101
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Fleming S, Ulijn RV. Design of nanostructures based on aromatic peptide amphiphiles. Chem Soc Rev 2014; 43:8150-77. [PMID: 25199102 DOI: 10.1039/c4cs00247d] [Citation(s) in RCA: 591] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aromatic peptide amphiphiles are gaining popularity as building blocks for the bottom-up fabrication of nanomaterials, including gels. These materials combine the simplicity of small molecules with the versatility of peptides, with a range of applications proposed in biomedicine, nanotechnology, food science, cosmetics, etc. Despite their simplicity, a wide range of self-assembly behaviours have been described. Due to varying conditions and protocols used, care should be taken when attempting to directly compare results from the literature. In this review, we rationalise the structural features which govern the self-assembly of aromatic peptide amphiphiles by focusing on four segments, (i) the N-terminal aromatic component, (ii) linker segment, (iii) peptide sequence, and (iv) C-terminus. It is clear that the molecular structure of these components significantly influences the self-assembly process and resultant supramolecular architectures. A number of modes of assembly have been proposed, including parallel, antiparallel, and interlocked antiparallel stacking conformations. In addition, the co-assembly arrangements of aromatic peptide amphiphiles are reviewed. Overall, this review elucidates the structural trends and design rules that underpin the field of aromatic peptide amphiphile assembly, paving the way to a more rational design of nanomaterials based on aromatic peptide amphiphiles.
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Affiliation(s)
- Scott Fleming
- WestCHEM/Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK.
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102
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Fanlo-Virgós H, Alba ANR, Hamieh S, Colomb-Delsuc M, Otto S. Transient substrate-induced catalyst formation in a dynamic molecular network. Angew Chem Int Ed Engl 2014; 53:11346-50. [PMID: 25169198 DOI: 10.1002/anie.201403480] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/02/2014] [Indexed: 11/06/2022]
Abstract
In biology enzyme concentrations are continuously regulated, yet for synthetic catalytic systems such regulatory mechanisms are underdeveloped. We now report how a substrate of a chemical reaction induces the formation of its own catalyst from a dynamic molecular network. After complete conversion of the substrate, the network disassembles the catalyst. These results open up new opportunities for controlling catalysis in synthetic chemical systems.
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Affiliation(s)
- Hugo Fanlo-Virgós
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands) http://www.otto-lab.com
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103
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Fanlo-Virgós H, Alba ANR, Hamieh S, Colomb-Delsuc M, Otto S. Transient Substrate-Induced Catalyst Formation in a Dynamic Molecular Network. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403480] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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104
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Biased and unbiased strategies to identify biologically active small molecules. Bioorg Med Chem 2014; 22:4474-89. [DOI: 10.1016/j.bmc.2014.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/03/2014] [Accepted: 04/10/2014] [Indexed: 12/20/2022]
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105
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Rancan M, Tessarolo J, Casarin M, Zanonato PL, Quici S, Armelao L. Double Level Selection in a Constitutional Dynamic Library of Coordination Driven Supramolecular Polygons. Inorg Chem 2014; 53:7276-87. [DOI: 10.1021/ic500573e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Marzio Rancan
- Department
of Chemical Sciences and INSTM, University of Padova, via Marzolo
1, 35131 Padova, Italy
- IENI−CNR, via
Marzolo 1, 35131 Padova, Italy
| | - Jacopo Tessarolo
- Department
of Chemical Sciences and INSTM, University of Padova, via Marzolo
1, 35131 Padova, Italy
- IENI−CNR, via
Marzolo 1, 35131 Padova, Italy
| | - Maurizio Casarin
- Department
of Chemical Sciences and INSTM, University of Padova, via Marzolo
1, 35131 Padova, Italy
| | - Pier Luigi Zanonato
- Department
of Chemical Sciences and INSTM, University of Padova, via Marzolo
1, 35131 Padova, Italy
| | - Silvio Quici
- ISTM−CNR, via C. Golgi, 19, 20133, Milano, Italy
| | - Lidia Armelao
- Department
of Chemical Sciences and INSTM, University of Padova, via Marzolo
1, 35131 Padova, Italy
- IENI−CNR, via
Marzolo 1, 35131 Padova, Italy
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106
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Weber L. In vitro combinatorial chemistry to create drug candidates. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 1:261-7. [PMID: 24981494 DOI: 10.1016/j.ddtec.2004.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In vitro combinatorial chemistry represents a variety of technologies where the selection and synthesis of novel molecules is performed in one integrated process. In its application towards drug discovery, the biological target is used to select and/or to amplify compounds out of a large pool of potential combinatorial compound library members. Recent examples provide a first proof-of-concept that dynamic combinatorial libraries or 'click chemistry' are able to discover highly potent and selective small molecule inhibitors of target enzymes.:
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Affiliation(s)
- Lutz Weber
- Morphochem AG, Gmunder Street 37-37A, 81379 München, Germany.
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107
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Matache M, Bogdan E, Hădade ND. Selective Host Molecules Obtained by Dynamic Adaptive Chemistry. Chemistry 2014; 20:2106-31. [DOI: 10.1002/chem.201303504] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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108
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Ballard N, Bon SAF. Dynamic uptake and release from poly(methacryloyl hydrazide) microgel particles through reversible hydrazide-aldehyde chemistry. Polym Chem 2014. [DOI: 10.1039/c4py00726c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The uptake and release time-profiles of aldehydes from aqueous formulations can be fine tuned using hydrazide functional microgels.
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Affiliation(s)
- Nicholas Ballard
- POLYMAT and Grupo de Ingeniería Química
- Dpto. de Química Aplicada
- University of the Basque Country UPV/EHU
- Donostia/San Sebastían, Spain
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109
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Misuraca MC, Moulin E, Ruff Y, Giuseppone N. Experimental and theoretical methods for the analyses of dynamic combinatorial libraries. NEW J CHEM 2014. [DOI: 10.1039/c4nj00304g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Progresses in spatial and temporal analytical tools open new avenues for the study and control of increasingly complex chemical systems.
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Affiliation(s)
- Maria Cristina Misuraca
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
| | - Emilie Moulin
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
| | - Yves Ruff
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
| | - Nicolas Giuseppone
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
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110
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Ulrich S, Dumy P. Probing secondary interactions in biomolecular recognition by dynamic combinatorial chemistry. Chem Commun (Camb) 2014; 50:5810-25. [DOI: 10.1039/c4cc00263f] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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111
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Abdelrahim MYM, Tanc M, Winum JY, Supuran CT, Barboiu M. Dominant behaviours in the expression of human carbonic anhydrase hCA I activity. Chem Commun (Camb) 2014; 50:8043-6. [DOI: 10.1039/c4cc03289f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic deconvolution ofDCLsof inhibitors (CAIs) and activators (CAAs) of hCA I show that the inhibitory effects dominate over the activating ones.
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Affiliation(s)
- M. Yahia M. Abdelrahim
- Adaptative Supramolecular Nanosystems Group
- Institut Européen des Membranes
- ENSCM/UMII/UMR-CNRS 5635
- 34095 Montpellier, Cedex 5, France
| | - Muhammet Tanc
- Università degli Studi di Firenze
- Polo Scientifico, Laboratorio di Chimica Bioinorganica
- 50019 Sesto Fiorentino (Florence), Italy
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS
- Ecole Nationale Supérieure de Chimie de Montpellier
- 34296 Montpellier Cedex, France
| | - Claudiu T. Supuran
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS
- Ecole Nationale Supérieure de Chimie de Montpellier
- 34296 Montpellier Cedex, France
| | - Mihail Barboiu
- Adaptative Supramolecular Nanosystems Group
- Institut Européen des Membranes
- ENSCM/UMII/UMR-CNRS 5635
- 34095 Montpellier, Cedex 5, France
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112
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Rasmussen B, Sørensen A, Gotfredsen H, Pittelkow M. Dynamic combinatorial chemistry with diselenides and disulfides in water. Chem Commun (Camb) 2014; 50:3716-8. [DOI: 10.1039/c4cc00523f] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diselenide exchange is introduced as a reversible reaction in dynamic combinatorial chemistry in water at physiological pH.
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Affiliation(s)
- Brian Rasmussen
- Department of Chemistry
- University of Copenhagen
- DK-2100 Copenhagen, Denmark
| | - Anne Sørensen
- Department of Chemistry
- University of Copenhagen
- DK-2100 Copenhagen, Denmark
| | - Henrik Gotfredsen
- Department of Chemistry
- University of Copenhagen
- DK-2100 Copenhagen, Denmark
| | - Michael Pittelkow
- Department of Chemistry
- University of Copenhagen
- DK-2100 Copenhagen, Denmark
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113
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Abstract
Guanosine (G) and isoguanosine (isoG) derivatives can self-assemble, yielding supramolecules that have found broad applications in diverse fields.
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Affiliation(s)
| | - Raphaël Rodriguez
- Institut de Chimie des Subtances Naturelles
- Centre National de la Recherche Scientifique
- Avenue de la Terrasse
- Gif-sur-Yvette, France
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114
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Gao Y, Berciu C, Kuang Y, Shi J, Nicastro D, Xu B. Probing nanoscale self-assembly of nonfluorescent small molecules inside live mammalian cells. ACS NANO 2013; 7:9055-63. [PMID: 24067160 PMCID: PMC3845088 DOI: 10.1021/nn403664n] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Like cellular proteins that form fibrillar nanostructures, small hydrogelator molecules self-assemble in water to generate molecular nanofibers. In contrast to the well-defined (dys)functions of endogenous protein filaments, the fate of intracellular assembly of small molecules remains largely unknown. Here we demonstrate the imaging of enzyme-triggered self-assembly of nonfluorescent small molecules by doping the molecular assemblies with a fluorescent hydrogelator. The cell fractionation experiments, fluorescent imaging, and electron microscopy indicate that the hydrogelators self-assemble and localize to the endoplasmic reticulum (ER) and are likely processed via the cellular secretory pathway (i.e., ER-Golgi-lysosomes/secretion). This work, as the first example of the use of correlative light and electron microscopy for probing the self-assembly of nonfluorescent small molecules inside live mammalian cells, not only establishes a general strategy to provide the spatiotemporal profile of the assemblies of small molecules inside cells but may lead to a new paradigm for regulating cellular functions based on the interactions between the assemblies of small molecules (e.g., molecular nanofibers) and subcellular organelles.
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Affiliation(s)
- Yuan Gao
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Cristina Berciu
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Yi Kuang
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Daniela Nicastro
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
- Corresponding Author:
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115
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Sharpless KB, Manetsch R. In situ click chemistry: a powerful means for lead discovery. Expert Opin Drug Discov 2013; 1:525-38. [PMID: 23506064 DOI: 10.1517/17460441.1.6.525] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combinatorial chemistry and parallel synthesis are important and regularly applied tools for lead identification and optimisation, although they are often accompanied by challenges related to the efficiency of library synthesis and the purity of the compound library. In the last decade, novel means of lead discovery approaches have been investigated where the biological target is actively involved in the synthesis of its own inhibitory compound. These fragment-based approaches, also termed target-guided synthesis (TGS), show great promise in lead discovery applications by combining the synthesis and screening of libraries of low molecular weight compounds in a single step. Of all the TGS methods, the kinetically controlled variant is the least well known, but it has the potential to emerge as a reliable lead discovery method. The kinetically controlled TGS approach, termed in situ click chemistry, is discussed in this article.
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Affiliation(s)
- K Barry Sharpless
- WM Keck Professor, Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC-315 La Jolla, CA 92037, USA.
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116
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Otsuka H. Reorganization of polymer structures based on dynamic covalent chemistry: polymer reactions by dynamic covalent exchanges of alkoxyamine units. Polym J 2013. [DOI: 10.1038/pj.2013.17] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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117
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Fischmann S, Lüning U. Dynamic Combinatorial Libraries of Macrocyclic Imines and Their Applications. Isr J Chem 2013. [DOI: 10.1002/ijch.201200092] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Svenja Fischmann
- Otto‐Diels‐Institut für Organische Chemie, Christian‐Albrechts‐Universität zu Kiel, Olshausenstr. 40, D‐24098 Kiel (Germany)
| | - Ulrich Lüning
- Otto‐Diels‐Institut für Organische Chemie, Christian‐Albrechts‐Universität zu Kiel, Olshausenstr. 40, D‐24098 Kiel (Germany) phone: +49‐431‐880‐2450 fax: +49‐431‐880‐1558
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118
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Levin E, Anaby A, Diesendruck CE, Berkovich-Berger D, Fuchs B, Lemcoff NG. Oligomerisation reactions of beta substituted thiols in water. RSC Adv 2013. [DOI: 10.1039/c2ra22131d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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119
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120
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Di Antonio M, Biffi G, Mariani A, Raiber EA, Rodriguez R, Balasubramanian S. Selective RNA versus DNA G-quadruplex targeting by in situ click chemistry. Angew Chem Int Ed Engl 2012; 51:11073-8. [PMID: 23038154 PMCID: PMC3652031 DOI: 10.1002/anie.201206281] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Indexed: 12/22/2022]
Abstract
It all clicks into place: A potent telomere-targeting small molecule has been identified by using the copper-free 1,3-dipolar cycloaddition of a series of alkyne and azide building blocks catalyzed by a non-Watson-Crick DNA secondary structure (see picture). This method rapidly identifies, otherwise unanticipated, potent small-molecule probes to selectively target a given RNA or DNA.
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Affiliation(s)
- Marco Di Antonio
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
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121
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Di Antonio M, Biffi G, Mariani A, Raiber EA, Rodriguez R, Balasubramanian S. Selective RNA Versus DNA G-Quadruplex Targeting by In Situ Click Chemistry. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206281] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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122
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Minkenberg CB, Homan B, Boekhoven J, Norder B, Koper GJM, Eelkema R, van Esch JH. Responsive wormlike micelles from dynamic covalent surfactants. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:13570-13576. [PMID: 22873840 DOI: 10.1021/la302294r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Dynamic covalent chemistry is a powerful tool for the construction of adaptive and stimulus-responsive nanosystems. Here we report on the spontaneous formation of dynamic covalent wormlike micelles from imine-based gemini surfactants, formed upon mixing aqueous solutions of two complementary non-surface-active precursors. Resulting from the reversibility of the dynamic covalent imine bond, the wormlike micelles can be switched between an isotropic solution and the assembled state, triggered by pH and temperature. Thermodynamic modeling of the reaction equilibria shows that, although mixtures of single- and double-tailed surfactants are formed, it is mainly the double-tailed surfactant that assembles into the wormlike micelles.
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Affiliation(s)
- Christophe B Minkenberg
- Self-Assembling Systems, Department of Chemical Engineering, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands
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123
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Joshi G, Anslyn EV. Dynamic thiol exchange with β-sulfido-α,β-unsaturated carbonyl compounds and dithianes. Org Lett 2012; 14:4714-7. [PMID: 22934665 PMCID: PMC3472802 DOI: 10.1021/ol301781u] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A reversible covalent bond exchange of thiols, β-sulfido-α,β-unsaturated carbonyls, and dithianes has been studied in DMSO and D(2)O/DMSO mixtures. The equilibrium between thiols and β-sulfido-α,β-unsaturated carbonyls is obtained within a few hours, while the equilibration starting with the β-dithiane carbonyls and thiols requires a few days. This time scale makes the system ideal for utilization in dynamic combinatorial chemistry.
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Affiliation(s)
- Gururaj Joshi
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Eric V. Anslyn
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
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124
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Sugino H, Kawai H, Umehara T, Fujiwara K, Suzuki T. Effects of Axle-Core, Macrocycle, and Side-Station Structures on the Threading and Hydrolysis Processes of Imine-Bridged Rotaxanes. Chemistry 2012; 18:13722-32. [DOI: 10.1002/chem.201200837] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 06/06/2012] [Indexed: 02/02/2023]
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125
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Hafezi N, Lehn JM. Adaptation of dynamic covalent systems of imine constituents to medium change by component redistribution under reversible phase separation. J Am Chem Soc 2012; 134:12861-8. [PMID: 22783895 DOI: 10.1021/ja305379c] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A dynamic covalent library of interconverting imine constituents, dissolved in an acetonitrile/water mixture, undergoes constitutional reorganization upon phase separation induced by a physical stimulus (heat) or a chemical effector (inorganic salt, carbohydrate, organic solvent). The process has been made reversible, regenerating the initial library upon phase reunification. It represents the behavior of a dynamic covalent library upon reversible phase separation and its adaptation to a phase change, with up-regulation in each phase of the fittest constituents by component selection. Finally, the system exemplifies the splitting of a 2D (square) constitutional dynamic network into a 3D (cube) one.
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Affiliation(s)
- Nema Hafezi
- Institut de Science et d'Ingénierie Supramoléculaires, ISIS Université de Strasbourg, Strasbourg 67000, France
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126
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Clipson AJ, Bhat VT, McNae I, Caniard AM, Campopiano DJ, Greaney MF. Bivalent enzyme inhibitors discovered using dynamic covalent chemistry. Chemistry 2012; 18:10562-70. [PMID: 22782854 DOI: 10.1002/chem.201201507] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Indexed: 12/25/2022]
Abstract
A bivalent dynamic covalent chemistry (DCC) system has been designed to selectively target members of the homodimeric glutathione-S-transferase (GST) enzyme family. The dynamic covalent libraries (DCLs) use aniline-catalysed acylhydrazone exchange between bivalent hydrazides and glutathione-conjugated aldehydes and the bis-hydrazides act as linkers to bridge between each glutathione binding site. The resultant DCLs were found to be compatible and highly responsive to templating with different GST isozymes, with the best results coming from the M and Schistosoma japonicum (Sj) class of GSTs, targets in cancer and tropical disease, respectively. The approach yielded compounds with selective, nanomolar affinity (K(i) =61 nM for mGSTM1-1) and demonstrates that DCC can be used to simultaneously interrogate binding sites on different subunits of a dimeric protein.
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Affiliation(s)
- Alexandra J Clipson
- School of Chemistry, University of Edinburgh, King's Buildings, West Mains Rd., Edinburgh, UK
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127
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Vendrell M, Zhai D, Er JC, Chang YT. Combinatorial strategies in fluorescent probe development. Chem Rev 2012; 112:4391-420. [PMID: 22616565 DOI: 10.1021/cr200355j] [Citation(s) in RCA: 462] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Marc Vendrell
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, 138667 Singapore.
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128
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Tanaka K, Shirotsuki S, Iwata T, Kageyama C, Tahara T, Nozaki S, Siwu ERO, Tamura S, Douke S, Murakami N, Onoe H, Watanabe Y, Fukase K. Template-assisted and self-activating clicked peptide as a synthetic mimic of the SH2 domain. ACS Chem Biol 2012; 7:637-45. [PMID: 22239652 DOI: 10.1021/cb2003175] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A new synthetic strategy for obtaining artificial receptors that selectively regulate and/or control specific protein/protein interactions was developed based on the template-assisted and the self-activating click reaction applied to a combinatorial library. Synthetic mimics of the Grb2-SH2 domain, examined as a model case, selectively bound to a target signaling protein to induce cytotoxicity and inhibit tumor growth in vivo.
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Affiliation(s)
- Katsunori Tanaka
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Sanae Shirotsuki
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Takayuki Iwata
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Chika Kageyama
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Tsuyoshi Tahara
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Satoshi Nozaki
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Eric R. O. Siwu
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
| | - Satoru Tamura
- Graduate School of Pharmaceutical
Sciences, Osaka University, 1-6 Yamada-oka,
Suita-shi, Osaka 565-0871, Japan
| | - Shunsuke Douke
- Graduate School of Pharmaceutical
Sciences, Osaka University, 1-6 Yamada-oka,
Suita-shi, Osaka 565-0871, Japan
| | - Nobutoshi Murakami
- Graduate School of Pharmaceutical
Sciences, Osaka University, 1-6 Yamada-oka,
Suita-shi, Osaka 565-0871, Japan
| | - Hirotaka Onoe
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Yasuyoshi Watanabe
- RIKEN Center for Molecular Imaging Science, 6-7-3 Minatojima-minamimachi,
Chuo-ku, Kobe-shi, Hyogo 650-0047, Japan
| | - Koichi Fukase
- Department
of Chemistry, Graduate
School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka-shi, Osaka 560-0043, Japan
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129
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Biros S, Hof F. Supramolecular Approaches to Medicinal Chemistry. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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130
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131
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132
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133
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Raindlová V, Pohl R, Hocek M. Synthesis of aldehyde-linked nucleotides and DNA and their bioconjugations with lysine and peptides through reductive amination. Chemistry 2012; 18:4080-7. [PMID: 22337599 DOI: 10.1002/chem.201103270] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Indexed: 11/06/2022]
Abstract
5-(5-Formylthienyl)-, 5-(4-formylphenyl)- and 5-(2-fluoro-5-formylphenyl)cytosine 2'-deoxyribonucleoside mono- (dC(R)MP) and triphosphates (dC(R)TP) were prepared by aqueous Suzuki-Miyaura cross-coupling of 5-iodocytosine nucleotides with the corresponding formylarylboronic acids. The dC(R)TPs were excellent substrates for DNA polymerases and were incorporated into DNA by primer extension or PCR. Reductive aminations of the model dC(R)MPs with lysine or lysine-containing tripeptide were studied and optimized. In aqueous phosphate buffer (pH 6.7) the yields of the reductive aminations with tripeptide III were up to 25 %. Bioconjugation of an aldehyde-containing DNA with a lysine-containing tripeptide was achieved through reductive amination in yields of up to 90 % in aqueous phosphate buffer.
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Affiliation(s)
- Veronika Raindlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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134
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Nishiyabu R, Teraoka S, Matsushima Y, Kubo Y. Fabrication of Soft Submicrospheres by Sequential Boronate Esterification and Their Dynamic Behavior. Chempluschem 2012. [DOI: 10.1002/cplu.201100008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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135
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136
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Hanessian S, Maianti JP, Ly VL, Deschênes-Simard B. Structural and kinetic study of self-assembling macrocyclic dimer natural product aminoglycoside66-40C and unnatural variants. Chem Sci 2012. [DOI: 10.1039/c1sc00538c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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137
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Eschenmoser A. Ätiologie potentiell primordialer Biomolekül-Strukturen: Vom Vitamin B12 zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens - ein Rückblick. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103672] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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138
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Eschenmoser A. Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl 2011; 50:12412-72. [PMID: 22162284 DOI: 10.1002/anie.201103672] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Indexed: 11/10/2022]
Abstract
"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.
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Affiliation(s)
- Albert Eschenmoser
- Organisch-chemisches Laboratorium der ETH Zürich, Hönggerberg, Wolfgang-Pauli-Str. 10, CHI H309, CH-8093 Zürich, Switzerland
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139
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Boutelle RC, Northrop BH. Substituent effects on the reversibility of furan-maleimide cycloadditions. J Org Chem 2011; 76:7994-8002. [PMID: 21866976 DOI: 10.1021/jo201606z] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The effects of furan and maleimide substitution on the dynamic reversibility of their Diels-Alder reactivity have been investigated computationally and by (1)H NMR spectroscopy. Furan and furan derivatives bearing methoxy, methyl, or formyl groups at their 2- or 3-positions were investigated with maleimide and maleimide derivatives bearing N-methyl, N-allyl, and N-phenyl substituents. Computational predictions indicate that electronic and regiochemical effects of furan substitution significantly influence their Diels-Alder reactivity with maleimide, with reaction free energies of exo adduct formation ranging from ΔG = -9.4 to 0.9 kcal/mol and transition state barriers to exo adduct formation ranging from ΔG(‡) = 18.9 to 25.6 kcal/mol. Much less variation was observed for the reactivity of N-substituted maleimide derivatives and furan, with reaction and transition state free energies each falling within a range of 1.1 kcal/mol. Dynamic exchange experiments monitored by (1)H NMR spectroscopy support computational predictions. The results indicate the reactivity and reversibility of furan-maleimide cycloadditions can be tuned significantly through the addition of appropriate substituents and have implications in the use of furan and maleimide derivatives in the construction of thermally responsive organic materials.
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Affiliation(s)
- Robert C Boutelle
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
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140
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Le Gresley A, Abdullah A, Desai P, Ghosh U, Gollapalli U, Kiran M, Lafon S. Scope of the Heck Reaction in the Synthesis of a New Family of Anthracene Diacrylamide G-Quadruplex Ligands. SYNTHETIC COMMUN 2011. [DOI: 10.1080/00397911.2010.505703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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141
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Combinatorially-generated library of 6-fluoroquinolone analogs as potential novel antitubercular agents: a chemometric and molecular modeling assessment. J Mol Model 2011; 18:1735-53. [DOI: 10.1007/s00894-011-1179-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 07/04/2011] [Indexed: 01/15/2023]
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142
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Li X, Chan YT, Casiano-Maldonado M, Yu J, Carri GA, Newkome GR, Wesdemiotis C. Separation and characterization of metallosupramolecular libraries by ion mobility mass spectrometry. Anal Chem 2011; 83:6667-74. [PMID: 21744807 DOI: 10.1021/ac201161u] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The self-assembly of Zn(II) ions and bis(terpyridine) (tpy) ligands carrying 120° or 180° angles between their metal binding sites was utilized to prepare metallosupramolecular libraries with the <tpy-Zn(II)-tpy> connectivity. These combinatorial libraries were separated and characterized by ion mobility mass spectrometry (IM MS) and tandem mass spectrometry (MS(2)). The 180°-angle building blocks generate exclusively linear complexes, which were used as standards to determine the architectures of the assemblies resulting from the 120°-angle ligands. The latter ligand geometry promotes the formation of macrocyclic hexamers, but other n-mers with smaller (n = 5) or larger ring sizes (n = 7-9) were identified as minor products, indicating that the angles in the bis(terpyridine) ligand and within the coordinative tpy-Zn(II)-tpy bonds are not as rigid, as previously believed. Macrocyclic and linear isomers were detected in penta- and heptameric assemblies; in the larger octa- and nonameric assemblies, ring-opened conformers with compact and folded geometries were observed in addition to linear extended and cyclic architectures. IM MS(2) experiments provided strong evidence that the macrocycles present in the libraries were already formed in solution, during the self-assembly process, not by dissociation of larger complexes in the gas phase. The IM MS/MS(2) methods provide a means to analyze, based on size and shape (architecture), supramolecular libraries that are not amenable to liquid chromatography, LC-MS, NMR, and/or X-ray techniques.
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Affiliation(s)
- Xiaopeng Li
- Department of Chemistry, The University of Akron, Akron, Ohio 44325, USA
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143
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Sahu S, Patel S, Mishra BK. Deoximation by cetyltrimethylammonium dichromate: A kinetic study. INT J CHEM KINET 2011. [DOI: 10.1002/kin.20576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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144
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Folmer-Andersen JF, Lehn JM. Thermoresponsive dynamers: thermally induced, reversible chain elongation of amphiphilic poly(acylhydrazones). J Am Chem Soc 2011; 133:10966-73. [PMID: 21639138 DOI: 10.1021/ja2035909] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A nanostructured poly(acylhydrazone), which is reversibly formed in acidic aqueous solution from di(aldehyde) and di(acylhydrazine) monomers with appended hexaglyme groups, was found to display lower critical solution (LCS) behavior. Remarkably, under acidic conditions in which polymerization is reversible, large and reversible molecular weight (M(w)) increases were observed in response to elevated temperatures, both below and above the LCS temperature. No variation in M(w) was evident under neutral and alkaline conditions, in which the acylhydrazone condensation is essentially irreversible. Results of turbidometry studies, size-exclusion chromatography-multiangle laser light scattering (SEC-MALLS), and transmission electron microscopy (TEM) suggest that heating the polymer below the LCS temperature leads to polymer growth with preservation of the characteristic nanostructured morphology, whereas the onset of the microphase separated state causes a fundamental change in morphology, in which the polymer chains aggregate into larger bundles and fibers. van't Hoff analysis of a small molecule model system indicates that the acylhydrazone condensation is enthalpy driven (ΔH(eq) = -8.2 ± 0.2 kcal·mol(-1) and ΔS(eq) = -11.1 ± 0.4 = cal·mol(-1)·K(-1)), which suggests that the observed polymer growth with temperature is not a consequence of the intrinsic thermodynamics of the intermonomer linkage but is likely the result of the thermoresponsive characteristics conferred by the multiple hexaglyme groups. The system described displays double control of the dynamer state by two orthogonal agents, heat and protons (pH). It also represents a prototype for dynamic materials displaying multiple control adaptive behavior.
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Affiliation(s)
- J Frantz Folmer-Andersen
- Institut de Science et d'Ingénierie Supramoléculaires, Université de Strasbourg, 8 Allée Gaspard-Monge, BP 70028, 67083 Strasbourg, France
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145
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Azéma L, Bathany K, Rayner B. 2'-O-Appended polyamines that increase triple-helix-forming oligonucleotide affinity are selected by dynamic combinatorial chemistry. Chembiochem 2011; 11:2513-6. [PMID: 21104718 DOI: 10.1002/cbic.201000538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Laurent Azéma
- U869, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France
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146
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Minkenberg CB, Li F, van Rijn P, Florusse L, Boekhoven J, Stuart MCA, Koper GJM, Eelkema R, van Esch JH. Responsive Vesicles from Dynamic Covalent Surfactants. Angew Chem Int Ed Engl 2011; 50:3421-4. [DOI: 10.1002/anie.201007401] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/26/2011] [Indexed: 12/11/2022]
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147
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Minkenberg CB, Li F, van Rijn P, Florusse L, Boekhoven J, Stuart MCA, Koper GJM, Eelkema R, van Esch JH. Responsive Vesicles from Dynamic Covalent Surfactants. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007401] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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148
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Lippert AR, Naganawa A, Keleshian VL, Bode JW. Synthesis of phototrappable shape-shifting molecules for adaptive guest binding. J Am Chem Soc 2011; 132:15790-9. [PMID: 20945902 DOI: 10.1021/ja107314p] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have designed and synthesized oligosubstituted bullvalenes 1 and 2 as adaptive molecules that can change their shapes in order to bind tightly to a suitable guest. By incorporation of a photolabile o-nitroveratryloxycarbonate (NVOC) group into bullvalenes 1 and 2, tightly binding species can be selectively isolated from a population of hundreds of interconverting structural isomers. Spontaneous strain-assisted Cope rearrangements allow these shape-shifting molecules to exist in a dynamic equilibrium of configurationally distinct valence isomers, as revealed by dynamic NMR and HPLC studies. When NVOC bullvalenes 1 and 2 were exposed to UV light, the cleavage of the NVOC group resulted in a mixture of static isomers of the corresponding bullvalone. Binding studies of NVOC bisporphyrin bullvalene 1 demonstrated that the dynamic isomeric equilibrium shifted in the presence of C(60), favoring configurations with more favorable binding affinities. Irradiation of a mixture of 1 and C(60) with UV light and isolation of the major static isomer yielded an isomer of bisporphyrin bullvalone with a binding affinity for C(60) that was ∼2 times larger than that of the nonadapted isomer bisporphyrin bullvalone 41.
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Affiliation(s)
- Alexander R Lippert
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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149
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Constitutional Dynamic Chemistry: Bridge from Supramolecular Chemistry to Adaptive Chemistry. CONSTITUTIONAL DYNAMIC CHEMISTRY 2011; 322:1-32. [DOI: 10.1007/128_2011_256] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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150
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Reversible covalent chemistries compatible with the principles of constitutional dynamic chemistry: new reactions to create more diversity. Top Curr Chem (Cham) 2011; 322:291-314. [PMID: 22025070 DOI: 10.1007/128_2011_277] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
An approach to make chemical diversity space more manageable is to search for smaller molecules, or fragments, and then combine or elaborate these fragments. Dynamic Combinatorial Chemistry (DCC) is a powerful approach whereby a number of molecular elements each with binding potential can be reversibly combined via covalent or noncovalent linkages to generate a dynamic library of products under thermodynamic equilibrium. Once a target molecule has been added, the distribution of products can be shifted to favor products that bind to the target. Thus the approach can be employed to identify products that selectively recognize the target. Although the size of the repertoire of reversible covalent reactions suitable for DCC has increased significantly over the past 5-10 years, the discovery of new reactions that satisfy all the criteria of reversibility and biocompatibility remains an exciting challenge for chemists. Increasing the number of chemical reactions will enable the engineering of larger and more diverse DCLs, which remains a key step toward a broader use of DCC. In this review, we aim to provide a nonexhaustive list of reversible covalent reactions that are compatible with the concept of DCC, focusing mainly on the most recent examples that were reported in the literature in the past 5 years.
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