanoBio Applied Technology
- Sungshin Women's University
- Seoul 01133
- Republic of Korea
| | - Suhyun Jung
- Department of Chemistry
- Center for NanoBio Applied Technology
- Sungshin Women's University
- Seoul 01133
- Republic of Korea
| | - Seongsoon Park
- Department of Chemistry
- Center for NanoBio Applied Technology
- Sungshin Women's University
- Seoul 01133
- Republic of Korea
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13
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Szymanska-Michalak A, Wawrzyniak D, Framski G, Stawinski J, Barciszewski J, Kraszewski A. New antiglioma zwitterionic pronucleotides with an FdUMP framework. Eur J Med Chem 2017; 144:682-691. [PMID: 29289891 DOI: 10.1016/j.ejmech.2017.12.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/24/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
We have designed and synthesized new 5-fluoro-2'-deoxyuridine 5'-phosphate pronucleotides which can function as potential agents against the glioblastoma multiforme tumor. Their anti-malignant potency has been tested against T98G, U-118 MG, U-87 MG gliomas, HeLa, and Caco-2 cancer cell lines, using MRC-5 healthy cells as a reference. Five of the sixteen compounds (4c, 4f-i) exhibited significant anticancer potency and high selectivity indices (SI 12-66). It is likely that these zwitterionic pronucleotides may function in a similar manner to zwitterionic phospholipids, by inducing cell membrane charge disorder, making the cell permeable to bioactive agents. The most promising therapeutic pronucleotides 4c, 4f-h, have high intestinal-blood uptake potency (Caco-2 cell line), and may be considered as potential, orally administrated, anticancer drugs.
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Affiliation(s)
| | - Dariusz Wawrzyniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Grzegorz Framski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Adam Kraszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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14
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Hrynchak I, Sousa E, Pinto M, Costa VM. The importance of drug metabolites synthesis: the case-study of cardiotoxic anticancer drugs. Drug Metab Rev 2017; 49:158-196. [DOI: 10.1080/03602532.2017.1316285] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ivanna Hrynchak
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- CIIMAR – Centro Interdisciplinar de Investigação Marinha e Ambiental, Matosinhos, Portugal
| | - Madalena Pinto
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- CIIMAR – Centro Interdisciplinar de Investigação Marinha e Ambiental, Matosinhos, Portugal
| | - Vera Marisa Costa
- Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, UCIBIO, REQUIMTE (Rede de Química e Tecnologia), Universidade do Porto, Porto, Portugal
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15
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Shah R, Strom A, Zhou A, Maize KM, Finzel BC, Wagner CR. Design, Synthesis, and Characterization of Sulfamide and Sulfamate Nucleotidomimetic Inhibitors of hHint1. ACS Med Chem Lett 2016; 7:780-4. [PMID: 27563403 DOI: 10.1021/acsmedchemlett.6b00169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/10/2016] [Indexed: 01/07/2023] Open
Abstract
Hint1 has recently emerged to be an important target of interest due to its involvement in the regulation of a broad range of CNS functions including opioid signaling, tolerance, neuropathic pain, and nicotine dependence. A series of inhibitors were rationally designed, synthesized, and tested for their inhibitory activity against hHint1 using isothermal titration calorimetry (ITC). The studies resulted in the development of the first small-molecule inhibitors of hHint1 with submicromolar binding affinities. A combination of thermodynamic and high-resolution X-ray crystallographic studies provides an insight into the biomolecular recognition of ligands by hHint1. These novel inhibitors have potential utility as molecular probes to better understand the role and function of hHint1 in the CNS.
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Affiliation(s)
- Rachit Shah
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Alexander Strom
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andrew Zhou
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kimberly M. Maize
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Barry C. Finzel
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carston R. Wagner
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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16
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De S, Groaz E, Margamuljana L, Herdewijn P. Syntheses of 5'-Nucleoside Monophosphate Derivatives with Unique Aminal, Hemiaminal, and Hemithioaminal Functionalities: A New Class of 5'-Peptidyl Nucleotides. Chemistry 2016; 22:8167-80. [PMID: 27136602 DOI: 10.1002/chem.201600721] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Indexed: 11/07/2022]
Abstract
A number of synthetically useful transformations have been developed to generate novel 5'-peptidyl nucleoside monophosphate analogues that incorporate sensitive phosphoaminal, -hemiaminal or -hemithioaminal functionalities. The strategies adopted entailed the coupling between dipeptides, which enclose a reactive Cα-functionalized glycine residue and phosphate or phosphorothioate moieties. These developments led to potentially powerful and general methodologies for the preparation of α-phosphorylated pseudopeptides as well as nucleoside monophosphate mimics. The resulting conjugates are of interest for a variety of important applications, which range from drug development to synthetic biology, as pronucleotides or artificial building blocks for the enzymatic synthesis of xenobiotic information systems. The potential of all dipeptide-TMP conjugates as pyrophosphate mimics in the DNA polymerization reaction was tested, and the influence of the nature of the linker was evaluated by in vitro chain elongation assay in the presence of wild-type microbial DNA polymerases.
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Affiliation(s)
- Swarup De
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Elisabetta Groaz
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Lia Margamuljana
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Minderbroedersstraat 10, 3000, Leuven, Belgium.
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17
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Lewandowska M, Ruszkowski P, Chojnacka K, Kleczewska N, Hoffmann M, Kacprzak K, Celewicz L. Synthesis and anticancer activity of some 5-fluoro-2'-deoxyuridine phosphoramidates. Bioorg Med Chem 2016; 24:2330-41. [PMID: 27073055 DOI: 10.1016/j.bmc.2016.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/25/2016] [Accepted: 04/01/2016] [Indexed: 10/22/2022]
Abstract
Two series of novel 4-chlorophenyl N-alkyl phosphoramidates of 3'-O-(t-butoxycarbonyl)-5-fluoro-2'-deoxyuridine (3'-BOC-FdU) (9a-9j) and 5-fluoro-2'-deoxyuridine (FdU) (10a-10j) were synthesized by means of phosphorylation of 3'-BOC-FdU (4) with 4-chlorophenyl phosphoroditriazolide (7), followed by a reaction with the appropriate amine. Phosphoramidates 9a-9j were converted to the corresponding 10a-10j by removal of the 3'-t-butoxycarbonyl protecting group (BOC) under acidic conditions. The synthesized phosphoramidates 9a-9j and 10a-10j were evaluated for their cytotoxic activity in five human cancer cell lines: cervical (HeLa), nasopharyngeal (KB), breast (MCF-7), liver (HepG2), osteosarcoma (143B) and normal human dermal fibroblast cell line (HDF) using the sulforhodamine B (SRB) assay. Two phosphoramidates 9b and 9j with the N-ethyl and N-(methoxy-(S)-alaninyl) substituents, respectively, displayed remarkable activity in all the investigated cancer cells, and the activity was considerably higher than that of the parent nucleoside 4 and FdU. Among phosphoramidates 10a-10j compound 10c with the N-(2,2,2-trifluoroethyl) substituent showed the highest activity. Phosphoramidate 10c was more active than the FdU in all the cancer cell lines tested.
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Affiliation(s)
- Marta Lewandowska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska St 89 b, 61-614 Poznań, Poland
| | - Piotr Ruszkowski
- Department of Pharmacology, Poznań University of Medical Sciences, Rokietnicka St 5 a, 60-806 Poznań, Poland
| | - Kinga Chojnacka
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska St 89 b, 61-614 Poznań, Poland
| | - Natalia Kleczewska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska St 89 b, 61-614 Poznań, Poland
| | - Marcin Hoffmann
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska St 89 b, 61-614 Poznań, Poland
| | - Karol Kacprzak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska St 89 b, 61-614 Poznań, Poland
| | - Lech Celewicz
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska St 89 b, 61-614 Poznań, Poland.
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18
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Sontakke VA, Lönnberg H, Ora M. 4-(Acetylthio)-2,2-dimethyl-3-oxobutyl and 4-( tert-Butyldisulfanyl)-2,2-dimethyl-3-oxobutyl as Protecting Groups for Nucleoside 5′-Phosphoramidates Derived from L-Alanine Methyl Ester. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Kubota K, Inaba SI, Nakano R, Watanabe M, Sakurai H, Fukushima Y, Ichikawa K, Takahashi T, Izumi T, Shinagawa A. Identification of activating enzymes of a novel FBPase inhibitor prodrug, CS-917. Pharmacol Res Perspect 2015; 3:e00138. [PMID: 26171222 PMCID: PMC4492754 DOI: 10.1002/prp2.138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/19/2015] [Accepted: 02/23/2015] [Indexed: 11/30/2022] Open
Abstract
CS-917 (MB06322) is a selective small compound inhibitor of fructose 1,6-bisphosphatase (FBPase), which is expected to be a novel drug for the treatment of type 2 diabetes by inhibiting gluconeogenesis. CS-917 is a bisamidate prodrug and activation of CS-917 requires a two-step enzyme catalyzed reaction. The first-step enzyme, esterase, catalyzes the conversion of CS-917 into the intermediate form (R-134450) and the second-step enzyme, phosphoramidase, catalyzes the conversion of R-134450 into the active form (R-125338). In this study, we biochemically purified the CS-917 esterase activity in monkey small intestine and liver. We identified cathepsin A (CTSA) and elastase 3B (ELA3B) as CS-917 esterases in the small intestine by mass spectrometry, whereas we found CTSA and carboxylesterase 1 (CES1) in monkey liver. We also purified R-134450 phosphoramidase activity in monkey liver and identified sphingomyelin phosphodiesterase, acid-like 3A (SMPADL3A), as an R-134450 phosphoramidase, which has not been reported to have any enzyme activity. Recombinant human CTSA, ELA3B, and CES1 showed CS-917 esterase activity and recombinant human SMPDL3A showed R-134450 phosphoramidase activity, which confirmed the identification of those enzymes. Identification of metabolic enzymes responsible for the activation process is the requisite first step to understanding the activation process, pharmacodynamics and pharmacokinetics of CS-917 at the molecular level. This is the first identification of a phosphoramidase other than histidine triad nucleotide-binding protein (HINT) family enzymes and SMPDL3A might generally contribute to activation of the other bisamidate prodrugs.
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Affiliation(s)
- Kazuishi Kubota
- Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co., Ltd. Tokyo, Japan
| | - Shin-Ichi Inaba
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd. Tokyo, Japan
| | - Rika Nakano
- Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co., Ltd. Tokyo, Japan
| | - Mihoko Watanabe
- Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co., Ltd. Tokyo, Japan
| | - Hidetaka Sakurai
- Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co., Ltd. Tokyo, Japan
| | - Yumiko Fukushima
- Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co., Ltd. Tokyo, Japan
| | - Kimihisa Ichikawa
- Biologics Technology Research Laboratories, Daiichi Sankyo Co., Ltd. Tokyo, Japan
| | - Tohru Takahashi
- New Modality Research Laboratories, Daiichi Sankyo Co., Ltd. Tokyo, Japan
| | - Takashi Izumi
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd. Tokyo, Japan
| | - Akira Shinagawa
- Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co., Ltd. Tokyo, Japan
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20
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Pradere U, Garnier-Amblard E, Coats SJ, Amblard F, Schinazi RF. Synthesis of nucleoside phosphate and phosphonate prodrugs. Chem Rev 2014; 114:9154-218. [PMID: 25144792 PMCID: PMC4173794 DOI: 10.1021/cr5002035] [Citation(s) in RCA: 386] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Ugo Pradere
- Center
for AIDS Research, Laboratory of Biochemical Pharmacology, Department
of Pediatrics, Emory University School of
Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
| | | | | | - Franck Amblard
- Center
for AIDS Research, Laboratory of Biochemical Pharmacology, Department
of Pediatrics, Emory University School of
Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
| | - Raymond F. Schinazi
- Center
for AIDS Research, Laboratory of Biochemical Pharmacology, Department
of Pediatrics, Emory University School of
Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
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21
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Sun Q, Li X, Gong S, Liu G, Shen L, Peng L. A novel synthesis of antiviral nucleoside phosphoramidate and thiophosphoramidate prodrugs via nucleoside H-phosphonamidates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 32:617-38. [PMID: 24138500 DOI: 10.1080/15257770.2013.838262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A novel and efficient method for the preparation of antiviral nucleoside 5'-H-phosphonamidates has been developed. The oxidization of the H-phosphonamidate intermediates with iodine and sulfur afforded nucleoside 5'-phosphoramidates and 5'-thiophosphoramidates in high yields.
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Affiliation(s)
- Qi Sun
- a Jiangxi Key Laboratory of Organic Chemistry , Jiangxi Science and Technology Normal University , Nanchang , Jiangxi , PR China
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22
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Sun Q, Sun J, Gong SS, Wang CJ, Pu SZ, Feng FD. Efficient synthesis of 5-hydroxymethyl-, 5-formyl-, and 5-carboxyl-2′-deoxycytidine and their triphosphates. RSC Adv 2014. [DOI: 10.1039/c4ra07670b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Efficient strategies for the preparation of high-quality 5-hydroxymethyl-, 5-formyl-, and 5-carboxyl-2′-deoxycytidine triphosphates and their parent nucleosides have been developed.
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Affiliation(s)
- Qi Sun
- Jiangxi Key Laboratory of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Nanchang, PR China
| | - Jian Sun
- Jiangxi Key Laboratory of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Nanchang, PR China
| | - Shan-Shan Gong
- Jiangxi Key Laboratory of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Nanchang, PR China
| | - Cheng-Jun Wang
- Jiangxi Key Laboratory of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Nanchang, PR China
| | - Shou-Zhi Pu
- Jiangxi Key Laboratory of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Nanchang, PR China
| | - Fu-De Feng
- Department of Polymer Science & Engineering
- College of Chemistry & Chemical Engineering
- Nanjing University
- Nanjing, PR China
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23
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Jang MY, Song XP, Froeyen M, Marlière P, Lescrinier E, Rozenski J, Herdewijn P. A synthetic substrate of DNA polymerase deviating from the bases, sugar, and leaving group of canonical deoxynucleoside triphosphates. ACTA ACUST UNITED AC 2013; 20:416-23. [PMID: 23521798 DOI: 10.1016/j.chembiol.2013.02.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 01/15/2013] [Accepted: 02/06/2013] [Indexed: 10/27/2022]
Abstract
The selection of artificial nucleic acids to be used for synthetic biology purposes is based on their structural and biochemical orthogonality to the natural system. We describe the example of a nucleotide mimic that functions as a substrate for polymerases and in which the carbohydrate moiety as well as the base moiety and the leaving group are different from that of the natural building blocks. The nucleotides themselves have two anomeric centers, and different leaving group properties of substituents at both anomeric centers need to be exploited to perform selective glycosylation reactions for their synthesis. In addition, the reversibility of the polymerase reaction at the level of the template has been demonstrated when pyrophosphate functions as leaving group and not with the alternative leaving groups.
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Affiliation(s)
- Mi-Yeon Jang
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, 3000, Belgium
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24
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Li S, Jia Y, Jacobson B, McCauley J, Kratzke R, Bitterman PB, Wagner CR. Treatment of breast and lung cancer cells with a N-7 benzyl guanosine monophosphate tryptamine phosphoramidate pronucleotide (4Ei-1) results in chemosensitization to gemcitabine and induced eIF4E proteasomal degradation. Mol Pharm 2013; 10:523-31. [PMID: 23289910 DOI: 10.1021/mp300699d] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The development of cancer and fibrotic diseases has been shown to be highly dependent on disregulation of cap-dependent translation. Binding protein eIF4E to N(7)-methylated guanosine capped mRNA has been found to be the rate-limiting step governing translation initiation, and therefore represents an attractive target for drug discovery. Our group has found that 7-benzyl guanosine monophosphate (7Bn-GMP) is a potent antagonist of eIF4E cap binding (K(d) = 0.8 μM). Recent X-ray crystallographic studies have revealed that the cap-dependent pocket undergoes a unique structural change in order to accommodate the benzyl group. Unfortunately, 7Bn-GMP is not cell permeable. Recently, we have prepared a tryptamine phosphoramidate prodrug of 7Bn-GMP, 4Ei-1, and shown that it is a substrate for human histidine triad nucleotide binding protein (hHINT1) and inhibits eIF4E initiated epithelial-mesenchymal transition (EMT) by Zebra fish embryo cells. To assess the intracellular uptake of 4Ei-1 and conversion to 7Bn-GMP by cancer cells, we developed a sensitive assay using LC-ESI-MS/MS for the intracellular quantitation of 4Ei-1 and 7Bn-GMP. When incubated with the breast cancer cell line MDA-231 or lung cancer cell lines H460, H383 and H2009, 4Ei-1 was found to be rapidly internalized and converted to 7Bn-GMP. Since oncogenic mRNAs are predicted to have the highest eIF4E requirement for translation, we carried out chemosensitization studies with 4Ei-1. The prodrug was found to chemosensitize both breast and lung cancer cells to nontoxic levels of gemcitabine. Further mechanistic studies revealed that the expressed levels of eIF4E were substantially reduced in cells treated with 4Ei-1 in a dose-dependent manner. The levels of eI4E could be restored by treatment with the proteasome inhibitor MG-132. Taken together, our results demonstrate that 4Ei-1 is likely to inhibit translation initiation by eIF4E cap binding by both antagonizing eIF4E cap binding and initiating eIF4E proteasomal degradation.
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Affiliation(s)
- Shui Li
- Department of Medicinal Chemistry and Department of Medicine, University of Minnesota , Minneapolis, Minnesota 55455, United States
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25
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Song XP, Bouillon C, Lescrinier E, Herdewijn P. Dipeptides as leaving group in the enzyme-catalyzed DNA synthesis. Chem Biodivers 2013; 9:2685-700. [PMID: 23255441 DOI: 10.1002/cbdv.201200261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Indexed: 01/22/2023]
Abstract
Conjugates of 2'-deoxyadenosine monophosphate with dipeptides have been synthesized and tested as substrates for several polymerases. Although the incorporation efficiency is not very high, it demonstrates that some of these dipeptides can be accommodated in the active site of polymerases and function as leaving groups in the enzymatic synthesis of DNA.
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Affiliation(s)
- Xiao-Ping Song
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven
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26
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Maiti M, Persoons L, Andrei G, Snoeck R, Balzarini J, Herdewijn P. Synthesis and anti-herpetic activity of phosphoramidate ProTides. ChemMedChem 2013; 8:985-93. [PMID: 23606629 DOI: 10.1002/cmdc.201300035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/15/2013] [Indexed: 01/28/2023]
Abstract
Among the many prodrug approaches aimed at delivering nucleoside monophosphates into cells, the phosphoramidate ProTide approach is one that has shown success, which has made it possible for some of the phosphoramidates to enter into clinical trials. Herein, we report the synthesis and antiviral activity of a series of phosphoramidate ProTides designed to bypass the thymidine kinase (TK) dependence of the parent nucleoside analogues. Phosphoramidate derivatives of (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) that contain L-alanine or pivaloyloxymethyl iminodiacetate (IDA-POM) exhibit anti-HSV-1 and anti-VZV activity in cell cultures, but they largely lost antiviral potency against TK-deficient virus strains. Among deazapurine nucleosides and their phosphoramidate derivatives, the 7-deazaadenine containing nucleosides and their phosphoramidate triester derivatives showed weak antiviral activity against VZV. Apparently, intracellular nucleotide delivery with these phosphoramidates is partly successful. However, none of the compound prodrugs showed superior activity to their parent drugs.
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Affiliation(s)
- Munmun Maiti
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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27
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Progress in the development of anti-hepatitis C virus nucleoside and nucleotide prodrugs. Future Med Chem 2012; 4:625-50. [PMID: 22458682 DOI: 10.4155/fmc.12.10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The search for new anti-hepatitis C virus (HCV) therapeutics continues as the current treatment, consisting of PEGylated IFN-α and ribavirin, is of limited efficacy, nonspecific and can cause significant side effects. Modified nucleoside analogues with improved efficacy and selectivity, may become the backbone of the future standard of care for anti-HCV therapies. Several families of modified nucleoside are known to inhibit HCV RNA-dependent RNA polymerase, a vital enzyme for viral replication. Ongoing efforts are focused on improvement of potency, selectivity and delivery of antiviral nucleoside analogues, with several recent promising advances into clinical trials. This review summarizes the current progress in the development of new anti-HCV nucleoside and nucleotide prodrugs.
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28
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Synthesis and study of cyclic pronucleotides of 5-fluoro-2'-deoxyuridine. Bioorg Med Chem Lett 2012; 22:4497-501. [PMID: 22738636 DOI: 10.1016/j.bmcl.2012.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 06/04/2012] [Indexed: 11/22/2022]
Abstract
A one-step method for the synthesis of cyclic pronucleotide (cProTide) derivatives of 5-fluoro-2'-deoxyuridine (FdUrd), utilizing a novel phosphoramidating reagent, is described. Stereochemistry at phosphorus was established by NMR studies and modeling. Cytotoxicity data of representative cProTide derivatives of FdUrd are presented. The observed cell-to-cell variations in activity suggests that it is feasible to screen for structural variations in the cProTide moiety favoring metabolic activation in cancer cells, which may lead to an increase in the therapeutic effectiveness of FdUrd. The method described is applicable to all anticancer and antiviral nucleoside analogs having both the 5'- and the 3'-OH groups available for modification, forming cProTide derivatives capable of delivering the 5'-monophosphates to cells.
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29
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Torabifard H, Fattahi A. Mechanisms and kinetics of thiotepa and tepa hydrolysis: DFT study. J Mol Model 2012; 18:3563-76. [DOI: 10.1007/s00894-012-1354-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 01/03/2012] [Indexed: 10/28/2022]
Affiliation(s)
- Hedieh Torabifard
- Department of Chemistry, Sharif University of Technology, P.O. BOX:11365-9516, Tehran, Iran
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30
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Yang S, Pannecouque C, Lescrinier E, Giraut A, Herdewijn P. Synthesis and in vitro enzymatic and antiviral evaluation of phosphoramidate d4T derivatives as chain terminators. Org Biomol Chem 2012; 10:146-53. [DOI: 10.1039/c1ob06214j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Maiti M, Michielssens S, Dyubankova N, Maiti M, Lescrinier E, Ceulemans A, Herdewijn P. Influence of the Nucleobase and Anchimeric Assistance of the Carboxyl Acid Groups in the Hydrolysis of Amino Acid Nucleoside Phosphoramidates. Chemistry 2011; 18:857-68. [DOI: 10.1002/chem.201102279] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 11/04/2011] [Indexed: 11/12/2022]
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32
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Matveeva EV, Shipov AE, Petrovskii PV, Odinets IL. Amino acids as suitable N-nucleophiles for the aza-Michael reaction of vinylphosphoryl compounds in water. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.09.111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Shevchuk MV, Metelitsa LA, Charochkina LL, Mogilevich SE, Rusanov EB, Sorochinsky AE, Khilya VP, Romanenko VD, Kukhar VP. Synthesis of N-(phosphonomethyl)glycine derivatives and studies of their immunotropic activity. Russ Chem Bull 2011. [DOI: 10.1007/s11172-011-0111-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Romanowska J, Sobkowski M, Szymańska-Michalak A, Kołodziej K, Dąbrowska A, Lipniacki A, Piasek A, Pietrusiewicz ZM, Figlerowicz M, Guranowski A, Boryski J, Stawiński J, Kraszewski A. Aryl H-Phosphonates 17: (N-Aryl)phosphoramidates of Pyrimidine Nucleoside Analogues and Their Synthesis, Selected Properties, and Anti-HIV Activity. J Med Chem 2011; 54:6482-91. [DOI: 10.1021/jm2001103] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joanna Romanowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Michał Sobkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | | | - Krystian Kołodziej
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | | | - Andrzej Lipniacki
- National Institute of Medicines, Chełmska 30/34, 00-725 Warsaw, Poland
| | - Andrzej Piasek
- National Institute of Medicines, Chełmska 30/34, 00-725 Warsaw, Poland
| | - Zofia M. Pietrusiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
- Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Andrzej Guranowski
- Faculty of Biochemistry and Biotechnology, Life Science University, Wołyńska 35, 60-637 Poznań, Poland
| | - Jerzy Boryski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jacek Stawiński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Adam Kraszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
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35
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Song XP, Bouillon C, Lescrinier E, Herdewijn P. Iminodipropionic acid as the leaving group for DNA polymerization by HIV-1 reverse transcriptase. Chembiochem 2011; 12:1868-80. [PMID: 21714056 DOI: 10.1002/cbic.201100160] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Indexed: 11/09/2022]
Abstract
Previous studies have demonstrated that some selected amino monoacids and amino diacids can function as leaving groups in the polymerase-catalyzed incorporation of deoxynucleotides into DNA. Among these, the iminodiacetic acid phosphoramidate of deoxyadenosine monophosphate (IDA-dAMP) represents an interesting example, as it could overcome some of the problems observed when using L-aspartic acid as the leaving group, that is, poor chain elongation. We have now synthesized and evaluated a series of IDA-dAMP analogues that bear either an extended aliphatic chain in the amino acid function, or a phosphonic acid moiety (substituting for the carboxylic acid function). Among these compounds, the nucleotide with an iminodipropionic acid leaving group (IDP-dAMP) was identified as the best substrate; the excellent single incorporation (91 % conversion to a P+1 strand at 50 μM) was at a substrate concentration ten times lower than that used for IDA-dAMP). This nucleotide also presented improved kinetics and elongation capability compared to IDA-dAMP. The analogues with T, G, and C base moieties were also investigated for their incorporation ability with HIV-1 RT. The incorporation efficiency was found to decrease in the order A>T>G>C. The properties of the iminodipropionic acid as the leaving group surpass those of previously evaluated leaving groups; this acid will be a prime candidate for in vivo testing.
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Affiliation(s)
- Xiao-Ping Song
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Minderbroederstraat 10, 3000 Leuven, Belgium
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Blotevogel J, Mayeno AN, Sale TC, Borch T. Prediction of contaminant persistence in aqueous phase: a quantum chemical approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:2236-2242. [PMID: 21332222 DOI: 10.1021/es1028662] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
At contaminated field sites where active remediation measures are not feasible, monitored natural attenuation is sometimes the only alternative for surface water or groundwater decontamination. However, due to slow degradation rates of some contaminants under natural conditions, attenuation processes and their performance assessment can take several years to decades to complete. Here, we apply quantum chemical calculations to predict contaminant persistence in the aqueous phase. For the test compound hexamethylphosphoramide (HMPA), P-N bond hydrolysis is the only thermodynamically favorable reaction that may lead to its degradation under reducing conditions. Through calculation of aqueous Gibbs free energies of activation for all potential reaction mechanisms, it is predicted that HMPA hydrolyzes via an acid-catalyzed mechanism at pH < 8.2, and an uncatalyzed mechanism at pH 8.2-8.5. The estimated half-lives of thousands to hundreds of thousands of years over the groundwater-typical pH range of 6.0 to 8.5 indicate that HMPA will be persistent in the absence of suitable oxidants. At pH 0, where the hydrolysis reaction is rapid enough to enable measurement, the experimentally determined rate constant and half-life are in excellent agreement with the predicted values. Since the quantum chemical methodology described herein can be applied to virtually any contaminant or reaction of interest, it is especially valuable for the prediction of persistence when slow reaction rates impede experimental investigations and appropriate QSARs are unavailable.
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Affiliation(s)
- Jens Blotevogel
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
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37
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Yang S, Froeyen M, Lescrinier E, Marlière P, Herdewijn P. 3-Phosphono-l-alanine as pyrophosphate mimic for DNA synthesis using HIV-1 reverse transcriptase. Org Biomol Chem 2011; 9:111-9. [DOI: 10.1039/c0ob00554a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Ozga M, Dolot R, Janicka M, Kaczmarek R, Krakowiak A. Histidine triad nucleotide-binding protein 1 (HINT-1) phosphoramidase transforms nucleoside 5'-O-phosphorothioates to nucleoside 5'-O-phosphates. J Biol Chem 2010; 285:40809-18. [PMID: 20940308 PMCID: PMC3003382 DOI: 10.1074/jbc.m110.162065] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 10/07/2010] [Indexed: 12/26/2022] Open
Abstract
Nucleoside 5'-O-phosphorothioates are formed in vivo as primary products of hydrolysis of oligo(nucleoside phosphorothioate)s (PS-oligos) that are applied as antisense therapeutic molecules. The biodistribution of PS-oligos and their pharmacokinetics have been widely reported, but little is known about their subsequent decay inside the organism. We suggest that the enzyme responsible for nucleoside 5'-O-monophosphorothioate ((d)NMPS) metabolism could be histidine triad nucleotide-binding protein 1 (Hint-1), a phosphoramidase belonging to the histidine triad (HIT) superfamily that is present in all forms of life. An additional, but usually ignored, activity of Hint-1 is its ability to catalyze the conversion of adenosine 5'-O-monophosphorothioate (AMPS) to 5'-O-monophosphate (AMP). By mutagenetic and biochemical studies, we defined the active site of Hint-1 and the kinetic parameters of the desulfuration reaction (P-S bond cleavage). Additionally, crystallographic analysis (resolution from 1.08 to 1.37 Å) of three engineered cysteine mutants showed the high similarity of their structures, which were not very different from the structure of WT Hint-1. Moreover, we found that not only AMPS but also other ribonucleoside and 2'-deoxyribonucleoside phosphorothioates are desulfurated by Hint-1 at the following relative rates: GMPS > AMPS > dGMPS ≥ CMPS > UMPS > dAMPS ≫ dCMPS > TMPS, and during the reaction, hydrogen sulfide, which is thought to be the third gaseous mediator, was released.
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Affiliation(s)
- Magdalena Ozga
- From the Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland
| | - Rafal Dolot
- From the Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland
| | - Magdalena Janicka
- From the Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland
| | - Renata Kaczmarek
- From the Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland
| | - Agnieszka Krakowiak
- From the Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland
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Chen WZ, Zhao YF. The Synthesis of Amino Acid Methyl Ester 5′-Phosphoamidates of Protected Uridine. PHOSPHORUS SULFUR 2010. [DOI: 10.1080/10426500903490237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- W. Z. Chen
- a Department of Chemistry and Key Laboratory for Chemical Biology of Fujian Province , Xiamen University , Xiamen, China
- b The Third Institute of Oceanography of the State Oceanic Administration , Xiamen, China
| | - Y. F. Zhao
- a Department of Chemistry and Key Laboratory for Chemical Biology of Fujian Province , Xiamen University , Xiamen, China
- c Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry , Tsinghua University , Beijing, China
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40
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Cheng J, Zhou X, Chou TF, Ghosh B, Liu B, Wagner CR. Identification of the amino acid-AZT-phosphoramidase by affinity T7 phage display selection. Bioorg Med Chem Lett 2009; 19:6379-81. [DOI: 10.1016/j.bmcl.2009.09.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2009] [Revised: 09/17/2009] [Accepted: 09/17/2009] [Indexed: 10/20/2022]
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41
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Peterson LW, McKenna CE. Prodrug approaches to improving the oral absorption of antiviral nucleotide analogues. Expert Opin Drug Deliv 2009; 6:405-20. [PMID: 19382883 DOI: 10.1517/17425240902824808] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Nucleotide analogues have been well accepted as therapeutic agents active against a number of viruses. However, their use as antiviral agents is limited by the need for phosphorylation by endogenous enzymes, and if the analogue is orally administered, by low bioavailability due to the presence of an ionizable diacid group. To circumvent these limitations, a number of prodrug approaches have been proposed. The ideal prodrug achieves delivery of a parent drug by attachment of a non-toxic moiety that is stable during transport and delivery, but is readily cleaved to release the parent drug once at the target. Here, a brief overview of several promising prodrug strategies currently under development is given.
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Affiliation(s)
- Larryn W Peterson
- University of Southern California, Department of Chemistry, Los Angeles, CA 90089-0744, USA.
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42
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Ahmadibeni Y, Tiwari RK, Sun G, Parang K. Synthesis of nucleoside mono-, di-, and triphosphoramidates from solid-phase cyclosaligenyl phosphitylating reagents. Org Lett 2009; 11:2157-60. [PMID: 19364114 DOI: 10.1021/ol900320r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloromethyl polystyrene resin was reacted with 5-hydroxysalicylaldehyde in the presence of potassium carbonate to afford polymer-bound 2-hydroxybenzaldehyde. Subsequent reduction with borane solution produced polymer-bound 2-hydroxybenzyl alcohol. The reaction of immobilized 2-hydroxybenzyl alcohol with appropriate phosphitylating reagents yielded solid-phase cycloSaligenyl mono-, di-, and triphosphitylating reagents, which were reacted with unprotected nucleosides, followed by iodine oxidation, deprotection of cyanoethoxy groups, and the basic cleavage, respectively, to afford 5'-O-nucleoside mono-, di-, and triphosphoramidates in 52-73% overall yield.
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Affiliation(s)
- Yousef Ahmadibeni
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, USA
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43
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Terrazas M, Marlière P, Herdewijn P. Enzymatically catalyzed DNA synthesis using L-Asp-dGMP, L-Asp-dCMP, and L-Asp-dTMP. Chem Biodivers 2008; 5:31-9. [PMID: 18205125 DOI: 10.1002/cbdv.200890013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The replacement of the pyrophosphate moiety of deoxynucleoside triphosphates by L-aspartic acid allows incorporation of natural deoxynucleosides into DNA using HIV reverse transcriptase (RT) as enzyme, while retaining the canonical base-pair selectivity. N-Methylation of the L-aspartic acid leaving group results in a reduced fidelity of incorporation.
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Affiliation(s)
- Montserrat Terrazas
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven.
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44
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Li P, Sergueeva ZA, Dobrikov M, Shaw BR. Nucleoside and Oligonucleoside Boranophosphates: Chemistry and Properties. Chem Rev 2007; 107:4746-96. [DOI: 10.1021/cr050009p] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ping Li
- Department of Chemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346
| | - Zinaida A. Sergueeva
- Department of Chemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346
| | - Mikhail Dobrikov
- Department of Chemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346
| | - Barbara Ramsay Shaw
- Department of Chemistry, Box 90346, Duke University, Durham, North Carolina 27708-0346
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45
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Adelfinskaya O, Herdewijn P. Amino acid phosphoramidate nucleotides as alternative substrates for HIV-1 reverse transcriptase. Angew Chem Int Ed Engl 2007; 46:4356-8. [PMID: 17443759 DOI: 10.1002/anie.200605016] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Olga Adelfinskaya
- Rega Institute for Medical Research, K U Leuven Laboratory of Medicinal Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium
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46
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Adelfinskaya O, Terrazas M, Froeyen M, Marlière P, Nauwelaerts K, Herdewijn P. Polymerase-catalyzed synthesis of DNA from phosphoramidate conjugates of deoxynucleotides and amino acids. Nucleic Acids Res 2007; 35:5060-72. [PMID: 17652326 PMCID: PMC1976459 DOI: 10.1093/nar/gkm498] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 11/20/2022] Open
Abstract
Some selected amino acids, in particular L-aspartic acid (L-Asp) and L-histidine (L-His), can function as leaving group during polymerase-catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. Although L-Asp-dAMP and L-His-dAMP bind, most probably, in a different way in the active site of the enzyme, aspartic acid and histidine can be considered as mimics of the pyrophosphate moiety of deoxyadenosine triphosphate. L-Aspartic acid is more efficient than D-aspartic acid as leaving group. Such P-N conjugates of amino acids and deoxynucleotides provide a novel experimental ground for diversifying nucleic acid metabolism in the field of synthetic biology.
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Affiliation(s)
- O. Adelfinskaya
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
| | - M. Terrazas
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
| | - M. Froeyen
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
| | - P. Marlière
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
| | - K. Nauwelaerts
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
| | - P. Herdewijn
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Department of Pharmaceutical Chemistry, Minderbroedersstraat 10, 3000 Leuven, Belgium and Genoscope - Centre National de Séquençage, 2 rue Gaston Crémieux CP5706, 91057 Evry cedex, France
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47
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Adelfinskaya O, Herdewijn P. Amino Acid Phosphoramidate Nucleotides as Alternative Substrates for HIV-1 Reverse Transcriptase. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200605016] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Krakowiak A, Kaczmarek R, Baraniak J, Wieczorek M, Stec WJ. Stereochemistry of rHint1 hydrolase assisted cleavage of P–N bond in nucleoside 5′-O-phosphoramidothioates. Chem Commun (Camb) 2007:2163-5. [PMID: 17520123 DOI: 10.1039/b615160d] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Hint-1 hydrolase assisted cleavage of the P-N bond in adenosine-5'-O-[N-(tryptophanylamide)]phosphoramidothioate proceeds with retention of configuration at the phosphorus atom which is consistent with the formation of a covalent enzyme-substrate complex.
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Affiliation(s)
- Agnieszka Krakowiak
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 112 Sienkiewicza Str., 90-363 Łódź, Poland
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49
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Choy CJ, Drontle DP, Wagner CR. Synthesis of amino acid phosphoramidate monoesters via H-phosphonate intermediates. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2006; Chapter 15:Unit 15.1. [PMID: 18428952 DOI: 10.1002/0471142700.nc1501s25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Diphenyl phosphite and bis(N,N-diisopropylamino)chlorophosphine are used as phosphitylating reagents to generate H-phosphonate monoesters. These H-phosphonate intermediates are subsequently oxidized with iodine to generate the 5'-nucleoside amino acid phosphoramidates.
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Affiliation(s)
- Cindy J Choy
- University of Minnesota, Minneapolis, Minnesota, USA
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50
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Zhu J, Han B, Fu H, Jiang Y, Zhao Y. Novel synthesis of nucleoside 5'-phosphoramidates through reaction of nucleoside triphosphates with amines mediated by trimethylsilyl chloride. J Org Chem 2006; 70:6676-9. [PMID: 16095286 DOI: 10.1021/jo050716i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reaction of nucleoside triphosphates (NTPs) with amines in pyridine mediated by trimethylsilyl chloride produced nucleoside 5'-phosphoramidates in moderate yields without any preprotection of nucleosides and amino acid methyl esters. The reaction pathway is very similar to the mechanism of the RNA capping reaction, DNA or RNA ligation reaction, and catalysis of hydrolases and nucleases involving the formation of covalent enzyme-NMP (nucleoside 5'-monophosphate) intermediates in biological systems, which could provide a valuable clue for the enzymatic reactions.
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Affiliation(s)
- Jigang Zhu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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