1
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Song Q, Cheng Z, Kariuki M, Hall SCL, Hill SK, Rho JY, Perrier S. Molecular Self-Assembly and Supramolecular Chemistry of Cyclic Peptides. Chem Rev 2021; 121:13936-13995. [PMID: 33938738 PMCID: PMC8824434 DOI: 10.1021/acs.chemrev.0c01291] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 01/19/2023]
Abstract
This Review focuses on the establishment and development of self-assemblies governed by the supramolecular interactions between cyclic peptides. The Review first describes the type of cyclic peptides able to assemble into tubular structures to form supramolecular cyclic peptide nanotubes. A range of cyclic peptides have been identified to have such properties, including α-peptides, β-peptides, α,γ-peptides, and peptides based on δ- and ε-amino acids. The Review covers the design and functionalization of these cyclic peptides and expands to a recent advance in the design and application of these materials through their conjugation to polymer chains to generate cyclic peptide-polymer conjugates nanostructures. The Review, then, concentrates on the challenges in characterizing these systems and presents an overview of the various analytical and characterization techniques used to date. This overview concludes with a critical survey of the various applications of the nanomaterials obtained from supramolecular cyclic peptide nanotubes, with a focus on biological and medical applications, ranging from ion channels and membrane insertion to antibacterial materials, anticancer drug delivery, gene delivery, and antiviral applications.
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Affiliation(s)
- Qiao Song
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Zihe Cheng
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Maria Kariuki
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | | | - Sophie K. Hill
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Julia Y. Rho
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Sébastien Perrier
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick Medical
School, University of Warwick, Coventry CV4 7AL, U.K.
- Faculty
of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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2
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Silk MR, Price JR, Mohanty B, Leiros HKS, Lund BA, Thompson PE, Chalmers DK. Side-Chain Interactions in d/l Peptide Nanotubes: Studies by Crystallography, NMR Spectroscopy and Molecular Dynamics. Chemistry 2021; 27:14489-14500. [PMID: 34415083 DOI: 10.1002/chem.202102106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/07/2022]
Abstract
Our understanding of the factors affecting the stability of cyclic d/l peptide (CP) nanotubes remains underdeveloped. In this work, we investigate the impact of side chain alignment, hydrophobicity and charge on CP nanotube stability through X-ray crystallography, NMR spectroscopy and molecular dynamics (MD) simulations. We characterise the distinct CP-CP alignments that can form and identify stable and unstable dimers by MD simulation. We measure H-bond half-lives of synthesised CPs by 1 H-D exchange experiments and find good correlation with predicted CP-CP stabilities. We find that hydrophobic amino acids improve CP dimer stability but experimentally reduce solubility. Charged amino acids either increase or decrease CP dimer stability depending on the relative orientation and composition of charged groups. X-ray crystal structures are solved for two CPs, revealing non-tubular folded conformations. Ultimately, this work will assist the educated design of stable tubular structures for potential applications in biomedicine.
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Affiliation(s)
- Mitchell R Silk
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Jason R Price
- Australian Synchrotron, The Australian Nuclear Science and Technology Organisation (ANSTO), 800 Blackburn Road, Clayton, VIC, 3168, Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Bjarte A Lund
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
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3
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Calvelo M, Lynch CI, Granja JR, Sansom MSP, Garcia-Fandiño R. Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes. ACS NANO 2021; 15:7053-7064. [PMID: 33739081 PMCID: PMC8485350 DOI: 10.1021/acsnano.1c00155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/15/2021] [Indexed: 05/23/2023]
Abstract
Self-assembling cyclic peptide nanotubes can form nanopores when they are inserted in lipid bilayers, acting as ion and/or water permeable channels. In order to improve the versatility of these systems, it is possible to specifically design cyclic peptides with a combination of natural and non-natural amino acids, enabling the control of the nature of the inner cavity of the channels. Here, the behavior of two types of self-assembling peptide motifs, alternating α-amino acids with γ- or δ-aminocycloalkanecarboxylic acids, is studied via molecular dynamics (MD) simulations. The behavior of water molecules in nanopores is expected to affect the properties of these channels and therefore merits detailed examination. A number of water models commonly used in MD simulations have been validated by how well they reproduce bulk water properties. However, it is less clear how these water models behave in the nanoconfined condition inside a channel. The behavior of four different water models-TIP3P, TIP4P, TIP4P/2005, and OPC-are evaluated in MD simulations of self-assembled cyclic peptide nanotubes of distinct composition and diameter. The dynamic behavior of the water molecules and ions in these designed artificial channels depends subtly on the water model used. TIP3P water molecules move faster than those of TIP4P, TIP4P/2005, and OPC. This demeanor is clearly observed in the filling of the nanotube, in water diffusion within the pore, and in the number and stability of hydrogen bonds of the peptides with water. It was also shown that the water model influences the simulated ion flux through the nanotubes, with TIP3P producing the greatest ion flux. Additionally, the two more recent models, TIP4P/2005 and OPC, which are known to reproduce the experimental self-diffusion coefficient of bulk water quite well, exhibit very similar results under the nanoconfined conditions studied here. Because none of these models have been parametrized specifically for waters confined in peptide nanotubes, this study provides a point of reference for further validation.
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Affiliation(s)
- Martin Calvelo
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Charlotte I. Lynch
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Juan R. Granja
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Rebeca Garcia-Fandiño
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
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4
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Rinaldi S. The Diverse World of Foldamers: Endless Possibilities of Self-Assembly. Molecules 2020; 25:E3276. [PMID: 32708440 PMCID: PMC7397133 DOI: 10.3390/molecules25143276] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.
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Affiliation(s)
- Samuele Rinaldi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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5
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Calvelo M, Lamas A, Guerra A, Amorín M, Garcia-Fandino R, Granja JR. Parallel Versus Antiparallel β-Sheet Structure in Cyclic Peptide Hybrids Containing γ- or δ-Cyclic Amino Acids. Chemistry 2020; 26:5846-5858. [PMID: 31999874 DOI: 10.1002/chem.201905554] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Indexed: 11/07/2022]
Abstract
Cyclic peptides with disc-shaped structures have emerged as potent building blocks for the preparation of new biomaterials in fields ranging from biological to material science. In this work, we analyze in depth the self-assembling properties of a new type of cyclic peptides based on the alternation of α-residues and cyclic δ-amino acids (α,δ-CPs). To examine the preferred stacking properties adopted by cyclic peptides bearing this type of amino acids, we carried out a synergistic in vitro/in silico approximation by using simple dimeric models and then extended to nanotubes. Although these new cyclic peptides (α,δ-CPs) can interact either in a parallel or antiparallel fashion, our results confirm that although the parallel β-sheet is more stable, it can be switched to the antiparallel stacking by choosing residues that can establish favorable cross-strand interactions. Moreover, the subsequent comparison by using the same methodology but applied to α,γ-CPs models, up to the moment assumed as antiparallel-like d,l-α-CPs, led to unforeseen conclusions that put into question preliminary conjectures about these systems. Surprisingly, they tend to adopt a parallel β-sheet directed by the skeleton interactions. These results imply a change of paradigm with respect to cyclic peptide designs that should be considered for dimers and nanotubes.
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Affiliation(s)
- Martín Calvelo
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Alejandro Lamas
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Arcadio Guerra
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Manuel Amorín
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Juan R Granja
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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6
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7
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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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8
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Silk MR, Mohanty B, Sampson JB, Scanlon MJ, Thompson PE, Chalmers DK. Controlled Construction of Cyclic d
/ l
Peptide Nanorods. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mitchell R. Silk
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Joanne B. Sampson
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Martin J. Scanlon
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - Philip E. Thompson
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
| | - David K. Chalmers
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville Victoria 3052 Australia
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9
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Silk MR, Mohanty B, Sampson JB, Scanlon MJ, Thompson PE, Chalmers DK. Controlled Construction of Cyclic d / l Peptide Nanorods. Angew Chem Int Ed Engl 2018; 58:596-601. [PMID: 30452108 DOI: 10.1002/anie.201811910] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 11/10/2022]
Abstract
Cyclic d / l peptides (CPs) assemble spontaneously via backbone H-bonding to form extended nanostructures. These modular materials have great potential as versatile bionanomaterials. However, the useful development of CP nanomaterials requires practical methods to direct and control their assembly. In this work, we present novel, heterogeneous, covalently linked CP tetramers that achieve local control over the CP subunit order and composition through coupling of amino acid side-chains using copper-activated azide-alkyne cycloaddition and disulfide bond formation. Cryo-transmission electron microscopy revealed the formation of highly ordered, fibrous nanostructures, while NMR studies showed that these systems have strong intramolecular H-bonding in solution. The introduction of inter-CP tethers is expected to enable the development of complex nanomaterials with controllable chemical properties, facilitating the development of precisely functionalized or "decorated" peptide nanostructures.
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Affiliation(s)
- Mitchell R Silk
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Joanne B Sampson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
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10
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Tabata Y, Uji H, Imai T, Kimura S. Two one-dimensional arrays of naphthyl and anthryl groups along peptide nanotubes prepared from cyclic peptides comprising α- and β-amino acids. SOFT MATTER 2018; 14:7597-7604. [PMID: 30215660 DOI: 10.1039/c8sm01627e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A novel cyclic hexapeptide composed of l-α-naphthylalanine, d-α-anthrylalanine, and four β-alanines (CP6) is synthesized and its molecular assembly into peptide nanotubes (PNTs) and the electronic properties arising from one-dimensional arrays of aromatic groups along the PNTs were investigated. CP6 with a combination of l- and d-α-amino acids is designed to self-assemble into PNTs with them stacking on top of each other under the constraint of maximizing the number of intermolecular hydrogen bonds between the cyclic peptides. Upon PNT formation, the respective side chains of l- and d-α-amino acids are aligned in line along the PNTs. The topological arrangement of the anthryl groups being in close proximity in the CP6 PNT is supported by higher photo-excited energy transfer, appearance of the induced Cotton effects, and the promoted photo-dimerization reaction upon PNT formation. AFM observations reveal that PNT bundles with diameters 5-15 nm are dielectric microcrystals having a piezoelectric coefficient of 2-6 pC N-1. Kelvin force microscopy observations show the generation of surface potentials over 100 mV owing to the one-dimensional array of the anthryl groups along PNTs. Incorporation of α-amino acids with opposite chirality into cyclic β-peptides is therefore an effective molecular design for the nano-architecture of PNTs displaying one-dimensional arrays of chromophores along PNTs.
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Affiliation(s)
- Yuki Tabata
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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11
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Silk MR, Newman J, Ratcliffe JC, White JF, Caradoc-Davies T, Price JR, Perrier S, Thompson PE, Chalmers DK. Parallel and antiparallel cyclic d/l peptide nanotubes. Chem Commun (Camb) 2017; 53:6613-6616. [PMID: 28581562 DOI: 10.1039/c7cc00846e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanotubes made from H-bonded cyclic d/l peptide (CP) subunits have great potential for the construction of nanomaterials of wide chemical and structural diversity but, to date, difficulties in structural characterisation have restricted development of these materials. We present the first crystal structures of continuous CP nanotubes with antiparallel and parallel stacking arrangements, assembled separately from two peptides; cyclo[(Asp-d-Leu-Lys-d-Leu)2] and cyclo[(Asp-d-Ala-Lys-d-Ala)2].
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Affiliation(s)
- Mitchell R Silk
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia.
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12
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Awada H, Grison CM, Charnay-Pouget F, Baltaze JP, Brisset F, Guillot R, Robin S, Hachem A, Jaber N, Naoufal D, Yazbeck O, Aitken DJ. Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure. J Org Chem 2017; 82:4819-4828. [PMID: 28398045 DOI: 10.1021/acs.joc.7b00494] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.
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Affiliation(s)
- Hawraà Awada
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France.,Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Claire M Grison
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Florence Charnay-Pouget
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Jean-Pierre Baltaze
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - François Brisset
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Régis Guillot
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Sylvie Robin
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France.,UFR Sciences Pharmaceutiques et Biologiques, Université Paris Descartes , 4 avenue de l'Observatoire, 75270 Paris cedex 06, France
| | - Ali Hachem
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Nada Jaber
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Daoud Naoufal
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Ogaritte Yazbeck
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - David J Aitken
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
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13
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Rodríguez-Vázquez N, Amorín M, Granja JR. Recent advances in controlling the internal and external properties of self-assembling cyclic peptide nanotubes and dimers. Org Biomol Chem 2017; 15:4490-4505. [DOI: 10.1039/c7ob00351j] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Tuning the internal and external properties of self-assembling cyclic peptide nanotubes.
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Affiliation(s)
- N. Rodríguez-Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - M. Amorín
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - J. R. Granja
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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14
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Calvelo M, Vázquez S, García-Fandiño R. Molecular dynamics simulations for designing biomimetic pores based on internally functionalized self-assembling α,γ-peptide nanotubes. Phys Chem Chem Phys 2016; 17:28586-601. [PMID: 26443433 DOI: 10.1039/c5cp04200c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A molecular dynamics study on internally functionalized peptide nanotubes composed of α- and γ-amino acids self-assembled in lipid bilayers is presented. One of the main advantages of peptide nanotubes composed of γ-amino acids is that the properties of their inner cavities can be tuned by introducing different functions on β-carbon of the γ-amino acid. In the work described here we studied the effect of the presence of different numbers of hydroxyl groups in different positions in the lumen of these channels when they are inserted into a lipid bilayer and assessed how they affect the structural and dynamic behavior of the modified peptide nanotubes as well as the transmembrane transport of different ions. The results provided atomic information about the effect of polar groups on the dynamic, structural and transport properties of this type of peptidic channel upon insertion into lipid bilayers, projecting a promising future for their use as biomimetic channels when properly inner-derivatized. Furthermore, the chemical versatility of the hydroxyl groups in the lumen of the peptide nanotubes would enable appealing applications for these channels, such as a controlled method for the activation/inactivation of the transmembrane transport along the nanopore.
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Affiliation(s)
- Martín Calvelo
- Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials, Campus Vida, Santiago de Compostela University, E-15782 Santiago de Compostela, Spain.
| | - Saulo Vázquez
- Department of Physical Chemistry, Center for Research in Biological Chemistry and Molecular Materials, Campus Vida, Santiago de Compostela University, E-15782 Santiago de Compostela, Spain
| | - Rebeca García-Fandiño
- Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials, Campus Vida, Santiago de Compostela University, E-15782 Santiago de Compostela, Spain.
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Design, synthesis, and characterization of new cyclic d,l-α-alternate amino acid peptides by capillary electrophoresis coupled to electrospray ionization mass spectrometry. Anal Biochem 2016; 502:8-15. [PMID: 26969790 DOI: 10.1016/j.ab.2016.02.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 11/21/2022]
Abstract
The self-assembly of peptide nanotubes (PNTs) depends on the structure and chemistry of cyclic peptide (CP) monomers, having an impact on their properties, making the choice of their monomers and their characterization a great challenge. We synthesized for the first time a new set of eight original CP sequences of 8, 10, and 12 d,l-α-alternate amino acids with a controlled internal diameter from 7 to 13 Å. They present various properties (e.g., diameter, global surface charge, hydrophobicity) that can open the way to new applications. Their structure and purity were determined thanks to a capillary electrophoresis coupled to electrospray ionization mass spectrometry (CE-ESI-MS) methodology developed for the first time for this purpose. The CPs were successfully separated in a basic hydro-organic background electrolyte (BGE, pH 8.0, H2O/EtOH 50:50, v/v) and analyzed in MS positive mode. The effect of CP structure on electrophoretic mobility was studied, and the mass spectra were deeply analyzed. This methodology allowed verifying their purity and the absence of linear peptide precursors as well as their stability when stored over several months. Therefore, we have developed a new CE-ESI-MS methodology for the structure and purity control of interesting potential precursors for PNTs that could be employed as nanoplatforms in diagnostics or as pseudo sieving tools for separative purposes.
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16
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Panciera M, Amorín M, Granja JR. Molecular Pom Poms from Self-Assembling α,γ-Cyclic Peptides. Chemistry 2014; 20:10260-5. [DOI: 10.1002/chem.201403319] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 02/02/2023]
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17
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Rodríguez-Vázquez N, Salzinger S, Silva LF, Amorín M, Granja JR. Synthesis of Cyclic γ-Amino Acids for Foldamers and Peptide Nanotubes. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201565] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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18
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Panciera M, Amorín M, Castedo L, Granja JR. Design of Stable β-Sheet-Based Cyclic Peptide Assemblies Assisted by Metal Coordination: Selective Homo- and Heterodimer Formation. Chemistry 2013; 19:4826-34. [DOI: 10.1002/chem.201203213] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 12/14/2012] [Indexed: 11/08/2022]
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19
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Martí-Centelles V, Burguete MI, Luis SV. Kinetic analysis for macrocyclizations involving anionic template at the transition state. ScientificWorldJournal 2012; 2012:748251. [PMID: 22666148 PMCID: PMC3347868 DOI: 10.1100/2012/748251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 12/19/2011] [Indexed: 12/04/2022] Open
Abstract
Several kinetic models for the macrocyclization of a C2 pseudopeptide with a dihalide through a SN2 reaction have been developed. These models not only focus on the kinetic analysis of the main macrocyclization reaction, but also consider the
competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.
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Affiliation(s)
- Vicente Martí-Centelles
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I, E12071 Castellón de la Plana, Spain
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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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21
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Chapman R, Danial M, Koh ML, Jolliffe KA, Perrier S. Design and properties of functional nanotubes from the self-assembly of cyclic peptide templates. Chem Soc Rev 2012; 41:6023-41. [DOI: 10.1039/c2cs35172b] [Citation(s) in RCA: 233] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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García-Fandiño R, Amorín M, Castedo L, Granja JR. Transmembrane ion transport by self-assembling α,γ-peptide nanotubes. Chem Sci 2012. [DOI: 10.1039/c2sc21068a] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Guerra A, Brea RJ, Amorín M, Castedo L, Granja JR. Self-assembling properties of all γ-cyclic peptides containing sugar amino acid residues. Org Biomol Chem 2012; 10:8762-6. [DOI: 10.1039/c2ob26612a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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24
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Hourani R, Zhang C, van der Weegen R, Ruiz L, Li C, Keten S, Helms BA, Xu T. Processable Cyclic Peptide Nanotubes with Tunable Interiors. J Am Chem Soc 2011; 133:15296-9. [DOI: 10.1021/ja2063082] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rami Hourani
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720-1760, United States
| | - Chen Zhang
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720-1760, United States
| | - Rob van der Weegen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Luis Ruiz
- Department of Civil & Environmental Engineering and Mechanical Engineering, Northwestern University, Evanston, Illinois 60208-3111, United States
| | - Changyi Li
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720-1760, United States
| | - Sinan Keten
- Department of Civil & Environmental Engineering and Mechanical Engineering, Northwestern University, Evanston, Illinois 60208-3111, United States
| | - Brett A. Helms
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ting Xu
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720-1760, United States
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25
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Foldamers containing γ-amino acid residues or their analogues: structural features and applications. Amino Acids 2011; 41:687-707. [DOI: 10.1007/s00726-011-0893-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 03/18/2011] [Indexed: 12/21/2022]
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26
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Pérez-Alvite MJ, Mosquera M, Castedo L, Granja JR. Toward the rational design of molecular rotors ion sensors based on α,γ-cyclic peptide dimers. Amino Acids 2011; 41:621-8. [DOI: 10.1007/s00726-011-0886-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 03/08/2011] [Indexed: 01/28/2023]
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27
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Hernández-Eguía LP, Brea RJ, Castedo L, Ballester P, Granja JR. Regioisomeric control induced by DABCO coordination to rotatable self-assembled bis- and tetraporphyrin α,γ-cyclic octapeptide dimers. Chemistry 2010; 17:1220-9. [PMID: 21243688 DOI: 10.1002/chem.201002271] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Indexed: 11/05/2022]
Abstract
The design and synthesis of two α,γ-cyclic octapeptides decorated with one and two Zn-porphyrin units in their periphery is described. In nonpolar organic solvents the α,γ-cyclic octapeptides quantitatively self-assemble into Zn-bis- or -tetraporphyrin architectures that could act as molecular tweezers. The self-assembly process, however, is not regioselective and affords a mixture of different regioisomers that are involved in chemical exchange processes. The regioisomers with the Zn-porphyrin units positioned in register with respect to each other are proposed to be the less abundant species in the solution mixture. It has been demonstrated that the coordination of 1,4-diazabicyclo[2.2.2]octane (DABCO) to the supramolecular bis- or tetraporphyrin tweezers is an effective way to achieve regioisomeric control of the self-assembled mixture of dimers. Thus, DABCO functions as an external molecular trigger and, when used under strict stoichiometric control with respect to the Zn-porphyrin units, provokes the exclusive formation of self-assembled dimers with a cofacial arrangement of Zn-porphyrin units through the formation of sandwich-type complexes. The use of excess DABCO fragments the sandwich complexes and affords open dimers of high stoichiometry with DABCO molecules axially monocoordinated to the Zn-porphyrin units, probably as a regioisomeric mixture. In the case of Zn-tetraporphyrin tweezers, the ditopic coordination of DABCO at the two binding sites shows a moderate positive cooperativity factor, αP=5. These assemblies have potential applications as light-induced energy and electron-transfer switches regulated by DABCO coordination; such applications would require the introduction of additional chromophores in the cyclic peptide scaffold.
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Affiliation(s)
- Laura P Hernández-Eguía
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain
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28
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Brea RJ, Pérez-Alvite MJ, Panciera M, Mosquera M, Castedo L, Granja JR. Highly Efficient and Directional Homo- and Heterodimeric Energy Transfer Materials Based on Fluorescently Derivatized α,γ-Cyclic Octapeptides. Chem Asian J 2010; 6:110-21. [DOI: 10.1002/asia.201000545] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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García-Fandiño R, Castedo L, Granja JR, Vázquez SA. Interaction and Dimerization Energies in Methyl-Blocked α,γ-Peptide Nanotube Segments. J Phys Chem B 2010; 114:4973-83. [DOI: 10.1021/jp910919k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rebeca García-Fandiño
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain, Departamento de Química Fundamental, Facultad de Ciencias, Universidad de A Coruña, 15071 A Coruña, Spain, and Departamento de Química Física, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Luis Castedo
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain, Departamento de Química Fundamental, Facultad de Ciencias, Universidad de A Coruña, 15071 A Coruña, Spain, and Departamento de Química Física, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Juan R. Granja
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain, Departamento de Química Fundamental, Facultad de Ciencias, Universidad de A Coruña, 15071 A Coruña, Spain, and Departamento de Química Física, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Saulo A. Vázquez
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain, Departamento de Química Fundamental, Facultad de Ciencias, Universidad de A Coruña, 15071 A Coruña, Spain, and Departamento de Química Física, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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30
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Affiliation(s)
- S. G. Ramkumar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - S. Ramakrishnan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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31
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García-Fandiño R, Granja JR, D'Abramo M, Orozco M. Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution. J Am Chem Soc 2010; 131:15678-86. [PMID: 19860480 DOI: 10.1021/ja903400n] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present here a molecular dynamics study on a promising class of peptide nanotubes with a partially hydrophobic inner cavity and an easy chemical functionalization of the lumen of the cylindrical structure. The structural and dynamical behavior of the nanotube in water, methanol, and chloroform has been analyzed using state of the art theoretical methods. The nanotube structure is always well preserved, but solvent-dependent dynamic alterations are evident. Such dynamic effects are surprisingly more severe in the most viscous solvent (water), as a consequence of the competition in polar solvents between intra- and intermolecular hydrogen bonds. Stiffness analysis from the collected trajectories helped us to characterize the equilibrium deformability of the nanotube, while steered dynamics simulations were used to determine the magnitude of free energy associated with nanotube growth. Analysis of the carrier and permeation properties of the compounds reveals surprising properties: (i) permeability for the most polar solvent (water), (ii) carrier properties for the most apolar solvent (chloroform), and (iii) neither good permeation nor carrier properties for the intermediate solvent in polarity (methanol). Results reported here constitute the most extensive characterization of these nanotubes presented to date and open many intriguing questions on their stability, dynamics, and transport/carrier properties.
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Affiliation(s)
- Rebeca García-Fandiño
- Institut de Recerca Biomèdica and Instituto Nacional de Bioinformatica, Parc Cientific de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
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32
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Alfonso I, Bru M, Burguete MI, García-Verdugo E, Luis S. Structural Diversity in the Self-Assembly of Pseudopeptidic Macrocycles. Chemistry 2010; 16:1246-55. [DOI: 10.1002/chem.200902196] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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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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34
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Brea RJ, Reiriz C, Granja JR. Towards functional bionanomaterials based on self-assembling cyclic peptide nanotubes. Chem Soc Rev 2009; 39:1448-56. [PMID: 20419200 DOI: 10.1039/b805753m] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In recent years, considerable effort has been devoted to the preparation of artificial nanotubular materials. One of the most successful approaches for the construction of noncovalently bonded nanotube entities is the self-assembly of cyclic polypeptides in stacks that are stabilized by hydrogen bonds. This tutorial review covers the history and current situation for synthetic organic nanostructures obtained from self-assembling cyclic peptides. In particular, we describe the evolution to cyclic peptides that not only allow the modification of the outer surface but also the inner cavity by paying special attention to peptide rings that contain cyclic gamma-amino acids. In this respect, we describe the synthesis, properties and application of a new class of homo- and heterodimeric supramolecular assemblies that are precursors of cyclic alpha,gamma-peptide nanotubes.
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Affiliation(s)
- Roberto J Brea
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
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35
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Zanuy D, Ballano G, Jiménez AI, Casanovas J, Haspel N, Cativiela C, Curcó D, Nussinov R, Alemán C. Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale. J Chem Inf Model 2009; 49:1623-9. [PMID: 19548653 DOI: 10.1021/ci9001487] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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36
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Guha S, Banerjee A. Macroporous Materials from Self-Assembling Synthetic Cyclic Peptide-Based Compounds and Deposition of Dipeptide-Capped Gold Nanoparticles on the Surfaces. MACROMOL CHEM PHYS 2009. [DOI: 10.1002/macp.200900261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Reiriz C, Brea RJ, Arranz R, Carrascosa JL, Garibotti A, Manning B, Valpuesta JM, Eritja R, Castedo L, Granja JR. α,γ-Peptide Nanotube Templating of One-Dimensional Parallel Fullerene Arrangements. J Am Chem Soc 2009; 131:11335-7. [DOI: 10.1021/ja904548q] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- César Reiriz
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, Centro Nacional de Biotecnología, CSIC, Darwin 3, E-28049 Madrid, Spain, and Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Spain
| | - Roberto J. Brea
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, Centro Nacional de Biotecnología, CSIC, Darwin 3, E-28049 Madrid, Spain, and Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Spain
| | - Rocío Arranz
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, Centro Nacional de Biotecnología, CSIC, Darwin 3, E-28049 Madrid, Spain, and Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Spain
| | - José L. Carrascosa
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, Centro Nacional de Biotecnología, CSIC, Darwin 3, E-28049 Madrid, Spain, and Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Spain
| | - Alejandra Garibotti
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, Centro Nacional de Biotecnología, CSIC, Darwin 3, E-28049 Madrid, Spain, and Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Spain
| | - Brendan Manning
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, Centro Nacional de Biotecnología, CSIC, Darwin 3, E-28049 Madrid, Spain, and Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Spain
| | - José M. Valpuesta
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, Centro Nacional de Biotecnología, CSIC, Darwin 3, E-28049 Madrid, Spain, and Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Spain
| | - Ramón Eritja
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, Centro Nacional de Biotecnología, CSIC, Darwin 3, E-28049 Madrid, Spain, and Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Spain
| | - Luis Castedo
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, Centro Nacional de Biotecnología, CSIC, Darwin 3, E-28049 Madrid, Spain, and Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Spain
| | - Juan R. Granja
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, Centro Nacional de Biotecnología, CSIC, Darwin 3, E-28049 Madrid, Spain, and Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 15, E-08028 Barcelona, Spain
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38
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Fischer L, Decossas M, Briand JP, Didierjean C, Guichard G. Control of Duplex Formation and Columnar Self-Assembly with Heterogeneous Amide/Urea Macrocycles. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Fischer L, Decossas M, Briand JP, Didierjean C, Guichard G. Control of Duplex Formation and Columnar Self-Assembly with Heterogeneous Amide/Urea Macrocycles. Angew Chem Int Ed Engl 2009; 48:1625-8. [DOI: 10.1002/anie.200804019] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Reiriz C, Amorín M, García-Fandiño R, Castedo L, Granja JR. α,γ-Cyclic peptide ensembles with a hydroxylated cavity. Org Biomol Chem 2009; 7:4358-61. [DOI: 10.1039/b911247m] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Tsikolia M, Hall AC, Suarez C, Nylander ZO, Wardlaw SM, Gibson ME, Valentine KL, Onyewadume LN, Ahove DA, Woodbury M, Mongare MM, Hall CD, Wang Z, Draghici B, Katritzky AR. Synthesis and characterization of a redox-active ion channel supporting cation flux in lipid bilayers. Org Biomol Chem 2009; 7:3862-70. [DOI: 10.1039/b907350g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Khakshoor O, Nowick JS. Artificial beta-sheets: chemical models of beta-sheets. Curr Opin Chem Biol 2008; 12:722-9. [PMID: 18775794 DOI: 10.1016/j.cbpa.2008.08.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 08/04/2008] [Indexed: 12/01/2022]
Abstract
Chemical models provide tools with which to simplify and study complicated biological systems. Forces and chemical processes that govern the structure, function, and interactions of a biomacromolecule can be explored with a simple, easy-to-study synthetic molecule. Chemical models of beta-sheet structures have helped to elucidate the factors influencing protein structures and functions. Chemical models that mimic beta-sheet quaternary structure and interactions are emerging as valuable tools with which to better understand and control protein recognition and protein aggregation.
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Affiliation(s)
- Omid Khakshoor
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
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43
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Alfonso I, Bolte M, Bru M, Burguete M, Luis S. Designed Folding of Pseudopeptides: The Transformation of a Configurationally Driven Preorganization into a Stereoselective Multicomponent Macrocyclization Reaction. Chemistry 2008; 14:8879-8891. [DOI: 10.1002/chem.200800726] [Citation(s) in RCA: 35] [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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Annunziata R, Benaglia M, Puglisi A, Raimondi L, Cozzi F. Synthesis of Some 2,2′:6′,2″-Terpyridines Disubstituted in Positions 6 and 6″ with Head-to-Tail Oriented Amino Acids and Dipeptides: A Simple Entry to a Reversible Inducer of Folding in Amino Acid Sequences. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800433] [Citation(s) in RCA: 3] [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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