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Nazari N, Bernard S, Fortin D, Marmin T, Gendron L, Dory YL. Triple Thorpe-Ingold Effect in the Synthesis of 18-Membered C 3 Symmetric Lactams Stacking as Endless Supramolecular Tubes. Chemistry 2023; 29:e202203717. [PMID: 36469732 DOI: 10.1002/chem.202203717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
Three C3 symmetric macrolactams were very efficiently cyclized from their linear precursors. Adequately located substituents are responsible for the enhancement of reactivity that is not observed in the unsubstituted parent. DFT calculations show that the properly folded cyclization precursor, the reactive conformer, is more populated than other conformers, leading to a decrease of free energy of activation. The crystal structure of the ring substituted with three very bulky esters indicates that tubular stacking is preserved.
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Affiliation(s)
- Niousha Nazari
- Laboratoire de Synthèse Supramoléculaire Département de Chimie, Université de Sherbrooke 2500, boulevard Université, Sherbrooke, Québec, J1K 2R1, Canada.,Institut de Pharmacologie et Centre de Recherche du CHUS, Université de Sherbrooke 3001, 12e avenue nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Sylvain Bernard
- Laboratoire de Synthèse Supramoléculaire Département de Chimie, Université de Sherbrooke 2500, boulevard Université, Sherbrooke, Québec, J1K 2R1, Canada.,Institut de Pharmacologie et Centre de Recherche du CHUS, Université de Sherbrooke 3001, 12e avenue nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Daniel Fortin
- Laboratoire de cristallographie, Université de Sherbrooke 2500, boulevard Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Thomas Marmin
- Laboratoire de Synthèse Supramoléculaire Département de Chimie, Université de Sherbrooke 2500, boulevard Université, Sherbrooke, Québec, J1K 2R1, Canada.,Institut de Pharmacologie et Centre de Recherche du CHUS, Université de Sherbrooke 3001, 12e avenue nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Louis Gendron
- Département de Pharmacologie-Biophysique 3001, 12e avenue nord, Sherbrooke, Québec, J1H 5N4, Canada.,Institut de Pharmacologie et Centre de Recherche du CHUS, Université de Sherbrooke 3001, 12e avenue nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Yves L Dory
- Laboratoire de Synthèse Supramoléculaire Département de Chimie, Université de Sherbrooke 2500, boulevard Université, Sherbrooke, Québec, J1K 2R1, Canada.,Institut de Pharmacologie et Centre de Recherche du CHUS, Université de Sherbrooke 3001, 12e avenue nord, Sherbrooke, Québec, J1H 5N4, Canada
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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: 65] [Impact Index Per Article: 21.7] [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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3
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Goldschmidt Gőz V, Pintér I, Harmat V, Perczel A. Approaches to Pyranuronic β-Sugar Amino Acid Building Blocks of Peptidosaccharide Foldamers. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - István Pintér
- Laboratory of Structural Chemistry and Biology; Institute of Chemistry; Eötvös University; Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - Veronika Harmat
- MTA-ELTE Protein Modeling Research Group; Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - András Perczel
- MTA-ELTE Protein Modeling Research Group; Pázmány Péter sétány 1/A 1117 Budapest Hungary
- Laboratory of Structural Chemistry and Biology; Institute of Chemistry; Eötvös University; Pázmány Péter sétány 1/A 1117 Budapest Hungary
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4
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Tabata Y, Mitani S, Kimura S. Peptide nanotube aligning side chains onto one side. J Pept Sci 2016; 22:391-6. [DOI: 10.1002/psc.2881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Yuki Tabata
- Department of Material Chemistry, Graduate School of Engineering; Kyoto University; Kyoto-Daigaku-Katsura Nishikyo-ku Kyoto 615-8510 Japan
| | - Shota Mitani
- Department of Material Chemistry, Graduate School of Engineering; Kyoto University; Kyoto-Daigaku-Katsura Nishikyo-ku Kyoto 615-8510 Japan
| | - Shunsaku Kimura
- Department of Material Chemistry, Graduate School of Engineering; Kyoto University; Kyoto-Daigaku-Katsura Nishikyo-ku Kyoto 615-8510 Japan
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Abstract
The self-assembly of different classes of peptide, including cyclic peptides, amyloid peptides and surfactant-like peptides into nanotube structures is reviewed. The modes of self-assembly are discussed. Additionally, applications in bionanotechnology and synthetic materials science are summarized.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD (UK).
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Feher-Voelger A, Borges-González J, Carrillo R, Morales EQ, González-Platas J, Martín T. Synthesis and conformational analysis of cyclic homooligomers from pyranoid ε-sugar amino acids. Chemistry 2014; 20:4007-22. [PMID: 24616150 DOI: 10.1002/chem.201303841] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/16/2013] [Indexed: 12/12/2022]
Abstract
New pyranoid ε-sugar amino acids were designed as building blocks, in which the carboxylic acid and the amine groups were placed in positions C2 and C3 with respect to the tetrahydropyran oxygen atom. By using standard solution-phase coupling procedures, cyclic homooligomers containing pyranoid ε-sugar amino acids were synthesized. Conformation analysis was performed by using NMR spectroscopic experiments, FTIR spectroscopic studies, X-ray analysis, and a theoretical conformation search. These studies reveal that the presence of a methoxy group in the position C4 of the pyran ring produces an important structural change in the cyclodipeptides. When the methoxy groups are present, the structure collapses through interresidue hydrogen bonds between the oxygen atoms of the pyran ring and the amide protons. However, when the cyclodipeptide lacks the methoxy groups, a U-shape structure is adopted, in which there is a hydrophilic concave face with four oxygen atoms and two amide protons directed toward the center of the cavity. Additionally, we found important evidence of the key role played by weak electrostatic interactions, such as the five-membered hydrogen-bonded pseudocycles (C5) between the amide protons and the ether oxygen atoms, in the conformation equilibrium of the macrocycles and in the cyclization step of the cyclic tetrapeptides.
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Affiliation(s)
- Andrés Feher-Voelger
- Instituto de Productos Naturales y Agrobiología-CSIC, Avda. Astrofísico Francisco Sánchez, 3, 38206-La Laguna, Tenerife (Spain), Fax: (+34) 922-260135
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Park S, Kwon TG, Lee SY. Controlled self-assembly and alignment of organic–magnetic hybrid microrods. POWDER TECHNOL 2013. [DOI: 10.1016/j.powtec.2013.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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9
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A compendium of cyclic sugar amino acids and their carbocyclic and heterocyclic nitrogen analogues. Amino Acids 2013; 45:613-89. [DOI: 10.1007/s00726-013-1521-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/21/2013] [Indexed: 12/19/2022]
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Ishihara Y, Kimura S. Peptide nanotube composed of cyclic tetra-β-peptide having polydiacetylene. Biopolymers 2012; 98:155-60. [DOI: 10.1002/bip.22029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/19/2012] [Accepted: 01/26/2012] [Indexed: 12/19/2022]
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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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12
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Handelman A, Beker P, Amdursky N, Rosenman G. Physics and engineering of peptide supramolecular nanostructures. Phys Chem Chem Phys 2012; 14:6391-408. [DOI: 10.1039/c2cp40157f] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Bernstein N, Kulp JL, Cato MA, Clark TD. Simulations of nanocylinders self-assembled from cyclic β-tripeptides. J Phys Chem A 2011; 114:11948-52. [PMID: 20961136 DOI: 10.1021/jp103447w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This paper examines the self-assembly of cyclic β-tripeptides using density functional theory. On the basis of literature precedents, these cyclic peptides were expected to self-assemble into cylindrical structures by stacking through backbone-backbone hydrogen bonding. Our calculations show that such stacking is energetically favorable, that the association energy per cyclic peptide decreases (becomes more favorable), and that the overall macrodipole moment of the cylindrical assembly increases with the number of stacked rings, for up to eight rings. For a structure in which two peptide ring units are joined through a single side chain-side chain covalent linker, the association energy between the two rings is favorable, albeit less so than for the unlinked rings. Significantly, the association energy in the dimers is only weakly dependent on the length (above a certain minimum) and conformation of the covalent linkers. Finally, as a plausible route for controlling assembly/disassembly of nanocylinders, we show that, for a pair of rings, each bearing a single amino-functionalized side chain, protonation of the amino group results in a strongly positive (unfavorable) association energy between the two rings.
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Taira J, Osada S, Hayashi R, Ueda T, Jelokhani-Niaraki M, Aoyagi H, Kodama H. Trans-Bilayer Ion Conduction by Proline Containing Cyclic Hexapeptides and Effects of Amino Acid Substitutions on Ion Conducting Properties. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20090272] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Soler M, Moorefield CN, Newkome GR. Hexameric Macrocyclic Architectures in Heterocyclic Chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2010. [DOI: 10.1016/s0065-2725(10)01001-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Kanzaki T, Horikawa Y, Makino A, Sugiyama J, Kimura S. Nanotube and Three-Way Nanotube Formation with Nonionic Amphiphilic Block Peptides. Macromol Biosci 2008; 8:1026-33. [DOI: 10.1002/mabi.200800071] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Mengel A, Reiser O, Aubé J. Synthesis and structural study of cyclic 5-aminovaleric acid-linked β-Ala–β-Ala dipeptides. Bioorg Med Chem Lett 2008; 18:5975-7. [DOI: 10.1016/j.bmcl.2008.07.082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2008] [Revised: 07/18/2008] [Accepted: 07/21/2008] [Indexed: 11/25/2022]
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18
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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: 57] [Impact Index Per Article: 3.6] [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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Oku H, Yamada K, Katakai R. Conformational change from antiparallel beta-sheet to alpha-helix in a series of depsipeptide, -(Leu-Leu-Lac)(n)-: syntheses, spectroscopic studies, and crystal structures of Boc-Leu-Lac-OEt and Boc-(Leu-Leu-Lac)(n)-OEt (n = 1, 2). Biopolymers 2008; 89:270-83. [PMID: 18067154 DOI: 10.1002/bip.20904] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The depsipeptides Boc-Leu-Lac-OEt (1) and Boc-(Leu-Leu-Lac)(n)-OEt (n = 1, 2) (2 and 3, respectively) (Boc = tert-butyloxycarbonyl, Lac = L-lactic acid residue) has been synthesized and studied by crystallographic, CD spectroscopic, and ESI-MS analyses. In the packing cells, those three compounds adopt beta-strand conformations. Each molecule is linked into a dimer (1) or an infinite assembly (2 and 3) by tight hydrogen bonds of the type NH...O==C. Interestingly, the hexamer, 3 shows the first example of antiparallel pleated beta-sheet crystal structure for a depsipeptide molecule. In the packing cells, especially for 3, the ester groups O--C==O are perpendicularly oriented to the amide groups NH--C==O and beta-sheet planes to avoid the interaction between --O--(ester) and O==C. Therefore, when the chain length become longer, the O...O==C repulsion interaction works as a beta-sheet breaker and hence promotes an alpha-helical structure as observed for Boc-(Leu-Leu-Lac)(3)-Leu-Leu-OEt (4) (Oku et al. Biopolymers 2004, 75, 242-254) and Boc-(Leu-Leu-Lac)(n)-OEt (n = 4-6) (5-7) (Katakai et al., Biopolymers 1996, 38, 285-290), in which the O...O==C repulsion does not cause significant structural changes in alpha-helical main chains. Therefore from the structural and spectroscopic analyses, we have found governing factors for the specificity in the beta-sheet and alpha-helix decision in this series of depsipeptides, -(Leu-Leu-Lac)(n)-.
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Affiliation(s)
- Hiroyuki Oku
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu, Gunma, Japan.
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20
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Kimura S. Molecular dipole engineering: new aspects of molecular dipoles in molecular architecture and their functions. Org Biomol Chem 2008; 6:1143-8. [DOI: 10.1039/b717898k] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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