1
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Bachurska-Szpala P, Chojnacki R, Pulka-Ziach K. Intramolecular lactam cross-linking of short oligoureas. J Pept Sci 2024:e3644. [PMID: 39010660 DOI: 10.1002/psc.3644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024]
Abstract
Oligourea foldamers are known to fold into 2.5-helices, stabilized by three-centered hydrogen bonds, which makes them conformationally more rigid than peptides. Nevertheless, the folding propensity and conformational stability in solution depend on the length of the oligomer, as well as the temperature, solvent, and so forth. In the peptide field, there are many approaches known for constraining the backbone in the folded conformation, including the stapling of side chains by disulfide bridges, lactam formation, ring closing metathesis reaction, and others. In this work, we linked side chains by lactam bridges of short oligoureas (four residues), containing Glu- and Lys-like residues. The designed oligoureas differed in the position of the Glu-like residue. Next, the conformational properties of linear and cyclic compounds were studied in protic solvent (methanol) by nuclear magnetic resonance and circular dichroism. Importantly, it was discovered that larger macrocycles (24-membered) are more tolerated with respect to the helical turn than smaller macrocycles (19-membered) under the studied conditions.
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2
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Grempka A, Dziubak D, Puszko AK, Bachurska-Szpala P, Ivanov M, Vilarinho PM, Pulka-Ziach K, Sek S. Stimuli-Responsive Oligourea Molecular Films. ACS APPLIED MATERIALS & INTERFACES 2024; 16:31817-31825. [PMID: 38848259 PMCID: PMC11194770 DOI: 10.1021/acsami.4c04767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
We have designed and synthesized a helical cysteamine-terminated oligourea foldamer composed of ten urea residues featuring side carboxyl and amine groups. The carboxyl group is located in proximity to the C-terminus of the oligourea and hence at the negative pole of the helix dipole. The amine group is located close to the N-terminus and hence at the positive pole of the helix dipole. Beyond the already remarkable dipole moment inherent in oligourea 2.5 helices, the incorporation of additional charges originating from the carboxylic and amine groups is supposed to impact the overall charge distribution along the molecule. These molecules were self-assembled into monolayers on a gold substrate, allowing us to investigate the influence of an electric field on these polar helices. By applying surface-enhanced infrared reflection-absorption spectroscopy, we proved that molecules within the monolayers tend to reorient themselves more vertically when a negative bias is applied to the surface. It was also found that surface-confined oligourea molecules affected by the external electric field tend to rearrange the electron density at urea groups, leading to the stabilization of the resonance structure with charge transfer character. The presence of the external electric field also affected the nanomechanical properties of the oligourea films, suggesting that molecules also tend to reorient in the ambient environment without an electrolyte solution. Under the same conditions, the helical oligourea displayed a robust piezoresponse, particularly noteworthy given the slender thickness of the monolayer, which measured approximately 1.2 nm. This observation demonstrates that thin molecular films composed of oligoureas may exhibit stimulus-responsive properties. This, in turn, may be used in nanotechnology systems as actuators or functional films, enabling precise control of their thickness in the range of even fractions of nanometers.
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Affiliation(s)
- Arkadiusz Grempka
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warsaw 02-089, Poland
| | - Damian Dziubak
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warsaw 02-089, Poland
| | - Anna K. Puszko
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | | | - Maxim Ivanov
- Department
of Materials and Ceramic Engineering & CICECO—Aveiro Institute
of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Paula M. Vilarinho
- Department
of Materials and Ceramic Engineering & CICECO—Aveiro Institute
of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | | | - Slawomir Sek
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warsaw 02-089, Poland
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3
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Szatko M, Forysiak W, Kozub S, Andruniów T, Szweda R. Revealing the Effect of Stereocontrol on Intermolecular Interactions between Abiotic, Sequence-Defined Polyurethanes and a Ligand. ACS Biomater Sci Eng 2024; 10:3727-3738. [PMID: 38804015 PMCID: PMC11167595 DOI: 10.1021/acsbiomaterials.4c00456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
The development of precision polymer synthesis has facilitated access to a diverse library of abiotic structures wherein chiral monomers are positioned at specific locations within macromolecular chains. These structures are anticipated to exhibit folding characteristics similar to those of biotic macromolecules and possess comparable functionalities. However, the extensive sequence space and numerous variables make selecting a sequence with the desired function challenging. Therefore, revealing sequence-function dependencies and developing practical tools are necessary to analyze their conformations and molecular interactions. In this study, we investigate the effect of stereochemistry, which dictates the spatial location of backbone and pendant groups, on the interaction between sequence-defined oligourethanes and bisphenol A ligands. Various methods are explored to analyze the receptor-like properties of model oligomers and the ligand. The accuracy of molecular dynamics simulations and experimental techniques is assessed to uncover the impact of discrete changes in stereochemical arrangements on the structures of the resulting complexes and their binding strengths. Detailed computational investigations providing atomistic details show that the formed complexes demonstrate significant structural diversity depending on the sequence of stereocenters, thus affecting the oligomer-ligand binding strength. Among the tested techniques, the fluorescence spectroscopy data, fitted to the Stern-Volmer equation, are consistently aligned with the calculations, thus validating the developed simulation methodology. The developed methodology opens a way to engineer the structure of sequence-defined oligomers with receptor-like functionality to explore their practical applications, e.g., as sensory materials.
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Affiliation(s)
- Maksymilian Szatko
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Weronika Forysiak
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Sara Kozub
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
| | - Tadeusz Andruniów
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Roza Szweda
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
- Center
for Advanced Technologies, Adam Mickiewicz
University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland
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4
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Forysiak W, Lizak A, Szweda R. Sequence of Monomers and Position of Stereocenters Matter for Thermal Properties of Stereocontrolled Oligourethanes. Chemphyschem 2024:e202400366. [PMID: 38753463 DOI: 10.1002/cphc.202400366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 05/18/2024]
Abstract
Polyurethanes are commodity materials used for multiple applications. In recent years, a new category of polyurethane material has emerged, characterized by the lack of polymer molar mass dispersity, control of the monomer arrangement in the chain, and even full stereocontrol. Various multistep synthesis strategies have been developed to fabricate sequence-defined polyurethanes. However, synthesizing stereocontrolled polyurethanes with a controlled sequence is still a challenge. Polyurethanes with structural precision, as represented by biopolymers, i. e. proteins or nucleic acids, have opened new application directions for these groups of materials. It has been shown that polyurethanes can be used as biomimetics, information carriers, molecular tags, and materials with strictly controlled properties. Precise synthesis of macromolecules allows us to fine-tune the properties of polymers to specific needs. Therefore, it is essential to collect information on the sequence-structure relationship of polymers. In our work, we present synthetic pathways to make sequence and stereo-defined oligourethanes. We demonstrate that structural details, i. e., the monomer sequences and position of the stereocenter, have a tremendous effect on the thermal properties of model oligourethanes. We show that the introduction of chirality by constitutional isomerization can be used to program the thermal characteristics of polymers, which are key features for material applications.
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Affiliation(s)
- Weronika Forysiak
- Łukasiewicz Research Network -, PORT Polish Centre for Technology Development, ul. Stabłowicka 147, 54-066, Wrocław, Poland
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383, Wrocław, Poland
| | - Agnieszka Lizak
- Łukasiewicz Research Network -, PORT Polish Centre for Technology Development, ul. Stabłowicka 147, 54-066, Wrocław, Poland
| | - Róża Szweda
- Łukasiewicz Research Network -, PORT Polish Centre for Technology Development, ul. Stabłowicka 147, 54-066, Wrocław, Poland
- Center for Advanced Technologies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
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5
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Perez Mellor AF, Brazard J, Kozub S, Bürgi T, Szweda R, Adachi TBM. Unveiling the Configurational Landscape of Carbamate: Paving the Way for Designing Functional Sequence-Defined Polymers. J Phys Chem A 2023; 127:7309-7322. [PMID: 37624607 PMCID: PMC10493977 DOI: 10.1021/acs.jpca.3c02442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/11/2023] [Indexed: 08/26/2023]
Abstract
Carbamate is an emerging class of a polymer backbone for constructing sequence-defined, abiotic polymers. It is expected that new functional materials can be de novo designed by controlling the primary polycarbamate sequence. While amino acids have been actively studied as building blocks for protein folding and peptide self-assembly, carbamates have not been widely investigated from this perspective. Here, we combined infrared (IR), vibrational circular dichroism (VCD), and nuclear magnetic resonance (NMR) spectroscopy with density functional theory (DFT) calculations to understand the conformation of carbamate monomer units in a nonpolar, aprotic environment (chloroform). Compared with amino acid building blocks, carbamates are more rigid, presumably due to the extended delocalization of π-electrons on the backbones. Cis configurations of the amide bond can be energetically stable in carbamates, whereas peptides often assume trans configurations at low energies. This study lays an essential foundation for future developments of carbamate-based sequence-defined polymer material design.
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Affiliation(s)
- Ariel F. Perez Mellor
- Department
of Physical Chemistry, Sciences II, University
of Geneva, 30, Quai Ernest Ansermet, Geneva 1211, Switzerland
| | - Johanna Brazard
- Department
of Physical Chemistry, Sciences II, University
of Geneva, 30, Quai Ernest Ansermet, Geneva 1211, Switzerland
| | - Sara Kozub
- Łukasiewicz
Research Network − PORT Polish Center for Technology Development, Stabłowicka 147, Wrocław 54-066, Poland
| | - Thomas Bürgi
- Department
of Physical Chemistry, Sciences II, University
of Geneva, 30, Quai Ernest Ansermet, Geneva 1211, Switzerland
| | - Roza Szweda
- Łukasiewicz
Research Network − PORT Polish Center for Technology Development, Stabłowicka 147, Wrocław 54-066, Poland
| | - Takuji B. M. Adachi
- Department
of Physical Chemistry, Sciences II, University
of Geneva, 30, Quai Ernest Ansermet, Geneva 1211, Switzerland
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6
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Sang P, Cai J. Unnatural helical peptidic foldamers as protein segment mimics. Chem Soc Rev 2023; 52:4843-4877. [PMID: 37401344 PMCID: PMC10389297 DOI: 10.1039/d2cs00395c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 07/05/2023]
Abstract
Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.
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Affiliation(s)
- Peng Sang
- Tianjian Laboratory of Advanced Biomedical Sciences, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA.
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7
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Kedzia K, Dobrzycki L, Wilczek M, Pulka-Ziach K. C-Terminal-Modified Oligourea Foldamers as a Result of Terminal Methyl Ester Reactions under Alkaline Conditions. Int J Mol Sci 2023; 24:ijms24076806. [PMID: 37047779 PMCID: PMC10094884 DOI: 10.3390/ijms24076806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/02/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023] Open
Abstract
Hybrids of short oligourea foldamers with residues of α, β and γ-amino acids esters at the C-terminus were obtained and subjected to a reaction with LiOH. There are two possible transformations under such conditions, one of which is ester hydrolysis and the formation of a carboxylic group and the other is the cyclization reaction after abstraction of a proton from urea by a base. We have investigated this reaction with difference C-terminal residue structures, as well as under different work-up conditions, especially for oligourea hybrids with α-amino acid esters. For these compounds, an oligourea-hydantoin combination is the product of cyclization. The stability of the hydantoin ring under alkaline conditions has been alsotested. Furthermore, this work reports data related to the structure of C-terminal-modified oligourea foldamers in solution and, for one compound, in the solid state. Helical folding is preserved both for cyclized and linear modifications, with oligourea-acid hybrids appearing to be more conformationally stable, as they are stabilized by an additional intramolecular hydrogen bond in comparison to cyclic derivatives.
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Affiliation(s)
- Katarzyna Kedzia
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Lukasz Dobrzycki
- Laboratory of Advanced Crystal Engineering, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Marcin Wilczek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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8
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Huguenot F, Vidal M. Phenyloxycarbonyl (Phoc) Carbamate: Chemioselective Reactivity and Tetra- n-butylammonium Fluoride Deprotection Study. ACS OMEGA 2022; 7:44861-44868. [PMID: 36530256 PMCID: PMC9753175 DOI: 10.1021/acsomega.2c04979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
We present the results of the chemoselective reactivity of phenylcarbamates. Phenylcarbamates of primary amines are reactive to form urea, and phenylcarbamates of secondary amines can be used as tags due to the existence of rotamers. Moreover, deprotection attempts to to recover the primary amines in use of a catalytic amount of TBAF show the possibility of obtaining the symmetrical urea from the corresponding phenylcarbamate. We have begun the study of the transformation of Phoc carbamates into the corresponding free amines by TBAF. We present here our most significant results concerning the sensitivity of this reaction in terms of the solvent and substrate.
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Affiliation(s)
- Florent Huguenot
- CNRS
UMR 8038 CiTCoM, Université de Paris, Faculté de Pharmacie
de Paris, 4 Avenue de
l’observatoire, Paris 75006, France
- INSERM
U 1268 Medicinal Chemistry and Translational Research, Paris 75006, France
| | - Michel Vidal
- CNRS
UMR 8038 CiTCoM, Université de Paris, Faculté de Pharmacie
de Paris, 4 Avenue de
l’observatoire, Paris 75006, France
- INSERM
U 1268 Medicinal Chemistry and Translational Research, Paris 75006, France
- UF
Biologie du médicament—Toxicologie, Hôpital Cochin, AP-HP, 27 Rue du Faubourg Saint
Jacques, Paris 75014, France
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9
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Cwynar P, Pasikowski P, Szweda R. One-pot approach for multi-step, iterative synthesis of sequence-defined oligocarbamates. Eur Polym J 2022. [DOI: 10.1016/j.eurpolymj.2022.111706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Gupta N, Wilczek M, Dobrzycki L, Pulka-Ziach K. Structural Consequences of N‐methylation of N‐terminus in Oligourea Foldamers. Chempluschem 2022; 87:e202200199. [DOI: 10.1002/cplu.202200199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/22/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Naveen Gupta
- University of Warsaw: Uniwersytet Warszawski Faculty of Chemistry Pastuera 1 02-093 Warsaw POLAND
| | - Marcin Wilczek
- University of Warsaw: Uniwersytet Warszawski Faculty of Chemistry Pasteura 1 02-093 Warsaw POLAND
| | - Lukasz Dobrzycki
- University of Warsaw: Uniwersytet Warszawski Faculty of Chemistry Zwirki i Wigury 101 02-089 Warsaw POLAND
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11
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Forysiak W, Kozub S, John L, Szweda R. Discrete oligourethanes of sequence-regulated properties – impact of stereocontrol. Polym Chem 2022. [DOI: 10.1039/d2py00299j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Properties and functions of natural biopolymers such as proteins are strongly dependent on the sequence of amino acid monomers. The regulation of the properties of synthetic polymers by controlling monomer...
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12
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Dziubak D, Puszko AK, Bachurska P, Pułka-Ziach K, Sęk S. Oligourea molecular lifter triggered by electric field. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2021.139634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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13
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Abstract
N,N'-linked oligoureas are a class of enantiopure, sequence-defined peptidomimetic oligomers without amino acids that form well-defined and predictable helical structures akin to the peptide α-helix. Oligourea-based foldamers combine a number of features-such as synthetic accessibility, sequence modularity, and folding fidelity-that bode well for their use in a range of applications from medicinal chemistry to catalysis. Moreover, it was recently recognized that this synthetic helical backbone can be combined with regular peptides to generate helically folded peptide-oligourea hybrids that display additional features in terms of helix mimicry and protein-surface recognition properties. Here we provide detailed protocols for the preparation of requested monomers and for the synthesis and purification of homo-oligoureas and peptide-oligourea hybrids.
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14
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Milbeo P, Simon M, Didierjean C, Wenger E, Aubert E, Martinez J, Amblard M, Calmès M, Legrand B. A bicyclic unit reversal to stabilize the 12/14-helix in mixed homochiral oligoureas. Chem Commun (Camb) 2020; 56:7921-7924. [DOI: 10.1039/d0cc02902e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Incorporation of highly constrained building blocks into oligoureas: a simple bicycle reversal leads to tunable 12/14-helices formation.
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Affiliation(s)
- Pierre Milbeo
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
| | - Matthieu Simon
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
| | | | | | | | - Jean Martinez
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
| | - Monique Calmès
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
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15
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Pulka-Ziach K, Antunes S, Perdriau C, Kauffmann B, Pasco M, Douat C, Guichard G. Postelongation Strategy for the Introduction of Guanidinium Units in the Main Chain of Helical Oligourea Foldamers. J Org Chem 2018; 83:2530-2541. [PMID: 29381363 DOI: 10.1021/acs.joc.7b01895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of hybrid urea-based foldamers containing isosteric guanidinium linkages at selected positions in the sequence is described. We used a postelongation approach whereby the guanidinium moiety is introduced by direct transformation of a parent oligo(urea/thiourea) foldamer precursor. The method involves activation of the thiourea by treatment with methyl iodide and subsequent reaction with amines. To avoid undesired cyclization with the preceding urea moiety, resulting in heterocyclic guanidinium formation in the main chain, the urea unit preceding the thiourea unit in the sequence was replaced by an isoatomic and isostructural γ-amino acid. The approach was extended to solid-phase techniques to accelerate the synthesis of longer and more functionalized sequences. Under optimized conditions, an octamer hybrid oligomer incorporating a central guanidinium linkage was obtained in good overall yield and purity. This work also reports data related to the structural consequences of urea by guanidinium replacements in solution and reveals that helical folding is substantially reduced in oligomers containing a guanidinium group.
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Affiliation(s)
- Karolina Pulka-Ziach
- Institut de Chimie et Biologie des Membranes et des Nano-objets 6 (CBMN), UMR 5248, Institut Européen de Chimie et Biologie, Université de Bordeaux, Centre National de la Recherche Scientifique (CNRS) , 2 rue Robert Escarpit, F-33607 Pessac, France.,Faculty of Chemistry, Universtiy of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Stéphanie Antunes
- Institut de Chimie et Biologie des Membranes et des Nano-objets 6 (CBMN), UMR 5248, Institut Européen de Chimie et Biologie, Université de Bordeaux, Centre National de la Recherche Scientifique (CNRS) , 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Camille Perdriau
- Institut de Chimie et Biologie des Membranes et des Nano-objets 6 (CBMN), UMR 5248, Institut Européen de Chimie et Biologie, Université de Bordeaux, Centre National de la Recherche Scientifique (CNRS) , 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie, UMS3033/US001, Université de Bordeaux, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS , F-33607 Pessac, France
| | - Morgane Pasco
- Institut de Chimie et Biologie des Membranes et des Nano-objets 6 (CBMN), UMR 5248, Institut Européen de Chimie et Biologie, Université de Bordeaux, Centre National de la Recherche Scientifique (CNRS) , 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Céline Douat
- Institut de Chimie et Biologie des Membranes et des Nano-objets 6 (CBMN), UMR 5248, Institut Européen de Chimie et Biologie, Université de Bordeaux, Centre National de la Recherche Scientifique (CNRS) , 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Gilles Guichard
- Institut de Chimie et Biologie des Membranes et des Nano-objets 6 (CBMN), UMR 5248, Institut Européen de Chimie et Biologie, Université de Bordeaux, Centre National de la Recherche Scientifique (CNRS) , 2 rue Robert Escarpit, F-33607 Pessac, France
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16
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Hongen T, Taniguchi T, Monde K. Modifying oligoalanine conformation by replacement of amide to ester linkage. Chirality 2018; 30:396-401. [DOI: 10.1002/chir.22823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Takahiro Hongen
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science; Hokkaido University; Sapporo Japan
| | - Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science; Hokkaido University; Sapporo Japan
| | - Kenji Monde
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science; Hokkaido University; Sapporo Japan
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Pulka-Ziach K, Sęk S. α-Helicomimetic foldamers as electron transfer mediators. NANOSCALE 2017; 9:14913-14920. [PMID: 28949361 DOI: 10.1039/c7nr05209j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
α-Helical peptides are known as efficient mediators of electron transfer; however, their use is limited to compounds longer that 7-10 residues. To overcome this limitation, α-helicomimetic foldamers, based on the oligourea backbone with the general formula [-CH(R)-CH2-NH-CO-NH]n, were synthesized. Oligoureas are known to adopt a robust 2.5-helical conformation where only four residues are enough to form stable 1.5 helical turns. This feature makes them great models to study the charge transfer process and the dependence of the mechanism of the electron transition on the length of the mediator. Two families of different chain length (2, 4 and 6 residues) oligoureas were synthesized with a thiol group attached to the δ+ or δ- helix dipole pole. This enables the adsorption of the molecules onto the gold surface, leading to the formation of self-assembled monolayers. The helicity of compounds was confirmed in solution and in the solid state. Such systems were used to study the electron transfer process by current sensing atomic force microscopy (CS-AFM). The results showed that oligoureas may act as electron transfer mediators. Additionally, it was shown by the increasing force applied to the AFM tip that the oligourea helix is more stable than the helix formed by peptides.
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Affiliation(s)
- K Pulka-Ziach
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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Antunes S, Douat C, Guichard G. Solid-Phase Synthesis of Hybrid Urea Oligomers Containing Conservative Thiourea Mutations. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Collie GW, Pulka-Ziach K, Guichard G. Surfactant-facilitated crystallisation of water-soluble foldamers. Chem Sci 2016; 7:3377-3383. [PMID: 29997832 PMCID: PMC6006954 DOI: 10.1039/c6sc00090h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/10/2016] [Indexed: 12/16/2022] Open
Abstract
Common surfactants promote the crystallisation of a series of water-soluble oligourea foldamers which had previously proven resistant to crystallisation efforts.
X-ray crystallography has played a major role in the advancement of foldamer research, however, obtaining well-formed single crystals of suitable quality for structure determination by X-ray diffraction methods is often rather challenging. Towards this end, we report here the ability of common surfactants to promote the crystallisation of a series of water-soluble oligourea foldamers which had previously proven highly resistant to crystallisation. Four high-resolution crystal structures are reported, suggesting certain surfactants could be potentially useful tools for the crystallisation of intractable water-soluble foldamers (or peptides).
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Affiliation(s)
- G W Collie
- Univ. Bordeaux , CBMN , UMR 5248 , Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33607 Pessac , France . .,CNRS , CBMN , UMR 5248 , F-33600 , Pessac , France
| | - K Pulka-Ziach
- Univ. Bordeaux , CBMN , UMR 5248 , Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33607 Pessac , France . .,CNRS , CBMN , UMR 5248 , F-33600 , Pessac , France
| | - G Guichard
- Univ. Bordeaux , CBMN , UMR 5248 , Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33607 Pessac , France . .,CNRS , CBMN , UMR 5248 , F-33600 , Pessac , France
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Shaping quaternary assemblies of water-soluble non-peptide helical foldamers by sequence manipulation. Nat Chem 2015; 7:871-8. [DOI: 10.1038/nchem.2353] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/19/2015] [Indexed: 12/28/2022]
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Balamurugan D, Muraleedharan KM. Conformational Switching in Heterochiral α,β2,3-Hybrid Peptides in Response to Solvent Polarity. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500534] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Balamurugan D, Muraleedharan KM. Can Helical Peptides Unwind One Turn at a Time? - Controlled Conformational Transitions in α,β(2,3)-Hybrid Peptides. Chemistry 2015; 21:9332-8. [PMID: 25980664 DOI: 10.1002/chem.201501198] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Indexed: 11/07/2022]
Abstract
Unfolding of helical trans-β(2,3) -hybrid peptides with (α-β)n α composition, when executed by increasing solvent polarity or temperature, proceeded in a systematic manner with the turns unwinding sequentially; C-terminal region of these peptides were first to unwind and the process propagated towards N terminus with more and more β residues equilibrating from the gauche to the anti rotameric state across Cα-Cβ . This is evidenced by clear change in their Cβ H signal splitting, (3)JCαH-CβH values, and sequential disappearance of i,i+2 NOEs.
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Affiliation(s)
- Dhayalan Balamurugan
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036 (India)
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Maury J, Le Bailly BAF, Raftery J, Clayden J. Conformational cooperativity between helical domains of differing geometry in oligoamide–oligourea foldamer chimeras. Chem Commun (Camb) 2015; 51:11802-5. [DOI: 10.1039/c5cc02995c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Two foldamer domains of different classes (urea and amide) remain in conformational communication, and adopt a well-defined global structure in solution, provided the interdomain hydrogen-bonds are suitably orientated.
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Affiliation(s)
- Julien Maury
- School of Chemistry
- University of Manchester
- Manchester M13 9PL
- UK
| | | | - James Raftery
- School of Chemistry
- University of Manchester
- Manchester M13 9PL
- UK
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Nelli YR, Antunes S, Salaün A, Thinon E, Massip S, Kauffmann B, Douat C, Guichard G. Isosteric Substitutions of Urea to Thiourea and Selenourea in Aliphatic Oligourea Foldamers: Site-Specific Perturbation of the Helix Geometry. Chemistry 2014; 21:2870-80. [DOI: 10.1002/chem.201405792] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Indexed: 01/05/2023]
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