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Dürr-Mayer T, Schmidt A, Wiesler S, Huck T, Mayer A, Jessen HJ. Non-Hydrolysable Analogues of Cyclic and Branched Condensed Phosphates: Chemistry and Chemical Proteomics. Chemistry 2023; 29:e202302400. [PMID: 37646539 DOI: 10.1002/chem.202302400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/18/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Studies into the biology of condensed phosphates almost exclusively cover linear polyphosphates. However, there is evidence for the presence of cyclic polyphosphates (metaphosphates) in organisms and for enzymatic digestion of branched phosphates (ultraphosphates) with alkaline phosphatase. Further research of non-linear condensed phosphates in biology would profit from interactome data of such molecules, however, their stability in biological media is limited. Here we present syntheses of modified, non-hydrolysable analogues of cyclic and branched condensed phosphates, called meta- and ultraphosphonates, and their application in a chemical proteomics approach using yeast cell extracts. We identify putative interactors with overlapping hits for structurally related capture compounds underlining the quality of our results. The datasets serve as starting point to study the biological relevance and functions of meta- and ultraphosphates. In addition, we examine the reactivity of meta- and ultraphosphonates with implications for their "hydrolysable" analogues: Efforts to increase the ring-sizes of meta- or cyclic ultraphosphonates revealed a strong preference to form trimetaphosphate-analogue structures by cyclization and/or ring-contraction. Using carbodiimides for condensation, the so far inaccessible dianhydro product of ultraphosphonate, corresponding to P4 O11 2- , was selectively obtained and then ring-opened by different nucleophiles yielding modified cyclic ultraphosphonates.
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Affiliation(s)
- Tobias Dürr-Mayer
- Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg im Breisgau, Germany
| | - Andrea Schmidt
- Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-CH-1066, Epalinges, Switzerland
| | - Stefan Wiesler
- Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg im Breisgau, Germany
| | - Tamara Huck
- Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg im Breisgau, Germany
| | - Andreas Mayer
- Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-CH-1066, Epalinges, Switzerland
| | - Henning J Jessen
- Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg im Breisgau, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg
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2
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Mordhorst S, Singh J, Mohr MKF, Hinkelmann R, Keppler M, Jessen HJ, Andexer JN. Several Polyphosphate Kinase 2 Enzymes Catalyse the Production of Adenosine 5'-Polyphosphates. Chembiochem 2019; 20:1019-1022. [PMID: 30549179 DOI: 10.1002/cbic.201800704] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Indexed: 11/08/2022]
Abstract
Polyphosphate kinases (PPKs) are involved in many metabolic processes; enzymes of the second family (PPK2) are responsible for nucleotide synthesis fuelled by the consumption of inorganic polyphosphate. They catalyse the phosphorylation of nucleotides with various numbers of phosphate residues, such as monophosphates or diphosphates. Hence, these enzymes are promising candidates for cofactor regeneration systems. Besides adenosine 5'-triphosphate, PPK2s also catalyse the synthesis of highly phosphorylated nucleotides in vitro, as shown here for adenosine 5'-tetraphosphate and adenosine 5'-pentaphosphate. These unusually phosphorylated adenosine 5'-polyphosphates add up to 50 % of the whole adenosine nucleotides in the assay. The two new products were chemically synthesised to serve as standards and compared with the two enzymatically produced compounds by high-performance ion chromatography and 31 P NMR analysis. This study shows that PPK2s are highly suitable for biocatalytic synthesis of different phosphorylated nucleotides.
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Affiliation(s)
- Silja Mordhorst
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Jyoti Singh
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Michael K F Mohr
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Rahel Hinkelmann
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Michael Keppler
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Jennifer N Andexer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
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3
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Forget SM, Smithen DA, Jee A, Jakeman DL. Mechanistic evaluation of a nucleoside tetraphosphate with a thymidylyltransferase. Biochemistry 2015; 54:1703-7. [PMID: 25647009 DOI: 10.1021/bi501438p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyrimidine polyphosphates were first detected in cells 5 decades ago; however, their biological significance remains only partially resolved. Such nucleoside polyphosphates are believed to be produced nonspecifically by promiscuous enzymes. Herein, synthetically prepared deoxythymidine 5'-tetraphosphate (p4dT) was evaluated with a thymidylyltransferase, Cps2L. We have identified p4dT as a substrate for Cps2L and evaluated the reaction pathway by analysis of products using high-performance liquid chromatography, liquid chromatography and tandem mass spectrometry, and 31P nuclear magnetic resonance spectroscopy. Product analysis confirmed production of dTDP-Glc and triphosphate (P3) and showed no trace of dTTP-Glc and PPi, which could arise from alternative pathways for the reaction mechanism.
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Affiliation(s)
- Stephanie M Forget
- Department of Chemistry, Dalhousie University , P.O. Box 15000, Halifax, Canada B3H 4R2
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Branson KM, Mertens HDT, Swarbrick JD, Fletcher JI, Kedzierski L, Gayler KR, Gooley PR, Smith BJ. Discovery of inhibitors of lupin diadenosine 5',5'''-P(1),P(4)-tetraphosphate hydrolase by virtual screening. Biochemistry 2009; 48:7614-20. [PMID: 19603790 DOI: 10.1021/bi900813x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel inhibitors of lupin diadenosine 5',5'''-P(1),P(4)-tetraphosphate (Ap(4)A) hydrolase have been identified by in silico screening of a large virtual chemical library. Compounds were ranked on the basis of a consensus from six scoring functions. From the top 100 ranked compounds six were selected and initially screened for inhibitory activity using a single concentration isothermal titration calorimetry assay. Two of these compounds that showed excellent solubility properties were further analyzed, but only one [NSC51531; 2-((8-hydroxy-4-(4-methyl-2-sulfoanilino)-9,10-dioxo-9,10-dihydro-1-anthracenyl)amino)-5-methylbenzenesulfonic acid] exhibited competitive inhibition with a K(i) of 1 microM. A structural analogue of this compound also exhibited competitive inhibition with a comparable K(i) of 2.9 microM. (1)H, (15)N NMR spectroscopy was used to map the binding site of NSC51531 on lupin Ap(4)A hydrolase and demonstrated that the compound bound specifically in the substrate-binding site, consistent with the competitive inhibition results. Binding of NSC51531 to the human form of Ap(4)A hydrolase is nonspecific, suggesting that this compound may represent a useful lead in the design of specific inhibitors of the plant-like form of Ap(4)A hydrolases.
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Affiliation(s)
- Kim M Branson
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
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Tölle M, Jankowski V, Schuchardt M, Wiedon A, Huang T, Hub F, Kowalska J, Jemielity J, Guranowski A, Loddenkemper C, Zidek W, Jankowski J, van der Giet M. Adenosine 5'-tetraphosphate is a highly potent purinergic endothelium-derived vasoconstrictor. Circ Res 2008; 103:1100-8. [PMID: 18832747 DOI: 10.1161/circresaha.108.177865] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Besides serving as a mechanical barrier, the endothelium has important regulatory functions. The discovery of nitric oxide revolutionized our understanding of vasoregulation. In contrast, the identity of endothelium-derived vasoconstrictive factors still remains uncertain. The supernatant from mechanically stimulated human microvascular endothelial cells elicited a potent vasoconstrictive response in the isolated perfused rat kidney. Whereas a nonselective purinoceptor blocker blocked this vasoactivity most potently, the inhibition of the endothelin receptor by BQ123 weakly affected that vasoconstrictive response. As a compound responsible for that vasoconstrictive effect, we have isolated from HMECs and identified the mononucleotide adenosine 5'-tetraphosphate (AP4). This nucleotide proved to be the most potent vasoactive purinergic mediator identified to date, exerting the vasoconstriction predominantly through activation of the P2X1 receptor. The intraarterial application of AP4 in a Wistar-Kyoto rat induced a strong increase of the mean arterial pressure. The plasma concentration of AP4 is in the nanomolar range, which, in vivo, induces a significant change in the mean arterial pressure. To our knowledge, AP4, which exerts vasoactive effects, is the most potent endogenous mononucleotide identified to date in mammals. The effects of AP4, the plasma concentration of AP4, and its release suggest that this compound functions as an important vasoregulator.
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Affiliation(s)
- Markus Tölle
- Medizinische Klinik IV-Nephrology, Charite-Campus Benjamin Franklin, Berlin, Germany
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Tammenkoski M, Koivula K, Cusanelli E, Zollo M, Steegborn C, Baykov AA, Lahti R. Human Metastasis Regulator Protein H-Prune is a Short-Chain Exopolyphosphatase. Biochemistry 2008; 47:9707-13. [DOI: 10.1021/bi8010847] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marko Tammenkoski
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Katja Koivula
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Emilio Cusanelli
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Massimo Zollo
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Clemens Steegborn
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Alexander A. Baykov
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Reijo Lahti
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland, Department of Biochemistry and Biotechnological Medicine, Via Pansini 5, University Federico II of Naples, Italy, c/o CEINGE, Centro di Ingegneria Genetica e Biotecnologie Avanzate, Naples, Italy, Department of Physiological Chemistry, Ruhr-University Bochum, 44801 Bochum, Germany, and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
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Guranowski A, Starzyńska E, Pietrowska-Borek M, Rejman D, Blackburn GM. Novel diadenosine polyphosphate analogs with oxymethylene bridges replacing oxygen in the polyphosphate chain: potential substrates and/or inhibitors of Ap4A hydrolases. FEBS J 2008; 276:1546-53. [PMID: 19210543 DOI: 10.1111/j.1742-4658.2009.06882.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dinucleoside polyphosphates (Np(n)N's; where N and N' are nucleosides and n = 3-6 phosphate residues) are naturally occurring compounds that may act as signaling molecules. One of the most successful approaches to understand their biological functions has been through the use of Np(n)N' analogs. Here, we present the results of studies using novel diadenosine polyphosphate analogs, with an oxymethylene group replacing one or two bridging oxygen(s) in the polyphosphate chain. These have been tested as potential substrates and/or inhibitors of the symmetrically acting Ap(4)A hydrolase [bis(5'-nucleosyl)-tetraphosphatase (symmetrical); EC 3.6.1.41] from E. coli and of two asymmetrically acting Ap(4)A hydrolases [bis(5'-nucleosyl)-tetraphosphatase (asymmetrical); EC 3.6.1.17] from humans and narrow-leaved lupin. The six chemically synthesized analogs were: ApCH(2)OpOCH(2)pA (1), ApOCH(2)pCH(2)OpA (2), ApOpCH(2)OpOpA (3), ApCH(2)OpOpOCH(2)pA (4), ApOCH(2)pOpCH(2)OpA (5) and ApOpOCH(2)pCH(2)OpOpA (6). The eukaryotic asymmetrical Ap(4)A hydrolases degrade two compounds, 3 and 5, as anticipated in their design. Analog 3 was cleaved to AMP (pA) and beta,gamma-methyleneoxy-ATP (pOCH(2)pOpA), whereas hydrolysis of analog 5 gave two molecules of alpha,beta-oxymethylene ADP (pCH(2)OpA). The relative rates of hydrolysis of these analogs were estimated. Some of the novel nucleotides were moderately good inhibitors of the asymmetrical hydrolases, having K(i) values within the range of the K(m) for Ap(4)A. By contrast, none of the six analogs were good substrates or inhibitors of the bacterial symmetrical Ap(4)A hydrolase.
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Affiliation(s)
- Andrzej Guranowski
- Department of Biochemistry and Biotechnology, University of Life Sciences, Poznań, Poland.
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