1
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Ebersbach B, Seichter W, Mazik M. Crystal structures of methyl 3,5-di-methyl-benzoate, 3,5-bis-(bromo-meth-yl)phenyl acetate and 5-hy-droxy-benzene-1,3-dicarbaldehyde. Acta Crystallogr E Crystallogr Commun 2022; 78:682-686. [PMID: 35855362 PMCID: PMC9260362 DOI: 10.1107/s2056989022005643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The crystal structures of the title compounds, methyl 3,5-di-methyl-benzoate (C10H12O2; 1), 3,5-bis-(bromo-meth-yl)phenyl acetate (C10H10Br2O2; 2) and 5-hy-droxy-benzene-1,3-dicarbaldehyde (C8H6O3; 3) were determined by single-crystal X-ray analysis. The crystals of 1 are composed of strands of C-H⋯O=C bonded mol-ecules, which are further arranged into layers. As a result of the presence of two bromo-methyl substituents in compound 2, mol-ecular dimers formed by crystallographically non-equivalent mol-ecules are connected to structurally different two-dimensional aggregates in which the bromine atoms participate in Br⋯Br bonds of type I and type II. In the case of compound 3, which possesses three donor/acceptor substituents, the mol-ecular association in the crystal creates a close three-dimensional network comprising Car-yl-H⋯Ohy-droxy, Cform-yl-H⋯Oform-yl and O-H⋯Oform-yl bonds.
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Affiliation(s)
- Ben Ebersbach
- Technische Universität Bergakademie Freiberg, Leipziger Str. 29, D-09596 Freiberg/Sachsen, Germany
| | - Wilhelm Seichter
- Technische Universität Bergakademie Freiberg, Leipziger Str. 29, D-09596 Freiberg/Sachsen, Germany
| | - Monika Mazik
- Technische Universität Bergakademie Freiberg, Leipziger Str. 29, D-09596 Freiberg/Sachsen, Germany
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2
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Danneberg F, Westemeier H, Horx P, Zellmann F, Dörr K, Kalden E, Zeiger M, Akpinar A, Berger R, Göbel MW. RNA Hydrolysis by Heterocyclic Amidines and Guanidines: Parameters Affecting Reactivity. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Friederike Danneberg
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Hauke Westemeier
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Philip Horx
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Felix Zellmann
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Kathrin Dörr
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Elisabeth Kalden
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Mirco Zeiger
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Abdullah Akpinar
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Robert Berger
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Michael W. Göbel
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
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3
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Werkhoven PR, Elwakiel M, Meuleman TJ, Quarles van Ufford HC, Kruijtzer JAW, Liskamp RMJ. Molecular construction of HIV-gp120 discontinuous epitope mimics by assembly of cyclic peptides on an orthogonal alkyne functionalized TAC-scaffold. Org Biomol Chem 2016; 14:701-710. [PMID: 26552661 DOI: 10.1039/c5ob02014j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mimics of discontinuous epitopes of for example bacterial or viral proteins may have considerable potential for the development of synthetic vaccines, especially if conserved epitopes can be mimicked. However, due to the structural complexity and size of discontinuous epitopes molecular construction of these mimics remains challeging. We present here a convergent route for the assembly of discontinuous epitope mimics by successive azide alkyne cycloaddition on an orthogonal alkyne functionalized scaffold. Here the synthesis of mimics of the HIV gp120 discontinuous epitope that interacts with the CD4 receptor is described. The resulting protein mimics are capable of inhibition of the gp120-CD4 interaction. The route is convergent, robust and should be applicable to other discontinuous epitopes.
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Affiliation(s)
- P R Werkhoven
- Division of Medicinal Chemistry & Chemical Biology, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, PO Box 80082, 3508 TB Utrecht, The Netherlands.
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4
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Wirth-Hamdoune D, Ullrich S, Scheffer U, Radanović T, Dürner G, Göbel MW. A Bis(guanidinium)alcohol Attached to a Hairpin Polyamide: Synthesis, DNA Binding, and Plasmid Cleavage. Chembiochem 2016; 17:506-14. [DOI: 10.1002/cbic.201500566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Daniela Wirth-Hamdoune
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Stefan Ullrich
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Ute Scheffer
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Toni Radanović
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Gerd Dürner
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Michael W. Göbel
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
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5
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2,6-Bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)pyridine and Its Benzene Analog as Nonmetallic Cleaving Agents of RNA Phosphodiester Linkages. Int J Mol Sci 2015; 16:17798-811. [PMID: 26247935 PMCID: PMC4581222 DOI: 10.3390/ijms160817798] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 07/13/2015] [Accepted: 07/28/2015] [Indexed: 01/10/2023] Open
Abstract
2,6-Bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)pyridine (11a) and 1,3-bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)benzene (11b) have been shown to accelerate at 50 mmol·L−1 concentration both the cleavage and mutual isomerization of uridylyl-3′,5′-uridine and uridylyl-2′,5′-uridine by up to two orders of magnitude. The catalytically active ionic forms are the tri- (in the case of 11b) tetra- and pentacations. The pyridine nitrogen is not critical for efficient catalysis, since the activity of 11b is even slightly higher than that of 11a. On the other hand, protonation of the pyridine nitrogen still makes 11a approximately four times more efficient as a catalyst, but only for the cleavage reaction. Interestingly, the respective reactions of adenylyl-3′,5′-adenosine were not accelerated, suggesting that the catalysis is base moiety selective.
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6
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Salvio R. The guanidinium unit in the catalysis of phosphoryl transfer reactions: from molecular spacers to nanostructured supports. Chemistry 2015; 21:10960-71. [PMID: 25940903 DOI: 10.1002/chem.201500789] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Examples of guanidinium-based artificial phosphodiesterases are illustrated in this review article. A wide set of collected catalytic systems are presented, from the early examples to the most recent developments of the use of this unit in the design of supramolecular catalysts. Special attention is dedicated to illustrate the operating catalytic mechanism and the role of guanidine/ium units in the catalysis. One or more of these units can act by themselves or in conjunction with other active units. The analogy with the mechanism of enzymatic systems is presented and discussed. In the last part of this overview, recent examples of guanidinophosphodiesterases based on nanostructured supports are reported, namely gold-monolayer-protected clusters and polymer brushes grafted to silica nanoparticles. The issue of the dependence of the catalytic performance on the preorganization of the spacer is tackled and discussed in terms of effective molarity, a parameter that can be taken as a quantitative measurement of this preorganization for both conventional molecular linker and nanosized supports.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Chimica and IMC-CNR, Sezione Meccanismi di Reazione, La Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 (Italy).
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7
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Brouwer AJ, van de Langemheen H, Liskamp RM. Expedient synthesis of a novel asymmetric selectively deprotectable derivative of the ATAC scaffold. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.04.084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Göbel MW, Roussev CD, Scheffer U. RNA Cleavage Catalyzed by Amphoteric Bis(acyl)guanidinium Derivatives. Helv Chim Acta 2014. [DOI: 10.1002/hlca.201300308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Baldini L, Cacciapaglia R, Casnati A, Mandolini L, Salvio R, Sansone F, Ungaro R. Upper rim guanidinocalix[4]arenes as artificial phosphodiesterases. J Org Chem 2012; 77:3381-9. [PMID: 22364173 DOI: 10.1021/jo300193y] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calix[4]arene derivatives, blocked in the cone conformation and functionalized with two to four guanidinium units at the upper rim were synthesized and investigated as catalysts in the cleavage of the RNA model compound 2-hydroxypropyl p-nitrophenyl phosphate. When compared with the behavior of a monofunctional model compound, the catalytic superiority of the calix[4]arene derivatives points to a high level of cooperation between catalytic groups. Combination of acidity measurements with the pH dependence of catalytic rates unequivocally shows that a necessary requisite for effective catalysis is the simultaneous presence, on the same molecular framework, of a neutral guanidine acting as a general base and a protonated guanidine acting as an electrophilic activator. The additional guanidinium (guanidine) group in the diprotonated (monoprotonated) trifunctional calix[4]arene acts as a more or less innocent spectator. This is not the case with the tetrasubstituted calix[4]arene, whose mono-, di-, and triprotonated forms are slightly less effective than the corresponding di- and triguanidinocalix[4]arene derivatives, most likely on account of a steric interference with HPNP caused by overcrowding.
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Affiliation(s)
- Laura Baldini
- Dipartimento di Chimica Organica e Industriale, Università degli Studi di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
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10
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11
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Salvio R, Cacciapaglia R, Mandolini L. General base-guanidinium cooperation in bifunctional artificial phosphodiesterases. J Org Chem 2011; 76:5438-43. [PMID: 21612212 DOI: 10.1021/jo2004007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Artificial phosphodiesterases that combine a guanidinium unit with a general base connected by a m-xylylene linker catalyze the transesterification of the RNA model compound 2-hydroxypropyl p-nitrophenyl phosphate (HPNP). The bifunctional catalysts presented in this work show varying extents of cooperation between catalytic units and a rate enhancement of 4 × 10(4) in the most favorable case.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Chimica and IMC-CNR Sezione Meccanismi di Reazione, Università La Sapienza, P.le Aldo Moro 5, 00185 Roma, Italy
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12
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Lönnberg H. Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic insight. Org Biomol Chem 2011; 9:1687-703. [PMID: 21258754 DOI: 10.1039/c0ob00486c] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
RNA molecules participate in many fundamental cellular processes either as a carrier of genetic information or as a catalyst, and hence, RNA has received increasing interest both as a chemotherapeutic agent and as a target of chemotherapy. In addition the dual nature of RNA has led to the RNA-world concept, i.e. an assumption that the evolution at an early stage of life was based on RNA-like oligomers that were responsible for the storage and transfer of information and as catalysts maintained primitive metabolism. Accordingly, the kinetics and mechanisms of the cleavage of RNA phosphodiester bonds have received interest and it is hoped they will shed light on the mechanisms of enzyme action and on the development of artificial enzymes. The major mechanistic findings concerning the cleavage by small molecules and ions and their significance for the development of efficient and biologically applicable artificial catalysts for RNA hydrolysis are surveyed in the present perspective.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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13
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Kuchelmeister HY, Schmuck C. An Efficient Synthesis of an Orthogonally Protected Aromatic Diamine as Scaffold for Tweezer Receptors with Two Different Arms. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900536] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Polyglycerol-bound phosphotriesterase enzyme model complexes for detection and hydrolysis of phosphorus species in aqueous solution. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.03.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Costa J, Balogh E, Turcry V, Tripier R, Le Baccon M, Chuburu F, Handel H, Helm L, Tóth E, Merbach AE. Unexpected Aggregation of Neutral, Xylene-Cored Dinuclear GdIII Chelates in Aqueous Solution. Chemistry 2006; 12:6841-51. [PMID: 16770815 DOI: 10.1002/chem.200501335] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have synthesized ditopic ligands L(1), L(2), and L(3) that contain two DO3A(3-) metal-chelating units with a xylene core as a noncoordinating linker (DO3A(3-) = 1,4,7,10-tetraazacyclododecane-1,4,7-triacetate; L(1) = 1,4-bis{[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane-1-yl]methyl}benzene; L(2) = 1,3-bis{[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane-1-yl]methyl}benzene; L(3) = 3,5-bis{[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecane-1-yl]methyl}benzoic acid). Aqueous solutions of the dinuclear Gd(III) complexes formed with the three ligands have been investigated in a variable-temperature, multiple-field (17)O NMR and (1)H relaxivity study. The (17)O longitudinal relaxation rates measured for the [Gd(2)L(1-3)(H2O)(2)] complexes show strong field dependence (2.35-9.4 T), which unambiguously proves the presence of slowly tumbling entities in solution. The proton relaxivities of the complexes, which are unexpectedly high for their molecular weight, and in particular the relaxivity peaks observed at 40-50 MHz also constitute experimental evidences of slow rotational motion. This was explained in terms of self-aggregation related to hydrophobic interactions, pi stacking between the aromatic linkers, or possible hydrogen bonding between the chelates. The longitudinal (17)O relaxation rates of the [Gd(2)L(1-3)(H2O)(2)] complexes have been analysed with the Lipari-Szabo approach, leading to local rotational correlation times tau(1)(298) of 150-250 ps and global rotational correlation times tau(g)(298) of 1.6-3.4 ns (c(Gd): 20-50 mM), where tau(1)(298) is attributed to local motions of the Gd segments, while tau(g)(298) describes the overall motion of the aggregates. The aggregates can be partially disrupted by phosphate addition; however, at high concentrations phosphate interferes in the first coordination sphere by replacing the coordinated water. In contrast to the parent [Gd(DO3A)(H2O)(1.9)], which presents a hydration equilibrium between mono- and dihydrated species, a hydration number of q = 1 was established for the [Ln(2)L(1-3)(H2O)(2)] chelates by (17)O chemical shift measurements on Ln = Gd and UV/Vis spectrophotometry for Ln = Eu. The exchange rate of the coordinated water is higher for [Gd(2)L(1-3)(H2O)(2)] complexes k(ex)(298) = 7.5-12.0 x 10(6) s(-1)) than for [Gd(DOTA)(H2O)](-). The proton relaxivity of the [Gd(2)L(1-3)(H2O)(2)] complexes strongly decreases with increasing pH. This is related to the deprotonation of the inner-sphere water, which has also been characterized by pH potentiometry. The protonation constants determined for this process are logK(OH) = 9.50 and 10.37 for [Gd(2)L(1)(H2O)(2)] and [Gd(2)L(3)(H2O)(2)], respectively.
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Affiliation(s)
- Jérôme Costa
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Chimie Inorganique et Bioinorganique, EPFL-BCH, 1015 Lausanne, Switzerland
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16
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Abstract
Mimicking the action of enzymes by simpler and more robust man-made catalysts has long inspired bioorganic chemists. During the past decade, mimics for RNA-cleaving enzymes, ribonucleases, or, more precisely, mimics of ribozymes that cleave RNA in sequence-selective rather than base-selective manner, have received special attention. These artificial ribonucleases are typically oligonucleotides (or their structural analogs) that bear a catalytically active conjugate group and catalyze sequence-selective hydrolysis of RNA phosphodiester bonds.
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Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014, Turku, Finland
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17
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Scheffer U, Strick A, Ludwig V, Peter S, Kalden E, Göbel MW. Metal-free catalysts for the hydrolysis of RNA derived from guanidines, 2-aminopyridines, and 2-aminobenzimidazoles. J Am Chem Soc 2005; 127:2211-7. [PMID: 15713099 DOI: 10.1021/ja0443934] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
2-aminopyridine and 2-aminobenzimidazole were chosen as structural analogues to substitute guanidinium groups in receptor molecules designed as phosphoryl transfer catalysts. Shifting the pKa of the guanidinium analogues toward 7 was expected to raise catalytic activities in aqueous buffer. Although the pKa's of both heterocycles are similar (6.2 and 7.0), only 2-aminobenzimidazole led to active RNA cleavers. All cleavage assays were run with fluorescently labeled substrates and a DNA sequencer. RNase contaminations would degrade RNA enantioselectively. In contrast, achiral catalysts such as 9b and 10b necessarily induce identical cleavage patterns in RNA and its mirror image. This principle allowed us to safely rule out contamination effects in this study. The most active catalysts, tris(2-aminobenzimidazoles) 9b and 10b, were shown by fluorescence correlation spectroscopy (FCS) to aggregate with oligonucleotides. However, at very low concentrations the compounds are still active in the nonaggregated state. Conjugates of 10b with antisense oligonucleotides or RNA binding peptides, therefore, will be promising candidates as site specific artificial ribonucleases.
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Affiliation(s)
- Ute Scheffer
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Marie-Curie-Str. 11, 60439 Frankfurt am Main, Germany
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18
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Krebs A, Ludwig V, Pfizer J, Dürner G, Göbel MW. Enantioselective synthesis of non-natural aromatic alpha-amino acids. Chemistry 2004; 10:544-53. [PMID: 14735523 DOI: 10.1002/chem.200305421] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We present two complementary methods for the stereoselective synthesis of non-natural alpha-amino acids with aromatic or heteroaromatic side chains. One approach is based on the chemical transformation of methionine, whereas the other applies the stereoselective Myers alkylation of glycine. The resulting product types differ in the linker length between glycine and the aromatic substituent. Since methionine and pseudoephedrine are available in both absolute configurations, R- or S-configured enantiopure amino acids with either C(2) or C(3) linkers can be obtained on gram scales. In each case the key step of the synthesis is hydroboration of the unsaturated building blocks 9 and 17, followed by palladium-catalyzed Suzuki cross-coupling with aryl halides. Attention must in certain cases be paid to the stereochemical integrity when basic Suzuki conditions are applied. Our initial difficulties are reported as well as the final "racemization-proof" procedures. The protecting groups chosen for the alpha-amino acids should be compatible with solid-phase peptide synthesis. This was confirmed by the successful synthesis of a series of tripeptides.
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Affiliation(s)
- Andreas Krebs
- Institute of Organic Chemistry and Chemical Biology, Marie-Curie Strasse 11, 60439 Frankfurt/Main, Germany
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19
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Kurz M, Göbel K, Hartel C, Göbel MW. Acridine-Labeled Primers as Tools for the Study of Nonenzymatic RNA Oligomerization. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19980810528] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Kurz K. Hydrolytische Spaltung von Nucleinsäuren-vom Enzymmechanismus zum Enzymmodell. CHEM UNSERER ZEIT 2004. [DOI: 10.1002/ciuz.19980320206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Opatz T, Liskamp RMJ. Synthesis and screening of libraries of synthetic tripodal receptor molecules with three different amino acid or peptide arms: identification of iron binders. JOURNAL OF COMBINATORIAL CHEMISTRY 2002; 4:275-84. [PMID: 12099844 DOI: 10.1021/cc020009s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel selectively deprotectable triazacyclophane scaffold was used for the design and split-mix synthesis of two libraries of solid-phase bound tripodal synthetic receptors possessing three different amino acid or peptidic arms. In the synthesis of the first library, the two outer arms consisted of amino acid Ala, Arg, Asp, Gln, Gly, Lys, Phe, Ser, Tyr, or Val and the middle arm consisted of amino acid Asn, Glu, His, Leu, or Pro. The second library contained amino acid and/or (di)peptide arms. The arms were different in all library members. The first outer arm consisted of amino acid(s) Ala, Arg, Gln, Phe, or Ser, the second outer arm consisted of amino acid(s) Asp, Gly, Lys, Tyr, or Val, and the middle arm consisted of amino acid(s) Asn, Glu, His, Leu, or Pro, leading to a 27 000 member library of synthetic tripodal receptor molecules. In on-bead screening experiments, a remarkable selectivity of some library members for Fe(3+) was observed and decoding of their structures by Edman degradation revealed consensus sequences with structural resemblance to non-heme iron proteins.
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Affiliation(s)
- Till Opatz
- Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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22
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Opatz T, Liskamp RM. A selectively deprotectable triazacyclophane scaffold for the construction of artificial receptors. Org Lett 2001; 3:3499-502. [PMID: 11678692 DOI: 10.1021/ol0101741] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text]. The synthesis of a triazacylclophane scaffold bearing a set of selectively removable protecting groups is described. This versatile scaffold, which can be linked to a solid support, allows the attachment of three different side chains and can therefore be used for the combinatorial synthesis of libraries of artificial receptor molecules of high structural diversity.
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Affiliation(s)
- T Opatz
- Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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23
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Monnee MC, Brouwer AJ, Verbeek LM, van Wageningen AM, Liskamp RM. Bio-inspired synthetic receptor molecules towards mimicry of vancomycin. Bioorg Med Chem Lett 2001; 11:1521-5. [PMID: 11412973 DOI: 10.1016/s0960-894x(01)00237-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A 512-member library of bio-inspired synthetic receptor molecules was prepared featuring a triazacyclophane scaffold. The purpose of this scaffold was to orient three (identical) peptide 'binding arms' in order to mimic an antibiotic binding cavity as is present in the vancomycin antibiotics. The library was screened with D-Ala-D-Ala and D-Ala-D-Lac containing ligands, which are present in the cell wall precursors of pathogenic bacteria. Screening and validation led to identification of a synthetic receptor capable of binding these ligands.
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Affiliation(s)
- M C Monnee
- Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, PO Box 80082, 3508 TB Utrecht, The Netherlands
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Bergstrom RC, Mayfield LD, Corey DR. A bridge between the RNA and protein worlds? Accelerating delivery of chemical reactivity to RNA and DNA by a specific short peptide (AAKK)(4). CHEMISTRY & BIOLOGY 2001; 8:199-205. [PMID: 11251293 DOI: 10.1016/s1074-5521(01)00004-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND RNA can catalyze diverse chemical reactions, leading to the hypothesis that an RNA world existed early in evolution. Today, however, catalysis by naturally occurring RNAs is rare and most chemical transformations within cells require proteins. This has led to interest in the design of small peptides capable of catalyzing chemical transformations. RESULTS We demonstrate that a short lysine-rich peptide (AAKK)(4) can deliver a nucleophile to DNA or RNA and amplify the rate of chemical modification by up to 3400-fold. We also tested similar peptides that contain ornithine or arginine in place of lysine, peptides with altered stereochemistry or orientation, and peptides containing eight lysines but with different spacing. Surprisingly, these similar peptides function much less well, suggesting that specific combinations of amino acids, charge distribution, and stereochemistry are necessary for the rate enhancement by (AAKK)(4). CONCLUSIONS By appending other reactive groups to (AAKK)(4) it should be possible to greatly expand the potential for small peptides to directly catalyze modification of DNA or RNA or to act as cofactors to promote ribozyme catalysis.
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Affiliation(s)
- R C Bergstrom
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-9041, USA
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Affiliation(s)
- K Michaelis
- Institut für Organische Chemie der Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
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Segura JL, Priego EM, Martı́n N. New functionalized and soluble bis-tetrathiafulvalene derivatives as building blocks in the construction of fullerene-derived electroactive triads. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)01309-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Affiliation(s)
- Yijun Pan
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Warren T. Ford
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078
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Zepik HH, Benner SA. Catalysts, Anticatalysts, and Receptors for Unactivated Phosphate Diesters in Water. J Org Chem 1999; 64:8080-8083. [PMID: 11674719 DOI: 10.1021/jo982418+] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A set of substituted bisguanidines have been prepared and examined for their ability to bind and catalyze the hydrolysis of uridylyl-3',5'-uridine (UpU), an unactivated RNA substrate in water. The unexpected result is that this set includes both catalysts (binding the transition state better than the ground state) and anticatalysts (binding the ground state better than the transition state), each with respectable rate enhancements and/or affinities, despite the fact that these molecules all have very similar structures. These results therefore show the level of sophistication that must be achieved in the conformational theory of small molecules if we hope to truly "design" supramolecular structures that bind preferentially to a transition state over the ground state.
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Affiliation(s)
- Helmut H. Zepik
- Departments of Chemistry and Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32611
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Schmuck C. Highly Stable Self-Association of 5-(Guanidiniocarbonyl)-1H-pyrrole-2-carboxylate in DMSO – The Importance of Electrostatic Interactions. European J Org Chem 1999. [DOI: 10.1002/(sici)1099-0690(199909)1999:9<2397::aid-ejoc2397>3.0.co;2-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Molenveld P, Engbersen JFJ, Reinhoudt DN. Dinuclear Bisimidazolyl-Cu(II) Calix[4]arenes as Metalloenzyme Models. Synthesis and Bifunctional Catalysis in Phosphate Diester Transesterification. J Org Chem 1999. [DOI: 10.1021/jo9905266] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Molenveld
- Laboratory of Supramolecular Chemistry and Technology, MESA+ Research Institute University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Johan F. J. Engbersen
- Laboratory of Supramolecular Chemistry and Technology, MESA+ Research Institute University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - David N. Reinhoudt
- Laboratory of Supramolecular Chemistry and Technology, MESA+ Research Institute University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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Löwik DWPM, Weingarten MD, Broekema M, Brouwer AJ, Still WC, Liskamp RMJ. Molekulare Pinzetten mit unterschiedlichem Biß – Erhöhung der Affinität synthetischer Rezeptoren durch Variation der Gelenkgruppe. Angew Chem Int Ed Engl 1998. [DOI: 10.1002/(sici)1521-3757(19980703)110:13/14<1947::aid-ange1947>3.0.co;2-e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Oivanen M, Kuusela S, Lönnberg H. Kinetics and Mechanisms for the Cleavage and Isomerization of the Phosphodiester Bonds of RNA by Brønsted Acids and Bases. Chem Rev 1998; 98:961-990. [PMID: 11848921 DOI: 10.1021/cr960425x] [Citation(s) in RCA: 358] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mikko Oivanen
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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Muche MS, Kamalaprija P, Göbel* MW. Reaction Cascade in the Supramolecular Phosphorylation of a Bis(Guanidinium) Diol. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)00513-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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