1
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Matsubara S, Okamoto Y, Yoshikawa M, Tsukiji S, Higuchi M. A Peptide Nanocage Constructed by Self-Assembly of Oligoproline Conjugates. Bioconjug Chem 2022; 33:1785-1788. [PMID: 35900377 DOI: 10.1021/acs.bioconjchem.2c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cage-like supramolecular assemblies called molecular cages, which possess attractive functions, have been prepared. Although biomolecule-based nanocages are required for biological/medical applications such as drug delivery systems, the majority of nanocages are constructed using aromatic compounds with lower biocompatibility and biodegradability. In this study, the construction of a peptide nanocage consisting of an oligoproline conjugate is demonstrated. The conjugate was easy to prepare and had high biocompatibility. The oligoproline moiety of the conjugate had a rigid, rod-like structure suitable for the backbone of the supramolecular nanocage. The conjugates self-assembled to form peptide nanocages with a huge inner cavity.
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Affiliation(s)
- Shogo Matsubara
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Yui Okamoto
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Masaru Yoshikawa
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.,Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Masahiro Higuchi
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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2
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Abstract
Artificial receptors able to recognise biologically relevant molecules or ions have gained interest in the chemical community because they offer a plethora of posibilities. Molecular cage compounds are polycyclic compounds with a cavity designed for the encapsulation of guest species. Once inside the host cavity, the substrate can be transported through membranes and protected from the action of enzymes or other reactive species, thus offering the possibility of interfering with biological systems. Commonly, enzymes have been an inspiration for chemists in the search and design of defined cavities for different purposes. However, the chemical preparation of molecular cages has struggled with many synthetic challenges but this effort is worthwhile as they are a very promising tool for many applications ranging from sensing, delivery, purification or even promotion of/prevention from chemical modifications. Since the early reports at the end of the 60s, this field has experienced a growing interest; this review summarises the progress in the preparation and study of cage-like compounds highlighting their importance in biological applications.
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Affiliation(s)
- Lucía Tapia
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Jordi Solà
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
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3
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Tapia L, Solozabal N, Solà J, Pérez Y, Miller WT, Alfonso I. Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages. Chemistry 2021; 27:9542-9549. [PMID: 33904620 PMCID: PMC8362067 DOI: 10.1002/chem.202100990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 12/15/2022]
Abstract
The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.
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Affiliation(s)
- Lucía Tapia
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Naiara Solozabal
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Jordi Solà
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Yolanda Pérez
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - W. Todd Miller
- Department of Physiology and BiophysicsStony Brook University and Department of Veterans Affairs Medical CenterStony BrookNY, 11794USA
| | - Ignacio Alfonso
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
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4
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Klepel F, Ravoo BJ. A dynamic combinatorial library for biomimetic recognition of dipeptides in water. Beilstein J Org Chem 2020; 16:1588-1595. [PMID: 32704325 PMCID: PMC7356556 DOI: 10.3762/bjoc.16.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/26/2020] [Indexed: 11/23/2022] Open
Abstract
Small peptides are involved in countless biological processes. Hence selective binding motifs for peptides can be powerful tools for labeling or inhibition. Finding those binding motifs, especially in water which competes for intermolecular H-bonds, poses an enormous challenge. A dynamic combinatorial library can be a powerful method to overcome this issue. We previously reported artificial receptors emerging form a dynamic combinatorial library of peptide building blocks. In this study we aimed to broaden this scope towards recognition of small peptides. Employing CXC peptide building blocks, we found that cyclic dimers of oxidized CFC bind to the aromatic peptides FF and YY (K ≈ 229–702 M−1), while AA binds significantly weaker (K ≈ 65–71 M−1).
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Affiliation(s)
- Florian Klepel
- Organic Chemistry Institute and Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, Correnstraße 40, 48149 Münster, Germany
| | - Bart Jan Ravoo
- Organic Chemistry Institute and Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, Correnstraße 40, 48149 Münster, Germany
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5
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Esteve F, Altava B, Bolte M, Burguete MI, García-Verdugo E, Luis SV. Highly Selective Anion Template Effect in the Synthesis of Constrained Pseudopeptidic Macrocyclic Cyclophanes. J Org Chem 2020; 85:1138-1145. [PMID: 31858803 DOI: 10.1021/acs.joc.9b03048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, we report the synthesis of a novel family of constrained pseudopeptidic macrocyclic compounds containing the hexahydropyrrolo[3,4-f]isoindolocyclophane scaffold and involving four coupled substitution reactions in the macrocyclization process. Although the increase in the number of steps involved in the macrocyclization could lead to a larger number of possible side products, the optimization of the methodology and the study of the driving forces have made it possible to obtain the desired macrocycles in excellent yields. A thorough computational study has been carried out to understand the macrocyclization process, and the results obtained nicely agree with experimental data. Moreover, the bromide anion had a clear catalytic template effect in the macrocyclization reaction, and surprisingly, the chloride anion had a negative template effect in opposition to the results obtained for analogous macrocycles. The parameters responsible for the specific kinetic template effect observed have been studied in detail.
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Affiliation(s)
- Ferran Esteve
- Departamento de Química Inorgánica y Orgánica , Universitat JaumeI , Av. Sos Baynat s/n , 12071 Castellón , Spain
| | - Belen Altava
- Departamento de Química Inorgánica y Orgánica , Universitat JaumeI , Av. Sos Baynat s/n , 12071 Castellón , Spain
| | - Michael Bolte
- Institut fur Anorganische Chemie , J. W. Goethe-Universitat Frankfurt , 60438 Frankfurt/Main , Germany
| | - M Isabel Burguete
- Departamento de Química Inorgánica y Orgánica , Universitat JaumeI , Av. Sos Baynat s/n , 12071 Castellón , Spain
| | - Eduardo García-Verdugo
- Departamento de Química Inorgánica y Orgánica , Universitat JaumeI , Av. Sos Baynat s/n , 12071 Castellón , Spain
| | - Santiago V Luis
- Departamento de Química Inorgánica y Orgánica , Universitat JaumeI , Av. Sos Baynat s/n , 12071 Castellón , Spain
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6
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Foianesi-Takeshige LH, Takahashi S, Tateishi T, Sekine R, Okazawa A, Zhu W, Kojima T, Harano K, Nakamura E, Sato H, Hiraoka S. Bifurcation of self-assembly pathways to sheet or cage controlled by kinetic template effect. Commun Chem 2019. [DOI: 10.1038/s42004-019-0232-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Abstract
The template effect is a key feature to control the arrangement of building blocks in assemblies, but its kinetic nature remains elusive compared to the thermodynamic aspects, with the exception of very simple reactions. Here we report a kinetic template effect in a self-assembled cage composed of flexible ditopic ligands and Pd(II) ions. Without template anion, a micrometer-sized sheet is kinetically trapped (off-pathway), which is converted into the thermodynamically most stable cage by the template anion. When the template anion is present from the start, the cage is selectively produced by the preferential cyclization of a dinuclear intermediate (on-pathway). Quantitative and numerical analyses of the self-assembly of the cage on the on-pathway revealed that the accelerating effect of the template is stronger for the early stage reactions of the self-assembly than for the final cage formation step itself, indicating the kinetic template effect.
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7
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Perretti MD, Pérez-Márquez LA, García-Rodríguez R, Carrillo R. Building Covalent Molecular Capsules by Thiol-Michael Addition Click Reaction. J Org Chem 2018; 84:840-850. [DOI: 10.1021/acs.joc.8b02677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Marcelle D. Perretti
- Instituto Universitario de Bio-Orgánica “Antonio González” (IUBO), Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez 2, 38200 La Laguna, Tenerife, Spain
| | - Lidia A. Pérez-Márquez
- Instituto Universitario de Bio-Orgánica “Antonio González” (IUBO), Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez 2, 38200 La Laguna, Tenerife, Spain
| | - Raúl García-Rodríguez
- GIR MIOMeT-IU Cinquima-Química Inorgánica, Facultad de Ciencias, Campus Miguel Delibes, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Romen Carrillo
- Instituto Universitario de Bio-Orgánica “Antonio González” (IUBO), Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez 2, 38200 La Laguna, Tenerife, Spain
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas (CSIC), Avda. Astrofísico Fco. Sánchez 3, 38206 La Laguna, Tenerife, Spain
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8
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Drożdż W, Bouillon C, Kotras C, Richeter S, Barboiu M, Clément S, Stefankiewicz AR, Ulrich S. Generation of Multicomponent Molecular Cages using Simultaneous Dynamic Covalent Reactions. Chemistry 2017; 23:18010-18018. [DOI: 10.1002/chem.201703868] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Wojciech Drożdż
- Faculty of Chemistry; Adam Mickiewicz University; Umultowska 89b 61-614 Poznań Poland
- Centre for Advanced Technologies; Adam Mickiewicz University; Umultowska 89c, 6 1-614 Poznań Poland
| | - Camille Bouillon
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 240 Avenue du Professeur Emile Jeanbrau 34296 Montpellier cedex 5 France
| | - Clément Kotras
- Institut Charles Gerhardt (ICGM), UMR 5253; Université de Montpellier, CNRS, ENSCM; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Sébastien Richeter
- Institut Charles Gerhardt (ICGM), UMR 5253; Université de Montpellier, CNRS, ENSCM; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Mihail Barboiu
- Institut Européen des Membranes (IEM), UMR 5635; Université de Montpellier, ENSCM, CNRS, Adaptive Supramolecular Nanosystems Group; Place Eugène Bataillon, CC 047 34095 Montpellier France
| | - Sébastien Clément
- Institut Charles Gerhardt (ICGM), UMR 5253; Université de Montpellier, CNRS, ENSCM; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Artur R. Stefankiewicz
- Faculty of Chemistry; Adam Mickiewicz University; Umultowska 89b 61-614 Poznań Poland
- Centre for Advanced Technologies; Adam Mickiewicz University; Umultowska 89c, 6 1-614 Poznań Poland
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 240 Avenue du Professeur Emile Jeanbrau 34296 Montpellier cedex 5 France
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9
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Bartolami E, Knoops J, Bessin Y, Fossépré M, Chamieh J, Dumy P, Surin M, Ulrich S. One-Pot Self-Assembly of Peptide-Based Cage-Type Nanostructures Using Orthogonal Ligations. Chemistry 2017; 23:14323-14331. [DOI: 10.1002/chem.201702974] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Eline Bartolami
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
- Present address: Department of Organic Chemistry; University of Geneva; 30 Quai Ernest Ansermet 1211 Geneva 4 Switzerland
| | - Jérémie Knoops
- Laboratory for Chemistry of Novel Materials; University of Mons-UMONS; 20, Place du Parc 7000 Mons Belgium
| | - Yannick Bessin
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials; University of Mons-UMONS; 20, Place du Parc 7000 Mons Belgium
| | - Joseph Chamieh
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials; University of Mons-UMONS; 20, Place du Parc 7000 Mons Belgium
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
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10
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Ulatowski F, Jurczak J. Oligocarboxylates as useful templates in dynamic combinatorial chemistry. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2016-1027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Dynamic combinatorial chemistry deals with systems (libraries) of multiple compounds formed by reversible reactions. Interactions of all library components with introduced template molecule are reflected in modification of library composition and are analysed simultaneously. In our studies we investigated a single-substrate dynamic combinatorial library of macrocycles, based on dipicolinic acid diamide, with disulphide bond exchange as the reversible reaction. The library components equipped with hydrogen bond donors interact with anionic guests – carboxylates which act as templates inducing amplification of selected library members. We proved that quantitative analysis of interactions with templates is possible, which led us to a novel method of analysis of association constants of static receptors introduced to the system. With a large set of carboxylates differing in number of anionic groups, size, shape, and flexibility of the linker, we proved that the library is very sensitive to structural parameters of the template. We also showed that with mediation of a photoswitchable azobenzene-based template it is possible to change the library composition by light stimulus. Similarly, with mediation of EDTA the library is sensitive to introduction of metal cations.
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11
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Sanna E, Escudero-Adán EC, López C, Ballester P, Rotger C, Costa A. Macrocyclic Tetraimines: Synthesis and Reversible Uptake of Diethyl Phthalate by a Porous Macrocycle. J Org Chem 2016; 81:5173-80. [DOI: 10.1021/acs.joc.6b00768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elena Sanna
- Department
of Chemistry, Universitat de les Illes Balears, 07122 Palma, Spain
| | - Eduardo C. Escudero-Adán
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avda. Països Catalans 16, 43007 Tarragona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Carlos López
- Department
of Chemistry, Universitat de les Illes Balears, 07122 Palma, Spain
| | - Pablo Ballester
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avda. Països Catalans 16, 43007 Tarragona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Carmen Rotger
- Department
of Chemistry, Universitat de les Illes Balears, 07122 Palma, Spain
| | - Antonio Costa
- Department
of Chemistry, Universitat de les Illes Balears, 07122 Palma, Spain
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12
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Szymański M, Wierzbicki M, Gilski M, Jędrzejewska H, Sztylko M, Cmoch P, Shkurenko A, Jaskólski M, Szumna A. Mechanochemical Encapsulation of Fullerenes in Peptidic Containers Prepared by Dynamic Chiral Self-Sorting and Self-Assembly. Chemistry 2016; 22:3148-55. [PMID: 26808958 DOI: 10.1002/chem.201504451] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Indexed: 01/24/2023]
Abstract
Molecular capsules composed of amino acid or peptide derivatives connected to resorcin[4]arene scaffolds through acylhydrazone linkers have been synthesized using dynamic covalent chemistry (DCC) and hydrogen-bond-based self-assembly. The dynamic character of the linkers and the preference of the peptides towards self-assembly into β-barrel-type motifs lead to the spontaneous amplification of formation of homochiral capsules from mixtures of different substrates. The capsules have cavities of around 800 Å(3) and exhibit good kinetic stability. Although they retain their dynamic character, which allows processes such as chiral self-sorting and chiral self-assembly to operate with high fidelity, guest complexation is hindered in solution. However, the quantitative complexation of even very large guests, such as fullerene C60 or C70 , is possible through the utilization of reversible covalent bonds or the application of mechanochemical methods. The NMR spectra show the influence of the chiral environment on the symmetry of the fullerene molecules, which results in the differentiation of diastereotopic carbon atoms for C70 , and the X-ray structures provide unique information on the modes of peptide-fullerene interactions.
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Affiliation(s)
- Marek Szymański
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Michał Wierzbicki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Mirosław Gilski
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Hanna Jędrzejewska
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Marcin Sztylko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Piotr Cmoch
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Aleksander Shkurenko
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Mariusz Jaskólski
- Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614, Poznan, Poland. .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| | - Agnieszka Szumna
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
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13
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Alfonso I. From simplicity to complex systems with bioinspired pseudopeptides. Chem Commun (Camb) 2016; 52:239-50. [DOI: 10.1039/c5cc07596c] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This feature article highlights some of the recent advances in creating complexity from simple pseudopeptidic molecules. The bioinspired approaches discussed here allowed an increase in the structural, chemical and interactional complexity (see figure).
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Affiliation(s)
- Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- Jordi Girona
- 18-26
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14
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Faggi E, Pérez Y, Luis SV, Alfonso I. Supramolecular protection from the enzymatic tyrosine phosphorylation in a polypeptide. Chem Commun (Camb) 2016; 52:8142-5. [DOI: 10.1039/c6cc03875a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two pseudopeptidic cages bind the EYE peptide motif of poly(EY) in buffered water, as shown by NMR and fluorescence spectroscopy. This supramolecular interaction protects the Tyr residues from the enzymatic phosphorylation by PTK.
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Affiliation(s)
- Enrico Faggi
- Department of Biological Chemistry and Molecular Modelling
- IQAC-CSIC
- Barcelona
- Spain
| | | | - Santiago V. Luis
- Department of Inorganic and Organic Chemistry
- ESTCE Universitat Jaume I
- Castellón
- Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling
- IQAC-CSIC
- Barcelona
- Spain
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15
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Kieryk P, Janczak J, Panek J, Miklitz M, Lisowski J. Chiral 2 + 3 Keto-Enamine Pseudocyclophanes Derived from 1,3,5-Triformylphloroglucinol. Org Lett 2015; 18:12-5. [DOI: 10.1021/acs.orglett.5b02989] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Przemysław Kieryk
- Department
of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Jan Janczak
- Institute
of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box
1410, 50-950, Wrocław, Poland
| | - Jarosław Panek
- Department
of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Marcin Miklitz
- Department
of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Jerzy Lisowski
- Department
of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
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16
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Faggi E, Vicent C, Luis SV, Alfonso I. Stereoselective recognition of the Ac-Glu-Tyr-OH dipeptide by pseudopeptidic cages. Org Biomol Chem 2015; 13:11721-31. [PMID: 26481115 DOI: 10.1039/c5ob01889g] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Pseudopeptidic molecular cages are appealing receptors since they can display different polar and non-polar interaction sites in a modular framework and a controlled disposition. Inspired by previous host-guest knowledge, two pseudopeptidic molecular cages based on serine and threonine (CySer and CyThr, respectively) were designed and synthesized as hosts for the binding of the four possible stereoisomers of the Ac-Glu-Tyr-OH dipeptide, a target sequence of tyrosine kinases. The careful NMR titration experiments in aqueous acetonitrile allowed the determination of the binding constants and reflected a difference in the stability of the corresponding diastereomeric host-guest complexes. The CySer cage proved to be slightly more efficient than the CyThr counterpart, although both showed similar stereoselectivity trends: LL > DD ≥ LD > DL. This stereoselective binding was retained in the gas phase, as shown by ESI-MS competition experiments using the enantiomer-labelled method (EL), as well as CID experiments. Thus, the MS-determined discriminations follow the same trends observed by NMR, suggesting that the stereoselectivity observed for these systems must be mainly dictated by the polar host-guest interactions. Despite the stereoselective binding of short peptide sequences in competitive media being a challenging issue in supramolecular chemistry, our results demonstrate the power of pseudopeptidic cages in molecular recognition with foreseen implications in chemical biology.
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Affiliation(s)
- Enrico Faggi
- Department of Biological Chemistry and Molecular Modeling, IQAC-CSIC, Jordi Girona, 18-26, E-08034, Barcelona, Spain.
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Martí-Centelles V, Pandey MD, Burguete MI, Luis SV. Macrocyclization Reactions: The Importance of Conformational, Configurational, and Template-Induced Preorganization. Chem Rev 2015; 115:8736-834. [DOI: 10.1021/acs.chemrev.5b00056] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Mrituanjay D. Pandey
- Departament de Química
Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - M. Isabel Burguete
- Departament de Química
Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - Santiago V. Luis
- Departament de Química
Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
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18
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Ulatowski F, Lichosyt D, Jurczak J. Introducing a static receptor to compete with a dynamic combinatorial library in template binding. Org Biomol Chem 2015; 13:10451-5. [DOI: 10.1039/c5ob01698c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Association constants can be obtained from HPLC analysis of a system comprising a dynamic combinatorial library and a static host.
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Affiliation(s)
- Filip Ulatowski
- Institute of Organic Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
| | - Dawid Lichosyt
- Institute of Organic Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
| | - Janusz Jurczak
- Institute of Organic Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
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19
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Abstract
Cyclic peptides provide excellent scaffolds for anion recognition and improved binding affinity and selectivity has been achieved through peptide backbone rigidification and the introduction of side chains bearing anion recognition groups.
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20
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Jędrzejewska H, Wierzbicki M, Cmoch P, Rissanen K, Szumna A. Dynamic Formation of Hybrid Peptidic Capsules by Chiral Self-Sorting and Self-Assembly. Angew Chem Int Ed Engl 2014; 53:13760-4. [DOI: 10.1002/anie.201407802] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/02/2014] [Indexed: 01/29/2023]
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21
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Jędrzejewska H, Wierzbicki M, Cmoch P, Rissanen K, Szumna A. Dynamic Formation of Hybrid Peptidic Capsules by Chiral Self-Sorting and Self-Assembly. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407802] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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22
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Ulatowski F, Sadowska-Kuzioła A, Jurczak J. "Choose-a-size" approach in dynamic combinatorial chemistry: a single substrate dynamic combinatorial library of oligomacrocycles that adapts to the size and shape of carboxylates. J Org Chem 2014; 79:9762-70. [PMID: 25280250 DOI: 10.1021/jo501956h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A neutral anion binding receptor based on dipicolinic acid diamide was equipped with thiol groups in the amidic side arms. After the thiol was oxidized to disulfide groups with I2, a mixture of cyclic oligomers (a library) was obtained. The distribution of macrocycles can be controlled kinetically during the oxidation process or thermodynamically at basic conditions via disulfide bond exchange. The library proved to be very sensitive to templation with various carboxylates in DMSO. The amplification pattern reflects the structural features of the anionic template and is sensitive to changes in the template's geometry. The application of carboxylates with multiple functional groups resulted in very strong amplification of the large penta- and hexameric macrocycles. The thermodynamic parameters of some templation effects were rationalized using a simple model and confirmed using competitive NMR titration.
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Affiliation(s)
- Filip Ulatowski
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
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23
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Evans NH, Beer PD. Advances in anion supramolecular chemistry: from recognition to chemical applications. Angew Chem Int Ed Engl 2014; 53:11716-54. [PMID: 25204549 DOI: 10.1002/anie.201309937] [Citation(s) in RCA: 415] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Indexed: 12/11/2022]
Abstract
Since the start of this millennium, remarkable progress in the binding and sensing of anions has been taking place, driven in part by discoveries in the use of hydrogen bonding, as well as the previously under-exploited anion-π interactions and halogen bonding. However, anion supramolecular chemistry has developed substantially beyond anion recognition, and now encompasses a diverse range of disciplines. Dramatic advance has been made in the anion-templated synthesis of macrocycles and interlocked molecular architectures, while the study of transmembrane anion transporters has flourished from almost nothing into a rapidly maturing field of research. The supramolecular chemistry of anions has also found real practical use in a variety of applications such as catalysis, ion extraction, and the use of anions as stimuli for responsive chemical systems.
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Affiliation(s)
- Nicholas H Evans
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB (UK).
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24
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Evans NH, Beer PD. Supramolekulare Chemie von Anionen: von der Erkennung zur chemischen Anwendung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309937] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Durot S, Taesch J, Heitz V. Multiporphyrinic cages: architectures and functions. Chem Rev 2014; 114:8542-78. [PMID: 25026396 DOI: 10.1021/cr400673y] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Stéphanie Durot
- Laboratoire de Synthèse des Assemblages Moléculaires Multifonctionnels, Institut de Chimie de Strasbourg, CNRS/UMR 7177 , 4, rue Blaise Pascal, 67000 Strasbourg, France
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26
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Martí I, Bolte M, Burguete MI, Vicent C, Alfonso I, Luis SV. Tight and Selective Caging of Chloride Ions by a Pseudopeptidic Host. Chemistry 2014; 20:7458-64. [DOI: 10.1002/chem.201303604] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 03/24/2014] [Indexed: 11/12/2022]
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Faggi E, Moure A, Bolte M, Vicent C, Luis SV, Alfonso I. Pseudopeptidic Cages as Receptors for N-Protected Dipeptides. J Org Chem 2014; 79:4590-601. [DOI: 10.1021/jo500629d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Enrico Faggi
- Departamento
de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Cataluña (IQAC-CSIC), Jordi Girona
18-26, E-08034 Barcelona, Spain
| | - Alejandra Moure
- Departamento
de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Cataluña (IQAC-CSIC), Jordi Girona
18-26, E-08034 Barcelona, Spain
| | - Michael Bolte
- Institut
für Anorganische Chemie, J.-W.-Goethe-Universität, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | | | | | - Ignacio Alfonso
- Departamento
de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Cataluña (IQAC-CSIC), Jordi Girona
18-26, E-08034 Barcelona, Spain
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28
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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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29
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Hasell T, Culshaw JL, Chong SY, Schmidtmann M, Little MA, Jelfs KE, Pyzer-Knapp EO, Shepherd H, Adams DJ, Day GM, Cooper AI. Controlling the Crystallization of Porous Organic Cages: Molecular Analogs of Isoreticular Frameworks Using Shape-Specific Directing Solvents. J Am Chem Soc 2014; 136:1438-48. [DOI: 10.1021/ja409594s] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Tom Hasell
- Department
of Chemistry and Centre for Materials Discovery, University of Liverpool, Crown St., Liverpool L69
7ZD, United Kingdom
| | - Jamie L. Culshaw
- Department
of Chemistry and Centre for Materials Discovery, University of Liverpool, Crown St., Liverpool L69
7ZD, United Kingdom
| | - Samantha Y. Chong
- Department
of Chemistry and Centre for Materials Discovery, University of Liverpool, Crown St., Liverpool L69
7ZD, United Kingdom
| | - Marc Schmidtmann
- Department
of Chemistry and Centre for Materials Discovery, University of Liverpool, Crown St., Liverpool L69
7ZD, United Kingdom
| | - Marc A. Little
- Department
of Chemistry and Centre for Materials Discovery, University of Liverpool, Crown St., Liverpool L69
7ZD, United Kingdom
| | - Kim E. Jelfs
- Department
of Chemistry and Centre for Materials Discovery, University of Liverpool, Crown St., Liverpool L69
7ZD, United Kingdom
| | - Edward O. Pyzer-Knapp
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Hilary Shepherd
- Department
of Chemistry and Centre for Materials Discovery, University of Liverpool, Crown St., Liverpool L69
7ZD, United Kingdom
| | - Dave J. Adams
- Department
of Chemistry and Centre for Materials Discovery, University of Liverpool, Crown St., Liverpool L69
7ZD, United Kingdom
| | - Graeme M. Day
- School
of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Andrew I. Cooper
- Department
of Chemistry and Centre for Materials Discovery, University of Liverpool, Crown St., Liverpool L69
7ZD, United Kingdom
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Abstract
For years researchers have tried to understand the molecular behavior of complex biomolecules through the development of small molecules that can partially mimic their function. Now researchers are implementing the reverse approach: using the structural and mechanistic knowledge obtained from those complex systems to design small molecules with defined properties and for specific applications. One successful strategy for constructing bioinspired, minimalistic molecules is to combine natural building blocks that provide functional elements with abiotic fragments that serve as structural scaffolds. Therefore pseudopeptidic compounds, most of them based on C2 symmetric structures, represent a unique opportunity to explore and evaluate this approach. Some of these molecules are as simple as two amino acids connected by a diamino spacer. The results in this Account show how bioinspired minimalistic pseudopeptides can form ordered structures, participate in the recognition and transcription of information events in molecular devices, and catalyze reactions. This strategy allows researchers to design and prepare a variety of open-chain and macrocyclic compounds leading to systems that can self-aggregate to form hierarchically ordered micro- and nanostructures. In addition, small changes in the molecule or external stimuli can regulate the self-aggregation pattern. In the same way, researchers can also tune the molecular movements of simple pseudopeptides through environmental factors, providing a means to control new molecular devices. In addition, some of the prepared model compounds have shown interesting properties in molecular recognition and even as sensors for several targets of interest. Finally we have observed remarkable catalytic activities from these types of molecules, although those results are still far from the efficiency shown by natural peptides. This family of pseudopeptidic compounds offers the opportunity for the more elaborate design of relatively simple abiotic but bioinspired systems that display specific properties. In addition, the results can provide additional information that will increase the molecular understanding of the basic principles that underlie the extraordinary behavior of natural systems.
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Affiliation(s)
- Santiago V. Luis
- Department of Inorganic and Organic Chemistry, ESTCE, University Jaume I, Castellón. Spain
| | - I. Alfonso
- Department of Biological Chemistry and Molecular Modeling, IQAC−CSIC, Barcelona, Spain
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31
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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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32
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Atcher J, Alfonso I. The effect of DMSO in the aqueous thiol–disulphide dynamic covalent chemistry of model pseudopeptides. RSC Adv 2013. [DOI: 10.1039/c3ra45811c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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33
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Faggi E, Luis SV, Alfonso I. Minimalistic amino amides as models to study N–H⋯π interactions and their implication in the side chain folding of pseudopeptidic molecules. RSC Adv 2013. [DOI: 10.1039/c3ra41843j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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34
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Martí I, Rubio J, Bolte M, Burguete MI, Vicent C, Quesada R, Alfonso I, Luis SV. Tuning Chloride Binding, Encapsulation, and Transport by Peripheral Substitution of Pseudopeptidic Tripodal Small Cages. Chemistry 2012; 18:16728-41. [DOI: 10.1002/chem.201202182] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Indexed: 11/05/2022]
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