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Kubik S. Synthetic Receptors Based on Abiotic Cyclo(pseudo)peptides. Molecules 2022; 27:2821. [PMID: 35566168 PMCID: PMC9103335 DOI: 10.3390/molecules27092821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Work on the use of cyclic peptides or pseudopeptides as synthetic receptors started even before the field of supramolecular chemistry was firmly established. Research initially focused on the development of synthetic ionophores and involved the use of macrocycles with a repeating sequence of subunits along the ring to facilitate the correlation between structure, conformation, and binding properties. Later, nonnatural amino acids as building blocks were also considered. With growing research in this area, cyclopeptides and related macrocycles developed into an important and structurally diverse receptor family. This review provides an overview of these developments, starting from the early years. The presented systems are classified according to characteristic structural elements present along the ring. Wherever possible, structural aspects are correlated with binding properties to illustrate how natural or nonnatural amino acids affect binding properties.
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Affiliation(s)
- Stefan Kubik
- Fachbereich Chemie-Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 54, 67663 Kaiserslautern, Germany
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Gorla L, Martí-Centelles V, Altava B, Burguete MI, Luis SV. The role of the side chain in the conformational and self-assembly patterns of C2-symmetric Val and Phe pseudopeptidic derivatives. CrystEngComm 2019. [DOI: 10.1039/c8ce02088d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Side chain as the main conformational and self-assembly structural factor for C2-pseudopeptides.
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Affiliation(s)
- Lingaraju Gorla
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | | | - Belén Altava
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | - M. Isabel Burguete
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | - Santiago V. Luis
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
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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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Escorihuela J, Burguete MI, Ujaque G, Lledós A, Luis SV. Mechanistic implications of the enantioselective addition of alkylzinc reagents to aldehydes catalyzed by nickel complexes with α-amino amide ligands. Org Biomol Chem 2016; 14:11125-11136. [DOI: 10.1039/c6ob01878e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The enantioselective alkylation of aldehydes catalysed by nickel(ii)-complexes derived from α-amino amides was studied by means of density functional theory (DFT) and ONIOM (B3LYP:UFF) calculations.
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Affiliation(s)
- Jorge Escorihuela
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- 12071 Castellón de la Plana
- Spain
| | - M. Isabel Burguete
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- 12071 Castellón de la Plana
- Spain
| | - Gregori Ujaque
- Unitat de Química Física
- Departament de Química
- Edifici Cn. Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - Agustí Lledós
- Unitat de Química Física
- Departament de Química
- Edifici Cn. Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - Santiago V. Luis
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- 12071 Castellón de la Plana
- Spain
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Wang Z, Islam MJ, Vukotic VN. Structural analysis of bis-bispidine tetraazamacrocycle: Long-range weak interactions in a channeled organic crystal. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.09.088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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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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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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Moure A, Luis SV, Alfonso I. Efficient Synthesis of Pseudopeptidic Molecular Cages. Chemistry 2012; 18:5496-500. [DOI: 10.1002/chem.201104045] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Revised: 02/24/2012] [Indexed: 11/11/2022]
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Martí-Centelles V, Burguete MI, Luis SV. Template Effects in SN2 Displacements for the Preparation of Pseudopeptidic Macrocycles. Chemistry 2012; 18:2409-22. [DOI: 10.1002/chem.201101416] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 09/20/2011] [Indexed: 11/07/2022]
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Martí I, Ferrer A, Escorihuela J, Burguete MI, Luis SV. Copper(ii) complexes of bis(amino amide) ligands: effect of changes in the amino acid residue. Dalton Trans 2012; 41:6764-76. [DOI: 10.1039/c2dt12459a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Crystal Structure of the N-Benzyloxycarbonyl-alanyl-phenylalanyl-methyl Ester: The Importance of the H-Bonding Pattern. CRYSTALS 2011. [DOI: 10.3390/cryst1030163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Martí-Centelles V, Kumar DK, White AJP, Luis SV, Vilar R. Zinc(ii) coordination polymers with pseudopeptidic ligands. CrystEngComm 2011. [DOI: 10.1039/c1ce05872j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Rubio J, Alfonso I, Bru M, Burguete MI, Luis SV. Gemini amphiphilic pseudopeptides: synthesis and preliminary study of their self-assembling properties. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.07.146] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Blasco S, Burguete MI, Clares MP, García-España E, Escorihuela J, Luis SV. Coordination of Cu2+ Ions to C2 Symmetric Pseudopeptides Derived from Valine. Inorg Chem 2010; 49:7841-52. [DOI: 10.1021/ic100748g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Salvador Blasco
- Instituto de Ciencia Molecular (ICMOL), Departamento de Química Inorgánica, Universidad de Valencia, C/Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain
| | - M. Isabel Burguete
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I, Avda. Sos Baynat s/n., 12071 Castellón, Spain
| | - M. Paz Clares
- Instituto de Ciencia Molecular (ICMOL), Departamento de Química Inorgánica, Universidad de Valencia, C/Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain
| | - Enrique García-España
- Instituto de Ciencia Molecular (ICMOL), Departamento de Química Inorgánica, Universidad de Valencia, C/Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain
| | - Jorge Escorihuela
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I, Avda. Sos Baynat s/n., 12071 Castellón, Spain
| | - Santiago V. Luis
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I, Avda. Sos Baynat s/n., 12071 Castellón, Spain
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Chiral bis(amino amides) as chiral solvating agents for enantiomeric excess determination of α-hydroxy and arylpropionic acids. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.tetasy.2010.05.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mehta G, Sen S. Modulating the preferred O-H...O hydrogen-bonding motif in a conformationally constrained environment through hydroxy-group derivatization. Acta Crystallogr C 2010; 66:o59-63. [PMID: 20124682 DOI: 10.1107/s0108270109054870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 12/21/2009] [Indexed: 11/10/2022] Open
Abstract
The crystal structures of three conformationally locked esters, namely the centrosymmetric tetrabenzoate of all-axial perhydronaphthalene-2,3,4a,6,7,8a-hexaol, viz. trans-4a,8a-dihydroxyperhydronaphthalene-2,3,6,7-tetrayl tetrabenzoate, C(38)H(34)O(10), and the diacetate and dibenzoate of all-axial perhydronaphthalene-2,3,4a,8a-tetraol, viz. (2R*,3R*,4aS*,8aS*)-4a,8a-dihydroxyperhydronaphthalene-2,3-diyl diacetate, C(14)H(22)O(6), and (2R*,3R*,4aS*,8aS*)-4a,8a-dihydroxyperhydronaphthalene-2,3-diyl dibenzoate, C(24)H(26)O(6), have been analyzed in order to examine the preference of their supramolecular assemblies towards competing inter- and intramolecular O-H...O hydrogen bonds. It was anticipated that the supramolecular assembly of the esters under study would adopt two principal hydrogen-bonding modes, namely one that employs intermolecular O-H...O hydrogen bonds (mode 1) and another that sacrifices those for intramolecular O-H...O hydrogen bonds and settles for a crystal packing dictated by weak intermolecular interactions alone (mode 2). Thus, while the molecular assembly of the two crystalline diacyl derivatives conformed to a combination of hydrogen-bonding modes 1 and 2, the crystal packing in the tetrabenzoate preferred to follow mode 2 exclusively.
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Affiliation(s)
- Goverdhan Mehta
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, Karnataka, India.
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Carrillo R, López-Rodríguez M, Martín VS, Martín T. Crystal structures of self-assembled nanotubes from flexible macrocycles by weak interactions. CrystEngComm 2010. [DOI: 10.1039/c001261k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Becerril J, Bolte M, Burguete MI, Escorihuela J, Galindo F, Luis SV. A simple peptidomimetic that self-associates on the solid state to form a nanoporous architecture containing chiral π-channels. CrystEngComm 2010. [DOI: 10.1039/b922172g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Liang XQ, Jia JT, Wu T, Li DP, Liu L, Tsolmon, Zhu GS. A spontaneously resoluted zinc–organic framework with nonlinear optical and ferroelectric properties generated from tetrazolate-ethyl ester ligand. CrystEngComm 2010. [DOI: 10.1039/c0ce00329h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pramanik A, Majumdar S, Das G. Aryl azo imidazoles assisted assembly of anion/anion–water through salt formation. CrystEngComm 2010. [DOI: 10.1039/b912454c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Xiao W, Chen C, Deng S, Mao X, Sun B, Zhang N. Supramolecular assembly of [H(4−n)BPTC]n− with pipzH22+: 1D negatively charged rectangular tubes and a 2D neutral fes 4·82 network. CrystEngComm 2010. [DOI: 10.1039/b922188c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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