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Palazzotti D, Sguilla M, Manfroni G, Cecchetti V, Astolfi A, Barreca ML. Small Molecule Drugs Targeting Viral Polymerases. Pharmaceuticals (Basel) 2024; 17:661. [PMID: 38794231 PMCID: PMC11124969 DOI: 10.3390/ph17050661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Small molecules that specifically target viral polymerases-crucial enzymes governing viral genome transcription and replication-play a pivotal role in combating viral infections. Presently, approved polymerase inhibitors cover nine human viruses, spanning both DNA and RNA viruses. This review provides a comprehensive analysis of these licensed drugs, encompassing nucleoside/nucleotide inhibitors (NIs), non-nucleoside inhibitors (NNIs), and mutagenic agents. For each compound, we describe the specific targeted virus and related polymerase enzyme, the mechanism of action, and the relevant bioactivity data. This wealth of information serves as a valuable resource for researchers actively engaged in antiviral drug discovery efforts, offering a complete overview of established strategies as well as insights for shaping the development of next-generation antiviral therapeutics.
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Affiliation(s)
| | | | | | | | | | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy; (D.P.); (M.S.); (G.M.); (V.C.); (A.A.)
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2
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Ruiz Puentes P, Rueda-Gensini L, Valderrama N, Hernández I, González C, Daza L, Muñoz-Camargo C, Cruz JC, Arbeláez P. Predicting target-ligand interactions with graph convolutional networks for interpretable pharmaceutical discovery. Sci Rep 2022; 12:8434. [PMID: 35589824 PMCID: PMC9119967 DOI: 10.1038/s41598-022-12180-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/05/2022] [Indexed: 02/08/2023] Open
Abstract
Drug Discovery is an active research area that demands great investments and generates low returns due to its inherent complexity and great costs. To identify potential therapeutic candidates more effectively, we propose protein–ligand with adversarial augmentations network (PLA-Net), a deep learning-based approach to predict target–ligand interactions. PLA-Net consists of a two-module deep graph convolutional network that considers ligands’ and targets’ most relevant chemical information, successfully combining them to find their binding capability. Moreover, we generate adversarial data augmentations that preserve relevant biological backgrounds and improve the interpretability of our model, highlighting the relevant substructures of the ligands reported to interact with the protein targets. Our experiments demonstrate that the joint ligand–target information and the adversarial augmentations significantly increase the interaction prediction performance. PLA-Net achieves 86.52% in mean average precision for 102 target proteins with perfect performance for 30 of them, in a curated version of actives as decoys dataset. Lastly, we accurately predict pharmacologically-relevant molecules when screening the ligands of ChEMBL and drug repurposing Hub datasets with the perfect-scoring targets.
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Affiliation(s)
- Paola Ruiz Puentes
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Laura Rueda-Gensini
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Natalia Valderrama
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Isabela Hernández
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Cristina González
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Laura Daza
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia.,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Carolina Muñoz-Camargo
- Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Juan C Cruz
- Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Pablo Arbeláez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogotá, 111711, Colombia. .,Department of Biomedical Engineering, Universidad de los Andes, Bogotá, 111711, Colombia.
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Farag B, Agili F, El‐Kalyoubi S, Said SA, Youssif S, Shehta W. Synthesis, Molecular Docking and Anticancer Activity of Some 5‐Aryl‐5,10‐dihydropyrido[2,3‐
d
:6,5‐
d′
]dipyrimidine‐2,4,6,8‐tetraone Derivatives and Pyrido[2,3‐
d
]pyrimidines. ChemistrySelect 2022. [DOI: 10.1002/slct.202103834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Basant Farag
- Department of Chemistry Faculty of Science Zagazig University Zagazig 44519 Egypt
| | - Fatimah Agili
- Department of Chemistry Faculty of Science (female section) Jazan University Jazan 82621 Saudi Arabia
| | - Samar El‐Kalyoubi
- Department of Pharmaceutical Organic Chemistry Faculty of Pharmacy (Girls) Al-Azhar University Cairo 11651 Egypt
| | - Said A. Said
- Department of Chemistry Faculty of Science Zagazig University Zagazig 44519 Egypt
| | - Shaker Youssif
- Department of Chemistry Faculty of Science Zagazig University Zagazig 44519 Egypt
| | - Wael Shehta
- Department of Chemistry Faculty of Science Zagazig University Zagazig 44519 Egypt
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4
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Philip S, Thomas PS, Mohanan K. Synthesis, characterization, fluorescence imaging, and cytotoxicity studies of a uracil-based azo derivative and its metal complexes. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201800275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Surya Philip
- Department of Chemistry; University of Kerala; Trivandrum India
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5
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Synthesis, reactivity, and biological activity of 5-aminouracil and its derivatives. Mol Divers 2015; 20:153-83. [DOI: 10.1007/s11030-015-9595-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/02/2015] [Indexed: 11/27/2022]
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6
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Fernández-Cureses G, de Castro S, Jimeno ML, Balzarini J, Camarasa MJ. Design, synthesis, and biological evaluation of unconventional aminopyrimidine, aminopurine, and amino-1,3,5-triazine methyloxynucleosides. ChemMedChem 2014; 10:321-35. [PMID: 25420933 DOI: 10.1002/cmdc.201402465] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Indexed: 12/11/2022]
Abstract
Herein we describe a class of unconventional nucleosides (methyloxynucleosides) that combine unconventional nucleobases such as substituted aminopyrimidines, aminopurines, or aminotriazines with unusual sugars in their structures. The allitollyl or altritollyl derivatives were pursued as ribonucleoside mimics, whereas the tetrahydrofuran analogues were pursued as their dideoxynucleoside analogues. The compounds showed poor, if any, activity against a broad range of RNA and DNA viruses, including human immunodeficiency virus (HIV). This inactivity may be due to lack of an efficient metabolic conversion into their corresponding 5'-triphosphates and poor affinity for their target enzymes (DNA/RNA polymerases). Several compounds showed cytostatic activity against proliferating human CD4(+) T-lymphocyte CEM cells and against several other tumor cell lines, including murine leukemia L1210 and human prostate PC3, kidney CAKI-1, and cervical carcinoma HeLa cells. A few compounds were inhibitory to Moloney murine sarcoma virus (MSV) in C3H/3T3 cell cultures, with the 2,6-diaminotri-O-benzyl-D-allitolyl- and -D-altritolyl pyrimidine analogues being the most potent among them. This series of unconventional nucleosides may represent a novel family of potential antiproliferative agents.
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Gümüs HP, Tamer Ö, Avci D, Tarcan E, Atalay Y. Theoretical investigations on nonlinear optical and spectroscopic properties of 6-(3,3,4,4,4-pentafluoro-2-hydroxy-1-butenyl)-2,4-pyrimidinedione: An efficient NLO material. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414130068] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Pir H, Günay N, Avcı D, Tamer Ö, Tarcan E, Atalay Y. Theoretical Investigation of 6-(3,3,4,4,4-Pentafluoro-2-Hydroxy-1-Butenyl)-2,4-Dimethoxy-Pyrimidine Molecule. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2014. [DOI: 10.1007/s13369-014-1131-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Krištafor S, Novaković I, Gazivoda Kraljević T, Kraljević Pavelić S, Lučin P, Westermaier Y, Pernot L, Scapozza L, Ametamey SM, Raić-Malić S. A new N-methyl thymine derivative comprising a dihydroxyisobutenyl unit as ligand for thymidine kinase of herpes simplex virus type 1 (HSV-1 TK). Bioorg Med Chem Lett 2011; 21:6161-5. [PMID: 21911293 DOI: 10.1016/j.bmcl.2011.07.115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 07/27/2011] [Accepted: 07/29/2011] [Indexed: 11/18/2022]
Affiliation(s)
- Svjetlana Krištafor
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, HR-10000 Zagreb, Croatia
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Kraljević TG, Petrović M, Krištafor S, Makuc D, Plavec J, Ross TL, Ametamey SM, Raić-Malić S. Methoxymethyl (MOM) group nitrogen protection of pyrimidines bearing C-6 acyclic side-chains. Molecules 2011; 16:5113-29. [PMID: 21694675 PMCID: PMC6264546 DOI: 10.3390/molecules16065113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 11/18/2022] Open
Abstract
Novel N-methoxymethylated (MOM) pyrimidine (4−13) and pyrimidine-2,4-diones (15−17) nucleoside mimetics in which an isobutyl side-chain is attached at the C-6 position of the pyrimidine moiety were synthesized. Synthetic methods viaO-persilylated or N-anionic uracil derivatives have been evaluated for the synthesis of N-1- and/or N-3-MOM pyrimidine derivatives with C-6 acyclic side-chains. A synthetic approach using an activated N-anionic pyrimidine derivative afforded the desired N,N-1,3-diMOM and N-1-MOM pyrimidines 4 and 5 in good yield. Introduction of fluorine into the side-chain was performed with DAST as the fluorinating reagent to give a N,N-1,3-diMOM pyrimidine 13 with a 1-fluoro-3-hydroxyisobutyl moiety at C-6. Conformational study of the monotritylated N-1-MOM pyrimidine 12 by the use of the NOE experiments revealed the predominant conformation of the compound to be one where the hydroxymethyl group in the C-6 side-chain is close to the N-1-MOM moiety, while the OMTr is in proximity to the CH3-5 group. Contrary to this no NOE enhancements between the N-1-MOM group and hydroxymethyl or fluoromethyl protons in 13 were observed, which suggested a nonrestricted rotation along the C-6 side-chain. Fluorinated N,N-1,3-diMOM pyrimidine 13 emerged as a model compound for development of tracer molecules for non-invasive imaging of gene expression using positron emission tomography (PET).
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Affiliation(s)
- Tatjana Gazivoda Kraljević
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia
- Author to whom correspondence should be addressed; (T.G.K.); (S.R.-M.); Tel.: +385-1-4597-213; Fax: +385-1-4597-224
| | - Martina Petrović
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia
| | - Svjetlana Krištafor
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia
| | - Damjan Makuc
- Slovenian NMR centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Exellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Exellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva cesta 5, SI-1000 Ljubljana, Slovenia
| | - Tobias L. Ross
- Radiopharmaceutical Chemistry, Institute of Nuclear Chemistry, Johannes Gutenberg-Universität, Fritz-Strassmann Weg 2, 55128 Mainz, Germany
| | - Simon M. Ametamey
- Center for Radiopharmaceutical Sciences, ETH Zurich (Swiss Federal Institute of Technology), Wolfgang-Pauli Strasse 10, CH-8093 Zurich, Switzerland
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia
- Author to whom correspondence should be addressed; (T.G.K.); (S.R.-M.); Tel.: +385-1-4597-213; Fax: +385-1-4597-224
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11
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Lin CF, Huang WS, Chou HH, Lin JT. Synthesis and characterization of cyclometalated iridium(III) complexes containing pyrimidine-based ligands. J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2009.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Krištafor S, Gazivoda T, Cetina M, Makuc D, Plavec J, Raić-Malić S. Synthesis and structural characterization of the C-6 fluoroalkylated pyrimidine derivatives. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2008.12.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Peters GJ, Ackland SP. Leading Article: Oncologic, Endocrine & Metabolic: New antimetabolites in preclinical and clinical development. Expert Opin Investig Drugs 2008. [DOI: 10.1517/13543784.5.6.637] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Godefridus J Peters
- Department of Oncology, Free University Hospital, PO Box 7075, 1007, MB, Amsterdam, The Netherlands
| | - Stephen P Ackland
- Department of Medical Oncology, Newcastle Mater Misericordiae Hospital, Waratah, 2298, Australia
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Prekupec S, Makuc D, Plavec J, Suman L, Kralj M, Pavelić K, Balzarini J, Clercq ED, Mintas M, Raić-Malić S. Novel C-6 Fluorinated Acyclic Side Chain Pyrimidine Derivatives: Synthesis, 1H and 13C NMR Conformational Studies, and Antiviral and Cytostatic Evaluations. J Med Chem 2007; 50:3037-45. [PMID: 17539622 DOI: 10.1021/jm0614329] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthetic route for introduction of a fluoroalkyl (7-12, 14), fluoroalkenyl (15 and 16), fluorophenylalkyl (17, 19, 20, and 22), and fluorophenylalkenyl (18, 21) side chain at C-6 of the pyrimidine involved the lithiation of the pyrimidine derivatives 3 and 3a and subsequent nucleophilic addition or substitution reactions of the organolithium intermediate thus obtained with various electrophiles. Conformational properties of the novel fluorinated pyrimidine derivatives were assessed by the use of 1D difference NOE enhancements and C-F coupling constants. Compounds 4-22 were evaluated for their antiviral and cytostatic activities. Of all compounds evaluated, the 5-bromopyrimidine derivatives 5 and 6 showed the highest inhibitory activities. Among the series of fluoroalkylated pyrimidines, which is generally more active than the series of fluorophenylalkylated pyrimidines, compounds 8 and 14 displayed moderate cytostatic activities against the tested tumor cell lines. Moreover, compound 8 containing a 2-fluoromethylpropyl side chain expressed some but not highly specific activity against varicella-zoster virus (VZV). From C-6 fluorophenylalkylated pyrimidine derivatives, 17a and 21 showed a slight activity against cytomegalovirus (CMV), VZV, and Coxsackie B4 virus, respectively. Besides, compounds 17a and 21 showed no cytotoxic effect.
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Affiliation(s)
- Svjetlana Prekupec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, P.O. Box 177, HR-10000 Zagreb, Croatia
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Johayem A, Raić-Malić S, Lazzati K, Schubiger PA, Scapozza L, Ametamey SM. Synthesis and characterization of a C6 nucleoside analogue for the in vivo imaging of the gene expression of herpes simplex virus type-1 thymidine kinase (HSV1 TK). Chem Biodivers 2007; 3:274-83. [PMID: 17193264 DOI: 10.1002/cbdv.200690030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The synthesis and biological evaluation of '6-(1,3-dihydroxyisobutyl)thymine' (DHBT; 1), which corresponds to 6-[3-hydroxy-2-(hydroxymethyl)propyl]-5-methylpyrimidine-2,4(1H,3H)-dione, is reported. DHBT (1) was designed as a new substrate for herpes simplex virus type-1 thymidine kinase (HSV1 TK). The compound was found to be exclusively phosphorylated by HSV1 TK, and to exhibit good binding affinity (Ki = 35.3+/-1.3 microM). Cell-proliferation assays with HSV1-TK-transduced human osteosarcoma cells (143B-TK+-HSV1-WT) and with both human-thymidine-kinase-1-negative (143B-TK-) and non-transduced parental (MG-63) cells indicate that 1 is less cytotoxic than the standard drug Ganciclovir. Thus, DHBT (1) represents a promising precursor of a nontoxic reporter probe for the monitoring of HSV1 TK gene expression by means of positron-emission tomography (PET).
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Affiliation(s)
- Anass Johayem
- Center for Radiopharmaceutical Science of the ETH, PSI, USZ, and D-CHAB, ETH Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich
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Srivastav NC, Manning T, Kunimoto DY, Kumar R. Studies on acyclic pyrimidines as inhibitors of mycobacteria. Bioorg Med Chem 2007; 15:2045-53. [PMID: 17218105 DOI: 10.1016/j.bmc.2006.12.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 12/15/2006] [Accepted: 12/21/2006] [Indexed: 10/23/2022]
Abstract
In vitro anti-mycobacterial activities of several 5-substituted acyclic pyrimidine nucleosides containing 1-(2-hydroxyethoxy)methyl and 1-[(2-hydroxy-1-(hydroxymethyl) ethoxy)methyl] acyclic moieties are investigated against three mycobacteria viz. Mycobacterium tuberculosis, Mycobacterium bovis, and Mycobacterium avium, which cause serious infections and mortality in healthy people as well as patients with AIDS. 1-(2-Hydroxyethoxy)methyl-5-(1-azido-2-haloethyl or 1-azidovinyl) analogs (4-7), 1-[(2-hydroxy-1-(hydroxymethyl)ethoxy)methyl]-5-decynyluracil (37), and 1-[(2-hydroxy-1-(hydroxymethyl)ethoxy)methyl]-5-dodecynyluracil (38) exhibited significant in vitro anti-tubercular activity against these mycobacteria.
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Affiliation(s)
- Naveen C Srivastav
- Department of Laboratory Medicine and Pathology, 1-41 Medical Sciences Building, University of Alberta, Edmonton, AB, Canada T6G 2H7
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Patel K, Trivedi S, Luo S, Zhu X, Pal D, Kern ER, Mitra AK. Synthesis, physicochemical properties and antiviral activities of ester prodrugs of ganciclovir. Int J Pharm 2005; 305:75-89. [PMID: 16242278 DOI: 10.1016/j.ijpharm.2005.08.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Revised: 08/30/2005] [Accepted: 08/31/2005] [Indexed: 12/01/2022]
Abstract
The purpose of this study was to synthesize a series of diester prodrugs of ganciclovir (GCV), for improving ocular and oral bioavailability and therapeutic activity. Solubility, logP, pH stability profile, in vitro antiviral activity, cytotoxicity, inhibition profile and ocular tissue hydrolysis of the GCV prodrugs were measured. Val-Val-GCV and Val-Gly-GCV diesters were found to exhibit greater aqueous stability compared to Val-GCV and Gly-Val-GCV while ocular tissue hydrolysis demonstrated Val-Gly-GCV and Gly-Val-GCV to be more stable. Val-Val-GCV and Val-GCV diesters were the most lipophilic compounds and were predicted to possess a partition coefficient 295- and 12-fold greater than that of GCV, respectively. All the prodrugs possess much higher aqueous solubility than the parent drug GCV. Ex vivo uptake in the rabbit eye indicates that the prodrugs have high uptake potential. The prodrugs showed no increase in cytotoxicity compared to GCV, instead there was a marked increase in their potency against human cytomegalovirus (HCMV) as well as HSV-1 and HSV-2. This should allow therapeutic response to be seen at a lower concentration that can be achieved more easily, than the drugs currently being used. In conclusion, the diester GCV prodrugs demonstrated excellent chemical stability, high aqueous solubility and markedly enhanced antiviral potency against the herpes viruses without any increase in cytotoxicity.
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Affiliation(s)
- Kunal Patel
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 5005 Rockhill Road, Kansas City, MO 64110-2499, USA
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Majumdar S, Tirucherai GS, Pal D, Mitra AK. Functional differences in nucleoside and nucleobase transporters expressed on the rabbit corneal epithelial cell line (SIRC) and isolated rabbit cornea. AAPS PHARMSCI 2003; 5:E15. [PMID: 12866942 PMCID: PMC2751523 DOI: 10.1208/ps050215] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The purpose of this study was to investigate the expression of nucleoside/nucleobase transporters on the Statens Seruminstitut rabbit corneal (SIRC) epithelial cell line and to evaluate SIRC as an in vitro screening tool for delineating the mechanism of corneal permeation of nucleoside analogs. SIRC cells (passages 410-425) were used to study uptake of [3H]thymidine, [3H]adenine, and [3H]ganciclovir. Transport of [3H]adenine and [3H]ganciclovir was studied across isolated rabbit cornea. Uptake and transport studies were performed for 2 minutes and 120 minutes, respectively, at 34 degrees C. Thymidine uptake by SIRC displayed saturable kinetics (K(m) = 595.9 +/- 80.4 microM, and V(max) = 289.5 +/- 17.2 pmol/min/mg protein). Uptake was inhibited by both purine and pyrimidine nucleosides but not by nucleobases. [3H]thymidine uptake was sodium and energy independent but was inhibited by nitrobenzylthioinosine at nanomolar concentrations. Adenine uptake by SIRC consisted of a saturable component (K(m) = 14.4 +/- 2.3 microM, V(max) = 0.4 +/- 0.04 nmol/min/mg protein) and a nonsaturable component. Uptake of adenine was inhibited by purine nucleobases but not by the nucleosides or pyrimidine nucleobases and was independent of sodium, energy, and nitrobenzylthioinosine. [3H]ganciclovir uptake involved a carrier-mediated component and was inhibited by the purine nucleobases but not by the nucleosides or pyrimidine nucleobases. However, transport of [3H]adenine across the isolated rabbit cornea was not inhibited by unlabeled adenine. Further, corneal permeability of ganciclovir across a 100-fold concentration range remained constant, indicating that ganciclovir permeates the cornea primarily by passive diffusion. Nucleoside and nucleobase transporters on rabbit cornea and corneal epithelial cell line, SIRC, are functionally different, undermining the utility of the SIRC cell line as an in vitro screening tool for elucidating the corneal permeation mechanism of nucleoside analogs.
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Affiliation(s)
- Soumyajit Majumdar
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 5005 Rockhill Road, 64110 Kansas City, MO
| | - Giridhar S. Tirucherai
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 5005 Rockhill Road, 64110 Kansas City, MO
- Department of Clinical Pharmacology, Quintiles Inc, 10245 Hickman Mills Drive, 64137 Kansas City, MO
| | - Dhanajay Pal
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 5005 Rockhill Road, 64110 Kansas City, MO
| | - Ashim K. Mitra
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 5005 Rockhill Road, 64110 Kansas City, MO
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Abstract
The available informations on the genotoxic effects in experimental systems of the antiherpesvirus nucleosides aciclovir, penciclovir, ganciclovir, brivudine and cidofovir as well as of the antiretrovirals zidovudine (AZT), lamivudine, zalcitabine (ddC), didanosine and stavudine are reviewed. Furthermore, data on carcinogenic activity of these drugs in laboratory rodents are compiled. Most nucleoside analogue antivirals induce chromosomal aberrations but are inactive in gene mutation assays. Carcinogenicity findings in mice and rats are variable but clearly positive for AZT and ddC. The possible mechanisms by which these agents may cause damage in the genetic information are still largely hypothetical, and experimental findings do not permit relevant extrapolations to the situation in man. There is no conclusive evidence that any of the drugs caused tumours in humans. The use of nucleoside analogues in antiviral therapy remains a pragmatic option that seems justified by risk/benefit assessment.
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Affiliation(s)
- P Wutzler
- Institute for Antiviral Chemotherapy, Friedrich Schiller University of Jena, Winzerlaer Str. 10, 07745, Jena, Germany
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20
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Poznański J, Felczak K, Kulikowski T, Remin M. 1H NMR conformational study of antiherpetic C5-substituted 2'-deoxyuridines: insight into the nature of structure-activity relationships. Biochem Biophys Res Commun 2000; 272:64-74. [PMID: 10872804 DOI: 10.1006/bbrc.2000.2725] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
1H NMR study and conformational analysis of a broad series of biologically important C5-substituted 2'-deoxyuridines, including alkyl, halogen, vinyl, hydroxymethyl, and hydroxy derivatives as well as nitro, formyl, trifluoromethyl, and dimethylamino substituents, is presented. A thorough analysis of chemical shifts in correlation with C5-substituent electronegativity as well as calculations by SCF semi-empirical method of the formal charge localized on C6 carbon is discussed in terms of charge distribution for electron attracting and electron donating groups. Conformation of the sugar ring is determined from proton-proton coupling constants and described in terms of pseudorotation between two main puckering domains C2'endo (S) and C3'endo (N). Generally, electron donating groups destabilise the N conformation, simultaneously decreasing the mean pseudorotation amplitude. Absolute assignments of the H5' and H5'' methylene protons in 1H NMR spectra permitted the unequivocal determination of molar fractions of the three classical exocyclic C4'-C5' rotamers gauche+, trans, and gauche-, and correlation of them with the sugar ring puckering domains. Conformation about the glycosidic bond is described in terms of equilibrium between two conformational regions, anti and syn. Finally, the role of the C5-substituent in the creation of cytotoxic activity is considered on the basis of a simplified model assuming that compound activity is a function of substituent polar surface, its molecular volume, and its molecule polarity defined at the relative partition of the polar atoms.
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Affiliation(s)
- J Poznański
- Department of Physics, University of Warsaw, Poland
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21
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Maury G. The enantioselectivity of enzymes involved in current antiviral therapy using nucleoside analogues: a new strategy? Antivir Chem Chemother 2000; 11:165-89. [PMID: 10901289 DOI: 10.1177/095632020001100301] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This review is primarily intended for synthetic bio-organic chemists and enzymologists who are interested in new strategies in the design of virus inhibitors. It is an attempt to assess the importance of the enzymatic properties of L-nucleosides and their analogues, particularly those that are active against viruses such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), herpes simplex virus (HSV), etc. Only data obtained with purified enzymes have been considered and discussed. The examined enzymes include nucleoside- or nucleotide-phosphorylating enzymes, catabolic enzymes, viral target enzymes and cellular polymerases. The enantioselectivities of these enzymes were determined from existing data and are significant only when a sufficient number of enantiomeric pairs of substrates could be examined. The reported data emphasize the weak enantioselectivities of cellular or viral nucleoside kinases and some viral DNA polymerases. Thus, cellular deoxycytidine kinase has a considerably relaxed enantioselectivity with respect to a large number of nucleosides or their analogues, and it occupies a strategic position in the intracellular activation of the compounds. Similarly, HIV-1 reverse transcriptase often has a relatively weak enantioselectivity and can be inhibited by the 5-triphosphates of a large series of L-nucleosides and analogues. In contrast, degradation enzymes, such as adenosine or cytidine deaminases, generally demonstrate strict enantioselectivities favouring D-enantiomers and are used by chemists in asymmetric syntheses. The weak enantioselectivities of some enzymes involved in nucleoside metabolism are more or less pronounced, and one enantiomer or the other is favoured depending on the substrate. This suggests that the low enantioselectivity is fortuitous and does not result from evolutionary pressure, since these enzymes do not create or modify asymmetric centres in substrates. The combined enantioselectivities of the enzymes examined in this review strongly suggest that the field of L-nucleosides and their analogues should be systematically explored in the search for new virus inhibitors.
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Affiliation(s)
- G Maury
- UMR 5625 du CNRS, Université Montpellier II, France.
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22
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de Vries EF, van Waarde A, Harmsen MC, Mulder NH, Vaalburg W, Hospers GA. [(11)C]FMAU and [(18)F]FHPG as PET tracers for herpes simplex virus thymidine kinase enzyme activity and human cytomegalovirus infections. Nucl Med Biol 2000; 27:113-9. [PMID: 10773539 DOI: 10.1016/s0969-8051(99)00105-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
[(11)C]-2'-Fluoro-5-methyl-1-beta-D-arabinofuranosyluracil ([(11)C]FMAU) and [(18)F]-9-[(3-fluoro-1-hydroxy-2-propoxy)methyl]guanine ([(18)F]FHPG), radiolabeled representatives of two classes of antiviral agents, were evaluated as tracers for measuring herpes simplex virus thymidine kinase (HSV-tk) enzyme activity after gene transfer and as tracers for localization of active human cytomegalovirus (HCMV) infections. In vitro accumulation experiments revealed that both [(11)C]FMAU and [(18)F]FHPG accumulated significantly more in HSV-tk expressing cells than they did in control cells. [(18)F]FHPG uptake in HSV-tk expressing cells, however, was found to depend strongly on the cell line used, which might be due to cell type dependent membrane transport or cell type dependent substrate specific susceptibility of the enzyme. In vitro, both tracers exhibited a good selectivity for accumulation in HCMV-infected human umbilical vein endothelial cells over uninfected cells. In contrast to [(18)F]FHPG, [(11)C]FMAU uptake in control cells was relatively high due to phosphorylation of the tracer by host kinases. Therefore, [(18)F]FHPG appears to be the more selective tracer not only to predict HSV-tk gene therapy outcome, but also to localize active HCMV infections with PET.
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Affiliation(s)
- E F de Vries
- PET Center, Groningen University Hospital, Groningen, The Netherlands.
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23
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Radke JR, White MW. A cell cycle model for the tachyzoite of Toxoplasma gondii using the Herpes simplex virus thymidine kinase. Mol Biochem Parasitol 1998; 94:237-47. [PMID: 9747974 DOI: 10.1016/s0166-6851(98)00074-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Toxoplasma gondii (RH strain) tachyzoites were transfected with a plasmid containing a fusion of the chloramphenicol acetyl transferase and the Herpes simplex virus-2 thymidine kinase coding regions and transgenic parasites obtained by chloramphenicol selection. CTK11, a single high expressing clone was isolated based on immunofluorescence and contained approximately five integrated copies of the fusion sequence. Lysates prepared from this clone displayed thymidine kinase activity of 2.9 pmol min(-1) microg(-1) protein, whereas thymidine kinase activity was not detected in lysates from the parental RH strain. Growth of CTK11 tachyzoites was fully inhibited in 5 microM ganciclovir and thymidine and in 2.5 microM 5-bromo-2'-deoxyuridine. While the inhibitory effects of ganciclovir were lethal, low concentrations of thymidine (10 microM) were largely reversible. Asynchronously growing CTK11 tachyzoites were found to contain major G1 (1 N) and S phase (1 N+) distributions as determined by relative propidium iodide fluorescence and with reference to the haploid (1 N) DNA content of a T. gondii sporozoite population. CTK11 tachyzoites blocked 4 h in 10 microM thymidine exhibited mean fluorescence consistent with a 1 N complement of DNA indicating growth was arrested in G1. Following the removal of excess thymidine, parasites immediately entered S phase, thus confirming the late G1 block. Parasites with a 2 N complement of DNA (G2 + M) first appear at 2 h post-release, while 1 N (G1) parasites re-appear at 3 h suggesting the length of S phase is < or = 2 h and that of G2 + M is < or = 1 h. Within 7 h, parasites had transited G2 + M and much of G1 and re-entered S of the subsequent cell cycle--a time consistent with the doubling of these parasites in culture. Thus, the CTK11 tachyzoite cell cycle is similar to those of higher eukaryotic cells and is characterized by major G1 and S phases and a relatively short G2 + M.
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Affiliation(s)
- J R Radke
- Department of Veterinary Molecular Biology, Montana State University, Bozeman 59717-3610, USA
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24
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Polo R, Moretó JM, Schick U, Ricart S. Reaction of Alkynyl Alkoxy Metal (Cr, W) Carbene Complexes with 1,3-Dinitrogen Systems. A Direct Entry to the Pyrimidine Skeleton. Organometallics 1998. [DOI: 10.1021/om9708945] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rolando Polo
- Departament de Química Orgànica Biològica, CID (CSIC), c/J. Girona 18-26, 08934-Barcelona, Spain
| | - Josep M. Moretó
- Departament de Química Orgànica Biològica, CID (CSIC), c/J. Girona 18-26, 08934-Barcelona, Spain
| | - Ute Schick
- Departament de Química Orgànica Biològica, CID (CSIC), c/J. Girona 18-26, 08934-Barcelona, Spain
| | - Susagna Ricart
- Departament de Química Orgànica Biològica, CID (CSIC), c/J. Girona 18-26, 08934-Barcelona, Spain
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Evrard A, Vian L, Aubert C, Cano JP. An in vitro nucleoside analog screening method for cancer gene therapy. Cell Biol Toxicol 1996; 12:345-50. [PMID: 9034632 DOI: 10.1007/bf00438169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Suicide genes that sensitize cells to drugs that are normally nontoxic at therapeutic levels represent an important approach in human gene therapy research. We have developed an in vitro screening assay to assess the modulation of nucleoside analogs after transfection of a vector expressing the herpes simplex virus thymidine kinase gene (HSV-TK). The thymidine kinase gene enhances nucleoside phosphorylation to nucleotides that kill cells by blocking DNA elongation. Cells lines used are 3T3-NIH fibroblasts (parental cells) and 3T3-TKc3 (HSV-TK gene-transfected 3T3-NIH). Two types of analysis are performed: a cytotoxicity assay, the neutral red uptake assay to assess the IC50 on the two cell lines, and an HPLC analysis coupled to a radiochemical flow detector to evaluate metabolic profiles after incubation of cells with tritiated analogs. Results show that cells expressing the HSV-TK gene are more sensitive than the parent cells to the effect of acyclovir or ganciclovir, the reference purine analog drugs, and also to the effect of pyrimidine analogs, bromodeoxyuridine, bromovinyldeoxyuridine, and ethyldeoxyuridine. Promising nucleoside analogs for gene therapy that can be achieved by HSV-TK could be evaluated using this model.
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Affiliation(s)
- A Evrard
- Laboratoire de Toxicologie, Faculté de Pharmacie, Montpellier, France
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26
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Thust R, Schacke M, Wutzler P. Cytogenetic genotoxicity of antiherpes virostatics in Chinese hamster V79-E cells. I. Purine nucleoside analogues. Antiviral Res 1996; 31:105-13. [PMID: 8793014 DOI: 10.1016/0166-3542(96)00961-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The antiherpes virostatics acyclovir (ACV), valaciclovir (VACV), penciclovir (PCV), famciclovir (FCV) and ganciclovir (GCV), which belong to the group of purine acyclic nucleoside analogues, were tested for clastogenic and sister chromatid exchange (SCE)-inducing activity in Chinese hamster V79-E cells upon chronic application with and without a recovery period. ACV induced borderline effects in both cytogenetic assays, a dose-dependent reduction of the mitotic index and an increasing cell cycle delay. With VACV and PCV only a decrease of the mitotic index and an increase of cell cycle delay were observed. FCV was negative with respect to the four parameters studied, presumably due to the incapacity of the target cells of metabolizing FCV to PCV. GCV was a very potent genotoxin in both assays. It induced a statistically significant SCE response even in the range of the cytomegalovirus IC50 of < 10 microM. By variation of the experimental protocol it was shown that SCEs are induced in the second cell cycle following exposure to GCV but not in the first one. It is assumed that the drugs under study are metabolized to their respective triphosphates and then inhibit DNA replication as detected by decreasing mitotic index and increasing cell cycle delay. In the case of GCV it is suggested that GCV-TP is incorporated into the target cell DNA and that chromosomal aberrations and SCEs are secondary lesions due to repair processes at the substituted template.
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Affiliation(s)
- R Thust
- Institute for Antiviral Chemotherapy, Friedrich Schiller University of Jena, Erfurt, Germany
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27
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Modified dideoxynucleosides: Synthesis of 2′-N-alkyl-3′-hydroxyalkyl-1′,2′-isoxazolidinyl thymidine and 5-fluorouridine derivatives. Tetrahedron 1996. [DOI: 10.1016/0040-4020(96)00437-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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28
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Abstract
Acyclovir is an effective drug for the treatment of HSV and VZV infections, which after phosphorylation to the triphosphate, inhibits viral DNA polymerase. Acyclovir has low oral bioavailability, therefore prodrugs have been developed, and the L-valyl ester, valaciclovir, recently has been licensed for the treatment of shingles. Ganciclovir is used against CMV, and famciclovir, a lipophilic prodrug of penciclovir, is marketed for shingles. The acyclic nucleoside phosphonates are active against thymidine kinase-resistant viral strains. Promising analogs are PMEA (in clinical trial for the treatment of AIDS) and (S)-HPMPC (good in vivo activity against HSV, VZV, CMV, and EBV). Oligonucleotides incorporating acyclic nucleosides at the 3'-and 5'-ends, or constituted of amino acyclic nucleosides, are resistant to cleavage by nucleases and may be useful in antisense and/or antigene therapy. HEPT is active against HIV-1: It binds in a hydrophic pocket on reverse transcriptase, rather than in the polymerase active site. Some acyclic nucleosides are potent inhibitors of purine and pyrimidine nucleoside phosphorylase. These compounds may have a therapeutic niche in combination therapy with antiviral and anticancer nucleosides, and in the treatment of diseases involving the T-cell.
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Affiliation(s)
- S Freeman
- Department of Pharmacy, University of Manchester, UK
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29
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Greenidge PA, Merz A, Folkers G. A pseudoreceptor modelling study of the varicella-zoster virus and human thymidine kinase binding sites. J Comput Aided Mol Des 1995; 9:473-8. [PMID: 8789189 DOI: 10.1007/bf00124318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A representative range of pyrimidine nucleoside analogues that are known to inhibit herpes simplex virus (HSV) replication have been used to construct receptor binding site models for the varicella-zoster virus (VZV) thymidine kinase (TK) and human TK1. Given a set of interacting ligands, superimposed in such a manner as to define a pharmacophore, the pseudoreceptor modelling technique Yak provides a means of building binding site models of macromolecules for which no three-dimensional experimental structures are available. Once the models have been evaluated by their ability to reproduce experimental binding data [Vedani et al., J. Am. Chem. Soc., 117 (1995) 4987], they can be used for predictive purposes. Calculated and experimental values of relative binding affinity are compared. Our models suggest that the substitution of one residue may be sufficient to determine ligand subtype affinity.
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30
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Mazzacano CA, Fallon AM. Evaluation of a viral thymidine kinase gene for suicide selection in transfected mosquito cells. INSECT MOLECULAR BIOLOGY 1995; 4:125-134. [PMID: 7551194 DOI: 10.1111/j.1365-2583.1995.tb00017.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
An Aedes albopictus cell line previously shown to be deficient in thymidine kinase activity was transfected with a thymidine kinase gene (tk) from Herpes simplex virus. Survival of the transfected lines in a 'TK+ selective medium' indicated that the viral gene was actively expressed at a level sufficient to rescue the TK-deficient phenotype of the parent line. Unlike the parental cells, TK+ transformants (TK6:hsv cells) were sensitive to 5-bromodeoxyuridine, and contained DNA corresponding to the constructs introduced by transfection. This TK selection system will facilitate recovery of other cotransfected, non-selectable mosquito genes in cultured cells. Transformed cells were treated with several antiviral drugs to define conditions for a 'suicide selection' system, in which cells expressing the viral thymidine kinase enzyme (TK) under the control of an inducible promoter would be selectively destroyed, whereas cells expressing the endogenous mosquito enzyme would remain relatively unaffected. The anti-herpetic drug (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) showed greater cytotoxicity against transformed cells expressing the viral enzyme, and less toxicity to wild-type mosquito cells. This cell culture system provides a model for initial evaluation of suicide selection systems that may ultimately be adapted to the mosquito using sex- or tissue-specific promoters to drive expression of heterologous genes.
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Affiliation(s)
- C A Mazzacano
- Department of Entomology, University of Minnesota, St Paul 55108, USA
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