1
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Kuznetsova VE, Shershov VE, Guseinov TO, Miftakhov RA, Solyev PN, Novikov RA, Levashova AI, Zasedatelev AS, Lapa SA, Chudinov AV. Synthesis of Cy5-Labelled C5-Alkynyl-modified cytidine triphosphates via Sonogashira coupling for DNA labelling. Bioorg Chem 2023; 131:106315. [PMID: 36528924 DOI: 10.1016/j.bioorg.2022.106315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/15/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
New applications of palladium-catalyzed Sonogashira-type cross-coupling reaction between C5-halogenated 2'-deoxycytidine-5'-monophosphate and novel cyanine dyes with a terminal alkyne group have been developed. The present methodology allows to synthesize of fluorescently labeled C5-nucleoside triphosphates with different acetylene linkers between the fluorophore and pyrimidine base in good to excellent yields under mild reaction conditions. Modified 2'-deoxycytidine-5'-triphosphates were shown to be good substrates for DNA polymerases and were incorporated into the DNA by polymerase chain reaction.
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Affiliation(s)
- Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Teimur O Guseinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Rinat A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Roman A Novikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna I Levashova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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2
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Cofactor and Process Engineering for Nicotinamide Recycling and Retention in Intensified Biocatalysis. Catalysts 2022. [DOI: 10.3390/catal12111454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
There is currently considerable interest in the intensification of biocatalytic processes to reduce the cost of goods for biocatalytically produced chemicals, including pharmaceuticals and advanced pharmaceutical intermediates. Continuous-flow biocatalysis shows considerable promise as a method for process intensification; however, the reliance of some reactions on the use of diffusible cofactors (such as the nicotinamide cofactors) has proven to be a technical barrier for key enzyme classes. This minireview covers attempts to overcome this limitation, including the cofactor recapture and recycling retention of chemically modified cofactors. For the latter, we also consider the state of science for cofactor modification, a field reinvigorated by the current interest in continuous-flow biocatalysis.
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3
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HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir. Sci Rep 2018; 8:1624. [PMID: 29374261 PMCID: PMC5785976 DOI: 10.1038/s41598-018-19602-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B virus (HBV) reverse transcriptase (RT) is essential for viral replication and is an important drug target. Nonetheless, the notorious insolubility of HBV RT has hindered experimental structural studies and structure-based drug design. Here, we demonstrate that a Q151M substitution alone at the nucleotide-binding site (N-site) of human immunodeficiency virus type-1 (HIV-1) RT renders HIV-1 highly sensitive to entecavir (ETV), a potent nucleoside analogue RT inhibitor (NRTI) against HBV. The results suggest that Met151 forms a transient hydrophobic interaction with the cyclopentyl methylene of ETV, a characteristic hydrophobic moiety of ETV. We thus solved the crystal structures of HIV-1 RTQ151M:DNA complex with bound dGTP or ETV-triphosphate (ETV-TP). The structures revealed that ETV-TP is accommodated at the N-site slightly apart from the ribose ring of the 3′-end nucleotide, compared to the position of bound dGTP and previously reported NRTI/dNTP. In addition, the protruding methylene group of bound ETV-TP directly pushes the side-chain of Met184 backward. Met184 is a key residue that confers ETV resistance upon substitution with smaller Ile/Val. These results provide novel insights into NRTI binding to the N-site and further provide important clues for the development of novel anti-HBV/HIV-1 RT inhibitors to overcome critical drug resistance.
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4
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Warminski M, Warminska Z, Kowalska J, Jemielity J. mRNA Cap Modification through Carbamate Chemistry: Synthesis of Amino- and Carboxy-Functionalised Cap Analogues Suitable for Labelling and Bioconjugation. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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5
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Monogalactosyl diacylglycerol, a replicative DNA polymerase inhibitor, from spinach enhances the anti-cell proliferation effect of gemcitabine in human pancreatic cancer cells. Biochim Biophys Acta Gen Subj 2013; 1830:2517-25. [DOI: 10.1016/j.bbagen.2012.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 10/25/2012] [Accepted: 11/10/2012] [Indexed: 02/05/2023]
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6
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D’Errico S, Oliviero G, Borbone N, Amato J, Piccialli V, Varra M, Mayol L, Piccialli G. Solid-phase synthesis of a new diphosphate 5-aminoimidazole-4-carboxamide riboside (AICAR) derivative and studies toward cyclic AICAR diphosphate ribose. Molecules 2011; 16:8110-8. [PMID: 21937970 PMCID: PMC6264535 DOI: 10.3390/molecules16098110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/09/2011] [Accepted: 09/13/2011] [Indexed: 11/17/2022] Open
Abstract
The solid-phase synthesis of the first example of a new diphosphate AICAR derivative is reported. The new substance is characterized by the presence of a 5'-phosphate group while a second phosphate moiety is installed on a 5-hydroxypentyl chain attached to the 4-N-position of AICAR. Cyclization of the diphosphate derivative by pyrophosphate bond formation allowed for the formation of a novel AICAR-based cyclic ADP-ribose (cADPR) mimic.
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Affiliation(s)
- Stefano D’Errico
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, 80131, Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, 80131, Napoli, Italy
- Facoltà di Scienze Biotecnologiche, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, 80131, Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, 80131, Napoli, Italy
| | - Jussara Amato
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, 80131, Napoli, Italy
| | - Vincenzo Piccialli
- Dipartimento di Chimica Organica e Biochimica, Università degli Studi di Napoli Federico II, Via Cynthia, 4, 80126, Napoli, Italy
| | - Michela Varra
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, 80131, Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, 80131, Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, 80131, Napoli, Italy
- Facoltà di Scienze Biotecnologiche, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, 80131, Napoli, Italy
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7
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Caton-Williams J, Smith M, Carrasco N, Huang Z. Protection-free one-pot synthesis of 2'-deoxynucleoside 5'-triphosphates and DNA polymerization. Org Lett 2011; 13:4156-9. [PMID: 21790120 DOI: 10.1021/ol201073e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By differentiating the functional groups on nucleosides, we have designed and developed a one-pot synthesis of deoxyribonucleoside 5'-triphosphates without any protection on the nucleosides. A facile synthesis is achieved by generating an in situ phosphitylating reagent that reacts selectively with the 5'-hydroxyl groups of the unprotected nucleosides. The synthesized triphosphates are of high quality and can be effectively incorporated into DNAs by DNA polymerase. This novel approach is straightforward and cost-effective for triphosphate synthesis.
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8
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Yanachkov IB, Dix EJ, Yanachkova MI, Wright GE. P1,P2-diimidazolyl derivatives of pyrophosphate and bis-phosphonates--synthesis, properties, and use in preparation of dinucleoside tetraphosphates and analogs. Org Biomol Chem 2011; 9:730-8. [PMID: 21082127 PMCID: PMC5705240 DOI: 10.1039/c0ob00542h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
P(1),P(2)-Diimidazolyl derivatives of pyrophosphate and halomethylene-bis-phosphonates have been synthesized and characterized, and the mechanism of their formation was studied. These reagents enable synthesis of dinucleoside tetraphosphates and tetraphosphonates conveniently and in high yields.
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9
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Liu X, Takahashi H, Harada Y, Ogawara T, Ogimura Y, Mizushina Y, Saneyoshi M, Yamaguchi T. 3'-Azido-2',3'-dideoxynucleoside 5'-triphosphates inhibit telomerase activity in vitro, and the corresponding nucleosides cause telomere shortening in human HL60 cells. Nucleic Acids Res 2007; 35:7140-9. [PMID: 17942424 PMCID: PMC2175342 DOI: 10.1093/nar/gkm859] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Telomerase adds telomeric DNA repeats to the ends of linear chromosomal DNA. 3′-Azido-3′-deoxythymidine 5′-triphosphate (AZTTP) is a known telomerase inhibitor. To obtain more selective and potent inhibitors that can be employed as tools for studying telomerase, we investigated the telomerase-inhibitory effects of purine nucleosides bearing a 3′-down azido group: 3′-azido-2′,3′-dideoxyguanosine (AZddG) 5′-triphosphate (AZddGTP), 3′-azido-2′,3′-dideoxy-6-thioguanosine (AZddSG) 5′-triphosphate (AZddSGTP), 3′-azido-2′,3′-dideoxyadenosine (AZddA) 5′-triphosphate (AZddATP) and 3′-azido-2′,3′-dideoxy-2-aminoadenosine (AZddAA) 5′-triphosphate (AZddAATP). Of these, AZddGTP showed the most potent inhibitory activity against HeLa cell telomerase. AZddGTP was significantly incorporated into the 3′-terminus of DNA by partially purified telomerase. However, AZddGTP did not exhibit significant inhibitory activity against DNA polymerases α and δ, suggesting that AZddGTP is a selective inhibitor of telomerase. We also investigated whether long-term treatment with these nucleosides could alter telomere length and growth rates of human HL60 cells in culture. Southern hybridization analysis of genomic DNA prepared from cells cultured in the presence of AZddG and AZddAA revealed reproducible telomere shortening.
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Affiliation(s)
- Xiaohong Liu
- Biotechnology Research Center, Teikyo University of Science and Technology, Uenohara, Yamanashi, Japan
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10
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Elphick LM, Lee SE, Gouverneur V, Mann DJ. Using chemical genetics and ATP analogues to dissect protein kinase function. ACS Chem Biol 2007; 2:299-314. [PMID: 17518431 DOI: 10.1021/cb700027u] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein kinases catalyze the transfer of the gamma-phosphate of ATP to a protein substrate and thereby profoundly alter the properties of the phosphorylated protein. The identification of the substrates of protein kinases has proven to be a very difficult task because of the multitude of structurally related protein kinases present in cells, their apparent redundancy of function, and the lack of absolute specificity of small-molecule inhibitors. Here, we review approaches that utilize chemical genetics to determine the functions and substrates of protein kinases, focusing on the design of ATP analogues and protein kinase binding site mutants.
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Affiliation(s)
- Lucy M Elphick
- Imperial College London, Cell Cycle Lab, Division of Cell and Molecular Biology, South Kensington, London SW7 2AZ, United Kingdom
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11
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Yamaguchi T, Saneyoshi M, Takahashi H, Hirokawa S, Amano R, Liu X, Inomata M, Maruyama T. Synthetic nucleosides and nucleotides. 43. Inhibition of vertebrate telomerases by carbocyclic oxetanocin g (C.OXT-G) triphosphate analogues and influence of C.OXT-G treatment on telomere length in human HL60 cells. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 25:539-51. [PMID: 16838844 DOI: 10.1080/15257770600684217] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Telomerase, responsible for telomere synthesis, is expressed in approximately 90% of human tumor cells but seldom in normal somatic cells. In this study, inhibition by carbocyclic oxetanocin G triphosphate (C. OXT-GTP) and its analogues was investigated in order to clarify the susceptibility of telomerase to various nucleotide analogues. C. OXT-GTP competitively inhibited telomerase activity with respect to dGTP However, C. OXT-GTP had a potent inhibitory effect on DNA polymerase alpha. It was examined whether the nucleoside (C. OXT-G) was able to alter telomere length in cultured human HL60 cells. Contrary to expectation, long-term treatment with 10 microM C. OXT-G was found to cause telomere lengthening.
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Affiliation(s)
- Toyofumi Yamaguchi
- Department of Biosciences and Biotechnology Research Center, Teikyo University of Science and Technology, Uenohara, Yamanashi, Japan.
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12
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Yamaguchi T, Saneyoshi M. Synthetic Nucleoside and Nucleotides. XXXIV. Photoaffinity Labeling of HIV Reverse Transcriptase: Synthesis and Utilization of 2′,3′-Dideoxy Uridylate Analogs Bearing Aryl(trifluor0methyl)-Diazirine Moiety. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319608002409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Toyofumi Yamaguchi
- a Department of Biological Sciences , The Nishi-Tokyo University , 2525 Yatsuzawa, Uenohara-machi, Kitatsuru-gun, Yamanashi , 409-01 , Japan
| | - Mineo Saneyoshi
- a Department of Biological Sciences , The Nishi-Tokyo University , 2525 Yatsuzawa, Uenohara-machi, Kitatsuru-gun, Yamanashi , 409-01 , Japan
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13
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Sekine M, Aoyagi M, Ushioda M, Ohkubo A, Seio K. Chemically Stabilized Phenylboranylidene Groups Having a Dimethoxytrityl Group as a Colorimetrically Detectable Protecting Group Designed forcis-1,2-Diol Functions of Ribonucleosides in the Solid-Phase Synthesis of m22,2G5‘ppT. J Org Chem 2005; 70:8400-8. [PMID: 16209584 DOI: 10.1021/jo051202m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
To not only improve the inherently poor stability of the phenylboranylidene group as a protecting group of the 2',3'-cis-diol function of ribonucleosides but also introduce a colorimetrically detectable function into its mother structure, various 2-[(dialkylamino)methyl]phenylboronic acid derivatives having a [(4,4'-dimethoxytrityl)oxy]methyl group were synthesized. The reaction of uridine with these substituted phenylboronic acid derivatives gave the corresponding 2',3'-O-phenylboranylideneuridine derivatives. The stability of these phenylboranylidene groups was examined. As a result, it was shown that the steric hindrance around the amino group greatly influenced the stability of the 2-substituted phenylboranylidene groups. The 2-aminomethyl-5-[[(4,4'-dimethoxytrityl)oxy]methyl]phenylboranylidene group was the most stable. Its 2-dimethylamino counterpart, the 2-[(dimethylamino)methyl]-5-[[(4,4'-dimethoxytrityl)oxy]methyl]phenylboranylidene group, was the second most stable. When the most and second stable protecting groups were applied to the synthesis of m(2)(2,2)G(5)(')ppT on controlled pore glass, the second stable protecting group showed the best result. The use of this DMTr-containing protecting group enabled us to estimate colorimetrically the amount of the m(2)(2,2)G residue that was incorporated into the reactive site of the pT-loaded CPG resin.
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Affiliation(s)
- Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, Division of Collaborative Research for Bioscience and Biotechnology, Midoriku, Yokohama 226-8501, Japan.
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14
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Synthesis of 8-vinyladenosine 5′-di- and 5′-triphosphate: evaluation of the diphosphate compound on ribonucleotide reductase. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)01151-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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16
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Abstract
Several coumarin-labeled nucleotides have been synthesized, based on 2'(3')-O-(2-aminoethyl)carbamoyl-ATP (edaATP). The fluorescent coumarins coupled with the free amino group are 7-diethylaminocoumarin-3-carboxylic acid (to give deac-edaATP), coumarin 343 (but-edaATP) and 7-ethylamino-8-bromocoumarin-3-carboxylic acid (mbc-edaATP). The carbamoyl linkage of these nucleotide analogs undergoes interconversion between 2'- and 3'-hydroxyl attachment very slowly, so that the 2'- and 3'-isomers were separated and stored with minimal equilibration. 3'-Deac-edaADP had fluorescence excitation and emission maxima at 430 nm and 477 nm, with a fluorescence quantum yield of 0.012. The equivalent data for 3'-but-edaADP are 445 nm, 494 nm, and 0.51, respectively, and for 3'-mbc-edaADP, 405 nm, 464 nm, and 0.62. The interaction with skeletal myosin subfragment 1 was measured in the absence and presence of actin. In each case the fluorescence was decreased when bound to subfragment 1, 3-fold for 3'-deac-edaADP, 7-fold for 3'-but-edaADP, and 11-fold for 3'-mbc-edaADP. Steady-state ATPase measurements and the kinetics of binding and release of nucleotides were similar to those reported for the natural nucleotide. Large fluorescence changes could be observed for the release of these analogs from actomyosin subfragment 1, enabling a direct measurement of the kinetics of this process. In the case of 3'-deac-edaADP a rate constant of 474 s(-1) was measured (at pH 7.0, 20 degrees C, and low ionic strength).
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Affiliation(s)
- M R Webb
- National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom.
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17
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Affiliation(s)
- K Burgess
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, and ISIS Pharmaceuticals, Carlsbad Research Center, 2292 Faraday Avenue, Carlsbad, California 920088
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18
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Marciacq F, Sauvaigo S, Issartel JP, Mouret JF, Molko D. Synthesis and enzymatic incorporation of morpholino thymidine-5′-triphosphate in DNA fragments. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)00842-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Padyukova NS, Dixon HBF, Efimtseva EV, Ermolinsky BS, Mikhailov SN, Karpeisky MY. Synthesis and Properties of Novel NTP Derivatives. ACTA ACUST UNITED AC 1999. [DOI: 10.1080/15257779908041633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Yamaguchi T, Tomikawa A, Hirai T, Kawaguchi T, Ohrui H, Saneyoshi M. Antileukemic Activities and Mechanism of Action of 2′-Deoxy-4′-methylcytidine and Related Nucleosides. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708006185] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Yanachkov I, Pan JY, Wessling-Resnick M, Wright GE. Synthesis and effect of nonhydrolyzable xanthosine triphosphate derivatives on prenylation of Rab5D136N. Mol Pharmacol 1997; 51:47-51. [PMID: 9016345 DOI: 10.1124/mol.51.1.47] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A novel and convenient method for nucleoside triphosphate synthesis was applied to the preparation of potentially nonhydrolyzable xanthosine triphosphate derivatives. The N-methylimidazolide of xanthosine 5'-monophosphate reacted rapidly with methylenediphosphonic acid and imidodiphosphonic acid to give xanthosine 5'-(beta, gamma-methylene)triphosphate and xanthosine 5'-(beta, gamma-imido)triphosphate, respectively, in good yields. Both compounds inhibited the xanthosine-diphosphate-dependent prenylation of a mutant of Rab5, Rab5D136N, the nucleotide specificity of which had been converted from GTP to xanthosine triphosphate. The results indicate that xanthosine 5'-(beta, gamma-methylene)triphosphate and xanthosine 5'-(beta, gamma-imido)triphosphate bound to the mutant protein with similar affinities and were not hydrolyzed under the assay conditions. These novel derivatives may be useful tools for the study of the role of individual GTPases mutated to xanthosine triphosphate specificity in the background of other GTP-binding proteins.
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Affiliation(s)
- I Yanachkov
- Department of Pharmacology and Molecular Toxicology, University of Massachusetts Medical School, Worcester 01655, USA
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22
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The development and application of photosensitive caged compounds to aid time-resolved structure determination of macromolecules. ACTA ACUST UNITED AC 1997. [DOI: 10.1098/rsta.1992.0063] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Rapid photochemical release of biologically active molecules, typically enzyme substrates or effectors of proteins, within crystals is likely to play an important role in time-resolved macromolecular crystallography. Photosensitive or ‘caged’ compounds in which functional groups are protected by the l-(2-nitrophenyl)ethyl group are potentially useful because many such compounds are efficiently and fairly rapidly photolysed (product quantum yield
ca.
0.5 and photolysis rate
ca.
100 s
-1
for esters of weakly acidic phosphates) and have proved effective probes of physiological mechanisms. However, their availability and successful application are unlikely to be universal, and in some cases limitations may arise because of low quantum yield, a photolysis rate that is slow compared with the mechanism being studied or the toxicity of the by-product, 2-nitrosoacetophenone. 3,5-Dinitrophenyl and 3,5'- dimethoxybenzoin esters are two other potentially useful photosensitive classes of compound (Kirby & Varvoglis, J.
chem. Soc. chem. Commun.
406 (1967); Sheehan
et al.
, J.
Am. chem. Soc
. 93, 7222-7228 (1971); Baldwin
et al., Tetrahedron
46, 6879-6884 (1990)). 3,5-Dinitrophenyl phosphate has a product quantum yield of 0.67 and releases P A at greater than 104 s_1. However the dinitrophenyl group is not generally photosensitive: for example the P 3-3,5-dinitrophenyl ester of ATP photolyses very inefficiently at pH 7. The S'A'-dimethoxybenzoin group is a promising photosensitive group for phosphate esters and the P
3
-3/,5'-dimethoxybenzoin ester of ATP photolyses at greater than 10
5
s
-1
at neutral pH and 20 °C though with only about 4% photolysis on 347 nm pulse irradiation.
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23
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Hazlett TL, Moore KJ, Lowe PN, Jameson DM, Eccleston JF. Solution dynamics of p21ras proteins bound with fluorescent nucleotides: a time-resolved fluorescence study. Biochemistry 1993; 32:13575-83. [PMID: 8257693 DOI: 10.1021/bi00212a025] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The solution dynamics of normal and transforming p21ras proteins in both the GTP- and GDP-bound forms were examined with time-resolved fluorescence spectroscopy. The fluorescent 2'(3')-O-(N-methylanthraniloyl) derivatives (mant derivatives) of GTP, dGTP, and GDP and the aminocoumarin and fluorescein derivatives of GTP and GDP were synthesized and used as reporter groups. The fluorescence lifetimes at 5 degrees C of the mant nucleotide derivatives increased from approximately 4 ns in solution to approximately 9 ns when bound to p21ras. At 30 degrees C, there was a 7.8% difference in lifetime between normal p21ras.mantGTP and p21ras.mantGDP, but no difference between similar complexes of the [Asp-12]p21ras protein. These data are consistent with steady-state fluorescence intensity differences among p21ras.mantGTP, p21ras.mantGDP, and the free nucleotides. Rotational correlation times for the mantGTP- and mantGDP-bound p21 proteins, N-ras, K-ras, and H-ras, were similar at 26 ns (5 degrees C), which is significantly longer than the 15-ns rotational correlation time predicted for a globular 21,000-Da protein. The p21-bound fluorescein and aminocoumarin nucleotide derivatives reported correlation times of 19 and 29 ns, respectively. Global analysis of the three fluorophore.p21 complexes with linked protein rotational correlation functions were best fit with a common rotational correlation time of 28 ns. Gel permeation chromatography of the GDP and mantGDP complexes of normal p21N-ras also showed greater apparent molecular weights than were expected in both cases, demonstrating that the high rotational correlation times obtained from time-resolved fluorescence measurements were not a result of the introduction of the fluorophore.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- T L Hazlett
- Department of Physics, University of Illinois at Urbana, Champaign 61801
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Corrie JE, Pizza C, Makwana J, King RW. Preparation and properties of an affinity support for purification of cyclic AMP receptor protein from Escherichia coli. Protein Expr Purif 1992; 3:417-20. [PMID: 1333861 DOI: 10.1016/s1046-5928(05)80044-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Reaction of cyclic AMP with 1,1'-carbonyldiimidazole produces an intermediate which reacts with primary amines to provide a stable 2'-O-carbamyl derivative. This chemistry has been used to tether cyclic AMP to a Sepharose gel. The resulting affinity support has been used to effect a simple, nondenaturing purification of cyclic AMP receptor protein from crude cell extracts.
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Affiliation(s)
- J E Corrie
- National Institute for Medical Research, London, United Kingdom
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25
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Corrie JET, Reid GP, Trentham DR, Hursthouse MB, Mazid MA. Synthesis and absolute stereochemistry of the two diastereoisomers of P3-1-(2-nitrophenyl)ethyl adenosine triphosphate (‘caged’ ATP). ACTA ACUST UNITED AC 1992. [DOI: 10.1039/p19920001015] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Cremo CR, Neuron JM, Yount RG. Interaction of myosin subfragment 1 with fluorescent ribose-modified nucleotides. A comparison of vanadate trapping and SH1-SH2 cross-linking. Biochemistry 1990; 29:3309-19. [PMID: 2110475 DOI: 10.1021/bi00465a023] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The environment near the ribose binding site of skeletal myosin subfragment 1 (S1) was investigated by use of two adenosine 5'-diphosphate analogues with fluorescent groups attached at the 2'- and 3'-hydroxyls of the ribose ring. We have compared steady-state and time-resolved fluorescent properties of the reversibly bound S1-nucleotide complexes and the complexes generated by N,N'-p-phenylenedimaleimide (pPDM) thiol cross-linking or vanadate (Vi) trapping. A new fluorescent probe, 2'(3')-O-[N-[2-[[[5-(dimethylamino)naphthyl]sulfonyl] amino]ethyl]carbamoyl]adenosine 5'-diphosphate (DEDA-ADP), which contains a base-stable carbamoyl linkage between the ribose ring and the fluorescent dansyl group, was synthesized and characterized. For comparison, we performed parallel experiments with 2'(3')-O-(N-methylanthraniloyl)adenosine 5'-diphosphate (MANT-ADP) [Hiratsuka, T. (1983) Biochim. Biophys. Acta 742, 496-508]. Solute quenching studies indicated that both analogues bound reversibly to a single cleft or pocket near the ribose binding site. However, steady-state polarization measurements indicated that the probes were not rigidly bound to the protein. The quantum yields of both fluorophores were higher for the complexes formed after trapping with pPDM or Vi than for the reversibly bound complexes. Both DEDA-ADP and MANT-ADP, respectively, had nearly homogeneous lifetimes free in solution (3.65 and 4.65 ns), reversibly bound to S1 (12.8 and 8.6 ns), and trapped on S1 by pPDM (12.7 and 8.7 ns) or Vi (12.8 and 8.6 ns). In contrast to the quantum yields, the lifetimes were not increased upon trapping, compared to those of the reversibly bound states. These results suggested that static quenching in the reversibly bound complex was relieved upon trapping. Taken together, the results suggest that there was a conformational change near the ribose binding site upon trapping by either pPDM or Vi. On the basis of the quantum yield, lifetime, polarization, and solute accessibility studies, we could not detect differences between the S1-pPDM-nucleotide analog complex and the S1-Vi-nucleotide analogue complex for either analogue. Thus, previously observed differences with the adenine modified nucleotide analogue 1,N6-ethenoadenosine diphosphate (epsilon ADP) could not be detected with these ribose-modified probes, indicating that structural differences may be localized to the adenine binding site and not transmitted to the region near the ribose ring.
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Affiliation(s)
- C R Cremo
- Department of Chemistry, Colorado College, Colorado Springs 80903
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28
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Nakashima H, Matsui T, Harada S, Kobayashi N, Matsuda A, Ueda T, Yamamoto N. Inhibition of replication and cytopathic effect of human T cell lymphotropic virus type III/lymphadenopathy-associated virus by 3'-azido-3'-deoxythymidine in vitro. Antimicrob Agents Chemother 1986; 30:933-7. [PMID: 2434024 PMCID: PMC180622 DOI: 10.1128/aac.30.6.933] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human T cell lymphotropic virus type III (HTLV-III)/lymphadenopathy-associated virus is the etiologic agent of the acquired immune deficiency syndrome (AIDS) and AIDS-related complex. The effect of 3'-azido-3'-deoxythymidine (AZT) on the HTLV-III/lymphadenopathy-associated virus infection was quantitatively studied with HTLV type I-carrying MT-4 cells. The AZT compound inhibited HTLV-III-induced cytopathic effect and virus-specific antigen expression in MT-4 cells at concentrations of 5 and 10 microM. In addition, a plaque-forming assay was performed to assess the effect of AZT on virus replication in MT-4 cells freshly infected with HTLV-III and in continuous HTLV-III-producing Molt-4/HTLV-III cells. Results showed that AZT efficiently and effectively inhibited the replication of HTLV-III in infected MT-4 cells. AZT is a strong inhibitor of reverse transcriptase activity of HTLV-III as a triphosphate, to such a degree that even 1.0 pM azido-TTP inhibits 50% of reverse transcriptase activity. However, it did not show any effect in the HTLV-III-producing cell line Molt-4/HTLV-III. Thus, AZT has no effect on virus replication of an already integrated virus. When 5 microM AZT was added to HTLV-III-infected MT-4 within 20 h after infection, a striking suppressive effect was noticed. This concentration was much lower than that which inhibits the growth of MT-4 cells. These results confirm those found in a previous report (H. Mitsuya, K. J. Weinhold, P. S. Furman, H. S. Clair, S. N. Lehrman, R. C. Gallo, D. Bolognesi, D. W. Barry, and S. Broder, Proc. Natl. Acad. Sci. USA 82:7096-7100, 1985) and suggest that AZT might be used as an experimental antiviral agent for AIDS and AIDS-related complex.
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Use of a vinyl phosphonate analog of ATP as a rotationally constrained probe of the C5′O5′ torsion angle in ATP complexed to methionine adenosyl transferase. Bioorg Chem 1985. [DOI: 10.1016/0045-2068(85)90029-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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30
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Yip KF, Albarella JP. Use of high-performance liquid chromatography in the preparation of flavin adenine dinucleotide analyte conjugates. J Chromatogr A 1985. [DOI: 10.1016/s0021-9673(01)87455-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Sawai H. SYNTHESIS AND PROPERTIES OF OLIGOADENYLIC ACIDS CONTAINING 2′-5′ PHOSPHORAMIDE LINKAGE. CHEM LETT 1984. [DOI: 10.1246/cl.1984.805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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32
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Synthesis of adenosine-5′-diphosphate using N,N'-acyldibenzotriazole. Pharm Chem J 1983. [DOI: 10.1007/bf00765028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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33
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Morris DL, Buckler RT. Colorimetric immunoassays using flavin adenine dinucleotide as label. Methods Enzymol 1983; 92:413-25. [PMID: 6855621 DOI: 10.1016/0076-6879(83)92035-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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