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Kavčič L, Ilc G, Wang B, Vlahoviček-Kahlina K, Jerić I, Plavec J. α-Hydrazino Acid Insertion Governs Peptide Organization in Solution by Local Structure Ordering. ACS OMEGA 2024; 9:22175-22185. [PMID: 38799301 PMCID: PMC11112695 DOI: 10.1021/acsomega.4c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/18/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]
Abstract
In this work, we have applied the concept of α-hydrazino acid insertion in a peptide sequence as a means of structurally organizing a potential protein-protein interactions (PPI) inhibitor. Hydrazino peptides characterized by the incorporation of an α-hydrazino acid at specific positions introduce an additional nitrogen atom into their backbone. This modification leads to a change in the electrostatic properties of the peptide and induces the restructuring of its hydrogen bonding network, resulting in conformational changes toward more stable structural motifs. Despite the successful use of synthetic hydrazino oligomers in binding to nucleic acids, the structural changes due to the incorporation of α-hydrazino acid into short natural peptides in solution are still poorly understood. Based on NMR data, we report structural models of p53-derived hydrazino peptides with elements of localized peptide structuring in the form of an α-, β-, or γ-turn as a result of hydrazino modification in the peptide backbone. The modifications could potentially lead to the preorganization of a helical secondary peptide structure in a solution that is favorable for binding to a biological receptor. Spectroscopically, we observed that the ensemble averaged rapidly interconverting conformations, including isomerization of the E-Z hydrazide bond. This further increases the adaptability by expanding the conformational space of hydrazine peptides as potential protein-protein interaction antagonists.
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Affiliation(s)
- Luka Kavčič
- Slovenian
NMR Centre, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | - Gregor Ilc
- Slovenian
NMR Centre, National Institute of Chemistry, Ljubljana 1000, Slovenia
- EN-FIST
Centre of Excellence, Ljubljana 1000, Slovenia
| | - Baifan Wang
- Slovenian
NMR Centre, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | | | - Ivanka Jerić
- Division
of Organic Chemistry and Biochemistry, Rudjer
Bošković Institute, Zagreb 10000, Croatia
| | - Janez Plavec
- Slovenian
NMR Centre, National Institute of Chemistry, Ljubljana 1000, Slovenia
- EN-FIST
Centre of Excellence, Ljubljana 1000, Slovenia
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Ljubljana 1000, Slovenia
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2
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Ibrahim MIA, Pickaert G, Stefan L, Jamart-Grégoire B, Bodiguel J, Averlant-Petit MC. Cyclohexamer [-(d-Phe-azaPhe-Ala) 2-]: good candidate to formulate supramolecular organogels. RSC Adv 2020; 10:43859-43869. [PMID: 35519698 PMCID: PMC9058333 DOI: 10.1039/d0ra07775e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/16/2020] [Indexed: 11/24/2022] Open
Abstract
Molecular self-assembly is a fascinating process which has become an area of great interest in supramolecular chemistry, as it leads in certain cases to molecular gels. Organogels formulated from low molecular weight compounds (LMWOGs) have attracted much interest in the past decades due to their applications as new soft materials. Herein, we report on the ability of the cyclic pseudopeptide cyclo-[-(d-Phe-azaPhe-Ala)2-] (2) to self-assemble in some aromatic solvents and to form organogels driven by non-covalent forces, mainly hydrogen bonding and π-stacking interactions. Comprehensive FTIR and NMR studies emphasized that this cyclic aza-peptide adopts a β-turn conformation at low concentration in toluene, while an equilibrium between the monomeric states (intramolecular forces) and the supramolecular structures (intra- and intermolecular forces) is established at high concentration (gel state). Rheological investigations of the organogels highlight the dependence of their stiffness (up to ∼4 kPa) and sol/gel transition temperatures (up to 100 °C) as a function of the solvent and concentration of gelator used. The formulation of fibrous structures confirmed the phenomenon of self-assembly. Finally, we found that cyclo-[-(d-Phe-azaPhe-Ala)2-] is an effective organogelator for application in phase selective gelation (PSG) of organic solvents from aqueous/organic mixtures with recovery percents up to 96%.
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Affiliation(s)
- Mohamed I A Ibrahim
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM), UMR 7375, CNRS, Université de Lorraine Nancy France
- Laboratory of Marine Chemistry, Marine Environment Division, National Institute of Oceanography and Fisheries, NIOF Egypt
| | - Guillaume Pickaert
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM), UMR 7375, CNRS, Université de Lorraine Nancy France
| | - Loïc Stefan
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM), UMR 7375, CNRS, Université de Lorraine Nancy France
| | - Brigitte Jamart-Grégoire
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM), UMR 7375, CNRS, Université de Lorraine Nancy France
| | - Jacques Bodiguel
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM), UMR 7375, CNRS, Université de Lorraine Nancy France
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3
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Jędrzejewska H, Szumna A. Peptide-based capsules with chirality-controlled functionalized interiors - rational design and amplification from dynamic combinatorial libraries. Chem Sci 2019; 10:4412-4421. [PMID: 31057768 PMCID: PMC6482442 DOI: 10.1039/c8sc05455j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/13/2019] [Indexed: 01/07/2023] Open
Abstract
Self-assembled capsules were designed by two approaches and synthesized using azapeptides of various chiralities attached to resorcin[4]arene by semicarbazone linkers.
Peptides are commonly perceived as inapplicable components for construction of porous structures. Due to their flexibility the design is difficult and shape persistence of such putative structures is diminished. Notwithstanding these limitations, the advantages of peptides as building blocks are numerous: they are functional and functionalizable, widely available, diverse and biocompatible. We aimed at the construction of discrete porous structures that exploit the inherent functionality of peptides by an approach that is inspired by nature: structural pockets are defined by the backbones of peptides while functionality is introduced by their side chains. In this work peptide ribbons were preorganized on a macrocyclic scaffold using azapeptide–aldehyde reactions. The resulting cavitands with semicarbazone linkers arrange the peptide backbones at positions that are suitable for self-assembly of dimeric capsules by formation of binding motifs that resemble eight-stranded β-barrels. Self-assembly properties and inside/outside positions of the side chains depend crucially on the chirality of peptides. By rational optimization of successive generations of capsules we have found that azapeptides containing three amino acids in a (l, d, d) sequence give well-defined dimeric capsules with side chains inside their cavities. Taking advantage of the reversibility of the reaction of semicarbazone formation we have also employed the dynamic covalent chemistry (DCC) for a combinatorial discovery of capsules that could not be rationally designed. Indeed, the results show that stable capsules with side chains positioned internally can be obtained even for shorter sequences but only for combination peptides of (l, l) and (d, l) chirality. The hybrid (l, l)(d, l) capsule is amplified directly from a reaction mixture containing two different peptides. All capsules gain substantial ordering upon self-assembly, which is manifested by a two orders of magnitude increase of the intensity of CD spectra of capsules compared with non-assembled analogs. Temperature-dependent CD measurements indicate that the capsules remain stable over the entire temperature range tested (20–100 °C). Circular dichroism coupled with TD DFT calculations, DOSY measurements and X-ray crystallography allow for elucidation of the structures in the solid state and in solution and guide their iterative evolution for the current goals.
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Affiliation(s)
- Hanna Jędrzejewska
- Institute of Organic Chemistry , Polish Academy of Sciences , Kasprzaka 44/52 , 01-224 Warsaw , Poland .
| | - Agnieszka Szumna
- Institute of Organic Chemistry , Polish Academy of Sciences , Kasprzaka 44/52 , 01-224 Warsaw , Poland .
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4
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Romero E, Moussodia RO, Jamart-Grégoire B, Acherar S. Synthesis and Conformational Analysis of 1:1 [α/α- N
α
-Bn-Hydrazino] and 1:1 [α- N
α
-Bn-Hydrazino/α] Trimers: Determination of the Δ δ
Value for the γ-Turn Structuration. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Eugénie Romero
- Laboratoire de Chimie Physique Macromoléculaire (LCPM); UMR CNRS-UL 7375; ENSIC; Université de Lorraine; 1 rue Grandville BP451 54001 Nancy France
| | - Ralph-Olivier Moussodia
- Laboratoire de Chimie Physique Macromoléculaire (LCPM); UMR CNRS-UL 7375; ENSIC; Université de Lorraine; 1 rue Grandville BP451 54001 Nancy France
| | - Brigitte Jamart-Grégoire
- Laboratoire de Chimie Physique Macromoléculaire (LCPM); UMR CNRS-UL 7375; ENSIC; Université de Lorraine; 1 rue Grandville BP451 54001 Nancy France
| | - Samir Acherar
- Laboratoire de Chimie Physique Macromoléculaire (LCPM); UMR CNRS-UL 7375; ENSIC; Université de Lorraine; 1 rue Grandville BP451 54001 Nancy France
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5
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Burade SS, Saha T, Bhuma N, Kumbhar N, Kotmale A, Rajamohanan PR, Gonnade RG, Talukdar P, Dhavale DD. Self-Assembly of Fluorinated Sugar Amino Acid Derived α,γ-Cyclic Peptides into Transmembrane Anion Transport. Org Lett 2017; 19:5948-5951. [DOI: 10.1021/acs.orglett.7b02942] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sachin S. Burade
- Garware
Research Center, Department of Chemistry, Savitribai Phule Pune University (formerly Pune University), Pune 411007, India
| | - Tanmoy Saha
- Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Naresh Bhuma
- Garware
Research Center, Department of Chemistry, Savitribai Phule Pune University (formerly Pune University), Pune 411007, India
| | - Navanath Kumbhar
- Garware
Research Center, Department of Chemistry, Savitribai Phule Pune University (formerly Pune University), Pune 411007, India
| | | | | | | | - Pinaki Talukdar
- Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Dilip D. Dhavale
- Garware
Research Center, Department of Chemistry, Savitribai Phule Pune University (formerly Pune University), Pune 411007, India
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Ibrahim MIA, Zhou Z, Deng C, Didierjean C, Vanderesse R, Bodiguel J, Averlant-Petit MC, Jamart-Grégoire B. Impact of Cα
-Chirality on Supramolecular Self-Assembly in Cyclo-2:1-[α/aza]-Hexamers (d
/l
-Phe-azaPhe-Ala)2. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700555] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mohamed Ibrahim Abdelmoneim Ibrahim
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
- Marine Chemistry Department; National Institute of Oceanography and Fisheries (NIOF); Qayet-Bey, El-Anfoushy 21557 Alexandria Egypt
| | - Zhou Zhou
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
| | - Cheng Deng
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
| | - Claude Didierjean
- Laboratoire de Cristallographie; Résonance Magnétique et Modélisation (CRM2); UMR 7036; CNRS; Université de Lorraine; Boulevard des Aiguillettes 56506 Vandoeuvre-lès-Nancy France
| | - Régis Vanderesse
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
| | - Jacques Bodiguel
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
| | - Marie-Christine Averlant-Petit
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
| | - Brigitte Jamart-Grégoire
- Laboratoire de Chimie-Physique Macromoléculaire (LCPM); UMR 7375; CNRS; Université de Lorraine; 1 rue Grandville, BP 20451 54001 Nancy France
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Mehawed Abdellatif M, Acherar S. Low-cost and multi-gram scale synthesis of chiral Nβ-Boc protected α-Nα-hydrazino diesters. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.02.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Romero E, Moussodia RO, Kriznik A, Wenger E, Acherar S, Jamart-Grégoire B. Spontaneous Self-Assembly of Fully Protected Ester 1:1 [α/α-N α-Bn-hydrazino] Pseudodipeptides into a Twisted Parallel β-Sheet in the Crystal State. J Org Chem 2016; 81:9037-9045. [PMID: 27627436 DOI: 10.1021/acs.joc.6b01680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous studies have demonstrated that amidic α/β-pseudodipeptides, 1:1 [α/α-Nα-Bn-hydrazino], have the ability to fold via a succession of γ-turn (C7 pseudocycle) and hydrazinoturn in CDCl3 solution, their amide terminals enabling the formation of an intramolecular H-bond network. Despite their lack of a primary amide terminals allowing the formation of the hydrazinoturn, their ester counterparts 1-4 were proven to self-assemble into C6 and C7 pseudocycles by intramolecular H-bonds in solution state and into an uncommon twisted parallel β-sheet through intermolecular H-bonding in the crystal state to form a supramolecular helix, with eight molecules needed to complete a full 360° rotation. Such self-organization (with eight molecules) has only been observed in a specific α/α-pseudodipeptide, depsipeptide (Boc-Leu-Lac-OEt). Relying on IR absorption, NMR, X-ray diffraction, and CD analyses, the aim of this study was to demonstrate that stereoisomers of ester 1:1 [α/α-Nα-Bn-hydrazino] pseudodipeptides 1-4 are able to self-assemble into this β-helical structure. The absolute configuration of the asymmetric Cα-atom of the α-amino acid residue influences the left- or right-handed twist without changing the pitch of the formed helix.
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Affiliation(s)
- Eugénie Romero
- Laboratoire de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375 , 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
| | - Ralph-Olivier Moussodia
- Laboratoire de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375 , 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
| | - Alexandre Kriznik
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Université de Lorraine-CNRS, UMR 7365 and Service Commun de Biophysique Interactions Moléculaires (SCBIM), Université de Lorraine, FR3209, Biopôle de l'Université de Lorraine, Campus Biologie Santé - Faculté de Médecine , 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Emmanuel Wenger
- Laboratoire de Crystallographie, Résonance Magnétique et Modélisations (CRM2), Université de Lorraine-CNRS, UMR 7036, Faculté des Sciences et Technologies , BP 70239, Boulevard des Aiguillettes, 54506 Vandœuvre-lès-Nancy cedex, France
| | - Samir Acherar
- Laboratoire de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375 , 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
| | - Brigitte Jamart-Grégoire
- Laboratoire de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375 , 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
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9
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Ghorai A, Achari B, Chattopadhyay P. Self-assembly of cyclic peptides and peptidomimetic macrocycles: linking structure with function. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.04.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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10
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Abstract
Hydrazino depsipeptides, a new class of backbone extended peptidomimetics were prepared by the Passerini reaction of α-hydrazino acids, carbonyl compounds and isocyanides.
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Affiliation(s)
- Josipa Suć
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Danijela Barić
- Division of Physical Chemistry
- Ruđer Bošković Institute
- 10 000 Zagreb
- Croatia
| | - Ivanka Jerić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
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