1
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Park G, Wralstad EC, Faginas-Lago N, Qian K, Raines RT, Bistoni G, Cummins CC. Pentaphosphorylation via the Anhydride of Dihydrogen Pentametaphosphate: Access to Nucleoside Hexa- and Heptaphosphates and Study of Their Interaction with Ribonuclease A. ACS CENTRAL SCIENCE 2024; 10:1415-1422. [PMID: 39071052 PMCID: PMC11273453 DOI: 10.1021/acscentsci.4c00835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024]
Abstract
Pentametaphosphate is the little studied cyclic pentamer of the metaphosphate ion, [PO3]5 5-. We show that the doubly protonated form of this pentamer can be selectively dehydrated to provide the anhydride [P5O14]3- (1). This trianion is the well-defined condensed phosphate component of a novel reagent for attachment of a pentaphosphate chain to biomolecules all in one go. Here, we demonstrate by extending adenosine monophosphate (AMP) and uridine monophosphate (UMP) to their corresponding nucleoside hexaphosphates, while adenosine diphosphate (ADP) and uridine diphosphate (UDP) are phosphate chain-extended to the corresponding nucleoside heptaphosphates. Such constructs are of interest for their potential biological function with respect to RNA-processing enzymes. Thus, we go on to investigate in detail the interaction of the polyanionic constructs with ribonuclease A, a model protein containing a polycationic active site and for which X-ray crystal structures are relatively straightforward to obtain. This work presents a combined experimental and quantum chemical approach to understanding the interactions of RNase A with the new nucleoside hexa- and heptaphosphate constructs.
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Affiliation(s)
- Gyeongjin Park
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Evans C. Wralstad
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Noelia Faginas-Lago
- Department
of Chemistry, Biology,and Biotechnology, University of Perugia, 06123, Perugia, Italy
| | - Kevin Qian
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Giovanni Bistoni
- Department
of Chemistry, Biology,and Biotechnology, University of Perugia, 06123, Perugia, Italy
| | - Christopher C. Cummins
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
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2
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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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3
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Shepard SM, Jessen HJ, Cummins CC. Beyond Triphosphates: Reagents and Methods for Chemical Oligophosphorylation. J Am Chem Soc 2022; 144:7517-7530. [PMID: 35471019 DOI: 10.1021/jacs.1c07990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligophosphates play essential roles in biochemistry, and considerable research has been directed toward the synthesis of both naturally occurring oligophosphates and their synthetic analogues. Greater attention has been given to mono-, di-, and triphosphates, as these are present in higher concentrations biologically and easier to synthesize. However, extended oligophosphates have potent biochemical roles, ranging from blood coagulation to HIV drug resistance. Sporadic reports have slowly built a niche body of literature related to the synthesis and study of extended oligophosphates, but newfound interests and developments have the potential to rapidly expand this field. Here we report on current methods to synthesize oligophosphates longer than triphosphates and comment on the most important future directions for this area of research. The state of the art has provided fairly robust methods for synthesizing nucleoside 5'-tetra- and pentaphosphates as well as dinucleoside 5',5'-oligophosphates. Future research should endeavor to push such syntheses to longer oligophosphates while developing synthetic methodologies for rarer morphologies such as 3'-nucleoside oligophosphates, polyphosphates, and phosphonate/thiophosphate analogues of these species.
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Affiliation(s)
- Scott M Shepard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg & Cluster of Excellence livMatS, FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
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4
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Haas TM, Wiesler S, Dürr‐Mayer T, Ripp A, Fouka P, Qiu D, Jessen HJ. The Aryne Phosphate Reaction**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Thomas M. Haas
- Institute of Organic Chemistry Albert-Ludwigs University Freiburg Albertstraße 21 79102 Freiburg im Breisgau Germany
| | - Stefan Wiesler
- Institute of Organic Chemistry Albert-Ludwigs University Freiburg Albertstraße 21 79102 Freiburg im Breisgau Germany
| | - Tobias Dürr‐Mayer
- Institute of Organic Chemistry Albert-Ludwigs University Freiburg Albertstraße 21 79102 Freiburg im Breisgau Germany
| | - Alexander Ripp
- Institute of Organic Chemistry Albert-Ludwigs University Freiburg Albertstraße 21 79102 Freiburg im Breisgau Germany
- DFG Cluster of Excellence “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS) 79110 Freiburg Germany
| | - Paraskevi Fouka
- Institute of Organic Chemistry Albert-Ludwigs University Freiburg Albertstraße 21 79102 Freiburg im Breisgau Germany
| | - Danye Qiu
- Institute of Organic Chemistry Albert-Ludwigs University Freiburg Albertstraße 21 79102 Freiburg im Breisgau Germany
| | - Henning J. Jessen
- Institute of Organic Chemistry Albert-Ludwigs University Freiburg Albertstraße 21 79102 Freiburg im Breisgau Germany
- DFG Cluster of Excellence “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS) 79110 Freiburg Germany
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5
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Haas TM, Wiesler S, Dürr-Mayer T, Ripp A, Fouka P, Qiu D, Jessen HJ. The Aryne Phosphate Reaction*. Angew Chem Int Ed Engl 2021; 61:e202113231. [PMID: 34727582 PMCID: PMC9299019 DOI: 10.1002/anie.202113231] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Indexed: 11/10/2022]
Abstract
Condensed phosphates are a critically important class of molecules in biochemistry. Non‐natural analogues are important for various applications, such as single‐molecule real‐time DNA sequencing. Often, such analogues contain more than three phosphate units in their oligophosphate chain. Consequently, investigations into phosphate reactivity enabling new ways of phosphate functionalization and oligophosphorylation are essential. Here, we scrutinize the potential of phosphates to act as arynophiles, paving the way for follow‐up oligophosphorylation reactions. The aryne phosphate reaction is a powerful tool to—depending on the perspective—(oligo)phosphorylate arenes or arylate (oligo‐cyclo)phosphates. Based on Kobayashi‐type o‐silylaryltriflates, the aryne phosphate reaction enables rapid entry into a broad spectrum of arylated products, like monophosphates, diphosphates, phosphodiesters and polyphosphates. The synthetic potential of these new transformations is demonstrated by efficient syntheses of nucleotide analogues and an unprecedented one‐flask octaphosphorylation.
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Affiliation(s)
- Thomas M Haas
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstraße 21, 79102, Freiburg im Breisgau, Germany
| | - Stefan Wiesler
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstraße 21, 79102, Freiburg im Breisgau, Germany
| | - Tobias Dürr-Mayer
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstraße 21, 79102, Freiburg im Breisgau, Germany
| | - Alexander Ripp
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstraße 21, 79102, Freiburg im Breisgau, Germany.,DFG Cluster of Excellence "Living, Adaptive and Energy-Autonomous Materials Systems" (livMatS), 79110, Freiburg, Germany
| | - Paraskevi Fouka
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstraße 21, 79102, Freiburg im Breisgau, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstraße 21, 79102, Freiburg im Breisgau, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, Albert-Ludwigs University Freiburg, Albertstraße 21, 79102, Freiburg im Breisgau, Germany.,DFG Cluster of Excellence "Living, Adaptive and Energy-Autonomous Materials Systems" (livMatS), 79110, Freiburg, Germany
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6
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Abstract
Condensed phosphates may exist as linear, cyclic or branched structures. Due to their important role in nature, linear polyphosphates have been well studied. In contrast, branched phosphates (ultraphosphates) remain largely uncharacterised, because they were already described in 1950 as exceedingly unstable in the presence of water, epitomized in the antibranching-rule. This rule lacks experimental backup, since, to the best of our knowledge, no rational synthesis of defined ultraphosphates is known. Consequently, detailed studies of their chemical properties, reactivity and potential biological relevance remain elusive. Here, we introduce a general synthesis of monodisperse ultraphosphates. Hydrolysis half-lives up to days call the antibranching-rule into question. We provide evidence for the interaction of an enzyme with ultraphosphates and discover a rearrangement linearizing the branched structure. Moreover, ultraphosphate can phosphorylate nucleophiles such as amino acids and nucleosides with implications for prebiotic chemistry. Our results provide an entry point into the uncharted territory of branched condensed phosphates. The “anti-branching rule”, introduced in 1950, excludes branched polyphosphates from biological relevance due to their supposedly rapid hydrolysis. Here, the authors synthesize monodisperse branched polyphosphates and demonstrate their unexpected stability in water, as well as provide evidence for their competence in phosphorylation.
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7
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Chizzolini F, Kent AD, Passalacqua LFM, Lupták A. Enzymatic RNA Production from NTPs Synthesized from Nucleosides and Trimetaphosphate*. Chembiochem 2021; 22:2098-2101. [PMID: 33798271 DOI: 10.1002/cbic.202100085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Indexed: 01/22/2023]
Abstract
A mechanism of nucleoside triphosphorylation would have been critical in an evolving "RNA world" to provide high-energy substrates for reactions such as RNA polymerization. However, synthetic approaches to produce ribonucleoside triphosphates (rNTPs) have suffered from conditions such as high temperatures or high pH that lead to increased RNA degradation, as well as substrate production that cannot sustain replication. Previous reports have demonstrated that cyclic trimetaphosphate (cTmp) can react with nucleosides to form rNTPs under prebiotically-relevant conditions, but their reaction rates were unknown and the influence of reaction conditions not well-characterized. Here we established a sensitive assay that allowed for the determination of second-order rate constants for all four rNTPs, ranging from 1.7×10-6 to 6.5×10-6 M-1 s-1 . The ATP reaction shows a linear dependence on pH and Mg2+ , and an enthalpy of activation of 88±4 kJ/mol. At millimolar nucleoside and cTmp concentrations, the rNTP production rate is sufficient to facilitate RNA synthesis by both T7 RNA polymerase and a polymerase ribozyme. We suggest that the optimized reaction of cTmp with nucleosides may provide a viable connection between prebiotic nucleotide synthesis and RNA replication.
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Affiliation(s)
- Fabio Chizzolini
- Department of Pharmaceutical Sciences, University of California at Irvine, Irvine, CA, 92617, USA
| | - Alexandra D Kent
- Department of Chemistry, University of California at Irvine, Irvine, CA, 92617, USA
| | - Luiz F M Passalacqua
- Department of Pharmaceutical Sciences, University of California at Irvine, Irvine, CA, 92617, USA
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California at Irvine, Irvine, CA, 92617, USA.,Department of Chemistry, University of California at Irvine, Irvine, CA, 92617, USA.,Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, 92617, USA
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8
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Shepard SM, Kim H, Bang QX, Alhokbany N, Cummins CC. Synthesis of α,δ-Disubstituted Tetraphosphates and Terminally-Functionalized Nucleoside Pentaphosphates. J Am Chem Soc 2020; 143:463-470. [PMID: 33375782 DOI: 10.1021/jacs.0c11884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The anion [P4O11]2-, employed as its bis(triphenylphosphine)iminium (PPN) salt, is shown herein to be a versatile reagent for nucleophile tetraphosphorylation. Treatment under anhydrous conditions with an alkylamine base and a nucleophile (HNuc1), such as an alcohol (neopentanol, cyclohexanol, 4-methylumbelliferone, and Boc-Tyr-OMe), an amine (propargylamine, diethylamine, morpholine, 3,5-dimethylaniline, and isopropylamine), dihydrogen phosphate, phenylphosphonate, azide ion, or methylidene triphenylphosphorane, results in nucleophile substituted tetrametaphosphates ([P4O11Nuc1]3-) as mixed PPN and alkylammonium salts in 59% to 99% yield. Treatment of the resulting functionalized tetrametaphosphates with a second nucleophile (HNuc2), such as hydroxide, a phenol (4-methylumbelliferone), an amine (propargylamine and ethanolamine), fluoride, or a nucleoside monophosphate (uridine monophosphate, deoxyadenosine monophosphate, and adenosine monophosphate), results in ring opening to linear tetraphosphates bearing one nucleophile on each end ([Nuc1(PO3)3PO2Nuc2]4-). When necessary, these linear tetraphosphates are purified by reverse phase or anion exchange HPLC, yielding triethylammonium or ammonium salts in 32% to 92% yield from [PPN]2[P4O11]. Phosphorylation of methylidene triphenylphosphorane as Nuc1 yields a new tetrametaphosphate-based ylide ([Ph3PCHP4O11]3-, 94% yield). Wittig olefination of 2',3'-O-isopropylidene-5'-deoxy-5'-uridylaldehyde using this ylide results in a 3'-deoxy-3',4'-didehydronucleotide derivative, isolated as the triethylammonium salt in 54% yield.
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Affiliation(s)
- Scott M Shepard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Hyehwang Kim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Qing Xin Bang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Norah Alhokbany
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
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9
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Domon K, Puripat M, Fujiyoshi K, Hatanaka M, Kawashima SA, Yamatsugu K, Kanai M. Catalytic Chemoselective O-Phosphorylation of Alcohols. ACS CENTRAL SCIENCE 2020; 6:283-292. [PMID: 32123747 PMCID: PMC7047436 DOI: 10.1021/acscentsci.9b01272] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Indexed: 05/16/2023]
Abstract
Phosphorylation of alcohols is a fundamentally important reaction in both life science and physical science. Product phosphate monoesters play key roles in living organisms, natural products, pharmaceuticals, and organic materials. Most of the chemical methods to date for synthesizing phosphate monoesters, however, require multistep sequences or are limited to specific types of substrates possibly due to harsh conditions. An alternative way to enable the simple production of phosphate monoesters from highly functionalized precursor alcohols is, thus, highly desired. We report herein a catalytic phosphorylation of alcohols with high functional group tolerance using tetrabutylammonium hydrogen sulfate (TBAHS) and phosphoenolpyruvic acid monopotassium salt (PEP-K) as the catalyst and phosphoryl donor, respectively. This method enables the direct introduction of a nonprotected phosphate group to the hydroxy group of a diverse menu of alcohol substrates, including functionalized small molecules, carbohydrates, and unprotected peptides. Nuclear magnetic resonance, mass spectrometric, and density functional theory analyses suggest that an unprecedented mixed anhydride species, generated from PEP-K and TBAHS, acts as an active phosphoryl donor in this reaction. This operationally simple and chemoselective catalytic phosphorylation allows for the efficient production of densely functionalized O-phosphorylated compounds, which are useful in diverse fields including biology and medicine.
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Affiliation(s)
- K. Domon
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. Puripat
- Institute
for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - K. Fujiyoshi
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. Hatanaka
- Institute
for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
- Graduate
School of Science and Technology, Data Science Center, NAIST, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - S. A. Kawashima
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - K. Yamatsugu
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. Kanai
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
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10
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Bezold D, Dürr T, Singh J, Jessen HJ. Cyclotriphosphate: A Brief History, Recent Developments, and Perspectives in Synthesis. Chemistry 2020; 26:2298-2308. [PMID: 31637774 PMCID: PMC7065162 DOI: 10.1002/chem.201904433] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/21/2019] [Indexed: 01/08/2023]
Abstract
There has been a recent upsurge in the study and application of approaches utilizing cyclotriphosphate 1 (cyclo-TP, also known as trimetaphosphate, TMP) and/or proceeding through its analogues in synthetic chemistry to access modified oligo- and polyphosphates. This is especially useful in the area of chemical nucleotide synthesis, but by no means restricted to it. Enabled by new high yielding and easy-to-implement methodologies, these approaches promise to open up an area of research that has previously been underappreciated. Additionally, refinements of concepts of prebiotic phosphorylation chemistry have been disclosed that ultimately rely on cyclo-TP 1 as a precursor, placing it as a potentially central compound in the emergence of life. Given the importance of such concepts for our understanding of prebiotic chemistry in combination with the need to readily access modified polyphosphates for structural and biological studies, this paper will discuss selected recent developments in the field of cyclo-TP chemistry, briefly touch on ultraphosphate chemistry, and highlight areas in which further developments can be expected.
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Affiliation(s)
- Dominik Bezold
- Institute of Organic ChemistryUniversity of Freiburg79104FreiburgGermany
| | - Tobias Dürr
- Institute of Organic ChemistryUniversity of Freiburg79104FreiburgGermany
| | - Jyoti Singh
- Institute of Organic ChemistryUniversity of Freiburg79104FreiburgGermany
| | - Henning J. Jessen
- Institute of Organic ChemistryUniversity of Freiburg79104FreiburgGermany
- Freiburg Research Institute for Advanced Studies (FRIAS)University of Freiburg79104FreiburgGermany
- Cluster of Excellence livMatS @ FIT—Freiburg Center for, Interactive Materials and Bioinspired TechnologiesUniversity of FreiburgGeorges-Köhler-Allee 10579110FreiburgGermany
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11
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Mohsen MG, Ji D, Kool ET. Polymerase synthesis of four-base DNA from two stable dimeric nucleotides. Nucleic Acids Res 2019; 47:9495-9501. [PMID: 31504784 PMCID: PMC6765132 DOI: 10.1093/nar/gkz741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/12/2019] [Accepted: 08/16/2019] [Indexed: 11/25/2022] Open
Abstract
We document the preparation and properties of dimerized pentaphosphate-bridged deoxynucleotides (dicaptides) that contain reactive components of two different nucleotides simultaneously. Importantly, dicaptides are found to be considerably more stable to hydrolysis than standard dNTPs. Steady-state kinetics studies show that the dimers exhibit reasonably good efficiency with the Klenow fragment of DNA polymerase I, and we identify thermostable enzymes that process them efficiently at high temperature. Experiments show that the dAp5dT dimer successfully acts as a combination of dATP and dTTP in primer extension reactions, and the dGp5dC dimer as a combination of dGTP and dCTP. The two dimers in combination promote successful 4-base primer extension. The final byproduct of the reaction, triphosphate, is shown to be less inhibitory to primer extension than pyrophosphate, the canonical byproduct. Finally, we document PCR amplification of DNA with two dimeric nucleotides, and show that the dimers can promote amplification under extended conditions when PCR with normal dNTPs fails. These dimeric nucleotides represent a novel and simple approach for increasing stability of nucleotides and avoiding inhibition from pyrophosphate.
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Affiliation(s)
- Michael G Mohsen
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Debin Ji
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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12
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Appy L, Chardet C, Peyrottes S, Roy B. Synthetic Strategies for Dinucleotides Synthesis. Molecules 2019; 24:molecules24234334. [PMID: 31783537 PMCID: PMC6930578 DOI: 10.3390/molecules24234334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Dinucleoside 5′,5′-polyphosphates (DNPs) are endogenous substances that play important intra- and extracellular roles in various biological processes, such as cell proliferation, regulation of enzymes, neurotransmission, platelet disaggregation and modulation of vascular tone. Various methodologies have been developed over the past fifty years to access these compounds, involving enzymatic processes or chemical procedures based either on P(III) or P(V) chemistry. Both solution-phase and solid-support strategies have been developed and are reported here. Recently, green chemistry approaches have emerged, offering attracting alternatives. This review outlines the main synthetic pathways for the preparation of dinucleoside 5′,5′-polyphosphates, focusing on pharmacologically relevant compounds, and highlighting recent advances.
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13
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Shepard SM, Windsor IW, Raines RT, Cummins CC. Nucleoside Tetra- and Pentaphosphates Prepared Using a Tetraphosphorylation Reagent Are Potent Inhibitors of Ribonuclease A. J Am Chem Soc 2019; 141:18400-18404. [PMID: 31651164 DOI: 10.1021/jacs.9b09760] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Adenosine and uridine 5'-tetra- and 5'-pentaphosphates were synthesized from an activated tetrametaphosphate ([PPN]2[P4O11], [PPN]2[1], PPN = bis(triphenylphosphine)iminium) and subsequently tested for inhibition of the enzymatic activity of ribonuclease A (RNase A). Reagent [PPN]2[1] reacts with unprotected uridine and adenosine in the presence of a base under anhydrous conditions to give nucleoside tetrametaphosphates. Ring opening of these intermediates with tetrabutylammonium hydroxide ([TBA][OH]) yields adenosine and uridine tetraphosphates (p4A, p4U) in 92% and 85% yields, respectively, from the starting nucleoside. Treatment of ([PPN]2[1]) with AMP or UMP yields nucleoside-monophosphate tetrametaphosphates (cp4pA, cp4pU) having limited aqueous stability. Ring opening of these ultraphosphates with [TBA][OH] yields p5A and p5U in 58% and 70% yield from AMP and UMP, respectively. We characterized inorganic and nucleoside-conjugated linear and cyclic oligophosphates as competitive inhibitors of RNase A. Increasing the chain length in both linear and cyclic inorganic oligophosphates resulted in improved binding affinity. Increasing the length of oligophosphates on the 5' position of adenosine beyond three had a deleterious effect on binding. Conversely, uridine nucleotides bearing 5' oligophosphates saw progressive increases in binding with chain length. We solved X-ray cocrystal structures of the highest affinity binders from several classes. The terminal phosphate of p5A binds in the P1 enzymic subsite and forces the oligophosphate to adopt a convoluted conformation, while the oligophosphate of p5U binds in several extended conformations, targeting multiple cationic regions of the active-site cleft.
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Affiliation(s)
- Scott M Shepard
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
| | - Ian W Windsor
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
| | - Ronald T Raines
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
| | - Christopher C Cummins
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
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14
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Singh J, Steck N, De D, Hofer A, Ripp A, Captain I, Keller M, Wender PA, Bhandari R, Jessen HJ. A Phosphoramidite Analogue of Cyclotriphosphate Enables Iterative Polyphosphorylations. Angew Chem Int Ed Engl 2019; 58:3928-3933. [DOI: 10.1002/anie.201814366] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Jyoti Singh
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Nicole Steck
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Debaditya De
- Laboratory of Cell Signaling, CDFD Hyderabad India
| | - Alexandre Hofer
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Alexander Ripp
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Ilya Captain
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Manfred Keller
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Paul A. Wender
- Stanford UniversityChemistry Department 333 Campus Drive Stanford CA 94305-5080 USA
| | | | - Henning J. Jessen
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
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15
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Singh J, Steck N, De D, Hofer A, Ripp A, Captain I, Keller M, Wender PA, Bhandari R, Jessen HJ. A Phosphoramidite Analogue of Cyclotriphosphate Enables Iterative Polyphosphorylations. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jyoti Singh
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Nicole Steck
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Debaditya De
- Laboratory of Cell Signaling, CDFD Hyderabad India
| | - Alexandre Hofer
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Alexander Ripp
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Ilya Captain
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Manfred Keller
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
| | - Paul A. Wender
- Stanford UniversityChemistry Department 333 Campus Drive Stanford CA 94305-5080 USA
| | | | - Henning J. Jessen
- University of FreiburgInstitute of Organic Chemistry Albertstrasse 21 79104 Freiburg Germany
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16
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Appy L, Depaix A, Bantreil X, Lamaty F, Peyrottes S, Roy B. Straightforward Ball-Milling Access to Dinucleoside 5',5'-Polyphosphates via Phosphorimidazolide Intermediates. Chemistry 2019; 25:2477-2481. [PMID: 30549335 DOI: 10.1002/chem.201805924] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 11/08/2022]
Abstract
A solvent-assisted mechanochemical approach to access symmetrical and mixed dinucleoside 5,5'-polyphosphates is reported. Under ball-milling conditions, nucleoside 5'-monophosphates were quantitatively activated using 1,1'-carbonyldiimidazole, forming their phosphorimidazolide derivatives. The addition of a nucleoside 5'-mono-, di- or triphosphate directly led to the formation of the corresponding dinucleotides. Benefits of the reported one-pot method include the use of unprotected nucleotides in their sodium or acid form, activation by the eco-friendly 1,1'-carbonyldiimidazole, non-dry conditions, short reaction time, high conversion rates, and easy setup and purification. This work offers new perspectives for the synthesis of nucleotide conjugates and analogues, combining the phosphorimidazolide approach and milling conditions.
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Affiliation(s)
- Lucie Appy
- Nucleosides & Phosphorylated Effectors, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1705, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Anaïs Depaix
- Nucleosides & Phosphorylated Effectors, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1705, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Xavier Bantreil
- Green Chemistry and Enabling Technologies, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1703, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Frédéric Lamaty
- Green Chemistry and Enabling Technologies, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1703, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Nucleosides & Phosphorylated Effectors, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1705, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Béatrice Roy
- Nucleosides & Phosphorylated Effectors, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, ENSCM, Université de Montpellier, Campus Triolet, cc1705, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
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17
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Shepard SM, Cummins CC. Functionalization of Intact Trimetaphosphate: A Triphosphorylating Reagent for C, N, and O Nucleophiles. J Am Chem Soc 2019; 141:1852-1856. [DOI: 10.1021/jacs.8b12204] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Scott M. Shepard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Christopher C. Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
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18
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Mohamady S, Taylor SD. Synthesis of Nucleoside-5'-O-Tetraphosphates from Activated Trimetaphosphate and Nucleoside-5'-O-Monophosphates. ACTA ACUST UNITED AC 2018; 75:e62. [PMID: 30307714 DOI: 10.1002/cpnc.62] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This article describes a straight-forward chemical method for the synthesis of nucleoside-5'-O-tetraphosphates, such as cytosine-, guanosine-, adenosine-, and uridine-5'-O-tetraphosphates, starting from the corresponding nucleoside monophosphates and trimetaphosphate, a readily available and inexpensive starting material. The procedure involves reacting the tri(tetrabutylammonium) salt of trimetaphosphate with mesitylenesulfonyl chloride and N-methylimidazole. The resulting activated cyclic trimetaphosphate is reacted with the tetrabutylammonium salts of nucleoside monophosphates. After quenching the reaction with buffer and high-performance liquid chromatography purification, the desired nucleoside-5'-O-tetraphosphates were obtained in yields of 84% to 86%. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Samy Mohamady
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada.,Current affiliation: Faculty of Pharmacy, The British University in Egypt, Al-Sherouk, Cairo, Egypt
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada
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19
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Azevedo C, Singh J, Steck N, Hofer A, Ruiz FA, Singh T, Jessen HJ, Saiardi A. Screening a Protein Array with Synthetic Biotinylated Inorganic Polyphosphate To Define the Human PolyP-ome. ACS Chem Biol 2018; 13:1958-1963. [PMID: 29924597 DOI: 10.1021/acschembio.8b00357] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Phenotypes are established by tight regulation on protein functions. This regulation can be mediated allosterically, through protein binding, and covalently, through post-translational modification (PTM). The integration of an ever-increasing number of PTMs into regulatory networks enables and defines the proteome complexity. Protein PTMs can occur enzymatically and nonenzymatically. Polyphosphorylation, which is a recently discovered PTM that belongs to the latter category, is the covalent attachment of the linear ortho-phosphate polymer called inorganic polyphosphate (polyP) to lysine residues. PolyP, which is ubiquitously present in nature, is also known to allosterically control protein function. To date, lack of reagents has prevented the systematic analysis of proteins covalently and/or allosterically associated with polyP. Here, we report on the chemical synthesis of biotin-modified monodisperse short-chain polyP (bio-polyP8-bio) and its subsequent use to screen a human proteome array to identify proteins that associate with polyP, thereby starting to define the human polyP-ome.
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Affiliation(s)
- Cristina Azevedo
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Jyoti Singh
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Nicole Steck
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Alexandre Hofer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Felix A. Ruiz
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, United Kingdom
- Research Unit, “Puerta del Mar” University Hospital, School of Medicine, and Institute of Biomedical Research Cadiz (INiBICA), University of Cadiz, Cadiz, Spain
| | - Tanya Singh
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Henning J. Jessen
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, United Kingdom
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20
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Hodgson DR. Physicochemical Aspects of Aqueous and Nonaqueous Approaches to the Preparation of Nucleosides, Nucleotides and Phosphate Ester Mimics. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Mungalpara D, Kelm H, Valkonen A, Rissanen K, Keller S, Kubik S. Oxoanion binding to a cyclic pseudopeptide containing 1,4-disubstituted 1,2,3-triazole moieties. Org Biomol Chem 2017; 15:102-113. [DOI: 10.1039/c6ob02172g] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The converging arrangement of hydrogen bond donors from amide NH and 1,2,3-triazole CH groups enables the described cyclic pseudopeptide to interact with oxoanions in water/DMSO mixtures.
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Affiliation(s)
- Disha Mungalpara
- Technische Universität Kaiserslautern
- Fachbereich Chemie – Organische Chemie
- 67663 Kaiserslautern
- Germany
| | - Harald Kelm
- Technische Universität Kaiserslautern
- Fachbereich Chemie – Anorganische Chemie
- 67663 Kaiserslautern
- Germany
| | - Arto Valkonen
- University of Jyvaskyla
- Department of Chemistry
- Nanoscience Center
- Jyvaskyla FI-40014
- Finland
| | - Kari Rissanen
- University of Jyvaskyla
- Department of Chemistry
- Nanoscience Center
- Jyvaskyla FI-40014
- Finland
| | - Sandro Keller
- University of Kaiserslautern
- Molecular Biophysics
- 67663 Kaiserslautern
- Germany
| | - Stefan Kubik
- Technische Universität Kaiserslautern
- Fachbereich Chemie – Organische Chemie
- 67663 Kaiserslautern
- Germany
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22
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One flask synthesis of 2′,3′-cyclic nucleoside monophosphates from unprotected nucleosides using activated cyclic trimetaphosphate. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.10.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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23
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Abstract
Focusing on the recent literature (since 2000), this review outlines the main synthetic approaches for the preparation of 5'-mono-, 5'-di-, and 5'-triphosphorylated nucleosides, also known as nucleotides, as well as several derivatives, namely, cyclic nucleotides and dinucleotides, dinucleoside 5',5'-polyphosphates, sugar nucleotides, and nucleolipids. Endogenous nucleotides and their analogues can be obtained enzymatically, which is often restricted to natural substrates, or chemically. In chemical synthesis, protected or unprotected nucleosides can be used as the starting material, depending on the nature of the reagents selected from P(III) or P(V) species. Both solution-phase and solid-support syntheses have been developed and are reported here. Although a considerable amount of research has been conducted in this field, further work is required because chemists are still faced with the challenge of developing a universal methodology that is compatible with a large variety of nucleoside analogues.
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Affiliation(s)
- Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Christian Périgaud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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24
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Hofer A, Marques E, Kieliger N, Gatter SKN, Jordi S, Ferrari E, Hofmann M, Fitzpatrick TB, Hottiger MO, Jessen HJ. Chemoselective Dimerization of Phosphates. Org Lett 2016; 18:3222-5. [PMID: 27308921 DOI: 10.1021/acs.orglett.6b01466] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A methodology for the synthesis of oligophosphate conjugates using phosphordiamidites is described. This strategy facilitates the straightforward preparation of C2-symmetric dinucleoside tri-, penta-, and heptaphosphates. Moreover, unsymmetric compounds such as thiamine adenosine triphosphate and thiamine cytidine triphosphate can be prepared. The material is used to study the inhibitory activity of thiaminylated nucleotides against adenosine diphosphate ribosyltransferases.
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Affiliation(s)
| | | | | | | | | | | | - Manuel Hofmann
- Plant Biochemistry & Physiology Laboratory, Department of Botany and Plant Biology, University of Geneva , Quai E. Ansermet 30, 1211 Geneva, Switzerland
| | - Teresa B Fitzpatrick
- Plant Biochemistry & Physiology Laboratory, Department of Botany and Plant Biology, University of Geneva , Quai E. Ansermet 30, 1211 Geneva, Switzerland
| | | | - Henning J Jessen
- Institute of Organic Chemistry, Albert-Ludwigs-University Freiburg , Albertstr. 21, 79104 Freiburg i. B., Germany
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25
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Mohamady S, Taylor SD. Synthesis of Nucleoside Triphosphates from 2'-3'-Protected Nucleosides Using Trimetaphosphate. Org Lett 2016; 18:580-3. [PMID: 26759914 DOI: 10.1021/acs.orglett.5b03624] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemists have been attempting to triphosphorylate nucleosides and other alcohols using trimetaphosphate (TriMP) since the 1960s. However, this route appears to have been abandoned due to poor yields. The first practical syntheses of nucleoside triphosphates (NTPs) are reported using TriMP as the key reagent. This was achieved by reacting the tetrabutylammonium salt of TriMP with mesitylenesulfonyl chloride in the presence of DABCO in pyridine followed by the addition of an appropriately protected nucleoside and phthalimide. Quenching the reaction with aqueous buffer followed by hydrolysis of the OH protecting groups gave the NTPs in good yield.
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Affiliation(s)
- Samy Mohamady
- Faculty of Pharmacy, The British University in Egypt , Cairo-Suez Desert Road, 11837 Cairo, Egypt
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
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26
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Sherstyuk YV, Abramova TV. How To Form a Phosphate Anhydride Linkage in Nucleotide Derivatives. Chembiochem 2015; 16:2562-70. [PMID: 26420042 DOI: 10.1002/cbic.201500406] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Indexed: 12/25/2022]
Abstract
The fundamental roles of nucleoside triphosphates and nucleotide cofactors such as NAD(+) in biochemistry are well known. In recent decades, continuing research has revealed the key role of 5'-capped RNA and 5',5'-dinucleoside polyphosphates in the regulation of vitally important physiological processes. Last but not least, the commercial potential of nucleoside triphosphate synthesis can hardly be overestimated. Nevertheless, despite decades of investigation and the obvious topicality of the research on the chemical synthesis of the nucleotide compounds containing phosphate anhydride linkages, none of the existing procedures can be considered an up-to-date "gold standard". However, there are a number of fruitful synthetic approaches to forming phosphate anhydride linkages in satisfactory yield. These are summarized in this concise review, organized by the type of active phosphorous intermediate and reagents used.
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Affiliation(s)
- Yuliya V Sherstyuk
- Laboratory of Organic Synthesis, Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Avenue, 8, Novosibirsk, 630090, Russia
| | - Tatyana V Abramova
- Laboratory of Organic Synthesis, Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Avenue, 8, Novosibirsk, 630090, Russia.
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27
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Hofer A, Cremosnik GS, Müller AC, Giambruno R, Trefzer C, Superti-Furga G, Bennett KL, Jessen HJ. A Modular Synthesis of Modified Phosphoanhydrides. Chemistry 2015; 21:10116-22. [PMID: 26033174 DOI: 10.1002/chem.201500838] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/11/2022]
Abstract
Phosphoanhydrides (P-anhydrides) are ubiquitously occurring modifications in nature. Nucleotides and their conjugates, for example, are among the most important building blocks and signaling molecules in cell biology. To study and manipulate their biological functions, a diverse range of analogues have been developed. Phosphate-modified analogues have been successfully applied to study proteins that depend on these abundant cellular building blocks, but very often both the preparation and purification of these molecules are challenging. This study discloses a general access to P-anhydrides, including different nucleotide probes, that greatly facilitates their preparation and isolation. The convenient and scalable synthesis of, for example, (18) O labeled nucleoside triphosphates holds promise for future applications in phosphoproteomics.
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Affiliation(s)
- Alexandre Hofer
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | - Gregor S Cremosnik
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA (UK)
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Roberto Giambruno
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Claudia Trefzer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Henning J Jessen
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland).
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28
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Sun Q, Sun J, Gong SS, Wang CJ, Wang XC. Synthesis of nucleoside tetraphosphates and dinucleoside pentaphosphates from nucleoside phosphoropiperidates via the activation of P(V)N bond. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2014.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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29
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Mohamady S, Taylor SD. Synthesis of nucleoside 5'-tetraphosphates containing terminal fluorescent labels via activated cyclic trimetaphosphate. J Org Chem 2014; 79:2308-13. [PMID: 24552623 DOI: 10.1021/jo500051y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2'-Deoxynucleotide 5'-tetraphosphates in which a fluorescent label is attached to the terminal phosphate are used as key reagents in high-throughput DNA sequencing techniques and in single nucleotide polymorphism typing assays. We demonstrate that this class of compounds can be prepared by reacting fluorophores such as 7-hydroxy-4-methylcoumarin, methylfluorescein, fluorescein and resorufin with an activated form of cyclic trimetaphosphate to give intermediate 11. Reaction of 11 with 2'-deoxynucleoside 5'-monophosphates or a nucleoside 5'-monophosphate gave the target compounds in good yield.
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Affiliation(s)
- Samy Mohamady
- Department of Chemistry, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada
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30
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Manna CM, Nassar MY, Tofan D, Chakarawet K, Cummins CC. Facile synthesis of mononuclear early transition-metal complexes of κ3cyclo-tetrametaphosphate ([P4O12]4−) and cyclo-trimetaphosphate ([P3O9]3−). Dalton Trans 2014; 43:1509-18. [DOI: 10.1039/c3dt52526k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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31
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Cremosnik GS, Hofer A, Jessen HJ. Iterative synthesis of nucleoside oligophosphates with phosphoramidites. Angew Chem Int Ed Engl 2013; 53:286-9. [PMID: 24222637 DOI: 10.1002/anie.201306265] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Indexed: 12/25/2022]
Abstract
P-Amidites can be used in iterative couplings to selectively give mixed P(III) -P(V) anhydrides. These intermediates can be oxidized followed by a rapid removal of the two terminal fluorenylmethyl groups. An iterative synthesis (coupling, oxidation, deprotection) of nucleoside oligophosphates can be carried out in solution and on a solid support. The coupling rates and yields are high, the procedures convenient (non-dry reagents and solvents, ambient conditions, unprotected nucleotides), and the purification is very simple. The method works with all canonical nucleosides and holds promise for significant simplification of the usually cumbersome process of P-anhydride bond construction.
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Affiliation(s)
- Gregor S Cremosnik
- Organic Chemistry Institute, University of Zürich (UZH), Winterthurerstrasse 190, 8057 Zürich (Switzerland)
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32
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Cremosnik GS, Hofer A, Jessen HJ. Iterative Synthese von Nukleosidoligophosphaten mit Phosphoramiditen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306265] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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