1
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Qian K, Hanf B, Cummins C, Fiedler D. Monodisperse Chemical Oligophosphorylation of Peptides via Protected Oligophosphorimidazolide Reagents. Angew Chem Int Ed Engl 2025; 64:e202419147. [PMID: 39625829 PMCID: PMC11891630 DOI: 10.1002/anie.202419147] [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: 10/04/2024] [Indexed: 12/17/2024]
Abstract
Protein poly- and oligophosphorylation are recently discovered post-translational modifications that remain poorly characterized due to (1) the difficulty of extracting endogenously polyphosphorylated species without degradation and (2) the absence of synthetic and analytical tools to prepare and characterize poly- and oligophosphorylated species in biochemical contexts. Herein, we report a methodology for the selective oligophosphorylation of peptides with monodisperse phosphate chain lengths (Pn=3-6). A library of oligophosphorimidazolide (oligoP-imidazolide) reagents featuring benzyl and o-nitrophenylethyl protecting groups was synthesized in moderate-to-good yields (65-93 %). These oligoP-imidazolide reagents enabled the selective and simultaneous conjugation of multiple phosphate units to phosphoryl nucleophiles, circumventing tedious iterative processes. The generalizability of this approach is illustrated by a substrate scope study that includes several biologically relevant phosphopeptide sequences, culminating in the synthesis of >60 examples of peptide oligophosphates (Pn=2-6). Moreover, we report the preparation of oligoP-diimidazolides (Pn=3-5) and discuss their application in generating unique condensed phosphate-peptide conjugates. We also demonstrate that human phospho-ubiquitin (pS65-Ub) is amenable to functionalization by our reagents. Overall, we envision the methods described here will enable future studies that characterize these newly discovered but poorly understood phosphorylation modes.
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Affiliation(s)
- Kevin Qian
- Department of ChemistryMassachusetts Institute of Technology (MIT)77 Massachusetts Ave.CambridgeMA-02139United States of America
| | - Björn Hanf
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Str. 1013125BerlinGermany
- Institut für ChemieHumboldt-Universität zu Berlin, GermanyBrook-Taylor-Str. 212489BerlinGermany
| | - Christopher Cummins
- Department of ChemistryMassachusetts Institute of Technology (MIT)77 Massachusetts Ave.CambridgeMA-02139United States of America
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Str. 1013125BerlinGermany
- Institut für ChemieHumboldt-Universität zu Berlin, GermanyBrook-Taylor-Str. 212489BerlinGermany
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2
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Tian Y, Chen DP, Chai Y, Li M, Wang XC, Du Z, Wu X, Quan ZJ. Direct conversion of various phosphate sources to a versatile P-X reagent [TBA][PO 2X 2] via redox-neutral halogenation. Nat Commun 2025; 16:2004. [PMID: 40011449 DOI: 10.1038/s41467-025-57255-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 02/13/2025] [Indexed: 02/28/2025] Open
Abstract
Inorganic phosphates hold significant potential as ideal natural building blocks, forming a fundamental basis for organic and biochemical synthesis. However, their limited solubility, inherent chemical stability, and low reactivity pose substantial challenges to converting phosphates into organophosphates under mild conditions. This study introduces an efficient method for the direct conversion of phosphates into P(V)-X reagents, [TBA][PO2X2] (X = Cl, F), via a redox-neutral halogenation process. This method utilizes cyanuric chloride (or cyanuric fluoride) as the halogenation reagent, in combination with 1-formylpyrrolidine and tetrabutylammonium chloride (TBAC), under ambient conditions. The approach enables effective halogenation conversion for various P(V) sources, including orthophosphates, pyrophosphoric acid, Na3P3O9 and P2O5. Furthermore, we demonstrate the synthetic utility of the P(V)-Cl reagent in the phosphorylation of diverse O-, S-, N- and C-nucleophiles. Key advantages of this conversion process include the use of inexpensive and readily available chemicals, the avoidance of high-energy redox reactions, and the generation of a reactive yet stable P(V)-X reagent.
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Affiliation(s)
- Yaling Tian
- Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, PR China
| | - Dong-Ping Chen
- Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, PR China
| | - Yao Chai
- Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, PR China
| | - Ming Li
- Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, PR China
| | - Xi-Cun Wang
- Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, PR China
| | - Zhengyin Du
- Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, PR China
| | - Xiaofeng Wu
- Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, PR China
- Materials Innovation Factory, and Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Zheng-Jun Quan
- Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, PR China.
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3
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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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4
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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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5
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Qian K, Shepard SM, Xin T, Park G, Cummins CC. Stabilized Molecular Diphosphorus Pentoxide, P 2O 5L 2 (L = N-Donor Base), in the Synthesis of Condensed Phosphate-Organic Molecule Conjugates. J Am Chem Soc 2023; 145:6045-6050. [PMID: 36913316 PMCID: PMC10038927 DOI: 10.1021/jacs.3c00211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Commercial phosphorus pentoxide reacts with some N-donor bases to give the adducts P2O5L2 and P4O10L3 (L = DABCO, pyridine, 4-tert-butylpyridine). The DABCO adducts were structurally characterized by single-crystal X-ray diffraction. It is proposed that P2O5L2 and P4O10L3 undergo interconversion through a "phosphate-walk" mechanism, which was evaluated using DFT calculations. P2O5(pyridine)2 (1) efficiently transfers monomeric diphosphorus pentoxide to phosphorus oxyanion nucleophiles, yielding substituted trimetaphosphates and cyclo-phosphonate-diphosphates (P3O8R)2- (R1 = nucleosidyl, phosphoryl, alkyl, aryl, vinyl, alkynyl, H, F). Hydrolytic ring-opening of these compounds forms linear derivatives [R1(PO3)2PO3H]3-, and nucleophilic ring-opening gives linear disubstituted [R1(PO3)2PO2R2]3- compounds.
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Affiliation(s)
- Kevin Qian
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Scott M Shepard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Tiansi Xin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Gyeongjin Park
- 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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6
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Lu H, Yi D, Feng H, Hou B, Hao J. Influence of the Crystal Structure of Melamine Trimetaphosphate 2D Supramolecules on the Properties of Polyamide 6. ACS APPLIED MATERIALS & INTERFACES 2023; 15:12393-12402. [PMID: 36802357 DOI: 10.1021/acsami.2c22760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
To explore the influence of the crystal structure difference of melamine trimetaphosphate (MAP) on the application performance of its polymer composites, an intumescent flame retardant with the optimal crystal type was designed and synthesized to improve the mechanical properties and flame retardancy of polyamide 6 (PA6). I-MAP and II-MAP were obtained using different concentrations of MA and sodium trimetaphosphate (STMP) in an acidic aqueous solution. The morphology, chemical composition, and thermal stability were comprehensively characterized by Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), X-ray diffraction (XRD), and thermogravimetric analysis (TGA). The dispersion, mechanical properties, and flame retardancy of PA6/I-MAP and PA6/II-MAP were evaluated by SEM, stress and strain, limiting oxygen index test (LOI), vertical burning test (UL-94), cone calorimetry (CONE) test, and char residue analysis. The conclusion is as follows: I-MAP and II-MAP have a greater influence on the physical properties of PA6 but less influence on the chemical properties. Compared with PA6/I-MAP, the tensile strength of PA6/II-MAP is 104.7% higher, the flame rating reaches V-0, and PHRR is reduced by 11.2%.
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Affiliation(s)
- Hongyu Lu
- National Engineering Research Center of Flame Retardant Materials, School of Materials Science and Engineering, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China
| | - Deqi Yi
- National Engineering Research Center of Flame Retardant Materials, School of Materials Science and Engineering, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China
| | - Haisheng Feng
- National Engineering Research Center of Flame Retardant Materials, School of Materials Science and Engineering, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China
| | - Boyou Hou
- National Engineering Research Center of Flame Retardant Materials, School of Materials Science and Engineering, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China
| | - Jianwei Hao
- National Engineering Research Center of Flame Retardant Materials, School of Materials Science and Engineering, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China
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7
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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: 14] [Impact Index Per Article: 4.7] [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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8
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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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9
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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; 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] [Grants] [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 ChemistryAlbert-Ludwigs University FreiburgAlbertstraße 2179102Freiburg im BreisgauGermany
| | - Stefan Wiesler
- Institute of Organic ChemistryAlbert-Ludwigs University FreiburgAlbertstraße 2179102Freiburg im BreisgauGermany
| | - Tobias Dürr‐Mayer
- Institute of Organic ChemistryAlbert-Ludwigs University FreiburgAlbertstraße 2179102Freiburg im BreisgauGermany
| | - Alexander Ripp
- Institute of Organic ChemistryAlbert-Ludwigs University FreiburgAlbertstraße 2179102Freiburg im BreisgauGermany
- DFG Cluster of Excellence “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS)79110FreiburgGermany
| | - Paraskevi Fouka
- Institute of Organic ChemistryAlbert-Ludwigs University FreiburgAlbertstraße 2179102Freiburg im BreisgauGermany
| | - Danye Qiu
- Institute of Organic ChemistryAlbert-Ludwigs University FreiburgAlbertstraße 2179102Freiburg im BreisgauGermany
| | - Henning J. Jessen
- Institute of Organic ChemistryAlbert-Ludwigs University FreiburgAlbertstraße 2179102Freiburg im BreisgauGermany
- DFG Cluster of Excellence “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS)79110FreiburgGermany
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10
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Jessen HJ, Dürr-Mayer T, Haas TM, Ripp A, Cummins CC. Lost in Condensation: Poly-, Cyclo-, and Ultraphosphates. Acc Chem Res 2021; 54:4036-4050. [PMID: 34648267 DOI: 10.1021/acs.accounts.1c00370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Much like linear, branched, and cyclic alkanes, condensed phosphates exist as linear, branched, and cyclic structures. Inasmuch as alkanes are the cornerstone of organic chemistry, generating an inexplorably large chemical space, a comparable richness in structures can be expected for condensed phosphates, as also for them the concepts of isomerism apply. Little of their chemical space has been charted, and only a few different synthesis methods are available to construct isomers of condensed phosphates. Here, we will discuss the application of phosphoramidites with one, two, or three P-N bonds that can be substituted selectively to access different condensed phosphates in a highly controllable manner. Work directed toward the further exploration of this chemical space will contribute to our understanding of the fundamental chemistry of phosphates.In biology, condensed phosphates play important roles in the form of inorganic representatives, such as pyrophosphate, polyphosphate, and cyclophosphate, and also in conjugation with organic molecules, such as esters and amidates. Phosphorus is one of the six biogenic elements; the omnipresence of phosphates in biology points toward their critical involvement in prebiotic chemistry and the emergence of life itself. Indeed, it is hard to imagine any life without phosphate. It is therefore desirable to achieve through synthesis a better understanding of the chemistry of the condensed phosphates to further explore their biology.There is a rich but underexplored chemistry of the family of condensed phosphates per se, which is further diversified by their conjugation to important biomolecules and metabolites. For example, proteins may be polyphosphorylated on lysins, a very recent addition to posttranslational modifications. Adenosine triphosphate, as a representative of the small molecules, on the other hand, is well known as the universal cellular energy currency. In this Account, we will describe our motivations and our approaches to construct, modify, and synthetically apply different representatives of the condensed phosphates. We also describe the generation of hybrids composed of cyclic and linear structures of different oxidation states and develop them into reagents of great utility. A pertinent example is provided in the step-economic synthesis of the magic spot nucleotides (p)ppGpp. Finally, we provide an overview of 31P NMR data collected over the years in our laboratories, helping as a waymarker for not getting lost in condensation.
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Affiliation(s)
- Henning J. Jessen
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT − Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Tobias Dürr-Mayer
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Thomas M. Haas
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Alexander Ripp
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT − Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Christopher C. Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
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11
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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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12
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Ripp A, Singh J, Jessen HJ. Rapid Synthesis of Nucleoside Triphosphates and Analogues. ACTA ACUST UNITED AC 2021; 81:e108. [PMID: 32391982 DOI: 10.1002/cpnc.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nucleoside triphosphates (NTPs) are essential biomolecules involved in almost all biological processes, and their study is therefore critical to understanding cellular biology. Here, we describe a chemical synthesis suitable for obtaining both natural and highly modified NTPs, which can, for example, be used as surrogates to probe biological processes. The approach includes the preparation of a reagent that enables the facile introduction and modification of three phosphate units: cyclic pyrophosphoryl P-amidite (c-PyPA), derived from pyrophosphate (PV ) and a reactive phosphoramidite (PIII ). By using non-hydrolyzable analogues of pyrophosphate, the reagent can be readily modified to obtain a family of non-hydrolyzable analogues containing CH2 , CF2 , CCl2 , and NH that are stable in solution for several weeks if stored appropriately. They enable the synthesis of NTPs by reaction with nucleosides to give deoxycyclotriphosphate esters that are then oxidized to cyclotriphosphate (cyclo-TP) esters. The use of different oxidizing agents provides an opportunity for modification at P-α. Furthermore, terminal modifications at P-γ can be introduced by linearization of the cyclo-TP ester with various nucleophiles. © 2020 The Authors. Basic Protocol 1: Synthesis of cyclic pyrophosphoryl P-amidite (c-PyPA) and derivatives (c-PyNH PA, c-PyCH2 PA, c-PyCCl2 PA, c-PyCF2 PA) Basic Protocol 2: Synthesis of 3'-azidothymidine 5'-γ-P-propargylamido triphosphates and analogues Basic Protocol 3: Synthesis of 2'-deoxythymidine 5'-γ-P-propargylamido triphosphate (15) Basic Protocol 4: Synthesis of adenosine 5'-γ-P-amido triphosphate (19) and adenosine 5'-γ-P-propargylamido triphosphate (20) Basic Protocol 5: Synthesis of d4T 5'-γ-propargylamido β,γ-(difluoromethylene)triphosphate Support Protocol: Synthesis of diisopropylphosphoramidous dichloride.
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Affiliation(s)
- Alexander Ripp
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany.,Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Freiburg, Germany
| | - Jyoti Singh
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany.,Freiburg Research Institute for Advanced Studies, University of Freiburg, Freiburg, Germany.,Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Freiburg, Germany
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13
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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: 1.3] [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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14
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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: 0.6] [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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15
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Mandala VS, Loh DM, Shepard SM, Geeson MB, Sergeyev IV, Nocera DG, Cummins CC, Hong M. Bacterial Phosphate Granules Contain Cyclic Polyphosphates: Evidence from 31P Solid-State NMR. J Am Chem Soc 2020; 142:18407-18421. [PMID: 33075224 DOI: 10.1021/jacs.0c06335] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Polyphosphates (polyPs) are ubiquitous polymers in living organisms from bacteria to mammals. They serve a wide variety of biological functions, ranging from energy storage to stress response. In the last two decades, polyPs have been primarily viewed as linear polymers with varying chain lengths. However, recent biochemical data show that small metaphosphates, cyclic oligomers of [PO3](-), can bind to the enzymes ribonuclease A and NAD kinase, raising the question of whether metaphosphates can occur naturally as products of biological activity. Before the 1980s, metaphosphates had been reported in polyPs extracted from various organisms, but these results are considered artifactual due to the extraction and purification protocols. Here, we employ nondestructive 31P solid-state NMR spectroscopy to investigate the chemical structure of polyphosphates in whole cells as well as insoluble fractions of the bacterium Xanthobacter autotrophicus. Isotropic and anisotropic 31P chemical shifts of hydrated whole cells indicate the coexistence of linear and cyclic phosphates. Under our cell growth conditions and the concentrated conditions of the solid-state NMR samples, we found substantial amounts of cyclic phosphates in X. autotrophicus, suggesting that in fresh cells metaphosphate concentrations can be significant. The cellular metaphosphates are identified by comparison with the 31P chemical shift anisotropy of synthetic metaphosphates of known structures. In X. autotrophicus, the metaphosphates have a chemical shift anisotropy that is consistent with an average size of 3-8 phosphate units. These metaphosphates are enriched in insoluble and electron-dense granules. Exogenous hexametaphosphate added to X. autotrophicus cell extracts is metabolized to trimetaphosphates, supporting the presence and biological role of metaphosphates in cells. The definitive evidence for the presence of metaphosphates, reported here in whole bacterial cells for the first time, opens the path for future investigations of the biological function of metaphosphates in many organisms.
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Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Daniel M Loh
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Scott M Shepard
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Michael B Geeson
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Ivan V Sergeyev
- Bruker Biospin, Billerica, Massachusetts 01821, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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16
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Abstract
The specific non-invasive control of intracellular signaling events requires advanced tools that enter cells by diffusion and are controllable by light. Here, we detail the synthesis and application of membrane-permeant caged inositol pyrophosphates with respect to cell entry and cell distribution. We recently published the synthesis of these tools as well as their effect on PH-domain localization in HeLa cells and oscillations of the intracellular calcium concentration in β-cells, which are known to drive insulin secretion. In this chapter, we discuss the possibilities and limitations when using cell-penetrating inositol pyrophosphates. We provide a detailed protocol for the application in live mouse β-cells and we discuss the image analysis needed for following effects on calcium signaling.
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17
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Geeson M, Cummins CC. Let's Make White Phosphorus Obsolete. ACS CENTRAL SCIENCE 2020; 6:848-860. [PMID: 32607432 PMCID: PMC7318074 DOI: 10.1021/acscentsci.0c00332] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Indexed: 05/20/2023]
Abstract
Industrial and laboratory methods for incorporating phosphorus atoms into molecules within the framework of Green Chemistry are in their infancy. Current practice requires large inputs of energy, involves toxic intermediates, and generates substantial waste. Furthermore, a negligible fraction of phosphorus-containing waste is recycled which in turn contributes to negative environmental impacts, such as eutrophication. Methods that begin to address some of these drawbacks are reviewed, and some key opportunities to be realized by pursuing organophosphorus chemistry under the principles of Green Chemistry are highlighted. Methods used by nature, or in the chemistry of other elements such as silicon, are discussed as model processes for the future of phosphorus in chemical synthesis.
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18
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Fialho DM, Roche TP, Hud NV. Prebiotic Syntheses of Noncanonical Nucleosides and Nucleotides. Chem Rev 2020; 120:4806-4830. [PMID: 32421316 DOI: 10.1021/acs.chemrev.0c00069] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The origin of nucleotides is a major question in origins-of-life research. Given the central importance of RNA in biology and the influential RNA World hypothesis, a great deal of this research has focused on finding possible prebiotic syntheses of the four canonical nucleotides of coding RNA. However, the use of nucleotides in other roles across the tree of life might be evidence that nucleotides have been used in noncoding roles for even longer than RNA has been used as a genetic polymer. Likewise, it is possible that early life utilized nucleotides other than the extant nucleotides as the monomers of informational polymers. Therefore, finding plausible prebiotic syntheses of potentially ancestral noncanonical nucleotides may be of great importance for understanding the origins and early evolution of life. Experimental investigations into abiotic noncanonical nucleotide synthesis reveal that many noncanonical nucleotides and related glycosides are formed much more easily than the canonical nucleotides. An analysis of the mechanisms by which nucleosides and nucleotides form in the solution phase or in drying-heating reactions from pre-existing sugars and heterocycles suggests that a wide variety of noncanonical nucleotides and related glycosides would have been present on the prebiotic Earth, if any such molecules were present.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
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19
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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: 22] [Impact Index Per Article: 4.4] [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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20
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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: 3.2] [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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21
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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: 18] [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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22
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Singh J, Ripp A, Haas TM, Qiu D, Keller M, Wender PA, Siegel JS, Baldridge KK, Jessen HJ. Synthesis of Modified Nucleoside Oligophosphates Simplified: Fast, Pure, and Protecting Group Free. J Am Chem Soc 2019; 141:15013-15017. [PMID: 31512870 PMCID: PMC10044464 DOI: 10.1021/jacs.9b08273] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Phosphoramidite analogues of modified cyclotriphosphates provide a general and step-economical synthesis of nucleoside triphosphates and analogues on scale without the need for protecting groups. These reagents enable rapid access to pure nucleoside oligophosphates and a range of other analogues that were previously difficult to obtain (e.g., NH, CH2, CCl2, and CF2 replacements for O, phosphono- and phosphoimidazolides, -morpholidates, -azidates, and -fluoridates). DFT calculations demonstrate that the selectivity of the cyclotriphosphate opening reactions proceeds via an in-line substitution mechanism that displaces the least charged leaving group.
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Affiliation(s)
- Jyoti Singh
- Institute of Organic Chemistry, University of Freiburg, D-79104 Freiburg, Germany
| | - Alexander Ripp
- Institute of Organic Chemistry, University of Freiburg, D-79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT − Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
| | - Thomas M. Haas
- Institute of Organic Chemistry, University of Freiburg, D-79104 Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, D-79104 Freiburg, Germany
| | - Manfred Keller
- Institute of Organic Chemistry, University of Freiburg, D-79104 Freiburg, Germany
| | - Paul A. Wender
- Chemistry Department, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Jay S. Siegel
- Health Science Platform, Tianjin University, Nankai District, Tianjin, PRC 30072
- Freiburg Research Institute for Advanced Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Kim K. Baldridge
- Health Science Platform, Tianjin University, Nankai District, Tianjin, PRC 30072
| | - Henning J. Jessen
- Institute of Organic Chemistry, University of Freiburg, D-79104 Freiburg, Germany
- Freiburg Research Institute for Advanced Studies, University of Freiburg, D-79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT − Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
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23
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Geeson MB, Ríos P, Transue WJ, Cummins CC. Orthophosphate and Sulfate Utilization for C-E (E = P, S) Bond Formation via Trichlorosilyl Phosphide and Sulfide Anions. J Am Chem Soc 2019; 141:6375-6384. [PMID: 30901207 DOI: 10.1021/jacs.9b01475] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reduction of phosphoric acid (H3PO4) or tetra- n-butylammonium bisulfate ([TBA][HSO4]) with trichlorosilane leads to the formation of the bis(trichlorosilyl)phosphide ([P(SiCl3)2]-, 1) and trichlorosilylsulfide ([Cl3SiS]-, 2) anions, respectively. Balanced equations for the formation of the TBA salts of anions 1 and 2 were formulated based on the identification of hexachlorodisiloxane and hydrogen gas as byproducts arising from these reductive processes: i) [H2PO4]- + 10HSiCl3 → 1 + 4O(SiCl3)2 + 6H2 for P and ii) [HSO4]- + 9HSiCl3 → 2 + 4O(SiCl3)2 + 5H2 for S. Hydrogen gas was identified by its subsequent use to hydrogenate an alkene ((-)-terpinen-4-ol) using Crabtree's catalyst ([(COD)Ir(py)(PCy3)][PF6], COD = 1,5-cyclooctadiene, py = pyridine, Cy = cyclohexyl). Phosphide 1 was generated in situ by the reaction of phosphoric acid and trichlorosilane and used to convert an alkyl chloride (1-chlorooctane) to the corresponding primary phosphine, which was isolated in 41% yield. Anion 1 was also prepared from [TBA][H2PO4] and isolated in 62% yield on a gram scale. Treatment of [TBA]1 with an excess of benzyl chloride leads to the formation of tetrabenzylphosphonium chloride, which was isolated in 61% yield. Sulfide 2 was used as a thionation reagent, converting benzophenone to thiobenzophenone in 62% yield. It also converted benzyl bromide to benzyl mercaptan in 55% yield. The TBA salt of trimetaphosphate ([TBA]3[P3O9]·2H2O), also a precursor to anion 1, was found to react with either trichlorosilane or silicon(IV) chloride to provide bis(trimetaphosphate)silicate, [TBA]2[Si(P3O9)2], characterized by NMR spectroscopy, X-ray crystallography, and elemental analysis. Trichlorosilane reduction of [TBA]2[Si(P3O9)2] also provided anion 1. The electronic structures of 1 and 2 were investigated using a suite of theoretical methods; the computational studies suggest that the trichlorosilyl ligand is a good π-acceptor and forms σ-bonds with a high degree of s character.
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Affiliation(s)
- Michael B Geeson
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Pablo Ríos
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Wesley J Transue
- 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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24
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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: 3.2] [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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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: 1.2] [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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