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Mauran L, Assailly C, Goudreau SR, Odaert B, Guichard G, Pasco M. Short Oligourea Foldamers as N- or C-Caps for Promoting α-Helix Formation in Water. Chembiochem 2024:e202400427. [PMID: 38943628 DOI: 10.1002/cbic.202400427] [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: 05/13/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/01/2024]
Abstract
While foldamers have been extensively studied as protein mimics and especially as α-helix mimics, their use as capping motif to enhance α-helix propensity remains comparatively much limited. In this study, we leverage the structural similarities between urea-based helical foldamers and α-helix to investigate the efficacy of oligoureas as N- or C-caps for reinforcing α-helical structures in water. Short oligoureas, comprising 3 to 4 residues, were strategically introduced at the N- or C-terminus of two peptide sequences (S-peptide and an Ala-rich model sequence). The impact of these foldamer insertions on peptide conformation was examined using electronic circular dichroism (ECD) and solution NMR. This research identifies specific foldamer sequences capable of promoting α-helicity when incorporated at either terminus of the peptides. Not only does this work broaden the application scope of foldamers, but it also provides valuable insights into novel strategies for modulating peptide conformation in aqueous environments. The findings presented in this study may have implications for peptide design and the development of bioactive foldamer-based peptide mimics.
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Affiliation(s)
- Laura Mauran
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600, Pessac, France
- IMMUPHARMA BIOTECH SAS, 15 rue de Bruxelles, 75009, Paris, France
| | - Coralie Assailly
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600, Pessac, France
| | | | - Benoît Odaert
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600, Pessac, France
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600, Pessac, France
| | - Morgane Pasco
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600, Pessac, France
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2
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Sukumar G, Rahul, Nayani K, Mainkar PS, Prashanth J, Sridhar B, Sarma AVS, Bharatam J, Chandrasekhar S. 6-Strand to Stable 10/12 Helix Conformational Switch by Incorporating Flexible β-hGly in the Homooligomers of Camphor Derived β-Amino Acid: NMR and X-Ray Crystallographic Evidence. Angew Chem Int Ed Engl 2024; 63:e202403321. [PMID: 38482551 DOI: 10.1002/anie.202403321] [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: 02/16/2024] [Indexed: 04/07/2024]
Abstract
Rational design of unnatural amino acid building blocks capable of stabilizing predictable secondary structures similar to protein fragments is pivotal for foldamer chemistry/catalysis. Here, we introduce novel β-amino acid building blocks: [1S,2R,4R]exoCDA and [1S,2S,4R]endoCDA, derived from the abundantly available R(+)-camphor, which is traditionally known for its medicinal value. Further, we demonstrate that the homooligomers of exoCDA adopt 6-strand conformation, which switches to a robust 10/12-helix simply by inserting flexible β-hGly spacer at alternate positions (1 : 1 β-hGly/exoCDA heterooligomers), as evident by DFT-calculations, solution-state NMR spectroscopy and X-ray crystallography. To the best of our knowledge, this is the first example of crystalline-state structure of left-handed 10/12-mixed helix, that is free from the conventional approach of employing β-amino acids of either alternate chirality or alternate β2/β3 substitutions, to access the 10/12-helix. The results also show that the homooligomers of heterochiral exoCDA don't adopt helical fold, instead exhibit banana-shaped strands, whereas the homodimers of the other diastereomer endoCDA, nucleate 8-membered turns. Furthermore, the homo-exoCDA and hetero-[β-hGly-exoCDA] oligomers are found to exhibit self-association properties with distinct morphological features. Overall, the results offer new possibilties of constructing discrete stable secondary and tertiary structures based on CDAs, which can accommodate flexible residues with desired side-chain substitutions.
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Affiliation(s)
- Genji Sukumar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Department of Chemistry, Adikavi Nannaya University, Rajamahendravaram, Andhra Pradesh, 533296, India
| | - Rahul
- Centre for NMR, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kiranmai Nayani
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prathama S Mainkar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jupally Prashanth
- Centre for X-ray Crystallography, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Balasubramanian Sridhar
- Centre for X-ray Crystallography, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Akella V S Sarma
- Centre for NMR, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jagadeesh Bharatam
- Centre for NMR, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Srivari Chandrasekhar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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3
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Just D, Palivec V, Bártová K, Bednárová L, Pazderková M, Císařová I, Martinez-Seara H, Jahn U. Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides. Commun Chem 2024; 7:114. [PMID: 38796536 PMCID: PMC11128005 DOI: 10.1038/s42004-024-01201-7] [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: 09/20/2023] [Accepted: 05/14/2024] [Indexed: 05/28/2024] Open
Abstract
Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,β,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,β,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.
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Affiliation(s)
- David Just
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Vladimír Palivec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843, Prague 2, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
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4
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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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5
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Liu B, Xing P. Hydrogen Bonded Foldamers with Axial Chirality: Chiroptical Properties and Applications. Chemistry 2023; 29:e202202665. [PMID: 36281580 DOI: 10.1002/chem.202202665] [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: 08/26/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Folding phenomenon refers to the formation of a specific conformation widely featured by the intramolecular interactions, which broadly exist in biomacromolecules, and are closely related to their structures and functions. A variety of oligomeric folded molecules have been designed and synthesized, namely "foldamer", exhibiting potentials in pharmaceutical and catalysis. Molecular folding is a promising strategy to transfer chirality from substituents to the whole skeleton, when chirality transfer, amplification, evolution, and other behaviors could be achieved. Investigating chirality using foldamer model deepens the understanding of the structure-function correlation in biomacromolecules and expands the molecular toolbox towards chiroptical and asymmetrical chemistry. Substitutes with abundant hydrogen bonding sites conjugated to a rotatable aryl group afford a parallel β-sheet-like conformation, which enables the emergence and manipulation of axial chirality. This concept aims to give a brief introduction and summary of the hydrogen bonded foldamers with anchored axial chirality, by taking some recent cases as examples. Design principles, control over axial chirality and applications are also reviewed.
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Affiliation(s)
- Bingyu Liu
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Pengyao Xing
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
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6
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Ur Rahim J, Ahmad SM, Amin T, Chowdhary R, Goswami A, Rai R. Synthesis, conformation and cytotoxic activity of short hybrid peptides containing conformationally constrained 1-(aminomethyl)cyclohexanecarboxylic acid and gabapentin. Peptides 2022; 158:170897. [PMID: 36279986 DOI: 10.1016/j.peptides.2022.170897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/08/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
Abstract
The present work describes the synthesis,conformation and cytotoxic activities of short β/γ hybrid peptides, Boc-β2,2-Ac6c-Gpn-NHMe, BG1; Boc-(β2,2-Ac6c-Gpn)2-OMe, BG2; Boc-(β2,2-Ac6c-Gpn)3-OMe, BG3; H-β2,2-Ac6c-Gpn-NHMe, BG4; H-(β2,2-Ac6c-Gpn)2-OMe, BG5; H-(β2,2-Ac6c-Gpn)3-OMe, BG6, Boc-β2,2-Ac6c-Gpn-OMe, BG7 and H-β2,2-Ac6c-Gpn-OMe, BG8. Mixed C6/C7 conformations were observed for β/γ hybrid peptides. Further, BG1-BG8 were screened against MCF-7 (Breast cancer), A549 (Lung Cancer), PC-3 (Prostate cancer), HCT-116 (Colon cancer), and MDA-MB-231 (Breast cancer) cell lines. Among all, BG6 exhibited potent cytotoxicity against all cancer cell lines with IC50 ranging from 1.6 μM to 6.3 μM with relatively low cytotoxicity against normal epithelial breast cell line fR-2 and human embryonic kidney cell line HEK-293. Minimal hemolytic activity was observed for BG6 against human erythrocytes. Peptide BG6 displayed anti-migratory and anti-invasive potentials showing strong interactions with intrinsic apoptotic markers Bcl-2, Bax, and cleaved-PARP, as well as the induction of the mitochondria maladjustment mediated apoptosis.
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Affiliation(s)
- Junaid Ur Rahim
- Natural Products and Medicinal Chemistry Division (NPMC), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu and Kashmir 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Syed Mudabir Ahmad
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu and Kashmir 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tanzeeba Amin
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu and Kashmir 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rubina Chowdhary
- Natural Products and Medicinal Chemistry Division (NPMC), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu and Kashmir 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anindya Goswami
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu and Kashmir 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Rajkishor Rai
- Natural Products and Medicinal Chemistry Division (NPMC), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu and Kashmir 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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7
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Wei H, Min J, Wang Y, Shen Y, Du Y, Su R, Qi W. Bioinspired porphyrin-peptide supramolecular assemblies and their applications. J Mater Chem B 2022; 10:9334-9348. [PMID: 36373597 DOI: 10.1039/d2tb01660e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Inspired by the hierarchical chiral assembly of porphyrin-proteins in photosynthetic systems, the hierarchical self-assembly of porphyrin-amino acids/peptides provides a novel strategy for constructing functional materials. How to artificially simulate the assembly of porphyrins, proteins, and other cofactors in the photosynthesis system to obtain persistent strong light capture, charge separation and catalytic reactions has become an important concern in the construction of biomimetic photosynthesis systems. This paper summarizes the different assembly strategies adopted in recent years, the effects of driving forces on self-assembly, and the application of porphyrin-peptides in catalysis and biomedicine, and briefly discusses the challenges and prospects for future research.
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Affiliation(s)
- Hao Wei
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China.
| | - Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China.
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China. .,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Yuhe Shen
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China.
| | - Yaohui Du
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China.
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
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8
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Debnath S, Ghosh S, Kumar D, Vasudev PG, Satpati P, Chatterjee S. Effect of differential backbone di-substitution of gamma amino acid residues on the conformation and assembly of their Fmoc derivatives in solid and solution states. Chem Asian J 2022; 17:e202200356. [PMID: 35603989 DOI: 10.1002/asia.202200356] [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: 04/06/2022] [Revised: 05/23/2022] [Indexed: 11/11/2022]
Abstract
We studied the effect of variable backbone dimethyl-substitution of γ amino acid residues (γ 2,2 , γ 3,3 and γ 4,4 ) on the conformation and assembly, in crystals and solution of their Fmoc derivatives. Crystal structure of γ 2,2 and γ 4,4 derivatives showed distinct conformations (open/close for γ 2,2 /γ 4,4 ) that differed in torsion angles, hydrogen-bonding and most importantly the π-π Fmoc-stacking interactions (relatively favorable for γ 4,4 -close). Fmoc derivatives existed in an equilibrium between major-monomeric (low energy, non-hydrogen bonded) and minor-dimeric (high energy, hydrogen bonded) populations in solution. Rate of major/minor population exchange was dependent on the position of substitution, highest being for γ 4,4 derivative. In solution, assembly of Fmoc derivatives was solvent dependent, but it was independent of the position of geminal substitution. Crystallization was primarily governed by the stabilization of high-energy dimer by favorable π-π stacking involving Fmoc moieties. High free-energy of the dimers (γ 2,2 -close, γ 3,3 -open/close) offset favorable stacking interactions and hindered crystallization.
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Affiliation(s)
- Swapna Debnath
- Indian Institute of Technology Guwahati, Department of chemistry, INDIA
| | - Suvankar Ghosh
- Indian Institute of Technology Guwahati, Bioscience and Bioengineering, INDIA
| | - Dinesh Kumar
- CSIR-CIMAP: Central Institute of Medicinal and Aromatic Plants CSIR, Plant Biotechnology Division, INDIA
| | - Prema G Vasudev
- CSIR-CIMAP: Central Institute of Medicinal and Aromatic Plants CSIR, Plant Biotechnology Division, INDIA
| | - Priyadarshi Satpati
- Indian Institute of Technology Guwahati, Bioscience and BIoengineering, INDIA
| | - Sunanda Chatterjee
- Indian Institute of Technology Guwahati, CHEMISTRY, IIT GUWAHATI, 781039, GUWAHATI, INDIA
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9
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Environmental Modulation of Chiral Prolinamide Catalysts for Stereodivergent Conjugate Addition. J Catal 2022; 406:126-133. [PMID: 35087258 PMCID: PMC8788998 DOI: 10.1016/j.jcat.2022.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Synthetic chiral catalysts generally rely on proximal functional groups or ligands for chiral induction. Enzymes often employ environmental chirality to achieve stereoselectivity. Environmentally controlled catalysis has benefits such as size and shape selectivity but is underexplored by chemists. We here report molecularly imprinted nanoparticles (MINPs) that utilized their environmental chirality to either augment or reverse the intrinsic selectivity of a chiral prolinamide cofactor. The latter ability allowed the catalyst to produce products otherwise disfavored in the conjugate addition of aldehyde to nitroalkene. The catalysis occurred in water at room temperature and afforded γ-nitroaldehydes with excellent yields (up to 94%) and ee (>90% in most cases). Up to 25:1 syn/anti and 1:6 syn/anti ratios were achieved through a combination of catalyst-derived and environmentally enabled selectivity. The high enantioselectivity of the MINP also made it possible for racemic catalysts to perform asymmetric catalysis, with up to 80% ee for the conjugate addition.
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10
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Shin YH, Yang H. Exploration of α/β/γ-peptidomimetics design for BH3 helical domains. Chem Commun (Camb) 2022; 58:945-948. [PMID: 34985060 DOI: 10.1039/d1cc05758h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Systematic incorporation of ring-constrained β- and γ-amino acid residues into α-helix mimetics engenders stable helical secondary structures. In this paper, functional α/β/γ-helical peptidomimetics were explored for mimicry of BH3 helical domains, Bim as a pioneering study. The Bim-based α/β/γ-peptides in an αγααβα-hexad repeat with five helical turns inhibited the interaction between Bak and Bcl-xL with excellent resistance towards proteolytic digestion. Further optimization of the α/β/γ-backbone strategy will considerably expand the utility of functional α/β/γ-peptidomimetics, in particular due to its prominent stability against proteolysis.
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Affiliation(s)
- Young-Hee Shin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Chemical Engineering & Biotechnology, Korea Polytechnic University, Siheung 15073, South Korea.
| | - Hyunjun Yang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
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11
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Legrand B, Maillard LT. α,β-Unsaturated γ-Peptide Foldamers. Chempluschem 2021; 86:629-645. [PMID: 33856125 DOI: 10.1002/cplu.202100045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/31/2021] [Indexed: 01/01/2023]
Abstract
Despite their concomitant emergence in the 1990s, γ-peptide foldamers have not developed as fast as β-peptide foldamers and to date, only a few γ-oligomer structures have been reported, and with sparse applications. Among these examples, sequences containing α,β-unsaturated γ-amino acids have recently drawn attention since the Z/E configurations of the double bond provide opposite planar restrictions leading to divergent conformational behaviors, from helix to extended structures. In this Review, we give a comprehensive overview of the developments of γ-peptide foldamers containing α,β-unsaturated γ-amino acids with examples of applications for health and catalysis, as well as materials science.
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Affiliation(s)
- Baptiste Legrand
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France., 15 Av. Charles Flahault BP 14 491, 34093, Montpellier Cedex 5, France
| | - Ludovic T Maillard
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France., 15 Av. Charles Flahault BP 14 491, 34093, Montpellier Cedex 5, France
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12
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Dey S, Misra R, Saseendran A, Pahan S, Gopi HN. Metal‐Coordinated Supramolecular Polymers from the Minimalistic Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sanjit Dey
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Rajkumar Misra
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Abhijith Saseendran
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Saikat Pahan
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Hosahudya N. Gopi
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
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13
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Dey S, Misra R, Saseendran A, Pahan S, Gopi HN. Metal‐Coordinated Supramolecular Polymers from the Minimalistic Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2021; 60:9863-9868. [DOI: 10.1002/anie.202015838] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/19/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Sanjit Dey
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Rajkumar Misra
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Abhijith Saseendran
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Saikat Pahan
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
| | - Hosahudya N. Gopi
- Department of Chemistry Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road Pune 411008 India
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14
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Affiliation(s)
- Zebediah C. Girvin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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15
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Reja RM, Kumar V, George G, Patel R, Puneeth Kumar DRGKR, Raghothama S, Gopi HN. Structural Investigation of Hybrid Peptide Foldamers Composed of α-Dipeptide Equivalent β-Oxy-δ 5 -amino Acids. Chemistry 2020; 26:4304-4309. [PMID: 31960517 DOI: 10.1002/chem.201904780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/15/2020] [Indexed: 01/05/2023]
Abstract
Due to their equivalent lengths, δ-amino acids can serve as surrogates of α-dipeptides. However, δ-amino acids with proteinogenic side chains have not been well studied because of synthetic difficulties and because of their insolubility in organic solvents. Recently we reported the spontaneous supramolecular gelation of δ-peptides composed of β(O)-δ5 -amino acids. Here, we report the incorporation of β(O)-δ5 -amino acids as guests into the host α-helix, α,γ-hybrid peptide 12-helix and their single-crystal conformations. In addition, we studied the solution conformations of hybrid peptides composed of 1:1 alternating α and β(O)-δ5 -amino acids. In contrast to the control α-helix structures, the crystal structure of peptides with β(O)-δ5 -amino acids exhibit α-helical conformations consisting of both 13- and 10-membered H-bonds. The α,δ-hybrid peptide adopted mixed 13/11-helix conformation in solution with alternating H-bond directionality. Crystal-structure analysis revealed that the α,γ4 -hybrid peptide accommodated the guest β(O)-δ5 -amino acid without significant deviation to the overall helix folding. The results reported here emphasize that β(O)-δ5 -amino acids with proteinogenic side chains can be accommodated into regular α-helix or 12-helix as guests without much deviation of the overall helix folding of the peptides.
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Affiliation(s)
- Rahi M Reja
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Vivek Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Gijo George
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Rajat Patel
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - DRGKoppalu R Puneeth Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | | | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
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16
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Tonali N, Correia I, Lesma J, Bernadat G, Ongeri S, Lequin O. Introducing sequential aza-amino acids units induces repeated β-turns and helical conformations in peptides. Org Biomol Chem 2020; 18:3452-3458. [PMID: 32091060 DOI: 10.1039/c9ob02654a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A major current issue in medicinal chemistry is the design of small peptide analogues resistant to proteolysis and able to adopt preferential conformations, while preserving the selectivity and efficiency of natural peptides. Whereas the introduction of one aza-Gly in peptides has proven numerous biological and structural interest, the conformational effect of sequential aza-Gly or aza-amino acids bearing side chains has not been investigated. In this work, experimental NMR and X-ray data together with in silico conformational studies reveal that the introduction of two consecutive aza-amino acids in pseudotripeptides induces the formation of stable hydrogen-bonded β-turn structures. Notably, this stabilization effect relies on the presence of side chains on aza-amino acids, as more flexible conformations are observed with aza-Gly residues. Remarkably, a longer aza/aza/α/aza/aza/α pseudohexapeptide containing substituted aza-amino acids adopts repeated β-turns conformations which interconvert with a fully helical structure mimicking a 310 helix.
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Affiliation(s)
- Nicolo Tonali
- Université Paris-Saclay, CNRS, BioCIS, 92290 Châtenay-Malabry, France.
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17
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Misra R, George G, Reja RM, Dey S, Raghothama S, Gopi HN. Structural insight into hybrid peptide ε-helices. Chem Commun (Camb) 2020; 56:2171-2173. [PMID: 31970340 DOI: 10.1039/c9cc07413a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unique ε-helical organizations (11-helices) from β,γ-hybrid peptides composed of chiral β3-amino acids along with achiral 3,3- or 4,4-dimethyl substituted γ-amino acids are disclosed.
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Affiliation(s)
- Rajkumar Misra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune-411021, India.
| | - Gijo George
- NMR Research Center, Indian Institute of Science, Bangalore-560012, India.
| | - Rahi M Reja
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune-411021, India.
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune-411021, India.
| | | | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune-411021, India.
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18
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Veeresh K, Gopi HN. Design of Helical Peptide Foldamers through α,β → β,γ Double-Bond Migration. Org Lett 2019; 21:4500-4504. [DOI: 10.1021/acs.orglett.9b01365] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kuruva Veeresh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Hosahudya N. Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411 008, India
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19
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Misra R, Saseendran A, Dey S, Gopi HN. Metal‐Helix Frameworks from Short Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2019; 58:2251-2255. [DOI: 10.1002/anie.201810849] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Rajkumar Misra
- Department of ChemistryIndian Institution of Science Education and Research Dr. Homi Bhabha Road Pune- 411008 India
| | - Abhijith Saseendran
- Department of ChemistryIndian Institution of Science Education and Research Dr. Homi Bhabha Road Pune- 411008 India
| | - Sanjit Dey
- Department of ChemistryIndian Institution of Science Education and Research Dr. Homi Bhabha Road Pune- 411008 India
| | - Hosahudya N. Gopi
- Department of ChemistryIndian Institution of Science Education and Research Dr. Homi Bhabha Road Pune- 411008 India
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20
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Misra R, Saseendran A, Dey S, Gopi HN. Metal-Helix Frameworks from Short Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201810849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rajkumar Misra
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 India
| | - Abhijith Saseendran
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 India
| | - Sanjit Dey
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 India
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 India
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21
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Enhancing Aromatic Foldamer Helix Dynamics to Probe Interactions with Protein Surfaces. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800855] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Debnath M, Das T, Podder D, Haldar D. α,ε-Hybrid Peptide Foldamers: Self-Assembly of Peptide with Trans Carbon-Carbon Double Bonds in the Backbone and Its Saturated Analogue. ACS OMEGA 2018; 3:8760-8768. [PMID: 31459008 PMCID: PMC6644893 DOI: 10.1021/acsomega.8b00832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/24/2018] [Indexed: 05/02/2023]
Abstract
The effect of geometrically rigid trans α,β-unsaturated ε-amino acids on the structure, folding, and assembly of α,ε-hybrid peptide foldamers has been reported. From single-crystal diffraction analysis, the unsaturated tetrapeptide 1 has stapler-pin-like structure but without intramolecular hydrogen bond. The asymmetric unit has two molecules that are stabilized by multiple intermolecular hydrogen bonding interactions as well as π-π stacking interactions between the aromatic rings of 3-aminocinnamic acid. Peptide 1 does not form organogel. But on hydrogenation, peptide 1 provides the saturated α,ε-hybrid peptide foldamer 2, which forms instant gel in most of the aromatic solvents. The gel exhibits high stability. The unsaturated peptide 1 has porous microsphere morphology, but saturated analogue 2 has ribbonlike morphology. The gel has been used efficiently for removal of cationic organic pollutants from waste water.
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23
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Misra R, Raja KMP, Hofmann HJ, Gopi HN. Modulating the Structural Properties of α,γ-Hybrid Peptides by α-Amino Acid Residues: Uniform 12-Helix Versus "Mixed" 12/10-Helix. Chemistry 2017; 23:16644-16652. [PMID: 28922503 DOI: 10.1002/chem.201703871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Indexed: 01/06/2023]
Abstract
The most important natural α- and 310 -helices are stabilized by unidirectional intramolecular hydrogen bonds along the helical cylinder. In contrast, we report here on 12/10-helical conformations with alternately changing hydrogen-bond directionality in sequences of α,γ-hybrid peptides P1-P5 [P1: Boc-Ala-Aic-Ala-Aic-COOH; P2: Boc-Leu-Aic-Leu-Aic-OEt; P3: Boc-Leu-Aic-Leu-Aic-Leu-Aic-Aib-OMe; P4: Boc-Ala-Aic-Ala-Aic-Ala-Aic-Ala-OMe; P5: Boc-Leu-Aic-Leu-Aic-Leu-Aic-Leu-Aic-Aib-OMe; Aic=4-aminoisocaproic acid, Aib=2-aminoisobutyric acid] composed of natural α-amino acids and the achiral γ4,4 -dimethyl substituted γ-amino acid Aic in solution and in single crystals. The helical conformations are stabilized by alternating i→i+3 and i→i-1 intramolecular hydrogen bonds. The experimental data are supported by ab initio MO calculations. Surprisingly, replacing the natural α-amino acids of the sequence by the achiral dialkyl amino acid Ac6 c [P6: Boc-Ac6 c-Aic-Ac6 c-Aic-Ac6 c-Aic-Ac6 c-Aic-Ac6 c-CONHMe; Ac6 c = 1-aminocyclohexane-1-carboxylic acid] led to a 12-helix with unidirectional hydrogen bonds showing an entirely different backbone conformation. The results presented here emphasize the influence of the structure of the α-amino acid residues in dictating the helix types in α,γ-hybrid peptide foldamers and demonstrate the consequences for folding of small structural variations in the monomers.
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Affiliation(s)
- Rajkumar Misra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India
| | - K Muruga Poopathi Raja
- Department of Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625 021, India
| | - Hans-Jörg Hofmann
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India
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24
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Richard M, Felten AS, Chrétien F, Averlant-Petit MC, Pellegrini-Moïse N. Synthesis and conformational studies of short mixed γ/α-glycopeptides based on sugar γ 3,3 -amino acids. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.10.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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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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26
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Misra R, Saseendran A, George G, Veeresh K, Raja KMP, Raghothama S, Hofmann HJ, Gopi HN. Structural Dimorphism of Achiral α,γ-Hybrid Peptide Foldamers: Coexistence of 12- and 15/17-Helices. Chemistry 2017; 23:3764-3772. [DOI: 10.1002/chem.201605753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Rajkumar Misra
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune 411021 India
| | - Abhijith Saseendran
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune 411021 India
| | - Gijo George
- NMR Research Center; Indian Institute of Science; Bangalore 560012 India
| | - Kuruva Veeresh
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune 411021 India
| | - K. Muruga Poopathi Raja
- Department of Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai 625 021 India
| | | | - Hans-Jörg Hofmann
- Institute of Biochemistry; Faculty of Biosciences, Pharmacy and Psychology; Talstraße 33 04103 Leipzig Germany
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune 411021 India
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27
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Malik A, Kumar MG, Bandyopadhyay A, Gopi HN. Helices with additional H-bonds: crystallographic conformations of α,γ-hybrid peptides helices composed of β-hydroxy γ-amino acids (statines). Biopolymers 2017; 108. [DOI: 10.1002/bip.22978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/05/2016] [Accepted: 08/25/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Ankita Malik
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
| | - Mothukuri Ganesh Kumar
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
| | - Anupam Bandyopadhyay
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
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28
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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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29
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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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30
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Fisher BF, Gellman SH. Impact of γ-Amino Acid Residue Preorganization on α/γ-Peptide Foldamer Helicity in Aqueous Solution. J Am Chem Soc 2016; 138:10766-9. [PMID: 27529788 DOI: 10.1021/jacs.6b06177] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
α/γ-Peptide foldamers containing either γ(4)-amino acid residues or ring-constrained γ-amino acid residues have been reported to adopt 12-helical secondary structure in nonpolar solvents and in the solid state. These observations have engendered speculation that the seemingly flexible γ(4) residues have a high intrinsic helical propensity and that residue-based preorganization may not significantly stabilize the 12-helical conformation. However, the prior studies were conducted in environments that favor intramolecular H-bond formation. Here, we use 2D-NMR to compare the ability of γ(4) residues and cyclic γ residues to support 12-helix formation in more challenging environments, methanol and water. Both γ residue types support 12-helical folding in methanol, but only the cyclically constrained γ residues promote helicity in water. These results demonstrate the importance of residue-based preorganization strategies for achieving stable folding among short foldamers in aqueous solution.
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Affiliation(s)
- Brian F Fisher
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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31
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Ganesh Kumar M, Thombare VJ, Katariya MM, Veeresh K, Raja KMP, Gopi HN. Non-classical Helices withcisCarbon-Carbon Double Bonds in the Backbone: Structural Features of α,γ-Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2016; 55:7847-51. [DOI: 10.1002/anie.201602861] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Mothukuri Ganesh Kumar
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Varsha J. Thombare
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Mona M. Katariya
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Kuruva Veeresh
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - K. Muruga Poopathi Raja
- Department of Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai- 625 021 India
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
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32
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Ganesh Kumar M, Thombare VJ, Katariya MM, Veeresh K, Raja KMP, Gopi HN. Non-classical Helices withcisCarbon-Carbon Double Bonds in the Backbone: Structural Features of α,γ-Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mothukuri Ganesh Kumar
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Varsha J. Thombare
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Mona M. Katariya
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Kuruva Veeresh
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - K. Muruga Poopathi Raja
- Department of Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai- 625 021 India
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
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33
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Hoang HN, Driver RW, Beyer RL, Hill TA, D. de Araujo A, Plisson F, Harrison RS, Goedecke L, Shepherd NE, Fairlie DP. Helix Nucleation by the Smallest Known α‐Helix in Water. Angew Chem Int Ed Engl 2016; 55:8275-9. [DOI: 10.1002/anie.201602079] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Huy N. Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Russell W. Driver
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Renée L. Beyer
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Aline D. de Araujo
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Fabien Plisson
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Rosemary S. Harrison
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Lena Goedecke
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Nicholas E. Shepherd
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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34
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Hoang HN, Driver RW, Beyer RL, Hill TA, D. de Araujo A, Plisson F, Harrison RS, Goedecke L, Shepherd NE, Fairlie DP. Helix Nucleation by the Smallest Known α‐Helix in Water. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Huy N. Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Russell W. Driver
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Renée L. Beyer
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Aline D. de Araujo
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Fabien Plisson
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Rosemary S. Harrison
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Lena Goedecke
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Nicholas E. Shepherd
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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35
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Grison CM, Robin S, Aitken DJ. 13-Helix folding of a β/γ-peptide manifold designed from a “minimal-constraint” blueprint. Chem Commun (Camb) 2016; 52:7802-5. [DOI: 10.1039/c6cc02142e] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A bottom-up design rationale was used to select an alternating β/γ-peptide motif which folds into a well-defined 13-helix in solution.
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Affiliation(s)
- Claire M. Grison
- CP3A Organic Synthesis Group
- ICMMO
- UMR 8182
- CNRS
- Université Paris-Sud
| | - Sylvie Robin
- CP3A Organic Synthesis Group
- ICMMO
- UMR 8182
- CNRS
- Université Paris-Sud
| | - David J. Aitken
- CP3A Organic Synthesis Group
- ICMMO
- UMR 8182
- CNRS
- Université Paris-Sud
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36
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Kudo M, Maurizot V, Masu H, Tanatani A, Huc I. Structural elucidation of foldamers with no long range conformational order. Chem Commun (Camb) 2015; 50:10090-3. [PMID: 25050415 DOI: 10.1039/c4cc03822c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The synthesis and structural investigation of aromatic-aliphatic oligoamide foldamers reveals a zig-zag tape conformation with local conformational variability that precludes long range order.
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Affiliation(s)
- Mayumi Kudo
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan.
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37
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Fisher BF, Guo L, Dolinar BS, Guzei IA, Gellman SH. Heterogeneous H-bonding in a foldamer helix. J Am Chem Soc 2015; 137:6484-7. [PMID: 25974390 DOI: 10.1021/jacs.5b03382] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Structural characterization of new α/γ-peptide foldamers containing the cyclically constrained γ-amino acid I is described. Crystallographic and 2D NMR analysis shows that γ residue I promotes the formation of a 12/10-helical secondary structure in α/γ-peptides. This helix contains two different types of internal H-bond, and the data show that the 12-atom C═O(i) → H-N(i+3) H-bond is more favorable than the 10-atom C═O(i) → H-N(i-1) H-bond. Several foldamer helices featuring topologically distinct H-bonds have been discovered, but our findings are the first to show that such H-bonds may differ in their favorability.
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Affiliation(s)
- Brian F Fisher
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Li Guo
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Brian S Dolinar
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ilia A Guzei
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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38
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Zhu J, Dong Z, Lei S, Cao L, Yang B, Li W, Zhang Y, Liu J, Shen J. Design of Aromatic Helical Polymers for STM Visualization: Imaging of Single and Double Helices with a Pattern of π-π Stacking. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410975] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Zhu J, Dong Z, Lei S, Cao L, Yang B, Li W, Zhang Y, Liu J, Shen J. Design of Aromatic Helical Polymers for STM Visualization: Imaging of Single and Double Helices with a Pattern of π-π Stacking. Angew Chem Int Ed Engl 2015; 54:3097-101. [DOI: 10.1002/anie.201410975] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/19/2014] [Indexed: 11/11/2022]
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40
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Wang Y, Frasconi M, Liu WG, Liu Z, Sarjeant AA, Nassar MS, Botros YY, Goddard WA, Stoddart JF. Folding of Oligoviologens Induced by Radical–Radical Interactions. J Am Chem Soc 2015; 137:876-85. [DOI: 10.1021/ja5111305] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yuping Wang
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Marco Frasconi
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Wei-Guang Liu
- Materials
and Process Simulation Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Zhichang Liu
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Amy A. Sarjeant
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Majed S. Nassar
- Joint
Center of Excellence in Integrated Nano-Systems (JCIN), King Abdul-Aziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Youssry Y. Botros
- Joint
Center of Excellence in Integrated Nano-Systems (JCIN), King Abdul-Aziz City for Science and Technology (KACST), P.O. Box 6086, Riyadh 11442, Saudi Arabia
- University
Research Office, Intel Corporation, Building RNB-6-61, 2200 Mission
College Boulevard, Santa Clara, California 95054, United States
| | - William A. Goddard
- Materials
and Process Simulation Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - J. Fraser Stoddart
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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41
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Grison CM, Robin S, Aitken DJ. The discovery of 9/8-ribbons, β/γ-peptides with curved shapes governed by a combined configuration-conformation code. Chem Commun (Camb) 2015; 51:16233-6. [DOI: 10.1039/c5cc07136d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The design of a β/γ-peptide reveals an unprecedented 9/8-ribbon whose curvature depends on the β-residue configuration and the γ-residue conformation.
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Affiliation(s)
- Claire M. Grison
- CP3A Organic Synthesis Group
- ICMMO-UMR 8182
- Université Paris-Sud
- Université Paris-Saclay
- 91405 Orsay cedex
| | - Sylvie Robin
- CP3A Organic Synthesis Group
- ICMMO-UMR 8182
- Université Paris-Sud
- Université Paris-Saclay
- 91405 Orsay cedex
| | - David J. Aitken
- CP3A Organic Synthesis Group
- ICMMO-UMR 8182
- Université Paris-Sud
- Université Paris-Saclay
- 91405 Orsay cedex
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42
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Giuliano MW, Maynard SJ, Almeida AM, Guo L, Guzei IA, Spencer LC, Gellman SH. A γ-Amino Acid That Favors 12/10-Helical Secondary Structure in α/γ-Peptides. J Am Chem Soc 2014; 136:15046-53. [DOI: 10.1021/ja5076585] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael W. Giuliano
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Stacy J. Maynard
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Aaron M. Almeida
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Li Guo
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lara C. Spencer
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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43
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Cabrele C, Martinek TA, Reiser O, Berlicki Ł. Peptides Containing β-Amino Acid Patterns: Challenges and Successes in Medicinal Chemistry. J Med Chem 2014; 57:9718-39. [DOI: 10.1021/jm5010896] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Chiara Cabrele
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Tamás A. Martinek
- SZTE-MTA
Lendulet Foldamer Research Group, Institute of Pharmaceutical Analysis, University of Szeged, Somogyi u. 6., H-6720 Szeged, Hungary
| | - Oliver Reiser
- Institute
of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Łukasz Berlicki
- Department
of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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44
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Stanovych A, Guillot R, Kouklovsky C, Miclet E, Alezra V. β,γ-Diamino acid: an original building block for hybrid α/γ-peptide synthesis with extra hydrogen bond donating group. Amino Acids 2014; 46:2753-7. [DOI: 10.1007/s00726-014-1831-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 08/21/2014] [Indexed: 01/01/2023]
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45
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Sharma GVM, Thodupunuri P, Sirisha K, Basha SJ, Gurava Reddy P, Sarma AVS. Design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational study. J Org Chem 2014; 79:8614-28. [PMID: 25180942 DOI: 10.1021/jo501267k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The present study is aimed at the design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational analysis (NMR, MD, and CD studies). The requisite peptides with heterogeneous backbones were prepared from β-, γ-, and δ-amino acids with carbohydrate side chains and α-amino acid, L-Ala. The α/β-peptides were prepared from (S)-β-Caa(l) (C-linked carbo-β-amino acid with D-lyxo furanoside side chain) and L-Ala with a 1:1 alternation. The α/β-peptides with "helix-turn" motif displayed a 11/9-helix nucleating a 13-atom H-bonding turn. The α/β-octapeptides showed the presence of HTH structures with bifurcated 11/15-H-bonded turn. Further, the α/β-hexapeptide with HT motif, independently on coupling with γ/α/γ/α- and δ/α/δ/α-tetrapeptides at the C-terminus provided access to the decapeptides with "hybrid HTH" motifs. The decapeptide ("α-β-α-β-α-β-γ-α-γ-α") showed a hybrid HTH with "11/9/11/9/11/16/9/12/10" H-bonding, while the decapeptide ("α-β-α-β-α-β-δ-α-δ-α") revealed the presence of a "11/9/11/9/11/17/9/13/11" helical pattern. The above peptides thus have shown compatibility between different types of helices and serendipitous bifurcated 11/16- and 11/17-turns. The present study thus provided the first opportunity for the design and study of "hybrid HTH" motifs with more than one kind of helical structures in them.
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Affiliation(s)
- Gangavaram V M Sharma
- Organic and Bimolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500 007, India
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46
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Jędrzejczak K, Hrynczyszyn P, Artym J, Kocięba M, Zimecki M, Zabrocki J, Jankowski S. Synthesis and biological activity of cyclolinopeptide A analogues modified with γ(3)-bis(homophenylalanine). Eur J Med Chem 2014; 86:515-27. [PMID: 25203781 DOI: 10.1016/j.ejmech.2014.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 09/01/2014] [Accepted: 09/04/2014] [Indexed: 01/01/2023]
Abstract
Cyclolinopeptide A, naturally occurring immunomodulatory nonapeptide, was modified with S or R-γ(3)-bis(homophenylalanine) in positions 3 or 4, or both 3 and 4. The replacement of one or both Phe residues by γ(3)-hhPhe led to decrease of their conformational flexibility in the analogues in comparison to CLA. All cyclic peptides, except 11, exist as isomers with the cis Pro-Pro peptide bond. Cyclic peptide 11 with single modification S-γ(3)-hhPhe(4) exists as a mixture of two isomers and the major isomer (89%) contains all peptide bonds of the trans geometry. The peptides were subjected to several immunological tests in vitro and in vivo. Linear peptides 1-8, precursors of CLA analogues 9-16, were not toxic against human peripheral blood mononuclear cells (PBMC) but cyclic analogues showed dose-dependent toxicity with exception of peptide 11. Linear peptides did not inhibit mitogen-induced PBMC proliferation whereas cyclic ones inhibited the proliferation in a dose-dependent manner. The actions of linear and cyclic peptides with regard to lipopolysaccharide (LPS) -induced tumour necrosis factor alpha (TNF α) production in whole human blood cultures were differential but particularly suppressive in the case of linear compound 6. Therefore, for in vivo tests compounds 6 and 11 were selected. The compounds showed comparable, suppressive actions in induction and effector phases of delayed type hypersensitivity as well as in the carrageenan-induced foot pad edema in mouse models. In summary, linear peptide 6 and cyclic peptide 11 are attractive as potential immune suppressor drugs.
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Affiliation(s)
- Karol Jędrzejczak
- Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924, Poland
| | - Paweł Hrynczyszyn
- Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924, Poland
| | - Jolanta Artym
- Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wroclaw, Poland
| | - Maja Kocięba
- Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wroclaw, Poland
| | - Michał Zimecki
- Institute of Immunology and Experimental Therapy, Polish Academy of Science, R. Weigla 12, 53-114 Wroclaw, Poland
| | - Janusz Zabrocki
- Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924, Poland; Peptaderm Ltd., Rydygiera 8, 01-793 Warsaw, Poland
| | - Stefan Jankowski
- Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Łódź, Żeromskiego 116, 90-924, Poland.
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47
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Xu JF, Niu LY, Chen YZ, Wu LZ, Tung CH, Yang QZ. Hydrogen Bonding Directed Self-Assembly of Small-Molecule Amphiphiles in Water. Org Lett 2014; 16:4016-9. [DOI: 10.1021/ol501841f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jiang-Fei Xu
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of the Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Li-Ya Niu
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Yu-Zhe Chen
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Li-Zhu Wu
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Chen-Ho Tung
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Qing-Zheng Yang
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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48
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Gord JR, Walsh PS, Fisher BF, Gellman SH, Zwier TS. Mimicking the First Turn of an α-Helix with an Unnatural Backbone: Conformation-Specific IR and UV Spectroscopy of Cyclically Constrained β/γ-Peptides. J Phys Chem B 2014; 118:8246-56. [PMID: 24694352 DOI: 10.1021/jp5015884] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Joseph R. Gord
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Patrick S. Walsh
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Brian F. Fisher
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Timothy S. Zwier
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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49
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Sonti R, Dinesh B, Basuroy K, Raghothama S, Shamala N, Balaram P. C12 helices in long hybrid (αγ)n peptides composed entirely of unconstrained residues with proteinogenic side chains. Org Lett 2014; 16:1656-9. [PMID: 24588077 DOI: 10.1021/ol500307p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Unconstrained γ(4) amino acid residues derived by homologation of proteinogenic amino acids facilitate helical folding in hybrid (αγ)n sequences. The C12 helical conformation for the decapeptide, Boc-[Leu-γ(4)(R)Val]5-OMe, is established in crystals by X-ray diffraction. A regular C12 helix is demonstrated by NMR studies of the 18 residue peptide, Boc-[Leu-γ(4)(R)Val]9-OMe, and a designed 16 residue (αγ)n peptide, incorporating variable side chains. Unconstrained (αγ)n peptides show an unexpectedly high propensity for helical folding in long polypeptide sequences.
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Affiliation(s)
- Rajesh Sonti
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, India, 560012
- NMR
Research Centre, Indian Institute of Science, Bangalore, India, 560012
| | - Bhimareddy Dinesh
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, India, 560012
| | - Krishnayan Basuroy
- Department
of Physics, Indian Institute of Science, Bangalore, India, 560012
| | | | | | - Padmanabhan Balaram
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, India, 560012
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Wani NA, Gupta VK, Kant R, Aravinda S, Rai R. Conformation of a terminally protected βγ hybrid dipeptide Boc-Ant-Gpn-OMe stabilized by C6/C7 hydrogen bonds. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2014; 70:46-9. [PMID: 24399225 DOI: 10.1107/s2053229613033044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 12/06/2013] [Indexed: 11/11/2022]
Abstract
The hybrid βγ dipeptide, methyl 2-[1-({2-[(tert-butoxycarbonyl)amino]benzamido}methyl)cyclohexyl]acetate (Boc-Ant-Gpn-OMe), C22H32N2O5, adopts a folded conformation stabilized by intramolecular six- (C6) and seven-membered (C7) hydrogen-bonded rings, together with weak C-H...O and C-H...π interactions, resulting in a ribbon-like structure.
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Affiliation(s)
- Naiem Ahmad Wani
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi 180 001, India
| | - Vivek Kumar Gupta
- X-ray Crystallography Laboratory, Post-Graduate Department of Physics & Electronics, University of Jammu, Jammu Tawi 180 006, India
| | - Rajni Kant
- X-ray Crystallography Laboratory, Post-Graduate Department of Physics & Electronics, University of Jammu, Jammu Tawi 180 006, India
| | - Subrayashastry Aravinda
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi 180 001, India
| | - Rajkishor Rai
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi 180 001, India
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