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Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3-Diketone-Modified Nucleotides and DNA for Cross-Linking with Arginine-Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021; 60:17383-17387. [PMID: 34107150 PMCID: PMC8362068 DOI: 10.1002/anie.202105126] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/27/2021] [Indexed: 12/28/2022]
Abstract
Linear or branched 1,3-diketone-linked thymidine 5'-O-mono- and triphosphate were synthesized through CuAAC click reaction of diketone-alkynes with 5-azidomethyl-dUMP or -dUTP. The triphosphates were good substrates for KOD XL DNA polymerase in primer extension synthesis of modified DNA. The nucleotide bearing linear 3,5-dioxohexyl group (HDO) efficiently reacted with arginine-containing peptides to form stable pyrimidine-linked conjugates, whereas the branched 2-acetyl-3-oxo-butyl (PDO) group was not reactive. Reaction with Lys or a terminal amino group formed enamine adducts that were prone to hydrolysis. This reactive HDO modification in DNA was used for bioconjugations and cross-linking with Arg-containing peptides or proteins (e.g. histones).
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Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
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2
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Ferey J, Da Silva D, Colas C, Lafite P, Topalis D, Roy V, Agrofoglio LA, Daniellou R, Maunit B. Monitoring of phosphorylation using immobilized kinases by on-line enzyme bioreactors hyphenated with High-Resolution Mass Spectrometry. Talanta 2019; 205:120120. [PMID: 31450426 DOI: 10.1016/j.talanta.2019.120120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 11/18/2022]
Abstract
Nucleosides analogues are the cornerstone of the treatment of several human diseases. They are especially at the forefront of antiviral therapy. Their therapeutic efficiency depends on their capacity to be converted to the active nucleoside triphosphate form through successive phosphorylation steps catalyzed by nucleoside/nucleotide kinases. In this context, it is mandatory to develop a rapid, reliable and sensitive enzyme activity test to evaluate their metabolic pathways. In this study, we report a proof of concept to directly monitor on-line nucleotide multiple phosphorylation. The methodology was developed by on-line enzyme bioreactors hyphenated with High-Resolution Mass Spectrometry detection. Human Thymidylate Kinase (hTMPK) and human Nucleoside Diphosphate Kinase (hNDPK) were covalently immobilized on functionalized silica beads, and packed into micro-bioreactors (40 μL). By continuous infusion of substrate into the bioreactors, the conversion of thymidine monophosphate (dTMP) into its di- (dTDP) and tri-phosphorylated (dTTP) forms was visualized by monitoring their Extracted Ion Chromatogram (EIC) of their [M - H]- ions. Both bioreactors were found to be robust and durable over 60 days (storage at 4 °C in ammonium acetate buffer), after 20 uses and more than 750 min of reaction, making them suitable for routine analysis. Each on-line conversion step was shown rapid (<5 min), efficient (conversion efficiency > 55%), precise and repeatable (CV < 3% for run-to-run analysis). The feasibility of the on-line multi-step conversion from dTMP to dTTP was also proved. In the context of selective antiviral therapy, this proof of concept was then applied to the monitoring of specificity of conversion of two synthesized Acyclic Nucleosides Phosphonates (ANPs), regarding human Thymidylate Kinase (hTMPK) and vaccina virus Thymidylate Kinase (vvTMPK).
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Affiliation(s)
- Justine Ferey
- Univ. Orléans, CNRS, ICOA, UMR 7311, F-45067, Orléans, France.
| | - David Da Silva
- Univ. Orléans, CNRS, ICOA, UMR 7311, F-45067, Orléans, France
| | - Cyril Colas
- Univ. Orléans, CNRS, ICOA, UMR 7311, F-45067, Orléans, France; CNRS, CBM, UPR 4301, Univ-Orléans, F-45071, Orléans, France
| | - Pierre Lafite
- Univ. Orléans, CNRS, ICOA, UMR 7311, F-45067, Orléans, France
| | - Dimitrios Topalis
- Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1043, 3000, Leuven, Belgium
| | - Vincent Roy
- Univ. Orléans, CNRS, ICOA, UMR 7311, F-45067, Orléans, France
| | | | | | - Benoît Maunit
- Univ. Orléans, CNRS, ICOA, UMR 7311, F-45067, Orléans, France
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Balaev VV, Lashkov AA, Gabdulkhakov AG, Dontsova MV, Seregina TA, Mironov AS, Betzel C, Mikhailov AM. Structural investigation of the thymidine phosphorylase from Salmonella typhimurium in the unliganded state and its complexes with thymidine and uridine. Acta Crystallogr F Struct Biol Commun 2016; 72:224-33. [PMID: 26919527 PMCID: PMC4774882 DOI: 10.1107/s2053230x1600162x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/26/2016] [Indexed: 11/10/2022] Open
Abstract
Highly specific thymidine phosphorylases catalyze the phosphorolytic cleavage of thymidine, with the help of a phosphate ion, resulting in thymine and 2-deoxy-α-D-ribose 1-phosphate. Thymidine phosphorylases do not catalyze the phosphorolysis of uridine, in contrast to nonspecific pyrimidine nucleoside phosphorylases and uridine phosphorylases. Understanding the mechanism of substrate specificity on the basis of the nucleoside is essential to support rational drug-discovery investigations of new antitumour and anti-infective drugs which are metabolized by thymidine phosphorylases. For this reason, X-ray structures of the thymidine phosphorylase from Salmonella typhimurium were solved and refined: the unliganded structure at 2.05 Å resolution (PDB entry 4xr5), the structure of the complex with thymidine at 2.55 Å resolution (PDB entry 4yek) and that of the complex with uridine at 2.43 Å resolution (PDB entry 4yyy). The various structural features of the enzyme which might be responsible for the specificity for thymidine and not for uridine were identified. The presence of the 2'-hydroxyl group in uridine results in a different position of the uridine furanose moiety compared with that of thymidine. This feature may be the key element of the substrate specificity. The specificity might also be associated with the opening/closure mechanism of the two-domain subunit structure of the enzyme.
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Affiliation(s)
- Vladislav V. Balaev
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Alexander A. Lashkov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Azat G. Gabdulkhakov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Maria V. Dontsova
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Tatiana A. Seregina
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1-st Dorozhny Proezd 1, Moscow 117545, Russian Federation
| | - Alexander S. Mironov
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1-st Dorozhny Proezd 1, Moscow 117545, Russian Federation
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Institute of Biochemistry and Molecular Biology, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Al’bert M. Mikhailov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
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Wang N, Jiang J, Li X, Tan H, Zheng J, Chen G, Jia Z. Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization. PLoS One 2015; 10:e0134879. [PMID: 26252214 PMCID: PMC4529217 DOI: 10.1371/journal.pone.0134879] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/14/2015] [Indexed: 11/18/2022] Open
Abstract
YhdE is a Maf-like (multicopy associated filamentation) protein that primarily acts as dTTPase to hydrolyze dTTP into dTMP and two phosphate molecules in cell metabolism pathway. Two crystal structures of YhdE have been previously determined, representing the open and closed active site conformations, respectively. Based on the structures, we have carried out molecular dynamics simulations and free energy calculations to investigate dTTP binding to and hydrolysis by YhdE. Our results suggest that YhdE closed state is structurally more compact than its open state at room temperature. YhdE open state is a favorable conformation for dTTP binding and closed state is a structurally favorable conformation for catalytic reaction. This observation is supported by the structure of YhdE homolog in complex with a nucleotide analog. Free energy calculations reveal that YhdE dimerization occurs preferentially in dTTP binding and is favorable for successive cooperative reaction. The key residues R11, R12 and K80, are found to contribute to the substrate stabilization. Further, YhdE dimerization and binding of dTTP induce the cooperative effect through a direct allosteric communication network in YhdE from the dTTP binding sites in the catalytic center to the intermolecular β-strand in YhdE dimer.
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Affiliation(s)
- Nan Wang
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Jiahong Jiang
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Xichen Li
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Hongwei Tan
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing, China
- * E-mail: (JMZ); (ZCJ)
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
- * E-mail: (JMZ); (ZCJ)
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5
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Abstract
Novel α,β-CH2 and β,γ-NH (1a) or α,β-NH and β,γ-CH2 (1b) "Met-Im" dTTPs were synthesized via monodemethylation of triethyl-dimethyl phosphorimido-bisphosphonate synthons (4a, 4b), formed via a base-induced [1,3]-rearrangement of precursors (3a, 3b) in a reaction with dimethyl or diethyl phosphochloridate. Anomerization during final bromotrimethylsilane (BTMS) deprotection after Mitsunobu conjugation with dT was avoided by microwave conditions. 1a was 9-fold more potent in inhibiting DNA polymerase β, attributed to an NH-group interaction with R183 in the active site.
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Affiliation(s)
- Anastasia P. Kadina
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Keriann Oertell
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Vinod K. Batra
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Myron F. Goodman
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
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Ivanov MA, Karpenko IL, Chernousova LN, Andreevskaia SN, Smirnova TG, Aleksandrova LA. [Synthesis and biological properties of α-thymidine 5'-aryl phosphonates]. Bioorg Khim 2015; 39:718-27. [PMID: 25696933 DOI: 10.1134/s1068162013060058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The interaction of CDI-activated diethyl phosphonoacetate with methyl 4-aminobenzoat or 3,5-difluoromethylphenylamine followed by treatment with Me3SiBr in DMF led to N-aryl aminocarbonylmethyl phosphonates and their ethyl esters. Their coupling with 3'-acetyl-α-thymidine followed by removal of the acetyl groups gave (α-D-thymidine-5'-il) N-[4-(methoxycarbonyl-, aminocarbonyl- and carboxy)phenyl]-aminocarbonylmethyl phosphonates, (α-D-thymidine-5'-il)-[3,5-bis(trifluoromethyl)phenylaminocarbonyl]methyl phosphonate and their ethyl esters. The phosphonates were stable in different conditions, low cytotoxic (in Vero and K562 cells) and were able to penetrate into K562 cells. The only ethyl ester of (α-D-thymidine-5'-il) N-[4-(methoxycarbonyl)phenyl]-aminocarbonylmethyl phosphonate in high concentration (200 μg/mL) inhibited in vitro the growth of laboratory sensitive strain of Mycobacterium tuberculosis H37Rv.
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7
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Vasilyeva SV, Levina AS, Li-Zhulanov NS, Shatskaya NV, Baiborodin SI, Repkova MN, Zarytova VF, Mazurkova NA, Silnikov VN. SiO₂ nanoparticles as platform for delivery of 3'-triazole analogues of AZT-triphosphate into cells. Bioorg Med Chem 2015; 23:2168-75. [PMID: 25801161 DOI: 10.1016/j.bmc.2015.02.063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 11/18/2022]
Abstract
A system for delivery of analogues of AZT-triphosphates (AZT*TP) based on SiO₂ nanoparticles was proposed. For this purpose, a simple and versatile method was developed for the preparation of SiO₂∼dNTP conjugates using the 'click'-reaction between AZTTP and premodified nanoparticles containing the alkyne groups. The substrate properties of SiO₂∼AZT*TP were tested using Klenow fragment and HIV reverse transcriptase. The 3'-triazole derivatives of thymidine triphosphate being a part of the SiO₂∼AZT*TP nanocomposites were shown to be incorporated into the growing DNA chain. It was shown by confocal microscopy that the proposed SiO₂∼AZT*TP nanocomposites penetrate into cells. These nanocomposites were shown to inhibit the reproduction of POX and Herpes viruses at nontoxic concentrations.
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Affiliation(s)
- Svetlana V Vasilyeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia.
| | - Asya S Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Nikolai S Li-Zhulanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Natalia V Shatskaya
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergei I Baiborodin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina N Repkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Valentina F Zarytova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
| | - Natalia A Mazurkova
- FBRI State Research Centre of Virology and Biotechnology 'Vector', Novosibirsk, Russia
| | - Vladimir N Silnikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, 630090 Novosibirsk, Russia
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Abstract
Post-synthesis DNA modification is a very useful method for DNA functionalization. This is achieved by using a modified NTP, which has a handle for further modifications, replacing the corresponding natural NTP in polymerase-catalyzed DNA synthesis. Subsequently, the handle can be used for further functionalization after PCR, preferably through a very fast reaction. Herein we describe polymerase-mediated incorporation of trans-cyclooctene modified thymidine triphosphate (TCO-TTP). Subsequently, the trans-cyclooctene group was reacted with a tetrazine tethered to other functional groups through a very fast click reaction. The utility of this DNA functionalization method was demonstrated with the incorporation of a boronic acid group and a fluorophore. The same approach was also successfully used in modifying a known aptamer for fluorescent labelling applications.
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Affiliation(s)
- Ke Wang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA.
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Saiko P, Steinmann MT, Schuster H, Graser G, Bressler S, Giessrigl B, Lackner A, Grusch M, Krupitza G, Bago-Horvath Z, Jaeger W, Fritzer-Szekeres M, Szekeres T. Epigallocatechin gallate, ellagic acid, and rosmarinic acid perturb dNTP pools and inhibit de novo DNA synthesis and proliferation of human HL-60 promyelocytic leukemia cells: Synergism with arabinofuranosylcytosine. Phytomedicine 2015; 22:213-22. [PMID: 25636891 DOI: 10.1016/j.phymed.2014.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 06/04/2023]
Abstract
Epigallocatechin gallate (EGCG), ellagic acid (EA) and rosmarinic acid (RA) are natural polyphenols exerting cancer chemopreventive effects. Ribonucleotide reductase (RR; EC 1.17.4.1) converts ribonucleoside diphosphates into deoxyribonucleoside diphosphates being essential for DNA replication, which is why the enzyme is considered an excellent target for anticancer therapy. EGCG, EA, and RA dose-dependently inhibited the growth of human HL-60 promyelocytic leukemia cells, exerted strong free radical scavenging potential, and significantly imbalanced nuclear deoxyribonucleoside triphosphate (dNTP) concentrations without distinctly affecting the protein levels of RR subunits (R1, R2, p53R2). Incorporation of (14)C-cytidine into nascent DNA of tumor cells was also significantly lowered, being equivalent to an inhibition of DNA synthesis. Consequently, treatment with EGCG and RA attenuated cells in the G0/G1 phase of the cell cycle, finally resulting in a pronounced induction of apoptosis. Sequential combination of EA and RA with the first-line antileukemic agent arabinofuranosylcytosine (AraC) synergistically potentiated the antiproliferative effect of AraC, whereas EGCG plus AraC yielded additive effects. Taken together, we show for the first time that EGCG, EA, and RA perturbed dNTP levels and inhibited cell proliferation in human HL-60 promyelocytic leukemia cells, with EGCG and RA causing a pronounced induction of apoptosis. Due to these effects and synergism with AraC, these food ingredients deserve further preclinical and in vivo testing as inhibitors of leukemic cell proliferation.
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Affiliation(s)
- Philipp Saiko
- Department of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Marie-Thérèse Steinmann
- Department of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Heike Schuster
- Department of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Geraldine Graser
- Department of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Sabine Bressler
- Department of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Benedikt Giessrigl
- Department of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Andreas Lackner
- Department of Medicine I, Division of Cancer Research, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | - Michael Grusch
- Department of Medicine I, Division of Cancer Research, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | - Georg Krupitza
- Department of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Zsuzsanna Bago-Horvath
- Department of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Walter Jaeger
- Department of Clinical Pharmacy and Diagnostics, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Monika Fritzer-Szekeres
- Department of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Thomas Szekeres
- Department of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.
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10
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Kono N, Arai H. [Regulation of the vitamin E level in the body by alpha-TTP, alpha-tocopherol-specific transfer protein]. Seikagaku 2014; 86:232-241. [PMID: 24864450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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11
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Cafarelli TM, Rands TJ, Godoy VG. The DinB•RecA complex of Escherichia coli mediates an efficient and high-fidelity response to ubiquitous alkylation lesions. Environ Mol Mutagen 2014; 55:92-102. [PMID: 24243543 DOI: 10.1002/em.21826] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/12/2013] [Indexed: 06/02/2023]
Abstract
Alkylation DNA lesions are ubiquitous, and result from normal cellular metabolism as well as from treatment with methylating agents and chemotherapeutics. DNA damage tolerance by translesion synthesis DNA polymerases has an important role in cellular resistance to alkylating agents. However, it is not yet known whether Escherichia coli (E. coli) DNA Pol IV (DinB) alkylation lesion bypass efficiency and fidelity in vitro are similar to those inferred by genetic analyses. We hypothesized that DinB-mediated bypass of 3-deaza-3-methyladenine, a stable analog of 3-methyladenine, the primary replication fork-stalling alkylation lesion, would be of high fidelity. We performed here the first kinetic analyses of E. coli DinB•RecA binary complexes. Whether alone or in a binary complex, DinB inserted the correct deoxyribonucleoside triphosphate (dNTP) opposite either lesion-containing or undamaged template; the incorporation of other dNTPs was largely inefficient. DinB prefers undamaged DNA, but the DinB•RecA binary complex increases its catalytic efficiency on lesion-containing template, perhaps as part of a regulatory mechanism to better respond to alkylation damage. Notably, we find that a DinB derivative with enhanced affinity for RecA, either alone or in a binary complex, is less efficient and has a lower fidelity than DinB or DinB•RecA. This finding contrasts our previous genetic analyses. Therefore, mutagenesis resulting from alkylation lesions is likely limited in cells by the activity of DinB•RecA. These two highly conserved proteins play an important role in maintaining genomic stability when cells are faced with ubiquitous DNA damage. Kinetic analyses are important to gain insights into the mechanism(s) regulating TLS DNA polymerases.
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Agostoni V, Chalati T, Horcajada P, Willaime H, Anand R, Semiramoth N, Baati T, Hall S, Maurin G, Chacun H, Bouchemal K, Martineau C, Taulelle F, Couvreur P, Rogez-Kreuz C, Clayette P, Monti S, Serre C, Gref R. Towards an improved anti-HIV activity of NRTI via metal-organic frameworks nanoparticles. Adv Healthc Mater 2013; 2:1630-7. [PMID: 23776182 DOI: 10.1002/adhm.201200454] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Indexed: 12/22/2022]
Abstract
Nanoscale mesoporous iron carboxylates metal-organic frameworks (nanoMOFs) have recently emerged as promising platforms for drug delivery, showing biodegradability, biocompatibility and important loading capability of challenging highly water-soluble drugs such as azidothymidine tryphosphate (AZT-TP). In this study, nanoMOFs made of iron trimesate (MIL-100) were able to act as efficient molecular sponges, quickly adsorbing up to 24 wt% AZT-TP with entrapment efficiencies close to 100%, without perturbation of the supramolecular crystalline organization. These data are in agreement with molecular modelling predictions, indicating maximal loadings of 33 wt% and preferential location of the drug in the large cages. Spectrophotometry, isothermal titration calorimetry, and solid state NMR investigations enable to gain insight on the mechanism of interaction of AZT and AZT-TP with the nanoMOFs, pointing out the crucial role of phosphates strongly coordinating with the unsaturated iron(III) sites. Finally, contrarily to the free AZT-TP, the loaded nanoparticles efficiently penetrate and release their cargo of active triphosphorylated AZT inside major HIV target cells, efficiently protecting against HIV infection.
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Affiliation(s)
- Valentina Agostoni
- Institut Galien, UMR 8612 CNRS Université Paris-Sud, Châtenay-Malabry, France
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Loranger MW, Beaton SA, Lines KL, Jakeman DL. Thiophosphate and thiophosphonate analogues of glucose-1-phosphate: synthesis and enzymatic activity with a thymidylyltransferase. Carbohydr Res 2013; 379:43-50. [PMID: 23872276 DOI: 10.1016/j.carres.2013.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/10/2013] [Accepted: 06/11/2013] [Indexed: 11/17/2022]
Abstract
Synthetic methods were investigated for the preparation of O and S-glucosyl thiophosphates and glucosyl 1C-thiophosphonate. Four protected glucosyl thiophosphate compounds were synthesized and characterized as precursors to glucose 1-thiophosphate. The effect of various reaction conditions and the nature of the carbohydrate and thiophosphate protecting groups and how they impact both the yields and α/β diastereoselectivity of the glucosyl thiophosphate products were explored. A novel isomerization from an O-linked to S-linked glucosyl thiophosphate was observed. α-D-Glucose-1C-thiophosphonate was synthesized and evaluated as a substrate for the thymidylyltransferase, Cps2L. Tandem mass spectrometric analysis determined the position of sulfur in the sugar nucleotide product.
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Affiliation(s)
- Matthew W Loranger
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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14
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Abstract
Inhibitors that covalently damage proteins or nucleic acids offer great potency, but are difficult to rationally design and suffer from poor specificity. Here we outline a general concept for constructing covalent inhibitors, called the two-component covalent inhibitor (TCCI). The approach takes advantage of two ligand analogs equipped with pre-reactive groups. Binding of the analogs to the adjacent sites of a target biopolymer brings the pre-reactive groups in close proximity and causes their interaction followed by covalent damage of the target. In the present study we used light-activated pre-reactive groups to inactivate a DNA polymerase. It was found that the efficiency of a traditional single-component inhibitor was greatly reduced in the presence of a non-target protein, while the TCCI was not significantly affected. Our findings suggest that TCCI approach has advantages in inactivation of biopolymers in complex multi-component systems.
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Affiliation(s)
- Evan M. Cornett
- Chemistry Department, University of Central Florida
- Burnett School of Biomedical Sciences, University of Central Florida
| | | | - Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida
- Burnett School of Biomedical Sciences, University of Central Florida
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15
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Li DG, Liu B, Zhou DW. Structural characterization of enzymatic products in the dTDP-d-Qui4NFo biosynthetic pathway using electrospray ionization tandem mass spectrometry. Rapid Commun Mass Spectrom 2013; 27:681-690. [PMID: 23418147 DOI: 10.1002/rcm.6501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 12/04/2012] [Accepted: 01/03/2013] [Indexed: 06/01/2023]
Abstract
RATIONALE Structural characterization of biosynthetic precursors is very important in assigning enzymatic function to proteins that have been identified as functional homologs on the basis of sequence homology alone. The objective of this study is to demonstrate the use of electrospray ionization tandem mass spectrometry (ESI-MS/MS) as a powerful technique for the characterization of enzymatic products in the biosynthetic pathway of deoxythymidine 5'-diphosphate-4-formamido-4,6-dideoxy-D-glucose (dTDP-D-Qui4NFo) in Providencia alcalifaciens O30. METHODS The glucose-1-phosphate thymidyltransferase (RmlA), dTDP-d-glucose 4,6-dehydratase (RmlB), dTDP-4-keto-6-deoxy-d-glucose aminotransferase (VioA), and formyltransferase (VioF) catalyzed reactions were directly monitored by ESI-MS, followed by a detailed structural characterization of the final enzymatic products using ESI-MS/MS in the negative-ion mode after minimal cleanup. RESULTS The biosynthetic pathway of dTDP-D-Qui4NFo, beginning from α-D-glucose-1-phosphate in four reaction steps catalyzed by RmlA, RmlB, VioA and VioF, was characterized solely by ESI-MS/MS. The results obtained were in good agreement with that of traditional high-performance liquid chromatography (HPLC) monitoring and preparation, as well as nuclear magnetic resonance (NMR) and ESI-MS structural characterization. CONCLUSIONS MS provides efficient and simple characterization of important unusual dTDP-sugar biosynthetic pathways in the O-chains of bacterial lipopolysaccharides.
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Affiliation(s)
- Dian-Ge Li
- TEDA School of Biological Sciences and Biotechnology, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin Research Center for Functional Genomics and Biochip, Ministry of Education, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China
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16
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Kirmizialtin S, Nguyen V, Johnson KA, Elber R. How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations. Structure 2012; 20:618-27. [PMID: 22483109 PMCID: PMC3322391 DOI: 10.1016/j.str.2012.02.018] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/21/2012] [Accepted: 02/23/2012] [Indexed: 11/26/2022]
Abstract
Nearly every enzyme undergoes a significant change in structure after binding it's substrate. Experimental and theoretical analyses of the role of changes in HIV reverse transcriptase structure in selecting a correct substrate are presented. Atomically detailed simulations using the Milestoning method predict a rate and free energy profile of the conformational change commensurate with experimental data. A large conformational change occurring on a millisecond timescale locks the correct nucleotide at the active site but promotes release of a mismatched nucleotide. The positions along the reaction coordinate that decide the yield of the reaction are not determined by the chemical step. Rather, the initial steps of weak substrate binding and protein conformational transition significantly enrich the yield of a reaction with a correct substrate, whereas the same steps diminish the reaction probability of an incorrect substrate.
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Affiliation(s)
- Serdal Kirmizialtin
- Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, 1 University Station, Austin, Texas 78712
| | - Virginia Nguyen
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway, MBB 3.122, Austin, Texas 78712, USA
| | - Kenneth A. Johnson
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway, MBB 3.122, Austin, Texas 78712, USA
| | - Ron Elber
- Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, 1 University Station, Austin, Texas 78712
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17
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Højland T, Veedu RN, Vester B, Wengel J. Enzymatic synthesis of DNA strands containing α-L-LNA (α-L-configured locked nucleic acid) thymine nucleotides. Artif DNA PNA XNA 2012; 3:14-21. [PMID: 22679529 PMCID: PMC3368812 DOI: 10.4161/adna.19272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We describe the first enzymatic incorporation of an α-L-LNA nucleotide into an oligonucleotide. It was found that the 5'-triphosphate of α-L-LNA is a substrate for the DNA polymerases KOD, 9°N(m), Phusion and HIV RT. Three dispersed α-L-LNA thymine nucleotides can be incorporated into DNA strands by all four polymerases, but they were unable to perform consecutive incorporations of α-L-LNA nucleotides. In addition it was found that primer extension can be achieved using templates containing one α-L-LNA nucleotide.
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Affiliation(s)
- Torben Højland
- Department of Physics, Chemistry and Pharmacy; Nucleic Acid Center; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense, Denmark
| | - Rakesh N. Veedu
- Department of Physics, Chemistry and Pharmacy; Nucleic Acid Center; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense, Denmark
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane, Australia
| | - Birte Vester
- Department of Physics, Chemistry and Pharmacy; Nucleic Acid Center; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy; Nucleic Acid Center; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense, Denmark
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18
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Abstract
Mix'n'match: Enzymatic total synthesis of TDP-D-olivose was achieved, starting from TDP-4-keto-6-deoxy-D-glucose, by combining three pathway enzymes with one cofactor-regenerating enzyme. The results also revealed that MtmC is a bifunctional enzyme that can perform a 4-ketoreduction necessary for D-olivose biosynthesis besides the previously found C-methyltransfer for D-mycarose biosynthesis.
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Affiliation(s)
- Guojun Wang
- Dr. G. Wang, Prof. Dr. M. K. Kharel, Dr. P. Pahari, Prof. Dr. J. Rohr Department of Pharmaceutical Sciences, University of Kentucky 789 South Limestone Street, Lexington, KY 40536-0596 (USA)
| | - Madan K. Kharel
- Dr. G. Wang, Prof. Dr. M. K. Kharel, Dr. P. Pahari, Prof. Dr. J. Rohr Department of Pharmaceutical Sciences, University of Kentucky 789 South Limestone Street, Lexington, KY 40536-0596 (USA)
- Prof. Dr. M. K. Kharel Present address: Midway College School of Pharmacy 120 Scott Perry Drive, Paintsville, KY 41240 (USA)
| | - Pallab Pahari
- Dr. G. Wang, Prof. Dr. M. K. Kharel, Dr. P. Pahari, Prof. Dr. J. Rohr Department of Pharmaceutical Sciences, University of Kentucky 789 South Limestone Street, Lexington, KY 40536-0596 (USA)
| | - Jürgen Rohr
- Dr. G. Wang, Prof. Dr. M. K. Kharel, Dr. P. Pahari, Prof. Dr. J. Rohr Department of Pharmaceutical Sciences, University of Kentucky 789 South Limestone Street, Lexington, KY 40536-0596 (USA)
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19
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Kharel MK, Lian H, Rohr J. Characterization of the TDP-D-ravidosamine biosynthetic pathway: one-pot enzymatic synthesis of TDP-D-ravidosamine from thymidine-5-phosphate and glucose-1-phosphate. Org Biomol Chem 2011; 9:1799-808. [PMID: 21264378 PMCID: PMC4482361 DOI: 10.1039/c0ob00854k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ravidomycin V and related compounds, e.g., FE35A-B, exhibit potent anticancer activities against various cancer cell lines in the presence of visible light. The amino sugar moieties (D-ravidosamine and its analogues, respectively) in these molecules contribute to the higher potencies of ravidomycin and analogues when compared to closely related compounds with neutral or branched sugars. Within the ravidomycin V biosynthetic gene cluster, five putative genes encoding NDP-D-ravidosamine biosynthetic enzymes were identified. Through the activities of the isolated enzymes in vitro, it is demonstrated that ravD, ravE, ravIM, ravAMT and ravNMT encode TDP-D-glucose synthase, TDP-4-keto-6-deoxy-D-glucose-4,6-dehydratase, TDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase, TDP-3-keto-6-deoxy-D-galactose-3-aminotransferase, and TDP-3-amino-3,6-dideoxy-D-galactose-N,N-dimethyl-transferase, respectively. A protocol for a one-pot enzymatic synthesis of TDP-D-ravidosamine has been developed. The results presented here now set the stage to produce TDP-D-ravidosamine routinely for glycosylation studies.
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Affiliation(s)
- Madan K. Kharel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Hui Lian
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
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20
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Dai C, Cheng Y, Cui J, Wang B. Click reactions and boronic acids: applications, issues, and potential solutions. Molecules 2010; 15:5768-81. [PMID: 20733546 PMCID: PMC6257766 DOI: 10.3390/molecules15085768] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 07/27/2010] [Accepted: 08/04/2010] [Indexed: 01/10/2023] Open
Abstract
Boronic acids have been widely used in a wide range of organic reactions, in the preparation of sensors for carbohydrates, and as potential pharmaceutical agents. With the growing importance of click reactions, inevitably they are also applied to the synthesis of compounds containing the boronic acid moiety. However, such applications have unique problems. Chief among them is the issue of copper-mediated boronic acid degradation in copper-assisted [2,3]-cycloadditions involving an alkyne and an azido compound as the starting materials. This review summarizes recent developments, analyzes potential issues, and discusses known as well as possible solutions.
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Affiliation(s)
| | | | | | - Binghe Wang
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, 30303, USA
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21
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Abstract
A long wavelength boronic acid-modified TTP (NB-TTP) has been synthesized and enzymatically incorporated into DNA. Such DNA shows intrinsic fluorescent changes upon carbohydrate addition.
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Affiliation(s)
- Xiaochuan Yang
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA. Fax: 4044135543; Tel: 4044135545;
| | - Chaofeng Dai
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA. Fax: 4044135543; Tel: 4044135545;
| | - Angie Dayan Calderon Molina
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA. Fax: 4044135543; Tel: 4044135545;
| | - Binghe Wang
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA. Fax: 4044135543; Tel: 4044135545;
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22
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Abstract
The three enzymes that constitute the de novo thymidylate synthesis pathway in mammals, cytoplasmic serine hydroxymethyltransferase (SHMT1), thymidylate synthase (TYMS) and dihydrofolate reductase (DHFR) undergo sumoylation and nuclear import during S-phase. In this study, we demonstrate that purified intact mouse liver nuclei convert dUMP to dTMP in the presence of NADPH and serine. Neither nuclear extracts nor intact nuclei exposed to aminomethylphosphonate, a SHMT inhibitor, exhibit thymidylate synthesis activity. Nuclei isolated from Shmt1(-/-) mouse livers retained 25% of thymidylate synthesis activity exhibited by nuclei isolated from wild type mice. This residual activity was due to the presence of a cytoplasmic/nuclear isozyme of SHMT encoded by Shmt2. Shmt2 is shown to encode two transcripts, one which encodes a protein that localizes exclusively to the mitochondria (SHMT2), and a second transcript that lacks exon 1 and encodes a protein that localizes to the cytoplasm and nucleus during S-phase (SHMT2alpha). The ability of Shmt2 to encode a cytoplasmic isozyme of SHMT may account for the viability of Shmt1(-/-) mice and provide redundancy that permitted the expansion of the human SHMT1 L474F polymorphism that impairs SHMT1 sumoylation and nuclear translocation.
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Affiliation(s)
- Donald D. Anderson
- Graduate Field of Biochemistry, Molecular and Cellular Biology, Cornell University, Ithaca, New York, United States of America
| | - Patrick J. Stover
- Graduate Field of Biochemistry, Molecular and Cellular Biology, Cornell University, Ithaca, New York, United States of America
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
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23
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Zipse H, Artin E, Wnuk S, Lohman GJS, Martino D, Griffin RG, Kacprzak S, Kaupp M, Hoffman B, Bennati M, Stubbe J, Lees N. Structure of the nucleotide radical formed during reaction of CDP/TTP with the E441Q-alpha2beta2 of E. coli ribonucleotide reductase. J Am Chem Soc 2009; 131:200-11. [PMID: 19128178 PMCID: PMC2651750 DOI: 10.1021/ja806693s] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Indexed: 11/28/2022]
Abstract
The Escherichia coli ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates to deoxynucleotides and requires a diferric-tyrosyl radical cofactor for catalysis. RNR is composed of a 1:1 complex of two homodimeric subunits: alpha and beta. Incubation of the E441Q-alpha mutant RNR with substrate CDP and allosteric effector TTP results in loss of the tyrosyl radical and formation of two new radicals on the 200 ms to min time scale. The first radical was previously established by stopped flow UV/vis spectroscopy and pulsed high field EPR spectroscopy to be a disulfide radical anion. The second radical was proposed to be a 4'-radical of a 3'-keto-2'-deoxycytidine 5'-diphosphate. To identify the structure of the nucleotide radical [1'-(2)H], [2'-(2)H], [4'-(2)H], [5'-(2)H], [U-(13)C, (15)N], [U-(15)N], and [5,6 -(2)H] CDP and [beta-(2)H] cysteine-alpha were synthesized and incubated with E441Q-alpha2beta2 and TTP. The nucleotide radical was examined by 9 GHz and 140 GHz pulsed EPR spectroscopy and 35 GHz ENDOR spectroscopy. Substitution of (2)H at C4' and C1' altered the observed hyperfine interactions of the nucleotide radical and established that the observed structure was not that predicted. DFT calculations (B3LYP/IGLO-III/B3LYP/TZVP) were carried out in an effort to recapitulate the spectroscopic observations and lead to a new structure consistent with all of the experimental data. The results indicate, unexpectedly, that the radical is a semidione nucleotide radical of cytidine 5'-diphosphate. The relationship of this radical to the disulfide radical anion is discussed.
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Affiliation(s)
- Hendrik Zipse
- Department of Chemistry and Biochemistry, Ludwig-Maximilians Universitaet Muenchen, 81377 Muenchen, Germany
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24
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Abstract
We describe a technique to synthesize DNA homopolymers on a surface using surface-initiated enzymatic polymerization (SIEP) with terminal deoxynucleotidyl transferase (TdTase), an enzyme that repetitively adds mononucleotides to the 3'-end of oligonucleotides. The thickness of the synthesized DNA layer was found to depend on the deoxymononucleotide monomer, in the order of dATP > dTTP > dGTP approximately dCTP. In addition, the composition and the surface density of oligonucleotide initiators were also important in controlling the extent of DNA polymerization. The extension of single-stranded DNA chains by SIEP was further verified by their binding to antibodies specific to oligonucleotides. TdTase-mediated SIEP can also be used to grow spatially defined three-dimensional DNA structures by soft lithography and is a new tool for bioinspired fabrication at the micro- and nanoscale.
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Affiliation(s)
- Dominic C Chow
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
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25
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Xia Q, Radzio J, Anderson KS, Sluis-Cremer N. Probing nonnucleoside inhibitor-induced active-site distortion in HIV-1 reverse transcriptase by transient kinetic analyses. Protein Sci 2007; 16:1728-37. [PMID: 17656585 PMCID: PMC2203366 DOI: 10.1110/ps.072829007] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTI) are a group of structurally diverse compounds that bind to a single site in HIV-1 reverse transcriptase (RT), termed the NNRTI-binding pocket (NNRTI-BP). NNRTI binding to RT induces conformational changes in the enzyme that affect key elements of the polymerase active site and also the association between the two protein subunits. To determine which conformational changes contribute to the mechanism of inhibition of HIV-1 reverse transcription, we used transient kinetic analyses to probe the catalytic events that occur directly at the enzyme's polymerase active site when the NNRTI-BP was occupied by nevirapine, efavirenz, or delavirdine. Our results demonstrate that all NNRTI-RT-template/primer (NNRTI-RT-T/P) complexes displayed a metal-dependent increase in dNTP binding affinity (K(d) ) and a metal-independent decrease in the maximum rate of dNTP incorporation (k (pol)). The magnitude of the decrease in k (pol) was dependent on the NNRTI used in the assay: Efavirenz caused the largest decrease followed by delavirdine and then nevirapine. Analyses that were designed to probe direct effects on phosphodiester bond formation suggested that the NNRTI mediate their effects on the chemistry step of the DNA polymerization reaction via an indirect manner. Because each of the NNRTI analyzed in this study exerted largely similar phenotypic effects on single nucleotide addition reactions, whereas each of them are known to exert differential effects on RT dimerization, we conclude that the NNRTI effects on subunit association do not directly contribute to the kinetic mechanism of inhibition of DNA polymerization.
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Affiliation(s)
- Qing Xia
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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26
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Rampazzo C, Fabris S, Franzolin E, Crovatto K, Frangini M, Bianchi V. Mitochondrial thymidine kinase and the enzymatic network regulating thymidine triphosphate pools in cultured human cells. J Biol Chem 2007; 282:34758-69. [PMID: 17913703 DOI: 10.1074/jbc.m705923200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In non-proliferating cells mitochondrial (mt) thymidine kinase (TK2) salvages thymidine derived from the extracellular milieu for the synthesis of mt dTTP. TK2 is a synthetic enzyme in a network of cytosolic and mt proteins with either synthetic or catabolic functions regulating the dTTP pool. In proliferating cultured cells the canonical cytosolic ribonucleotide reductase (R1-R2) is the prominent synthetic enzyme that by de novo synthesis provides most of dTTP for mt DNA replication. In non-proliferating cells p53R2 substitutes for R2. Catabolic enzymes safeguard the size of the dTTP pool: thymidine phosphorylase by degradation of thymidine and deoxyribonucleotidases by degradation of dTMP. Genetic deficiencies in three of the participants in the network, TK2, p53R2, or thymidine phosphorylase, result in severe mt DNA pathologies. Here we demonstrate the interdependence of the different enzymes of the network. We quantify changes in the size and turnover of the dTTP pool after inhibition of TK2 by RNA interference, of p53R2 with hydroxyurea, and of thymidine phosphorylase with 5-bromouracil. In proliferating cells the de novo pathway dominates, supporting large cytosolic and mt dTTP pools, whereas TK2 is dispensable, even in cells lacking the cytosolic thymidine kinase. In non-proliferating cells the small dTTP pools depend on the activities of both R1-p53R2 and TK2. The activity of TK2 is curbed by thymidine phosphorylase, which degrades thymidine in the cytoplasm, thus limiting the availability of thymidine for phosphorylation by TK2 in mitochondria. The dTTP pool shows an exquisite sensitivity to variations of thymidine concentrations at the nanomolar level.
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Affiliation(s)
- Chiara Rampazzo
- Department of Biology, University of Padova, Via Ugo Bassi 58B, Padova I-35131, Italy
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27
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Wang Y, Xu Y, Perepelov AV, Qi Y, Knirel YA, Wang L, Feng L. Biochemical characterization of dTDP-D-Qui4N and dTDP-D-Qui4NAc biosynthetic pathways in Shigella dysenteriae type 7 and Escherichia coli O7. J Bacteriol 2007; 189:8626-35. [PMID: 17905981 PMCID: PMC2168959 DOI: 10.1128/jb.00777-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
O-antigen variation due to the presence of different types of sugars and sugar linkages is important for the survival of bacteria threatened by host immune systems. The O antigens of Shigella dysenteriae type 7 and Escherichia coli O7 contain 4-(N-acetylglycyl)amino-4,6-dideoxy-d-glucose (d-Qui4NGlyAc) and 4-acetamido-4,6-dideoxy-d-glucose (d-Qui4NAc), respectively, which are sugars not often found in studied polysaccharides. In this study, we characterized the biosynthetic pathways for dTDP-d-Qui4N and dTDP-d-Qui4NAc (the nucleotide-activated precursors of d-Qui4NGlyAc and d-Qui4NAc in O antigens). Predicted genes involved in the synthesis of the two sugars were cloned, and the gene products were overexpressed and purified as His-tagged fusion proteins. In vitro enzymatic reactions were carried out using the purified proteins, and the reaction products were analyzed by capillary electrophoresis, electrospray ionization-mass spectrometry, and nuclear magnetic resonance spectroscopy. It is shown that in S. dysenteriae type 7 and E. coli O7, dTDP-d-Qui4N is synthesized from alpha-d-glucose-1-phosphate in three reaction steps catalyzed by glucose-1-phosphate thymidyltransferase (RmlA), dTDP-d-glucose 4,6-dehydratase (RmlB), and dTDP-4-keto-6-deoxy-d-glucose aminotransferase (VioA). An additional acetyltransferase (VioB) catalyzes the conversion of dTDP-d-Qui4N into dTDP-d-Qui4NAc in E. coli O7. Kinetic parameters and some other properties of VioA and VioB are described and differences between VioA proteins from S. dysenteriae type 7 (VioA(D7)) and E. coli O7 (VioA(O7)) discussed. To our knowledge, this is the first time that functions of VioA and VioB have been biochemically characterized. This study provides valuable enzyme sources for the production of dTDP-d-Qui4N and dTDP-d-Qui4NAc, which are potentially useful in the pharmaceutical industry for drug development.
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Affiliation(s)
- Ying Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, People's Republic of China.
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28
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Ma X, Ke T, Mao P, Jin X, Ma L, He G. The mutagenic properties of BrdUTP in a random mutagenesis process. Mol Biol Rep 2007; 35:663-7. [PMID: 17874205 DOI: 10.1007/s11033-007-9137-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Accepted: 08/29/2007] [Indexed: 11/26/2022]
Abstract
To explore the mutagenic properties of the nucleotide analogue bromodeoxyuridine triphosphate (BrdUTP), the wild type alpha-amylase (xamy) gene from Xanthomonas campestris pv. campestris 8004 was used as a mutational target. It was mutated using PCR techniques to partially replace deoxythymidine triphosphate (dTTP) with BrdUTP. A total of 18 mutants were selected for DNA sequencing from the mutagenesis libraries by their ability to hydrolyze the starch. The results showed that 70% of the total mutations were single base-pair substitutions; BrdUTP also induced deletion and insertion mutation types. Among single base-pair substitutions, the predominant mutation type is transition (84%), but three kinds of transversions (16%) were also detected. It thus mainly induces A:T --> G:C and T:A --> C:G transitions. This result indicated that when bromouracil is present as a deoxyribonucleoside triphosphate substrate it mainly paired with dAMP, and when it is present as a template base it could pair with free dGTP. Three mutational hot spots induced by BrdUTP were revealed in this work.
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Affiliation(s)
- Xiangdong Ma
- College of Life Science, Hubei University, Wuhan, 430062, China
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29
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Abstract
Triphosphate of a thymidine analogue bearing acridone was prepared from a modified thymidine nucleotide with a terminal amino group at C5 position and an acridone derivative as a new fluorecsent-tagged nucleotide. The acridone-tagged nucleotide was incorporated into DNA enzymatically during PCR using KOD Dash DNA polymerase. Further, we introduced the acridone derivative into an amino-modified DNA chemically by post-synthetic modification, and investigated their fluorescence properties and hybridization ability. The new fluorescent-labeled DNA bearing acridone will be useful as a DNA probe.
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Affiliation(s)
- Tomoya Hasegawa
- Department of Applied Chemistry, Faculty of Engineering, Gunma University, 1-5-1 Tenjin-chou, Kiryu, Gunma 376-8515, Japan
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30
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Lefebvre I, Puy JY, Perrin C, Périgaud C. Quantification of zidovudine and its monophosphate in cell extracts by on-line solid-phase extraction coupled to liquid chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 858:2-7. [PMID: 17870675 DOI: 10.1016/j.jchromb.2007.07.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Revised: 06/15/2007] [Accepted: 07/19/2007] [Indexed: 11/17/2022]
Abstract
A simple and rapid analytical method for the simultaneous quantification of zidovudine (AZT) and its monophosphate (AZTMP) in cell extracts has been developed using high-performance liquid chromatography (HPLC) with on-line solid-phase extraction and 2-aminoethyl-3'-azido-2',3'-dideoxythymidin-5'-yl phosphodiester sodium salt as internal standard (IS). The cell extract samples were directly injected on a short reversed-phase precolumn using an aqueous buffer containing an ion-pairing reagent as a mobile phase. Under these conditions, the analytes were retained on the precolumn whereas the proteins were discarded. The analytes were then transferred onto the analytical column by increasing the strength of the eluent. The calibration curve was linear over a concentration range of 0.5-100 microg/ml. Inter- and intra-day accuracy and precision results satisfied the accepted criteria for bioanalytical validation. This method was used to study the decomposition pathway of a model pronucleotide in an in vitro approach.
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Affiliation(s)
- I Lefebvre
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-UM1-UM2, Université Montpellier 2, case courrier 1705, place Eugène Bataillon, 34095 Montpellier Cédex 05, France.
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31
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Abstract
The 2′-deoxyguanosine-3′,5′-diphosphate, 2′-deoxyadenosine-3′,5′-diphosphate, 2′-deoxycytidine-3′,5′-diphosphate and 2′-deoxythymidine-3′,5′-diphosphate systems are the smallest units of a DNA single strand. Exploring these comprehensive subunits with reliable density functional methods enables one to approach reasonable predictions of the properties of DNA single strands. With these models, DNA single strands are found to have a strong tendency to capture low-energy electrons. The vertical attachment energies (VEAs) predicted for 3′,5′-dTDP (0.17 eV) and 3′,5′-dGDP (0.14 eV) indicate that both the thymine-rich and the guanine-rich DNA single strands have the ability to capture electrons. The adiabatic electron affinities (AEAs) of the nucleotides considered here range from 0.22 to 0.52 eV and follow the order 3′,5′-dTDP > 3′,5′-dCDP > 3′,5′-dGDP > 3′,5′-dADP. A substantial increase in the AEA is observed compared to that of the corresponding nucleic acid bases and the corresponding nucleosides. Furthermore, aqueous solution simulations dramatically increase the electron attracting properties of the DNA single strands. The present investigation illustrates that in the gas phase, the excess electron is situated both on the nucleobase and on the phosphate moiety for DNA single strands. However, the distribution of the extra negative charge is uneven. The attached electron favors the base moiety for the pyrimidine, while it prefers the 3′-phosphate subunit for the purine DNA single strands. In contrast, the attached electron is tightly bound to the base fragment for the cytidine, thymidine and adenosine nucleotides, while it almost exclusively resides in the vicinity of the 3′-phosphate group for the guanosine nucleotides due to the solvent effects. The comparatively low vertical detachment energies (VDEs) predicted for 3′,5′-dADP− (0.26 eV) and 3′,5′-dGDP− (0.32 eV) indicate that electron detachment might compete with reactions having high activation barriers such as glycosidic bond breakage. However, the radical anions of the pyrimidine nucleotides with high VDE are expected to be electronically stable. Thus the base-centered radical anions of the pyrimidine nucleotides might be the possible intermediates for DNA single-strand breakage.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, P. R. China and Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602-2525, USA
- *To whom correspondence should be addressed.+86-21-5080-6720+86-21-5080-7088 Correspondence may also be addressed to Henry F. Schaefer III.+1-706-542-2067+1-706-542-0406
| | - Yaoming Xie
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, P. R. China and Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602-2525, USA
| | - Henry F. Schaefer
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, P. R. China and Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602-2525, USA
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32
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Johansson E, Thymark M, Bynck JH, Fanø M, Larsen S, Willemoës M. Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme. FEBS J 2007; 274:4188-98. [PMID: 17651436 DOI: 10.1111/j.1742-4658.2007.05945.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The trimeric dCTP deaminase produces dUTP that is hydrolysed to dUMP by the structurally closely related dUTPase. This pathway provides 70-80% of the total dUMP as a precursor for dTTP. Accordingly, dCTP deaminase is regulated by dTTP, which increases the substrate concentration for half-maximal activity and the cooperativity of dCTP saturation. Likewise, increasing concentrations of dCTP increase the cooperativity of dTTP inhibition. Previous structural studies showed that the complexes of inactive mutant protein, E138A, with dUTP or dCTP bound, and wild-type enzyme with dUTP bound were all highly similar and characterized by having an ordered C-terminal. When comparing with a new structure in which dTTP is bound to the active site of E138A, the region between Val120 and His125 was found to be in a new conformation. This and the previous conformation were mutually exclusive within the trimer. Also, the dCTP complex of the inactive H121A was found to have residues 120-125 in this new conformation, indicating that it renders the enzyme inactive. The C-terminal fold was found to be disordered for both new complexes. We suggest that the cooperative kinetics are imposed by a dTTP-dependent lag of product formation observed in presteady-state kinetics. This lag may be derived from a slow equilibration between an inactive and an active conformation of dCTP deaminase represented by the dTTP complex and the dUTP/dCTP complex, respectively. The dCTP deaminase then resembles a simple concerted system subjected to effector binding, but without the use of an allosteric site.
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Affiliation(s)
- Eva Johansson
- Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Denmark.
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33
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Chi LM, Lam SL. NMR investigation of primer-template models: structural effect of sequence downstream of a thymine template on mutagenesis in DNA replication. Biochemistry 2007; 46:9292-300. [PMID: 17658896 DOI: 10.1021/bi700865e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Misaligned structures can occur in primer-templates during DNA replication, which can be bypassed and extended by low-fidelity polymerases and ultimately lead to mutations. In this study, we have investigated how the nucleotide downstream of a thymine template affects the primer-template structures upon misincorporation of dNTPs. The base pair structures at the replicating sites of a set of primer-template models containing either a G or an A downstream of the thymine template have been determined using NMR spectroscopy. Incorporation of dCTP and dTTP opposite 5'-GT and 5'-AT templates, respectively, can result in misaligned structures with a T-bulge. Depending on the downstream sequence, subsequent extension of the primers may stabilize the misaligned structures or cause the formation of mismatched structures. These results provide alternative pathways for base substitution and deletion errors during DNA replication by low-fidelity polymerases.
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Affiliation(s)
- Lai Man Chi
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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34
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Völker J, Klump HH, Breslauer KJ. The energetics of i-DNA tetraplex structures formed intermolecularly by d(TC5) and intramolecularly by d[(C5T3)3C5]. Biopolymers 2007; 86:136-47. [PMID: 17330895 DOI: 10.1002/bip.20712] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cytosine-rich DNA at low pH adopts an antiparallel tetraplex structure via the intercalation of two partially protonated, parallel stranded duplexes. This intriguing structural motif has been named i-DNA. We have used a combination of spectroscopic and calorimetric techniques to characterize the properties of an intermolecular i-DNA formed by d(TC(5)) and an intramolecular i-DNA formed by d[(C(5)T(3))(3)C(5)]. Our measurements reveal that both i-DNA complexes are enthalpically stabilized by 6.5-7.0 kcal/mol(base) and entropically destabilized by 20 cal/mol(base)/K. These values are about 50% larger than the corresponding enthalpy and entropy values per base for Watson and Crick duplexes and for Hoogsteen triplexes, while being similar to per base enthalpy and entropy values reported for G-quadruplexes. Our data also reveal a positive heat capacity change between 20 and 30 cal/mol(base)/K, values similar to that reported for polymeric Watson & Crick DNA duplexes. Solution-dependent studies reveal the overall thermal and thermodynamic stability of i-DNA complexes to be dictated by an interplay between pH and ionic strength. Based on the thermodynamic data measured, we discuss the feasibility of i-DNA formation in the context of conventional DNA sequences, while commenting on potential roles for this structural motif in biological regulatory mechanisms.
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Affiliation(s)
- Jens Völker
- Department of Chemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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35
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Abstract
Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found, for example, in such macrolide antibiotics as erthyromycin, azithromycin, and clarithromycin. The efficacies of these macrolide antibiotics are markedly reduced in the absence of desosamine. In the bacterium Streptomyces venezuelae, six enzymes are required for the production of dTDP-desosamine. The focus of this X-ray crystallographic analysis is the third enzyme in the pathway, a PLP-dependent aminotransferase referred to as DesI. The structure of DesI was solved in complex with its product, dTDP-4-amino-4,6-dideoxyglucose, to a nominal resolution of 2.1 A. Each subunit of the dimeric enzyme contains 12 alpha-helices and 14 beta-strands. Three cis-peptides are observed in each subunit, Phe 330, Pro 332, and Pro 339. The two active sites of the enzyme are located in clefts at the subunit/subunit interface. Electron density corresponding to the bound product clearly demonstrates a covalent bond between the amino group of the product and C-4' of the PLP cofactor. Interestingly, there are no hydrogen-bonding interactions between the protein and the dideoxyglucosyl group of the product (within 3.2 A). The only other sugar-modifying aminotransferase whose structure is known in the presence of product is PseC from Helicobacter pylori. This enzyme, as opposed to DesI, catalyzes amino transfer to the axial position of the sugar. A superposition of the two active sites for these proteins reveals that the major differences in ligand binding occur in the orientations of the deoxyglucosyl and phosphoryl groups. Indeed, the nearly 180 degrees difference in hexose orientation explains the equatorial versus axial amino transfer exhibited by DesI and PseC, respectively.
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Affiliation(s)
| | - Hazel M. Holden
- To whom correspondence should be addressed. FAX: 608−262−1319 PHONE: 608−262−4988
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36
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Ruiz J, Villa MD, Rodríguez V, Cutillas N, Vicente C, López G, Bautista D. A novel metal-binding mode of thymine nucleobases: N3 and O4 chelation. Inorg Chem 2007; 46:5448-9. [PMID: 17567007 DOI: 10.1021/ic700843s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The syntheses and crystal structures of the first examples of an anionic 1-methylthymine [deprotonated at the endocyclic NH group N(3)] acting as a chelating ligand for the cis-Pd(C6F3H2)2 and cis-Pd(C6F5)2 moieties through N(3) and O(4) are reported.
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Affiliation(s)
- José Ruiz
- Departamento de Química Inorgánica and SUIC, Edificio SACE, Universidad de Murcia, 30071 Murcia, Spain.
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37
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Neschastnova AA, Gasanova VK, Belitskiĭ GA, Iakubovskaia MG, Dolinnaia NG. [Chemical cleavage of DNA with single base mismatches for detection of mutations of unknown localization]. Mol Biol (Mosk) 2007; 41:535-43. [PMID: 17685231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The most promising approach for detection of random point mutations relies upon the DNA chemical cleavage near associated mismatching base pairs. In our study, the series of heteroduplexes with all types of mismatches and extrahelical nucleotide residues surrounded by both A x T and G x C pairs were performed via hybridization of 50-mer synthetic oligonucleotides differing in only one nucleotide at the central position. The chemical cleavage of DNA duplexes immobilized on magnetic beads by means of biotin-streptavidin interaction was carried out with chemicals, which able to attack only nucleobases flipped out of the base stack: potassium permanganate and hydroxylamine reacting to T and C respectively. The chemical reactivity of different mismatches was shown to correlate clearly with the target local structure in a particular sequence context. This work makes up for a deficiency in systematic study of DNA cleavage near mismatches in dependence on their type, orientation and flanking nucleotides. The model system elaborated may be applied to estimate the sensitivity of the methodology and to control the possibility of false-positive and false-negative result appearance, when different protocols for detection of DNA mutations are used. The modification of heteroduplex mixtures by potassium permanganate and hydroxylamine allows to reveal any non-canonical base pair and suggest its type and neighboring nucleotides from the nature of chemical as well as its localization from the length of cleavage products.
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38
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Kohli E, Han HY, Zeman AD, Vinogradov SV. Formulations of biodegradable Nanogel carriers with 5'-triphosphates of nucleoside analogs that display a reduced cytotoxicity and enhanced drug activity. J Control Release 2007; 121:19-27. [PMID: 17509713 PMCID: PMC2000331 DOI: 10.1016/j.jconrel.2007.04.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Accepted: 04/11/2007] [Indexed: 12/11/2022]
Abstract
Therapies including nucleoside analogs are associated with severe toxic side effects and acquirement of drug resistance. We have previously reported the drug delivery in the form of 5'-triphosphates (NTP) encapsulated in cross-linked cationic networks of polyethylenimine (PEI) and PEG/Pluronic polymers (Nanogels). In this study, Nanogels, containing biodegradable PEI that could easily dissociate in reducing cytosolic environment and form products with minimal toxicity, were synthesized and displayed low cytotoxicity. Toxicity of Nanogels was clearly dependent on the total positive charge of carriers and was 5-6 fold lower for carriers loaded with NTP. Though intracellular ATP level was immediately reduced by ca. 50% following the treatment with Nanogels, it was largely restored 24 h later. Effect of Nanogels on various respiratory components of cells was reversible too, and, therefore, resulted in low immediate cell death. Nanogel alone and formulations with AZT-TP demonstrated a much lower mitochondrial toxicity than AZT. As an example of potential antiviral applications of low-toxic Nanogel carriers, a 5'-triphosphorylated Ribavirin-Nanogel formulation was prepared that demonstrated a 30-fold decrease in effective drug concentration (EC(90)) and, totally, a 10-fold increase in selectivity index compared to the drug alone in MDCK cells infected with influenza A virus.
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39
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Lennerstrand J, Chu CK, Schinazi RF. Biochemical studies on the mechanism of human immunodeficiency virus type 1 reverse transcriptase resistance to 1-(beta-D-dioxolane)thymine triphosphate. Antimicrob Agents Chemother 2007; 51:2078-84. [PMID: 17403997 PMCID: PMC1891359 DOI: 10.1128/aac.00119-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large panel of drug-resistant mutants of human immunodeficiency virus type 1 reverse transcriptase (RT) was used to study the mechanisms of resistance to 1-(beta-d-dioxolane)thymine triphosphate (DOT-TP) and other nucleotide analogs. RT containing thymidine analog-associated mutations (TAM) or RT with a T69S-SG insertion in combination with TAM removed 3'-azido-3'-deoxythymidine-5'-monophosphate or tenofovir more efficiently than DOT-monophosphate from chain-terminated DNA primer/template through ATP-mediated pyrophosphorolysis. For non-ATP-dependent discrimination toward DOT-TP, high levels of resistance were found for RT bearing the Q151M mutation with family mutations, while RT bearing only the M184V or the Y115F mutation conferred no resistance to DOT-TP. A lower degree of resistance to DOT-TP than to tenofovir diphosphate or carbovir-TP was found for RT containing the K65R mutation. In the present studies, 1-(beta-d-dioxolane)guanine triphosphate, another nucleotide with a dioxolane sugar moiety, showed a resistance profile similar to that of DOT-TP. The results suggest that DOT, compared with other approved nucleoside analogs, is overall more resilient to mutations such as TAM, M184V, and K65R, which are commonly found in viruses derived from subjects failing multinucleoside therapy.
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Affiliation(s)
- Johan Lennerstrand
- Laboratory of Biochemical Pharmacology, Emory University/Veterans Affairs Medical Center, 1670 Clairmont Rd., Medical Research 151-H, Decatur, GA 30033, USA
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40
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Ducho C, Görbig U, Jessel S, Gisch N, Balzarini J, Meier C. Bis-cycloSal-d4T-monophosphates: drugs that deliver two molecules of bioactive nucleotides. J Med Chem 2007; 50:1335-46. [PMID: 17328534 DOI: 10.1021/jm0611713] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bis-cycloSal-d4T-monophosphates have been synthesized as potentially anti-HIV active "dimeric" prodrugs of 2',3'-dideoxy-2',3'-didehydrothymidine monophosphate (d4TMP). These pronucleotides display a mask-drug ratio of 1:2, a novelty in the field of pronucleotides. Both bis-cycloSal-d4TMP 6 and bis-5-methyl-cycloSal-d4TMP 7 showed increased hydrolytic stability as compared to their "monomeric" counterparts and a completely selective hydrolytic release of d4TMP. The hydrolysis pathway was investigated via 31P NMR spectroscopy. Moreover, due to the steric bulkiness, compound 6 already displayed strongly reduced inhibitor potency toward human butyrylcholinesterase (BChE), while compound 7 turned out to be devoid of any inhibitory activity against BChE. Partial separation of the diastereomeric mixture of 6 revealed strong dependence of the pronucleotides' properties on the stereochemistry at the phosphorus centers. Both 6 and 7 showed good activity against HIV-1 and HIV-2 in wild-type CEM cells in vitro. These compounds were significantly more potent than the parent nucleoside d4T 1 in HIV-2-infected TK-deficient CEM cells, indicating an efficient TK-bypass.
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Affiliation(s)
- Christian Ducho
- Department of Chemistry, Organic Chemistry, Faculty of Science, University of Hamburg, Martin-Luther-King-Platz 6, D-20146 Hamburg, Germany
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41
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Abstract
Nanogels are colloidal microgel carriers that have been recently introduced as a prospective drug delivery system for nucleotide therapeutics. The crosslinked protonated polymer network of nanogels binds oppositely charged drug molecules, encapsulating them into submicron particles with a core-shell structure. The nanogel network also provides a suitable template for chemical engineering, surface modification and vectorisation. This review reveals recent attempts to develop novel drug formulations of nanogels with antiviral and antiproliferative nucleoside analogs in the active form of 5'-triphosphates, discusses structural approaches to the optimisation of nanogel properties, and discusses the development of targeted nanogel drug formulations for systemic administration. Notably, nanogels can improve the CNS penetration of nucleoside analogs that are otherwise restricted from passing across the blood-brain barrier. The latest findings reviewed here demonstrate an efficient intracellular release of nucleoside analogs, encouraging further applications of nanogel carriers for targeted drug delivery.
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Affiliation(s)
- Serguei V Vinogradov
- University of Nebraska Medical Center, Department of Pharmaceutical Sciencess, College of Pharmacy and Center for Drug Delivery and Nanomedicine, Omaha, NE 68198-5830, USA.
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42
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Lin N, Yan J, Huang Z, Altier C, Li M, Carrasco N, Suyemoto M, Johnston L, Wang S, Wang Q, Fang H, Caton-Williams J, Wang B. Design and synthesis of boronic-acid-labeled thymidine triphosphate for incorporation into DNA. Nucleic Acids Res 2007; 35:1222-9. [PMID: 17267413 PMCID: PMC1851626 DOI: 10.1093/nar/gkl1091] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The boronic acid moiety is a versatile functional group useful in carbohydrate recognition, glycoprotein pull-down, inhibition of hydrolytic enzymes and boron neutron capture therapy. The incorporation of the boronic-acid group into DNA could lead to molecules of various biological functions. We have successfully synthesized a boronic acid-labeled thymidine triphosphate (B-TTP) linked through a 14-atom tether and effectively incorporated it into DNA by enzymatic polymerization. The synthesis was achieved using the Huisgen cycloaddition as the key reaction. We have demonstrated that DNA polymerase can effectively recognize the boronic acid-labeled DNA as the template for DNA polymerization, that allows PCR amplification of boronic acid-labeled DNA. DNA polymerase recognitions of the B-TTP as a substrate and the boronic acid-labeled DNA as a template are critical issues for the development of DNA-based lectin mimics via in vitro selection.
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Affiliation(s)
- Na Lin
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Jun Yan
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Zhen Huang
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Craig Altier
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Minyong Li
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Nicolas Carrasco
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Mitsu Suyemoto
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Lynette Johnston
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Siming Wang
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Qian Wang
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Hao Fang
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Julianne Caton-Williams
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
| | - Binghe Wang
- Department of Chemistry and Center for Biotechnology and Drug Design, Campus Box 4098, Georgia State University, Atlanta, GA 30302-4098, USA, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, NC 27606, USA and Department of Chemistry and Biochemistry, 631 Sumter St. University of South Carolina, Columbia, SC 29202, USA
- *To whom correspondence should be addressed. Tel: +1 404 651 0289; Fax: +1 404 654 5827;
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43
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Abstract
Control of nanostructure formation by a diblock-type supramacromolecule via biocomplementary hydrogen bonding has been achieved. Two different homopolymers, poly(4-trimethylsilylstyrene) and poly(styrene-d8), that are end-decorated with complementary oligonucleotides, i.e., thymidine phosphates and deoxyadenosine phosphates, were prepared by using the phosphoramidite method and blended successively. Association behavior in a blend solution was examined with NMR, and a cast bulk film obtained from the solution has been confirmed to show a nanophase-separated structure by transmission electron microscopy and X-ray scattering. Suppression of this nanostructure formation of a block-type supramacromolecule was also attained by adding a smaller agent as an inhibitor.
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Affiliation(s)
- Atsushi Noro
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
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Oelschlaeger P, Klahn M, Beard WA, Wilson SH, Warshel A. Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects. J Mol Biol 2006; 366:687-701. [PMID: 17174326 PMCID: PMC1859854 DOI: 10.1016/j.jmb.2006.10.095] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 10/14/2006] [Accepted: 10/28/2006] [Indexed: 11/17/2022]
Abstract
Human DNA polymerase beta (pol beta) fills gaps in DNA as part of base excision DNA repair. Due to its small size it is a convenient model enzyme for other DNA polymerases. Its active site contains two Mg(2+) ions, of which one binds an incoming dNTP and one catalyzes its condensation with the DNA primer strand. Simulating such binuclear metalloenzymes accurately but computationally efficiently is a challenging task. Here, we present a magnesium-cationic dummy atom approach that can easily be implemented in molecular mechanical force fields such as the ENZYMIX or the AMBER force fields. All properties investigated here, namely, structure and energetics of both Michaelis complexes and transition state (TS) complexes were represented more accurately using the magnesium-cationic dummy atom model than using the traditional one-atom representation for Mg(2+) ions. The improved agreement between calculated free energies of binding of TS models to different pol beta variants and the experimentally determined activation free energies indicates that this model will be useful in studying mutational effects on catalytic efficiency and fidelity of DNA polymerases. The model should also have broad applicability to the modeling of other magnesium-containing proteins.
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Affiliation(s)
- Peter Oelschlaeger
- University of Southern California, Department of Chemistry, Los Angeles, California
- *Corresponding authors: Peter Oelschlaeger, University of Southern California, Department of Chemistry, SGM 418, 3620, McClintock Ave., Los Angeles, CA 90089-1062, Phone: (213) 740 7671, Fax: (213) 740 2701, E-mail: ., Arieh Warshel, University of Southern California, Department of Chemistry, SGM 418, 3620, McClintock Ave., Los Angeles, CA 90089-1062, Phone: (213) 740 4114, Fax: (213) 740 2701, E-mail:
| | - Marco Klahn
- University of Southern California, Department of Chemistry, Los Angeles, California
| | - William A. Beard
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Arieh Warshel
- University of Southern California, Department of Chemistry, Los Angeles, California
- *Corresponding authors: Peter Oelschlaeger, University of Southern California, Department of Chemistry, SGM 418, 3620, McClintock Ave., Los Angeles, CA 90089-1062, Phone: (213) 740 7671, Fax: (213) 740 2701, E-mail: ., Arieh Warshel, University of Southern California, Department of Chemistry, SGM 418, 3620, McClintock Ave., Los Angeles, CA 90089-1062, Phone: (213) 740 4114, Fax: (213) 740 2701, E-mail:
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45
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Affiliation(s)
- Ping-hui Szu
- Division of Medicinal Chemistry, College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
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46
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Hillaireau H, Le Doan T, Appel M, Couvreur P. Hybrid polymer nanocapsules enhance in vitro delivery of azidothymidine-triphosphate to macrophages. J Control Release 2006; 116:346-52. [PMID: 17113178 DOI: 10.1016/j.jconrel.2006.09.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 09/22/2006] [Accepted: 09/28/2006] [Indexed: 11/26/2022]
Abstract
One of the main limitations in the use of nucleoside reverse transcriptase inhibitors (NRTIs) such as azidothymidine (AZT) lies in their poor intracellular activation by cellular kinases into their active tri-phosphorylated form. Thus, the direct administration of triphosphate NRTIs like azidothymidine-triphosphate (AZT-TP), has been considered for bypassing this metabolic bottleneck, but these molecules do not diffuse intracellularly, due to their too hydrophilic character. Therefore, poly(iso-butylcyanoacrylate) (PIBCA) aqueous-cored nanocapsules have been tested as carriers to overcome the cellular delivery of AZT-TP. However, encapsulation of AZT-TP remained challenging because this molecule, due to its relatively low molecular weight, rapidly leaked out of the nanocapsules. In this study, we show that association of AZT-TP to a cationic polymer such as poly(ethyleneimine) (PEI) allowed to reach high entrapment efficiency of AZT-TP in PIBCA nanocapsules (up to 90%) as well as gradual in vitro release. The resulting hybrid PIBCA/PEI nanocapsules efficiently delivered AZT-TP in vitro to macrophages: the cellular uptake was increased by 30-fold compared to the free molecule, reaching relevant cellular concentrations for therapeutic purposes.
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Affiliation(s)
- Hervé Hillaireau
- University Paris Sud, UMR CNRS 8612, 5, rue J. B. Clément, 92296 Châtenay-Malabry, France
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Dong C, Major LL, Srikannathasan V, Errey JC, Giraud MF, Lam JS, Graninger M, Messner P, McNeil MR, Field RA, Whitfield C, Naismith JH. RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation. J Mol Biol 2006; 365:146-59. [PMID: 17046787 PMCID: PMC1805628 DOI: 10.1016/j.jmb.2006.09.063] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 09/21/2006] [Accepted: 09/22/2006] [Indexed: 11/27/2022]
Abstract
The striking feature of carbohydrates is their constitutional, conformational and configurational diversity. Biology has harnessed this diversity and manipulates carbohydrate residues in a variety of ways, one of which is epimerization. RmlC catalyzes the epimerization of the C3' and C5' positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose. RmlC is the third enzyme of the rhamnose pathway, and represents a validated anti-bacterial drug target. Although several structures of the enzyme have been reported, the mechanism and the nature of the intermediates have remained obscure. Despite its relatively small size (22 kDa), RmlC catalyzes four stereospecific proton transfers and the substrate undergoes a major conformational change during the course of the transformation. Here we report the structure of RmlC from several organisms in complex with product and product mimics. We have probed site-directed mutants by assay and by deuterium exchange. The combination of structural and biochemical data has allowed us to assign key residues and identify the conformation of the carbohydrate during turnover. Clear knowledge of the chemical structure of RmlC reaction intermediates may offer new opportunities for rational drug design.
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Affiliation(s)
- Changjiang Dong
- Centre for Biomolecular Sciences, The University, St. Andrews KY16 9ST, UK
| | - Louise L. Major
- Centre for Biomolecular Sciences, The University, St. Andrews KY16 9ST, UK
| | | | - James C. Errey
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Joseph S. Lam
- Department of Molecular & Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - Michael Graninger
- Zentrum für NanoBiotechnologie, Universität für Bodenkultur Wien, A-1180, Vienna, Austria
| | - Paul Messner
- Zentrum für NanoBiotechnologie, Universität für Bodenkultur Wien, A-1180, Vienna, Austria
| | - Michael R. McNeil
- Department of Microbiology, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert A. Field
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | - Chris Whitfield
- Department of Molecular & Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
| | - James H. Naismith
- Centre for Biomolecular Sciences, The University, St. Andrews KY16 9ST, UK
- Address Correspondence to James H Naismith, Centre for Biomolecular Sciences, The University, St Andrews KY16 9ST, UK. Phone 44-1334-463792 Fax 44-1334-462595 Email
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Rajwanshi VK, Prhavc M, Fagan P, Brooks JL, Hurd T, Cook PD, Wang G. Synthesis of 5'-triphosphate mimics (P3Ms) of 3'-azido-3',5'-dideoxythymidine and 3',5'-dideoxy-5'-difluoromethylenethymidine as HIV-1 reverse transcriptase inhibitors. Nucleosides Nucleotides Nucleic Acids 2006; 24:179-89. [PMID: 15892257 DOI: 10.1081/ncn-55707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
3'-Azido-3',5-dideoxythymidine 5'-phosphonate and 3',5'-dideoxy-5'-difluoromethylenethymidine 5'-phosphonate were prepared by multistep syntheses. The nucleoside 5'-phosphonates were converted to their triphosphates and triphosphate mimics (P3Ms) containing beta,gamma-difluoromethylene, beta,gamma-dichloromethylene, or beta,gamma-imodo by condensation with pyrophosphate or pyrophosphate mimics, respectively. Inhibition of HIV-1 reverse transcriptase by the nucleoside P3Ms is briefly discussed.
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Affiliation(s)
- Vivek K Rajwanshi
- Research Laboratories, Biota, Inc., 2232 Rutherford Road, Carlsbad, CA 92008, USA
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Rungrotmongkol T, Mulholland AJ, Hannongbua S. Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex. J Mol Graph Model 2006; 26:1-13. [PMID: 17046299 DOI: 10.1016/j.jmgm.2006.09.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Revised: 09/07/2006] [Accepted: 09/10/2006] [Indexed: 11/16/2022]
Abstract
We have investigated the structure and dynamics of the HIV-1 reverse transcriptase (HIV-RT) active site, by modelling the active conformation of the HIV-1 RT/DNA/deoxythymidine triphosphate (dTTP) ternary complex. This has included molecular dynamics simulations with the CHARMM27 force field, and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Three different ternary systems were studied to investigate the effects of different protonation states of the dTTP substrate (a deprotonated and two different mono-protonated triphosphate forms of dTTP at the active site), and the effects of different possible protonation state of potentially catalytic aspartate residues (Asp185 and Asp186) were tested. Several potentially important hydrogen-bonding interactions with amino acids and bound water molecules in the deoxyribonucleoside triphosphate (dNTP) binding pocket were examined. The model of the deprotonated form of the dTTP substrate with the two aspartates in their charged (basic) form seemed to be the most stable and its orientation was in good agreement with X-ray crystallographic structure. In addition, two different semiempirical (AM1/CHARMM and PM3/CHARMM) QM/MM methods were tested for the HIV-RT system, in structural optimizations. Both methods provided conformations of the triphosphate moiety in either fully deprotonated or mono-protonated forms, which agreed well with the experimental structure of dTTP. The only significant difference between the AM1/CHARMM and PM3/CHARMM minimized structures is that the PM3/CHARMM Palpha-O3' optimized distance (important for nucleotide addition) is longer by 0.66 A in the deprotonated system but shorter by 0.37 A in the mono-protonated triphosphate system as compared with those obtained from AM1/CHARMM minimized structure. The obtained results suggest that both of these QM/MM methods, and the stochastic boundary molecular dynamics approach applied in this work, can give reasonable results for modelling the catalytically active complex of this important enzyme. The results provide insight into the structure and interactions of the active site of this important enzyme, with implications for its mechanism, which may be useful in inhibitor design.
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Zhang L, Rechkoblit O, Wang L, Patel DJ, Shapiro R, Broyde S. Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies. Nucleic Acids Res 2006; 34:3326-37. [PMID: 16820532 PMCID: PMC1500869 DOI: 10.1093/nar/gkl425] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Bulky carcinogen-DNA adducts commonly cause replicative polymerases to stall, leading to a switch to bypass polymerases. We have investigated nucleotide incorporation opposite the major adduct of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in the DinB family polymerase, Dpo4, using molecular modeling and molecular dynamics (MD) simulations. PhIP, the most prevalent heterocyclic aromatic amine formed by cooking of proteinaceous food, is mutagenic in mammalian cells and is implicated in mammary and colon tumors. Our results show that the dG-C8-PhIP adduct can be accommodated in the spacious major groove Dpo4 open pocket, with Dpo4 capable of incorporating dCTP, dTTP or dATP opposite the adduct reasonably well. However, the PhIP ring system on the minor groove side would seriously disturb the active site, regardless of the presence and identity of dNTP. Furthermore, the simulations indicate that dATP and dTTP are better incorporated in the damaged system than in their respective mismatched but unmodified controls, suggesting that the PhIP adduct enhances incorporation of these mismatches. Finally, bulky C8-dG adducts, situated in the major groove, are likely to impede translocation in this polymerase (Rechkoblit et al. (2006), PLoS Biol., 4, e11). However, N2-dG adducts, which can reside on the minor groove side, appear to cause less hindrance when in this position.
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Affiliation(s)
| | - Olga Rechkoblit
- Structural Biology Program, Memorial Sloan-Kettering Cancer CenterNew York, NY, USA
| | - Lihua Wang
- Department of Biology, New York UniversityNew York, NY, USA
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer CenterNew York, NY, USA
| | | | - Suse Broyde
- Department of Biology, New York UniversityNew York, NY, USA
- To whom correspondence should be addressed. Tel: +1 212 998 8231; Fax: +1 212 995 4015;
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