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Jacobson KA, Salmaso V, Suresh RR, Tosh DK. Expanding the repertoire of methanocarba nucleosides from purinergic signaling to diverse targets. RSC Med Chem 2021; 12:1808-1825. [PMID: 34825182 PMCID: PMC8597424 DOI: 10.1039/d1md00167a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022] Open
Abstract
Nucleoside derivatives are well represented as pharmaceuticals due to their druglike physicochemical properties, and some nucleoside drugs are designed to act on receptors. The purinergic signaling pathways for extracellular nucleosides and nucleotides, consisting of adenosine receptors, P2Y/P2X receptors for nucleotides, and enzymes such as adenosine (ribo)kinase, have been extensively studied. A general modification, i.e. a constrained, bicyclic ring system (bicyclo[3.1.0]hexane, also called methanocarba) substituted in place of a furanose ring, can increase nucleoside/nucleotide potency and/or selectivity at purinergic and antiviral targets and in interactions at diverse and unconventional targets. Compared to other common drug discovery scaffolds containing planar rings, methanocarba nucleosides display greater sp3 character (i.e. more favorable as drug-like molecules) and can manifest as sterically-constrained North (N) or South (S) conformations. Initially weak, off-target interactions of (N)-methanocarba adenosine derivatives were detected as leads that were structurally optimized to enhance activity and selectivity toward target proteins that normally do not recognize nucleosides. By this approach, novel modulators for 5HT2 serotonin and κ-opioid receptors, dopamine (DAT) and ATP-binding cassette (ABC) transporters were found, and previously undetected antiviral activities were revealed. Thus, through methanocarba nucleoside synthesis, structure-activity relationships, and multi-target pharmacology, a robust purinergic receptor scaffold has been repurposed to satisfy the pharmacophoric requirements of various GPCRs, enzymes and transporters.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
| | - Veronica Salmaso
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
| | - R Rama Suresh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
| | - Dilip K Tosh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
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Rabelo VWH, Romeiro NC, Paixão ICNDP, Abreu PA. Mechanism of resistance to acyclovir in thymidine kinase mutants from Herpes simplex virus type 1: a computational approach. J Biomol Struct Dyn 2019; 38:2116-2127. [DOI: 10.1080/07391102.2019.1625443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Vitor Won-Held Rabelo
- Programa de Pós-graduação em Ciências e Biotecnologia, Instituto de Biologia, Universidade Federal Fluminense - Campus do Valonguinho, Niterói, Brazil
| | - Nelilma Correia Romeiro
- Laboratório Integrado de Computação Científica, Universidade Federal do Rio de Janeiro - Campus Macaé, Brazil
| | | | - Paula Alvarez Abreu
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Brazil
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Toti KS, Osborne D, Ciancetta A, Boison D, Jacobson KA. South (S)- and North (N)-Methanocarba-7-Deazaadenosine Analogues as Inhibitors of Human Adenosine Kinase. J Med Chem 2016; 59:6860-77. [PMID: 27410258 PMCID: PMC5032833 DOI: 10.1021/acs.jmedchem.6b00689] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Adenosine kinase (AdK) inhibitors raise endogenous adenosine levels, particularly in disease states, and have potential for treatment of seizures, neurodegeneration, and inflammation. On the basis of the South (S) ribose conformation and molecular dynamics (MD) analysis of nucleoside inhibitors bound in AdK X-ray crystallographic structures, (S)- and North (N)-methanocarba (bicyclo[3.1.0]hexane) derivatives of known inhibitors were prepared and compared as human (h) AdK inhibitors. 5'-Hydroxy (34, MRS4202 (S); 55, MRS4380 (N)) and 5'-deoxy 38a (MRS4203 (S)) analogues, containing 7- and N(6)-NH phenyl groups in 7-deazaadenine, robustly inhibited AdK activity (IC50 ∼ 100 nM), while the 5'-hydroxy derivative 30 lacking the phenyl substituents was weak. Docking in the hAdK X-ray structure and MD simulation suggested a mode of binding similar to 5'-deoxy-5-iodotubercidin and other known inhibitors. Thus, a structure-based design approach for further potency enhancement is possible. The potent AdK inhibitors in this study are ready to be further tested in animal models of epilepsy.
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Affiliation(s)
- Kiran S Toti
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Danielle Osborne
- Robert Stone Dow Neurobiology Laboratories, Legacy Research Institute , 1225 NE Second Avenue, Portland, Oregon 97232, United States
| | - Antonella Ciancetta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Detlev Boison
- Robert Stone Dow Neurobiology Laboratories, Legacy Research Institute , 1225 NE Second Avenue, Portland, Oregon 97232, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892-0810, United States
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Sjuvarsson E, Marquez VE, Eriksson S. Selective Phosphorylation of South and North-Cytidine and Adenosine Methanocarba-Nucleosides by Human Nucleoside and Nucleotide Kinases Correlates with Their Growth Inhibitory Effects on Cultured Cells. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 34:544-64. [PMID: 26167664 DOI: 10.1080/15257770.2015.1031248] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Here bicyclo[3.1.0]hexane locked deoxycytidine (S-MCdC, N-MCdC), and deoxyadenosine analogs (S-MCdA and N-MCdA) were examined as substrates for purified preparations of human deoxynucleoside kinases: dCK, dGK, TK2, TK1, the ribonucleoside kinase UCK2, two NMP kinases (CMPK1, TMPK) and a NDP kinase. dCK can be important for the first step of phosphorylation of S-MCdC in cells, but S-MCdCMP was not a substrate for CMPK1, TMPK, or NDPK. dCK and dGK had a preference for the S-MCdA whereas N-MCdA was not a substrate for dCK, TK1, UCK2, TK2, dGK nucleoside kinases. The cell growth experiments suggested that N-MCdC and S-MCdA could be activated in cells by cellular kinases so that a triphosphate metabolite was formed. List of abbreviations: ddC, 2', 3'-didioxycytosine, Zalcitabine; 3TC, β-L-(-)-2',3'-dideoxy-3'-thiacytidine, Lamivudine; CdA, 2-cloro-2'-deoxyadenosine, Cladribine; AraA, 9-β-D-arabinofuranosyladenine; hCNT 1-3, human Concentrative Nucleoside Transporter type 1, 2 and 3; hENT 1-4, human Equilibrative Nucleoside Transporter type 1, 2, 3, and 4.
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Affiliation(s)
- Elena Sjuvarsson
- a Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences , VHC , Uppsala , Sweden
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Bernstein DI, Bravo FJ, Pullum DA, Shen H, Wang M, Rahman A, Glazer RI, Cardin RD. Efficacy of N-methanocarbathymidine against genital herpes simplex virus type 2 shedding and infection in guinea pigs. Antivir Chem Chemother 2016; 24:19-27. [PMID: 26149263 DOI: 10.1177/2040206614566581] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Current approved nucleoside therapies for genital herpes simplex virus (HSV) infections are effective but improved therapies are needed for treatment of both acute and recurrent diseases. METHODS The effects of N-methanocarbathymidine were evaluated and compared to acyclovir using guinea pig models of acute and recurrent infection. For acute disease following intravaginal inoculation of 10(6 )pfu HSV-2 (MS strain), animals were treated intraperitoneally beginning 24 h post-infection, and the effects on disease severity, vaginal virus replication, subsequent recurrences, and latent virus loads were evaluated. For evaluation of recurrent infection, animals were treated for 21 days beginning 14 days after infection and disease recurrence and recurrent shedding were evaluated. RESULTS Treatment of the acute disease with N-methanocarbathymidine significantly reduced the severity of acute disease and decreased acute vaginal virus shedding more effectively than acyclovir. Significantly, none of the animals developed visible disease in the high-dose N-methanocarbathymidine group and this was the only group in which the number of days with recurrent virus shedding was reduced. Treatment of recurrent disease was equivalent to acyclovir when acyclovir was continuously supplied in the drinking water. CONCLUSION N-methanocarbathymidine was effective as therapy for acute and recurrent genital HSV-2 disease in the guinea pig models.
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Affiliation(s)
- David I Bernstein
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Fernando J Bravo
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Derek A Pullum
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Hui Shen
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Mei Wang
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Rhonda D Cardin
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
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Yang L, Mo X, Yang H, Dai H, Tan F. Testing the sensitivities of noncognate inhibitors to varicella zoster virus thymidine kinase: implications for postherpetic neuralgia therapy with existing agents. J Mol Model 2014; 20:2321. [DOI: 10.1007/s00894-014-2321-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 05/27/2014] [Indexed: 11/29/2022]
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Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD. Automating crystallographic structure solution and refinement of protein-ligand complexes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:144-54. [PMID: 24419387 PMCID: PMC3919266 DOI: 10.1107/s139900471302748x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/07/2013] [Indexed: 11/29/2022]
Abstract
High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation.
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Affiliation(s)
- Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Nigel W. Moriarty
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Herbert E. Klei
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Gábor Bunkóczi
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Jeffrey J. Headd
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Airlie J. McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Robert D. Oeffner
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | | | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720-1762, USA
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Meščić A, Krištafor S, Novaković I, Osmanović A, Müller U, Završnik D, Ametamey SM, Scapozza L, Raić-Malić S. C-5 hydroxyethyl and hydroxypropyl acyclonucleosides as substrates for thymidine kinase of herpes simplex virus type 1 (HSV-1 TK): syntheses and biological evaluation. Molecules 2013; 18:5104-24. [PMID: 23644977 PMCID: PMC6270122 DOI: 10.3390/molecules18055104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/16/2013] [Accepted: 04/25/2013] [Indexed: 11/16/2022] Open
Abstract
The efficient syntheses of 5-(2-hydroxyethyl)- and 5-(3-hydroxypropyl)-substituted pyrimidine derivatives bearing 2,3-dihydroxypropyl, acyclovir-, ganciclovir- and penciclovir-like side chains are reported. A synthetic approach that included the alkylation of an N-anionic-5-substituted pyrimidine intermediate (method A) provided the target acyclonucleosides in significantly higher overall yields in comparison to those obtained by method B using sylilation reaction. The phosphorylation assays of novel compounds as potential substrates for thymidine kinase of herpes simplex virus type 1 (HSV-1 TK) showed that solely pyrimidine 5-substituted acyclonucleosides with a penciclovir-like side chain acted as a fraudulent substrates of HSV-1 TK. Moreover, the uracil derivative with penciclovir-like side chain with less bulky 2-hydroxyethyl substituent at C-5 proved to be a better substrate than the corresponding one with a 3-hydroxypropyl substituent. Therefore, this acyclonucleoside was selected as a lead compound for the development of a positron emission tomography HSV-1 TK activity imaging agent.
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Affiliation(s)
- Andrijana Meščić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia; E-Mails: (A.M.); (S.K.)
| | - Svjetlana Krištafor
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia; E-Mails: (A.M.); (S.K.)
| | - Ivana Novaković
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland; E-Mails: (I.N.); (L.S.)
| | - Amar Osmanović
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Sarajevo, Zmaja od Bosne 8, BIH-71 000 Sarajevo, Bosnia and Herzegovina; E-Mails: (A.O.); (D.Z.)
| | - Ursina Müller
- Center for Radiopharmaceutical Sciences, ETH Zurich (Swiss Federal Institute of Technology), Wolfgang-Pauli Strasse 10, CH-8093 Zurich, Switzerland; E-Mails: (U.M.); (S.M.A.)
| | - Davorka Završnik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Sarajevo, Zmaja od Bosne 8, BIH-71 000 Sarajevo, Bosnia and Herzegovina; E-Mails: (A.O.); (D.Z.)
| | - Simon M. Ametamey
- Center for Radiopharmaceutical Sciences, ETH Zurich (Swiss Federal Institute of Technology), Wolfgang-Pauli Strasse 10, CH-8093 Zurich, Switzerland; E-Mails: (U.M.); (S.M.A.)
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland; E-Mails: (I.N.); (L.S.)
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia; E-Mails: (A.M.); (S.K.)
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Martić M, Pernot L, Westermaier Y, Perozzo R, Kraljević TG, Krištafor S, Raić-Malić S, Scapozza L, Ametamey S. Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:293-315. [PMID: 21623543 DOI: 10.1080/15257770.2011.581258] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Novel C-6 substituted pyrimidine derivatives are good substrates of herpes simplex virus type 1 thymidine kinase (HSV1-TK). Enzyme kinetic experiments showed that our lead compound, N-methyl DHBT (N-methyl-6-(1,3-dihydroxyisobutyl) thymine; N-Me DHBT), is phosphorylated at a similar rate compared to "gold standard" 9-[4-fluoro-3-(hydroxymethyl)butyl]guanine, FHBG, (K(m) = 10 ± 0.3 μM; k(cat) = 0.036 ± 0.015 sec(-1)). Additionally, it does not show cytotoxic properties on B16F1 cells up to a concentration of 10 mM. The x-ray analysis of the crystal structures of HSV1-TK with N-Me DHBT and of HSV1-TK with the fluorinated derivative N-Me FHBT confirmed the binding mode predicted by docking studies and their substrate characteristics. Moreover, the crystal structure of HSV1-TK with N-Me DHBT revealed an additional water-mediated H-bond interesting for the design of further analogues.
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Affiliation(s)
- Miljen Martić
- Center for Pharmaceutical Science of ETH, PSI and USZ, ETH Zurich, Zurich, Switzerland
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Bernstein DI, Bravo FJ, Clark JR, Earwood JD, Rahman A, Glazer R, Cardin RD. N-Methanocarbathymidine is more effective than acyclovir for treating neonatal herpes simplex virus infection in guinea pigs. Antiviral Res 2011; 92:386-8. [PMID: 21924293 DOI: 10.1016/j.antiviral.2011.08.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 08/22/2011] [Accepted: 08/23/2011] [Indexed: 11/25/2022]
Abstract
The outcome of neonatal herpes simplex (HSV) infection, even after therapy with high dose acyclovir (ACV), is not optimum. We therefore evaluated N-Methanocarbathymidine ((N)-MCT) using the guinea pig model of neonatal herpes. Treatment with ACV (60 mg/kg/day) was compared to doses of 1, 5, and 25 mg/kg/day of (N)-MCT initiated 1, 2, or 3 days postinoculation (dpi). Both ACV and (N)-MCT significantly improved survival, but only (N)-MCT significantly reduced the number of animals with symptoms when begun at 1 dpi. When therapy was begun at 2 dpi, only (N)-MCT (1, 5, or 25 mg/kg/day) significantly increased survival. In fact, (N)-MCT improved survival up to 3 dpi, the last time point evaluated. (N)-MCT was highly effective and superior to high dose ACV therapy for the treatment of neonatal herpes in the guinea pig model.
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Affiliation(s)
- David I Bernstein
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States.
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Niculescu-Duvaz D, Negoita-Giras G, Niculescu-Duvaz I, Hedley D, Springer CJ. Directed Enzyme Prodrug Therapies. PRODRUGS AND TARGETED DELIVERY 2011. [DOI: 10.1002/9783527633166.ch12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Antiviral Activity of 4'-thioIDU and Thymidine Analogs against Orthopoxviruses. Viruses 2010; 2:1968-1983. [PMID: 21994716 PMCID: PMC3185742 DOI: 10.3390/v2091968] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 08/20/2010] [Accepted: 09/07/2010] [Indexed: 11/17/2022] Open
Abstract
The search for effective therapies for orthopoxvirus infections has identified diverse classes of molecules with antiviral activity. Pyrimidine analogs, such as 5-iodo-2'-deoxyuridine (idoxuridine, IDU) were among the first compounds identified with antiviral activity against a number of orthopoxviruses and have been reported to be active both in vitro and in animal models of infection. More recently, additional analogs have been reported to have improved antiviral activity against orthopoxviruses including several derivatives of deoxyuridine with large substituents in the 5 position, as well as analogs with modifications in the deoxyribose moiety including (north)-methanocarbathymidine, and 5-iodo-4'-thio-2'-deoxyuridine (4'-thioIDU). The latter molecule has proven to have good antiviral activity against the orthopoxviruses both in vitro and in vivo and has the potential to be an effective therapy in humans.
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Michel BY, Strazewski P. Total syntheses of a conformationally locked North-type methanocarba puromycin analogue and a dinucleotide derivative. Chemistry 2009; 15:6244-57. [PMID: 19441002 DOI: 10.1002/chem.200802629] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An original synthetic approach for the first synthesis of an enantiopure methanocarba puromycin (3'-alpha-aminoacylamino-3'-deoxyadenosine) analogue and its cytidine dinucleotide derivative is described. Each compound is conformationally locked in a North-type pucker and exhibits both a pseudoaxial hydroxy group and a pseudoequatorial aminoacyl group. The syntheses were accomplished from D-ribose in 18 and 19 steps, respectively, with key steps being a ring-closing metathesis, a Luche reduction, a Simmons-Smith cyclopropanation, a Mitsunobu coupling, a Mattocks bromoacetylation, a regioselective and a stereoselective nucleophilic substitution, a chemoselective phosphoramidite coupling and a Staudinger-Vilarrasa coupling. Both molecules are being tested for peptidyl transfer efficiency in ribosomes for comparison with the peptidyl transfer kinetics of natural puromycin and other natural and synthetic ribosomal A site substrates.
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Affiliation(s)
- Benoît Y Michel
- UMR 5246, CNRS, Laboratoire de Synthèse de Biomolécules, Université Claude Bernard Lyon 1, Villeurbanne, Université de Lyon, 69622 Lyon, France
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Mehellou Y, Balzarini J, McGuigan C. An investigation into the anti-HIV activity of 2′,3′-didehydro-2′,3′-dideoxyuridine (d4U) and 2′,3′-dideoxyuridine (ddU) phosphoramidate ‘ProTide’ derivatives. Org Biomol Chem 2009; 7:2548-53. [DOI: 10.1039/b904276h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Melman A, Zhong M, Marquez VE, Jacobson KA. Synthesis of enantiomerically pure (S)-methanocarbaribo uracil nucleoside derivatives for use as antiviral agents and P2Y receptor ligands. J Org Chem 2008; 73:8085-8. [PMID: 18811198 DOI: 10.1021/jo801224j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed an approach toward enantiomerically pure (S)-methanocarba ribonucleosides based on several functional group transformations on a sensitive bicyclo[3.1.0]hexane system. D-ribose was transformed into methanocarba alcohol 3 followed by conversion of the OH group to a nitrile with inversion of configuration at C4. The nitrile group was subsequently reduced in two stages to the 5'-hydroxymethyl group. An ester group appended to a tertiary carbon (C1) was transformed to an amino group as a nucleobase precursor.
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Affiliation(s)
- Artem Melman
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699, USA
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Smee DF, Hurst BL, Wong MH, Glazer RI, Rahman A, Sidwell RW. Efficacy of N-methanocarbathymidine in treating mice infected intranasally with the IHD and WR strains of vaccinia virus. Antiviral Res 2007; 76:124-9. [PMID: 17658623 PMCID: PMC2268765 DOI: 10.1016/j.antiviral.2007.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2006] [Revised: 04/23/2007] [Accepted: 06/18/2007] [Indexed: 10/23/2022]
Abstract
N-Methanocarbathymidine [(N)-MCT] is a newly identified inhibitor of orthopoxvirus replication in cell culture and in mice. Limited published animal studies indicated the compound is effective by intraperitoneal (i.p.) route at 10-100 mg/(kg day). More extensive studies using different treatment regimens in intranasally infected mice were conducted in order to further explore the potential of this compound compared to cidofovir in treating vaccinia virus infections. (N)-MCT was given twice a day for 7 days, whereas cidofovir was administered once a day for 2 days, each starting 24h after virus exposure for most experiments. (N)-MCT was not toxic up to 1000 mg/(kg day) by the i.p. treatment route. Oral and i.p. treatment regimens with (N)-MCT were directly compared during a vaccinia virus (IHD strain) infection, indicating that the nucleoside has good oral bioavailability in mice. Treatments by i.p. route with (N)-MCT (100 mg/(kg day)) reduced lung, nasal, and brain virus titers during an IHD virus infection, but not nearly to the same extent as i.p. cidofovir (100 mg/(kg day)). Treatment with both compounds decreased liver, spleen, and kidney virus titers, as well as reduced lung consolidation scores and lung weights. Onset of treatment could be delayed by 2 days with (N)-MCT and by 3 days with cidofovir, providing significant survival benefit during the IHD virus infection. Against a vaccinia virus (WR strain) infection in mice, i.p. (N)-MCT treatment prevented death at 500 mg/(kg day), which was comparable in activity to i.p. cidofovir (100 mg/(kg day)). Significant reductions in tissue virus titers occurred with both treatment regimens. (N)-MCT could be further pursued for its potential to treat orthopoxvirus infections in humans.
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Affiliation(s)
- Donald F Smee
- Institute for Antiviral Research, Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-5600, USA
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17
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Comin MJ, Agbaria R, Ben-Kasus T, Huleihel M, Liao C, Sun G, Nicklaus MC, Deschamps JR, Parrish DA, Marquez VE. Sculpting the bicyclo[3.1.0]hexane template of carbocyclic nucleosides to improve recognition by herpes thymidine kinase. J Am Chem Soc 2007; 129:6216-22. [PMID: 17451242 DOI: 10.1021/ja0688732] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The replacement of the furanose ring by a cyclopentane in nucleosides generates a group of analogues known generically as carbocyclic nucleosides. These compounds have increased chemical and enzymatic stability due to the absence of a true glycosyl bond that characterizes conventional nucleosides. The additional fusion of a cyclopropane ring to the cyclopentane produces a bicyclo[3.1.0]hexane system that depending on its location relative to the nucleobase is able to lock the embedded cyclopentane ring into conformations that mimic the typical north and south conformations of the furanose ring in conventional nucleosides. These bicyclo[3.1.0]hexane templates have already provided important clues to differentiate the contrasting conformational preferences between kinases and polymerases. Herein, we describe the design, synthesis, and phosphorylation pattern of a new bicyclo[3.1.0]hexane thymidine analogue that seems to possess an ideal spatial distribution of pharmacophores for an optimal interaction with herpes simplex 1 thymidine kinase. The bicyclo[3.1.0]hexane template represents a privileged rigid template for sculpting other carbocyclic nucleosides to meet the demands of specific receptors.
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Affiliation(s)
- Maria J Comin
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, 376 Boyles Street, Frederick, Maryland 21702, USA
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18
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Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WTM, Mortenson PN, Murray CW. Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem 2007; 50:726-41. [PMID: 17300160 DOI: 10.1021/jm061277y] [Citation(s) in RCA: 447] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A procedure for analyzing and classifying publicly available crystal structures has been developed. It has been used to identify high-resolution protein-ligand complexes that can be assessed by reconstructing the electron density for the ligand using the deposited structure factors. The complexes have been clustered according to the protein sequences, and clusters have been discarded if they do not represent proteins thought to be of direct interest to the pharmaceutical or agrochemical industry. Rules have been used to exclude complexes containing non-drug-like ligands. One complex from each cluster has been selected where a structure of sufficient quality was available. The final Astex diverse set contains 85 diverse, relevant protein-ligand complexes, which have been prepared in a format suitable for docking and are to be made freely available to the entire research community (http://www.ccdc.cam.ac.uk). The performance of the docking program GOLD against the new set is assessed using a variety of protocols. Relatively unbiased protocols give success rates of approximately 80% for redocking into native structures, but it is possible to get success rates of over 90% with some protocols.
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Affiliation(s)
- Michael J Hartshorn
- Astex Therapeutics, Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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19
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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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20
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Structure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design. BMC STRUCTURAL BIOLOGY 2006; 6:22. [PMID: 17062140 PMCID: PMC1636055 DOI: 10.1186/1472-6807-6-22] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Accepted: 10/24/2006] [Indexed: 11/23/2022]
Abstract
Background Development of countermeasures to bioterrorist threats such as those posed by the smallpox virus (variola), include vaccination and drug development. Selective activation of nucleoside analogues by virus-encoded thymidine (dThd) kinases (TK) represents one of the most successful strategies for antiviral chemotherapy as demonstrated for anti-herpes drugs. Vaccinia virus TK is a close orthologue of variola TK but also shares a relatively high sequence identity to human type 2 TK (hTK), thus achieving drug selectivity relative to the host enzyme is challenging. Results In order to identify any differences compared to hTK that may be exploitable in drug design, we have determined the crystal structure of VVTK, in complex with thymidine 5'-triphosphate (dTTP). Although most of the active site residues are conserved between hTK and VVTK, we observe a difference in conformation of residues Asp-43 and Arg-45. The equivalent residues in hTK hydrogen bond to dTTP, whereas in subunit D of VVTK, Asp-43 and Arg-45 adopt a different conformation preventing interaction with this nucleotide. Asp-43 and Arg-45 are present in a flexible loop, which is disordered in subunits A, B and C. The observed difference in conformation and flexibility may also explain the ability of VVTK to phosphorylate (South)-methanocarbathymine whereas, in contrast, no substrate activity with hTK is reported for this compound. Conclusion The difference in conformation for Asp-43 and Arg-45 could thus be used in drug design to generate VVTK/Variola TK-selective nucleoside analogue substrates and/or inhibitors that have lower affinity for hTK.
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21
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Iqbal J, Scapozza L, Folkers G, Müller CE. Development and validation of a capillary electrophoresis method for the characterization of herpes simplex virus type 1 (HSV-1) thymidine kinase substrates and inhibitors. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 846:281-90. [PMID: 17023224 DOI: 10.1016/j.jchromb.2006.09.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 08/31/2006] [Accepted: 09/08/2006] [Indexed: 11/16/2022]
Abstract
A fast, convenient capillary electrophoresis (CE) method was developed for monitoring the enzymatic reaction of herpes simplex virus type 1 thymidine kinase (HSV-1 TK). The reaction was performed in a test tube followed by quantitative analysis of the products. The optimized CE conditions were as follows: polyacrylamide-coated capillary (20 cm effective length x 50 microm), electrokinetic injection for 30s, 50 mM phosphate buffer at pH 6.5, constant current of -60 microA, UV detection at 210 nm, UMP or cAMP were used as internal standards. Phosphorylated products eluted within less than 7 min. The limits of detection were 0.36 microM for dTMP and 0.86 microM for GMP. The method was used to study enzyme kinetics, and to investigate alternative substrates and inhibitors.
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Affiliation(s)
- Jamshed Iqbal
- Pharmaceutical Institute, Department of Pharmaceutical Chemistry Poppelsdorf, University of Bonn, Kreuzbergweg 26, D-53115 Bonn, Germany
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22
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Marquez VE, Hughes SH, Sei S, Agbaria R. The history of N-methanocarbathymidine: The investigation of a conformational concept leads to the discovery of a potent and selective nucleoside antiviral agent. Antiviral Res 2006; 71:268-75. [PMID: 16730077 DOI: 10.1016/j.antiviral.2006.04.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 04/11/2006] [Accepted: 04/13/2006] [Indexed: 10/24/2022]
Abstract
Conformationally locked (North)-methanocarbathymidine (N-MCT) and (South)-methanocarbathymidine (S-MCT) have been used to investigate the conformational preferences of kinases and polymerases. The herpes kinases show a distinct bias for S-MCT, while DNA polymerases almost exclusively incorporate the North 5'-triphosphate (N-MCT-TP). Only N-MCT demonstrated potent antiviral activity against herpes simplex viruses (HSV-1 and 2) and Kaposi's sarcoma-associated herpesvirus (KSHV). The activity of N-MCT depends on its metabolic transformation to N-MCT-TP by the herpes kinases (HSV-tk or KSHV-tk), which catalyze the mono and diphosphorylation steps; cellular kinases generate the triphosphate. N-MCT at a dose of 5.6 mg/kg was totally protective for mice inoculated intranasally with HSV-1. Tumor cells that are not responsive to antiviral therapy became sensitive to N-MCT if the cells expressed HSV-tk. N-MCT given twice daily (100 mg/kg) for 7 days completely inhibited the growth of MC38 tumors derived from cells that express HSV-tk in mice while exhibiting no effect on tumors derived from non-transduced cells. After i.p. administration, N-MCT was rapidly absorbed and distributed in all organs examined with slow penetration into brain and testes. N-MCT-TP was also a potent inhibitor of HIV replication in human osteosarcoma (HOS) cells expressing HSV-tk.
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Affiliation(s)
- Victor E Marquez
- Laboratory of Medicinal Chemistry, National Cancer Institute at Frederick, P.O. Box B, Building 539, Frederick, MD 21702, USA.
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Prichard MN, Keith KA, Quenelle DC, Kern ER. Activity and mechanism of action of N-methanocarbathymidine against herpesvirus and orthopoxvirus infections. Antimicrob Agents Chemother 2006; 50:1336-41. [PMID: 16569849 PMCID: PMC1426929 DOI: 10.1128/aac.50.4.1336-1341.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N-Methanocarbathymidine [(N)-MCT] is a conformationally locked nucleoside analog that is active against some herpesviruses and orthopoxviruses in vitro. The antiviral activity of this molecule is dependent on the type I thymidine kinase (TK) in herpes simplex virus and also appears to be dependent on the type II TK expressed by cowpox and vaccinia viruses, suggesting that it is a substrate for both of these divergent forms of the enzyme. The drug is also a good inhibitor of viral DNA synthesis in both viruses and is consistent with inhibition of the viral DNA polymerase once it is activated by the viral TK homologs. This mechanism of action explains the rather unusual spectrum of activity, which is limited to orthopoxviruses, alphaherpesviruses, and Epstein-Barr virus, since these viruses express molecules with TK activity that can phosphorylate and thus activate the drug. The compound is also effective in vivo and reduces the mortality of mice infected with orthopoxviruses, as well as those infected with herpes simplex virus type 1 when treatment is initiated 24 h after infection. These results indicate that (N)-MCT is active in vitro and in vivo, and its mechanism of action suggests that the molecule may be an effective therapeutic for orthopoxvirus and herpesvirus infections, thus warranting further development.
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Affiliation(s)
- Mark N Prichard
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL 35233, USA.
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Smee DF, Wandersee MK, Bailey KW, Wong MH, Chu CK, Gadthula S, Sidwell RW. Cell line dependency for antiviral activity and in vivo efficacy of N-methanocarbathymidine against orthopoxvirus infections in mice. Antiviral Res 2006; 73:69-77. [PMID: 16712967 DOI: 10.1016/j.antiviral.2006.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 04/12/2006] [Accepted: 04/13/2006] [Indexed: 10/24/2022]
Abstract
A novel carbocyclic thymidine analog, N-methanocarbathymidine [(N)-MCT], was evaluated for inhibition of orthopoxvirus infections. Efficacy in vitro was assessed by plaque reduction assays against wild-type and cidofovir-resistant strains of cowpox and vaccinia viruses in nine different cell lines. Minimal differences were seen in antiviral activity against wild-type and cidofovir-resistant viruses. (N)-MCT's efficacy was affected by the cell line used for assay, with 50% poxvirus-inhibitory concentrations in cells as follows: mouse=0.6-2.2 microM, rabbit=52-90 microM, monkey=87 to >1000 microM, and human=39-220 microM. Limited studies performed with carbocyclic thymidine indicated a similar cell line dependency for antiviral activity. (N)-MCT did not inhibit actively dividing uninfected cells at 1000 microM. The potency of (N)-MCT against an S-variant thymidine kinase-deficient vaccinia virus was similar to that seen against S-variant and wild-type viruses in mouse, monkey, and human cells, implicating a cellular enzyme in the phosphorylation of the compound. Mice were intranasally infected with cowpox and vaccinia viruses followed 24h later by intraperitoneal treatment with (N)-MCT (twice a day for 7 days) or cidofovir (once a day for 2 days). (N)-MCT treatment at 100 and 30 mg/kg/day resulted in 90 and 20% survival from cowpox virus infection, respectively, compared to 0% survival in the placebo group. Statistically significant reductions in lung virus titers on day 5 occurred in 10, 30, and 100mg/kg/day treated mice. These same doses were also active against a lethal vaccinia virus (WR strain) challenge, and protection was seen down to 10mg/kg/day against a lethal vaccinia virus (IHD strain) infection. Cidofovir (100mg/kg/day) protected animals from death in all three infections.
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Affiliation(s)
- Donald F Smee
- Institute for Antiviral Research, Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-5600, USA.
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25
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Zhu W, Burnette A, Dorjsuren D, Roberts PE, Huleihel M, Shoemaker RH, Marquez VE, Agbaria R, Sei S. Potent antiviral activity of north-methanocarbathymidine against Kaposi's sarcoma-associated herpesvirus. Antimicrob Agents Chemother 2006; 49:4965-73. [PMID: 16304159 PMCID: PMC1315933 DOI: 10.1128/aac.49.12.4965-4973.2005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) infection is a prerequisite for the development of Kaposi's sarcoma (KS). Blocking lytic KSHV replication may hinder KS tumorigenesis. Here, we report potent in vitro anti-KSHV activity of 2'-exo-methanocarbathymidine [North-methanocarbathymidine (N-MCT)], a thymidine analog with a pseudosugar ring locked in the northern conformation, which has previously been shown to block the replication of herpes simplex virus types 1 and 2. N-MCT inhibited KSHV virion production in lytically induced KSHV-infected BCBL-1 cells with a substantially lower 50% inhibitory concentration (IC50) than those of cidofovir (CDV) and ganciclovir (GCV) (IC50, mean +/- standard deviation: 0.08 +/- 0.03, 0.42 +/- 0.07, and 0.96 +/- 0.49 microM for N-MCT, CDV, and GCV, respectively). The reduction in KSHV virion production was accompanied by a corresponding decrease in KSHV DNA levels in the N-MCT-treated BCBL-1 cells, indicating that the compound blocked lytic KSHV DNA replication. A time- and dose-dependent accumulation of N-MCT-triphosphate (TP) was demonstrated in lytically induced BCBL-1 cells, while uninfected cells showed virtually no accumulation. The levels of N-MCT-TP were significantly decreased in the presence of 5'-ethynylthymidine, a potent inhibitor of herpesvirus thymidine kinase, resulting in the abrogation of anti-KSHV activity of N-MCT. N-MCT-TP more effectively blocked in vitro DNA synthesis by KSHV DNA polymerase with an IC50 of 6.24 +/- 0.08 microM (mean +/- standard deviation) compared to CDV-diphosphate (14.70 +/-2.47 microM) or GCV-TP (24.59 +/- 5.60 microM). Taken together, N-MCT is a highly potent and target-specific anti-KSHV agent which inhibits lytic KSHV DNA synthesis through its triphosphate metabolite produced in KSHV-infected cells expressing a virally encoded thymidine kinase.
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Affiliation(s)
- Weimin Zhu
- Laboratory of Antiviral Drug Mechanisms, SAIC-Frederick, Frederick, Maryland 21702, USA
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26
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Marquez VE, Choi Y, Comin MJ, Russ P, George C, Huleihel M, Ben-Kasus T, Agbaria R. Understanding How the Herpes Thymidine Kinase Orchestrates Optimal Sugar and Nucleobase Conformations To Accommodate Its Substrate at the Active Site: A Chemical Approach. J Am Chem Soc 2005; 127:15145-50. [PMID: 16248655 DOI: 10.1021/ja053789s] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The herpes virus thymidine kinase (HSV-tk) is a critical enzyme for the activation of anti-HSV nucleosides. However, a successful therapeutic outcome depends not only on the activity of this enzyme but also on the ability of the compound(s) to interact effectively with cellular kinases and with the target viral or cellular DNA polymerases. Herein, we describe the synthesis and study of two nucleoside analogues built on a conformationally locked bicyclo[3.1.0]hexane template designed to investigate the conformational preferences of HSV-tk for the 2'-deoxyribose ring. Intimately associated with the conformation of the 2'-deoxyribose ring is the value of the C-N torsion angle chi, which positions the nucleobase into two different domains (syn or anti). The often-conflicting sugar and nucleobase conformational parameters were studied using North and South methanocarbadeoxythymidine analogues (6 and 7), which forced HSV-tk to make a clear choice in the conformation of the substrate. The results provide new insights into the mechanism of action of this enzyme, which cannot be gleaned from a static X-ray crystal structure.
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Affiliation(s)
- Victor E Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA.
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27
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Birringer MS, Claus MT, Folkers G, Kloer DP, Schulz GE, Scapozza L. Structure of a type II thymidine kinase with bound dTTP. FEBS Lett 2005; 579:1376-82. [PMID: 15733844 DOI: 10.1016/j.febslet.2005.01.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Revised: 12/06/2004] [Accepted: 01/09/2005] [Indexed: 11/23/2022]
Abstract
The structure of human cytosolic thymidine kinase in complex with its feedback inhibitor 2'-deoxythymidine-5'-triphosphate was determined. This structure is the first representative of the type II thymidine kinases found in several pathogens. The structure deviates strongly from the known structures of type I thymidine kinases such as the Herpes simplex enzyme. It contains a zinc-binding domain with four cysteines complexing a structural zinc ion. Interestingly, the backbone atoms of the type II enzyme bind thymine via hydrogen-bonds, in contrast to type I, where side chains are involved. This results in a specificity difference exploited for antiviral therapy. The presented structure will foster the development of new drugs and prodrugs for numerous therapeutic applications.
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Affiliation(s)
- Markus S Birringer
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Wolfgang-Pauli Strasse 10, 8093 Zurich, Switzerland
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