1
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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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2
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Park HS, Lee JY, Kang YK. Exploring helix structures of γ-peptides based on 2-(aminomethyl)cyclopentanecarboxylic acid. Biopolymers 2024; 115:e23575. [PMID: 38465777 DOI: 10.1002/bip.23575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/12/2024]
Abstract
Conformational search and density functional theory calculations were performed to explore the preferences of helical structures for chiro-specific oligo-γ-peptides of 2-(aminomethyl)cyclopentanecarboxylic acid (γAmc5) with a cyclopentyl constraint on the Cα-Cβ bond in solution. The dimer and tetramer of γAmc5 (1) with homochiral (1S, 2S) configurations exhibited a strong preference for the 9-membered helix foldamer in solution, except for the tetramer in water. However, the oligomers of γAmc5 (1) longer than tetramer preferentially adopted a right-handed (P)-2.614-helix (H1-14) as the peptide sequence becomes longer and as solvent polarity increases. The high stabilities for H1-14 foldamers of γAmc5 (1) in solution were ascribed to the favored solvation free energies. The calculated mean backbone torsion angles for H1-14 helix foldamers of γAmc5 (1) were similar to those calculated for oligomers of other γ-residues with cyclopentane or cyclohexane rings. However, the substitution of cyclopentane constraints on the Cα-Cβ bond of the γAmc5 (1) residue resulted in different conformational preferences and/or handedness of helix foldamers. In particular, the pyrrolidine-substituted analogs of the H1-14 foldamers of γAmc5 (1) with adjacent amine diads substituted at a proximal distance are expected to be potential catalysts for the crossed aldol condensation in nonpolar and polar solvents.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing, Cheju Halla University, Cheju, Republic of Korea
| | - Joo Yun Lee
- AI Team, Yunovia Co., Ltd., Hwaseong-si, Gyeonggi, Republic of Korea
| | - Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
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3
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Reza D, Balo R, Otero JM, Fletcher AM, García-Fandino R, Sánchez-Pedregal VM, Davies SG, Estévez RJ, Estévez JC. β-Peptides incorporating polyhydroxylated cyclohexane β-amino acid: synthesis and conformational study. Org Biomol Chem 2023; 21:8535-8547. [PMID: 37840474 DOI: 10.1039/d3ob00906h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
We describe the synthesis of trihydroxylated cyclohexane β-amino acids from (-)-shikimic acid, in their cis and trans configuration, and the incorporation of the trans isomer into a trans-2-aminocyclohexanecarboxylic acid peptide chain. Subsequently, the hydroxyl groups were partially or totally deprotected. The structural study of the new peptides by FTIR, CD, solution NMR and DFT calculations revealed that they all fold into a 14-helix secondary structure, similarly to the homooligomer of trans-2-aminocyclohexanecarboxylic acid. This means that the high degree of substitution of the cyclohexane ring of the new residue is compatible with the adoption of a stable helical secondary structure and opens opportunities for the design of more elaborate peptidic foldamers with oriented polar substituents at selected positions of the cycloalkane residues.
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Affiliation(s)
- David Reza
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
| | - Rosalino Balo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - José M Otero
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
| | - Ai M Fletcher
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Rebeca García-Fandino
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Víctor M Sánchez-Pedregal
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Stephen G Davies
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ramón J Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Juan C Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
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4
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Seo N, Son H, Kim Y, Guzei IA, Kang P, Choi SH. Exploring a β-Amino Acid with a Seven-Membered Ring Constraint as a Foldamer Building Block for Nontraditional Helices. Org Lett 2023; 25:7497-7501. [PMID: 37800878 DOI: 10.1021/acs.orglett.3c02746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
We explored trans- and cis-2-aminocycloheptanecarboxylic acid (ACHpC) as potential building blocks for helical foldamers. trans-ACHpC does not show sufficient folding propensity in unnatural peptides. cis-ACHpC promotes nontraditional helices of two unnatural peptide backbones: the 11/9-helix for 1:1 α/β-peptides and the 12/10-helix for β-peptides with interconvertible handedness. The two opposite-handed 12/10-helices rapidly interconvert in solution by pseudorotation of the two twist chair forms of the cycloheptane moiety in each cis-ACHpC residue.
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Affiliation(s)
- Nuri Seo
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hoyang Son
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Yonghan Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Ilia A Guzei
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Philjae Kang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
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5
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Chen YK, Simon IA, Maslov I, Oyarce-Pino IE, Kulkarni K, Hopper D, Aguilar MI, Vankadari N, Broughton BR, Del Borgo MP. A switch in N-terminal capping of β-peptides creates novel self-assembled nanoparticles. RSC Adv 2023; 13:29401-29407. [PMID: 37818265 PMCID: PMC10561372 DOI: 10.1039/d3ra04514e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023] Open
Abstract
Small tripeptides composed entirely of β3-amino acids have been shown to self-assemble into fibres following acylation of the N-terminus. Given the use of Fmoc as a strategy to initiate self-assembly in α-peptides, we hypothesized that the acyl cap can be replaced by an Fmoc without perturbation to the self-assembly and enable simpler synthetic protocols. We therefore replaced the N-acyl cap for an Fmoc group and herein we show that these Fmoc-protected β3-peptides produce regular spherical particles, rather than fibrous structures, that are stable and capable of encapsulating cargo. We then demonstrated that these particles were able to deliver cargo to cells without any obvious signs of cytotoxicity. This is the first description of such regular nanoparticles derived from Fmoc-protected β3-peptides.
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Affiliation(s)
- Yi-Kai Chen
- Department of Pharmacology, Monash University Clayton VIC 3800 Australia
- Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
| | - Isabella A Simon
- Department of Pharmacology, Monash University Clayton VIC 3800 Australia
- Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
| | - Ivan Maslov
- Department of Pharmacology, Monash University Clayton VIC 3800 Australia
- Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
| | - Ivan E Oyarce-Pino
- Department of Pharmacology, Monash University Clayton VIC 3800 Australia
- Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
| | - Ketav Kulkarni
- Department of Biochemistry & Molecular Biology, Monash University Clayton VIC 3800 Australia
- Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
| | - Denham Hopper
- Department of Pharmacology, Monash University Clayton VIC 3800 Australia
- Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry & Molecular Biology, Monash University Clayton VIC 3800 Australia
- Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
| | - Naveen Vankadari
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Melbourne VIC 3000 Australia
| | - Brad Rs Broughton
- Department of Pharmacology, Monash University Clayton VIC 3800 Australia
- Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
| | - Mark P Del Borgo
- Department of Pharmacology, Monash University Clayton VIC 3800 Australia
- Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
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6
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Boruah A, Roy A. Advances in hybrid peptide-based self-assembly systems and their applications. Biomater Sci 2022; 10:4694-4723. [PMID: 35899853 DOI: 10.1039/d2bm00775d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembly of peptides demonstrates a great potential for designing highly ordered, finely tailored supramolecular arrangements enriched with high specificity, improved efficacy and biological activity. Along with natural peptides, hybrid peptide systems composed of natural and chemically diverse unnatural amino acids have been used in various fields, including drug delivery, wound healing, potent inhibition of diseases, and prevention of biomaterial related diseases to name a few. In this review, we provide a brief outline of various methods that have been utilized for obtaining fascinating structures that create an avenue to reproduce a range of functions resulting from these folds. An overview of different self-assembled structures as well as their applications will also be provided. We believe that this review is very relevant to the current scenario and will cover conformations of hybrid peptides and resulting self-assemblies from the late 20th century through 2022. This review aims to be a comprehensive and reliable account of the hybrid peptide-based self-assembly owing to its enormous influence in understanding and mimicking biological processes.
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Affiliation(s)
- Alpana Boruah
- Applied Organic Chemistry Group, Chemical Sciences and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and Technology (CSIR-NEIST), Pulibor, Jorhat-785006, Assam, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Arup Roy
- Applied Organic Chemistry Group, Chemical Sciences and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and Technology (CSIR-NEIST), Pulibor, Jorhat-785006, Assam, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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7
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Shankar S, Jyothi D, Rahim JU, Pal PC, Singh UP, Rai R. Conformation of Achiral α/β Hybrid Peptides Containing Glycine and 1‐Aminocyclohexaneacetic Acid. ChemistrySelect 2022. [DOI: 10.1002/slct.202104453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sudha Shankar
- Natural Products & Medicinal Chemistry Division (NPMC) CSIR-Indian Institute of Integrative Medicine (CSIR-IIIM) Jammu 180001 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Deeti Jyothi
- CSIR-Indian Institute of Chemical Biology (CSIR-IICB) Kolkata 700032 India
| | - Junaid ur Rahim
- Natural Products & Medicinal Chemistry Division (NPMC) CSIR-Indian Institute of Integrative Medicine (CSIR-IIIM) Jammu 180001 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Purna Chandra Pal
- CSIR-Indian Institute of Chemical Biology (CSIR-IICB) Kolkata 700032 India
| | - Umesh Prasad Singh
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- CSIR-Indian Institute of Chemical Biology (CSIR-IICB) Kolkata 700032 India
| | - Rajkishor Rai
- Natural Products & Medicinal Chemistry Division (NPMC) CSIR-Indian Institute of Integrative Medicine (CSIR-IIIM) Jammu 180001 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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8
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Choi S, Shim J, Kang P, Choi SH. Effect of a cis-4-aminopiperidine-3-carboxylic acid ( cis-APiC) residue on mixed-helical folding of unnatural peptides. Org Biomol Chem 2021; 20:613-618. [PMID: 34951620 DOI: 10.1039/d1ob02223g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The α/β-peptide 11/9-helix and the β-peptide 12/10-helix belong to "mixed" helices, in which two types of hydrogen bonds with opposite directionality alternate along the helical axis. cis-2-Aminocyclohexanecarboxylic acid (cis-ACHC) is known to promote these mixed helices and stabilize the helical propensity more than other acyclic β-residues. Application of a mixed-helical backbone still requires sufficient solubility in aqueous solution. In this regard, we chose cis-4-aminopiperidine-3-carboxylic acid (cis-APiC) as a foldamer building block that can provide both sufficient aqueous solubility and mixed-helical propensity. Conformational analyses of α/β- and β-peptides containing a cis-APiC residue by circular dichroism spectroscopy and single-crystal X-ray crystallography suggest that the incorporation of cis-APiC instead of cis-ACHC can enhance the aqueous solubility of the mixed-helical peptides without any adverse effect on helical folding. In addition, the ratio between right- and left-handed 12/10-helices of β-peptides can be rationalized by relative energies between the local conformations of the cis-APiC residue.
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Affiliation(s)
- Sunglim Choi
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Jihyun Shim
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Philjae Kang
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea.
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9
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Choi S, Choi SH. Synthesis and conformational analysis of an
anti
‐β
2,
3
‐amino
acid as a building block for unnatural peptide helices. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sunglim Choi
- Department of Chemistry Yonsei University Seoul Korea
| | - Soo Hyuk Choi
- Department of Chemistry Yonsei University Seoul Korea
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10
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Szefczyk M. Peptide foldamer-based self-assembled nanostructures containing cyclic beta-amino acids. NANOSCALE 2021; 13:11325-11333. [PMID: 34190303 DOI: 10.1039/d1nr02220b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Peptide soft materials belong to an emerging branch of materials sciences due to their growing importance as responsive materials in diagnostics, therapeutics, and biomedical applications. The diversity provided by easily modifiable peptide sequences can be further increased by introducing nonnatural amino acids such as cyclic β-amino acids, leading to the formation of foldamers. Moreover, it is possible to combine peptide chains with other polymers, aromatic compounds, etc. to create hybrids with completely new properties and applications. In this review, we focus on the cis/trans enantiomers of three cyclic β-amino acids: 2-aminocyclobutane-1-carboxylic acid (ACBC), 2-aminocyclopentane-1-carboxylic acid (ACPC) and 2-aminocyclohexane-1-carboxylic acid (ACHC). The peptides discussed here either contain exclusively β-amino acids or are α,β-peptides, and they undergo self-assembly by forming different interactions that lead to the creation of well-defined nanostructures.
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Affiliation(s)
- Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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11
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Shankar S, Junaid Ur Rahim, Rai R. Self-Assembly in Peptides Containing β-and γ-amino Acids. Curr Protein Pept Sci 2020; 21:584-597. [DOI: 10.2174/1389203721666200127112244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/07/2019] [Accepted: 10/07/2019] [Indexed: 12/17/2022]
Abstract
The peptides containing β-and γ-amino acids as building blocks display well-defined secondary
structures with unique morphologies. The ability of such peptides to self-assemble into complex
structures of controlled geometries has been exploited in biomedical applications. Herein, we have
provided an updated overview about the peptides containing β-and γ-amino acids considering the significance
and advancement in the area of development of peptide-based biomaterials having diverse
applications.
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Affiliation(s)
- Sudha Shankar
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
| | - Junaid Ur Rahim
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
| | - Rajkishor Rai
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
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12
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Rinaldi S. The Diverse World of Foldamers: Endless Possibilities of Self-Assembly. Molecules 2020; 25:E3276. [PMID: 32708440 PMCID: PMC7397133 DOI: 10.3390/molecules25143276] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.
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Affiliation(s)
- Samuele Rinaldi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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13
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Blodgett KN, Jang G, Kim S, Kim MK, Choi SH, Zwier TS. Coexistence of Left- and Right-Handed 12/10-Mixed Helices in Cyclically Constrained β-Peptides and Directed Formation of Single-Handed Helices upon Site-Specific Methylation. J Phys Chem A 2020; 124:5856-5870. [PMID: 32497433 DOI: 10.1021/acs.jpca.0c03545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The inherent conformational preferences of the neutral β-peptide foldamer series, Ac-(ACHC)n-NHBn, n = 2-4, are studied in the gas phase using conformation-specific IR-UV double resonance methods. The cyclically constrained chiral β-amino acid cis-2-aminocyclohexane carboxylic acid (ACHC) is designed to bring both right- and left-handed helices into close energetic proximity. Comparison of the infrared spectra in the NH stretch and amide I/II regions with the predictions of DFT calculations lead to the unambiguous assignment of four out of the six observed conformations of the molecules in this series, while corroborating computational and spectral evidence, affords tentative assignments of the remaining two conformers for which IR data were not recorded. The observed structures fall into one of two conformational families: a right-handed 12/10-mixed helix or its "cap-disrupted" left-handed helical analogue, which coexist with significant populations. Site-specific and stereospecific methylation on the cyclohexane backbone at the dipeptide (n = 2) level is also tested as a means to sterically lock in a predetermined cyclohexane chair conformation. These substitutions are proven to be a means of selectively driving formation of one helical screw sense or the other. Calculated relative energies and free energies of all possible structures for the molecules provide strong supporting evidence that the rigid nature of the ACHC residue confers unusual stability to the 12/10-mixed helix conformation, regardless of local environment, temperature, or C-terminal capping unit. The simultaneous presence of both handed helices offers unique opportunities for future studies of their interconversion.
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Affiliation(s)
- Karl N Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Geunhyuk Jang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Sojung Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Min Kyung Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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14
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Aloisi A, Christensen NJ, Sørensen KK, Guilbaud-Chéreau C, Jensen KJ, Bianco A. Synthesis and Characterization of Adamantane-Containing Heteropeptides with a Chirality Switch. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Adriano Aloisi
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry; ISIS; University of Strasbourg; UPR 3572 67000 Strasbourg France
| | - Niels Johan Christensen
- Department of Chemistry; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Kasper K. Sørensen
- Department of Chemistry; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Chloé Guilbaud-Chéreau
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry; ISIS; University of Strasbourg; UPR 3572 67000 Strasbourg France
| | - Knud J. Jensen
- Department of Chemistry; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Alberto Bianco
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry; ISIS; University of Strasbourg; UPR 3572 67000 Strasbourg France
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15
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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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16
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Nizami B, Bereczki-Szakál D, Varró N, el Battioui K, Nagaraj VU, Szigyártó IC, Mándity I, Beke-Somfai T. FoldamerDB: a database of peptidic foldamers. Nucleic Acids Res 2020; 48:D1122-D1128. [PMID: 31686102 PMCID: PMC7145536 DOI: 10.1093/nar/gkz993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/10/2019] [Accepted: 10/17/2019] [Indexed: 01/04/2023] Open
Abstract
Foldamers are non-natural oligomers that mimic the structural behaviour of natural peptides, proteins and nucleotides by folding into a well-defined 3D conformation in solution. Since their first description about two decades ago, numerous studies have been undertaken dealing with the design, synthesis, characterization and application of foldamers. They have huge application potential as antimicrobial, anticancer and anti-HIV agents and in materials science. Despite their importance, there is no publicly available web resource providing comprehensive information on these compounds. Here we describe FoldamerDB, an open-source, fully annotated and manually curated database of peptidic foldamers. FoldamerDB holds the information about the sequence, structure and biological activities of the foldamer entries. It contains the information on over 1319 species and 1018 activities, collected from more than 160 research papers. The web-interface is designed to be clutter-free, user-friendly and it is compatible with devices of different screen sizes. The interface allows the user to search the database, browse and filter the foldamers using multiple criteria. It also offers a detailed help page to assist new users. FoldamerDB is hoped to bridge the gap in the freely available web-based resources on foldamers and will be of interest to diverse groups of scientists from chemists to biologists. The database can be accessed at http://foldamerdb.ttk.hu/.
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Affiliation(s)
- Bilal Nizami
- MTA TTK Lendület Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Magyar Tudósok krt. 2, Hungary
| | - Dorottya Bereczki-Szakál
- MTA TTK Lendület Artificial Transporter Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Magyar Tudósok krt. 2, Hungary
| | - Nikolett Varró
- MTA TTK Lendület Artificial Transporter Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Magyar Tudósok krt. 2, Hungary
| | - Kamal el Battioui
- MTA TTK Lendület Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Magyar Tudósok krt. 2, Hungary
| | - Vignesh U Nagaraj
- MTA TTK Lendület Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Magyar Tudósok krt. 2, Hungary
| | - Imola Cs Szigyártó
- MTA TTK Lendület Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Magyar Tudósok krt. 2, Hungary
| | - István Mándity
- MTA TTK Lendület Artificial Transporter Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Magyar Tudósok krt. 2, Hungary
| | - Tamás Beke-Somfai
- MTA TTK Lendület Biomolecular Self-Assembly Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Magyar Tudósok krt. 2, Hungary
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17
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Chan MHY, Leung SYL, Yam VWW. Rational Design of Multi-Stimuli-Responsive Scaffolds: Synthesis of Luminescent Oligo(ethynylpyridine)-Containing Alkynylplatinum(II) Polypyridine Foldamers Stabilized by Pt···Pt Interactions. J Am Chem Soc 2019; 141:12312-12321. [DOI: 10.1021/jacs.9b04447] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Michael Ho-Yeung Chan
- Institute of Molecular Functional Materials (Areas of Excellence Scheme, University Grants Committee (Hong Kong)) and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People’s Republic of China
| | - Sammual Yu-Lut Leung
- Institute of Molecular Functional Materials (Areas of Excellence Scheme, University Grants Committee (Hong Kong)) and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People’s Republic of China
| | - Vivian Wing-Wah Yam
- Institute of Molecular Functional Materials (Areas of Excellence Scheme, University Grants Committee (Hong Kong)) and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People’s Republic of China
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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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Bera S, Gazit E. Self-assembly of Functional Nanostructures by Short Helical Peptide Building Blocks. Protein Pept Lett 2019; 26:88-97. [PMID: 30227810 PMCID: PMC6416463 DOI: 10.2174/0929866525666180917163142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/28/2018] [Accepted: 09/11/2018] [Indexed: 12/03/2022]
Abstract
The self-assembly of short peptide building blocks into well-ordered nanostructures is a key direction in bionanotechnology. The formation of β -sheet organizations by short peptides is well explored, leading to the development of a wide range of functional assemblies. Likewise, many natural proteinaceous materials, such as silk and amyloid fibrils, are based on β-sheet structures. In contrast, collagen, the most abundant protein in mammals, is based on helical arrangement. Similar to β-sheet structures, short helical peptides have been recently discovered to possess a diverse set of functionalities with the potential to fabricate artificial self-assembling materials. Here, we outline the functional roles of self-assembled nanostructures formed by short helical peptides and their potential as artificial materials. We focus on the association between self-assembled mesoscale structures and their material function and demonstrate the way by which this class of building blocks bears the potential for diverse applications, such as the future fabrication of smart devices.
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Affiliation(s)
- Santu Bera
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv
University, Ramat Aviv 69978, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv
University, Ramat Aviv 69978, Israel
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20
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Nekkaa I, Bogdán D, Gáti T, Béni S, Juhász T, Palkó M, Paragi G, Tóth GK, Fülöp F, Mándity IM. Flow-chemistry enabled efficient synthesis of β-peptides: backbone topology vs. helix formation. Chem Commun (Camb) 2019; 55:3061-3064. [DOI: 10.1039/c8cc10147g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Enantiodiscriminative helix formation was observed for β-peptide H14 helices when enantiomers of bridged bicyclic residues were introduced.
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21
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Simon M, Milbeo P, Liu H, André C, Wenger E, Martinez J, Amblard M, Aubert E, Legrand B, Calmès M. 12/10‐Helix in Mixed β‐Peptides Alternating Bicyclic and Acyclic β‐Amino Acids: Probing the Relationship between Bicyclic Side Chain and Helix Stability. Chemistry 2018; 24:18795-18800. [DOI: 10.1002/chem.201804404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Matthieu Simon
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Pierre Milbeo
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Hongtao Liu
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Christophe André
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Emmanuel Wenger
- CRM2UMR 7063 CNRS Université de Lorraine Boulevard des Aiguilletes 54506 Vandoeuvre-lès-Nancy Cedex France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Emmanuel Aubert
- CRM2UMR 7063 CNRS Université de Lorraine Boulevard des Aiguilletes 54506 Vandoeuvre-lès-Nancy Cedex France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
| | - Monique Calmès
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247CNRS-Université Montpellier-ENSCM 34093 Montpellier cedex 5 France
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22
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Sussman F, Sánchez-Pedregal VM, Estévez JC, Balo R, Jiménez-Barbero J, Ardá A, Gimeno A, Royo M, Villaverde MC, Estévez RJ. Environmental Effects Determine the Structure of Potential β-Amino Acid Based Foldamers. Chemistry 2018; 24:10625-10629. [DOI: 10.1002/chem.201801953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/24/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Fredy Sussman
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Víctor M. Sánchez-Pedregal
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Juan C. Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Rosalino Balo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition & Host-Pathogen Interactions Unit; CIC bioGUNE; Bizkaia Technology Park, Building 801A 48170 Derio Spain
- Ikerbasque; Basque Foundation for Science; Maria Diaz de Haro 13 48009 Bilbao Spain
- Department of Organic Chemistry II, Faculty of Science & Technology; University of the Basque Country; 48940 Leioa Spain
| | - Ana Ardá
- Molecular Recognition & Host-Pathogen Interactions Unit; CIC bioGUNE; Bizkaia Technology Park, Building 801A 48170 Derio Spain
| | - Ana Gimeno
- Molecular Recognition & Host-Pathogen Interactions Unit; CIC bioGUNE; Bizkaia Technology Park, Building 801A 48170 Derio Spain
| | - Miriam Royo
- Combinatorial Chemistry Unit; Barcelona Science Park; Baldiri Reixac 10 08028 Barcelona Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN); Barcelona Science Park; Baldiri Reixac 10 08028 Barcelona Spain
| | - M. Carmen Villaverde
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Ramón J. Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
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23
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Goldschmidt Gőz V, Pintér I, Harmat V, Perczel A. Approaches to Pyranuronic β-Sugar Amino Acid Building Blocks of Peptidosaccharide Foldamers. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - István Pintér
- Laboratory of Structural Chemistry and Biology; Institute of Chemistry; Eötvös University; Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - Veronika Harmat
- MTA-ELTE Protein Modeling Research Group; Pázmány Péter sétány 1/A 1117 Budapest Hungary
| | - András Perczel
- MTA-ELTE Protein Modeling Research Group; Pázmány Péter sétány 1/A 1117 Budapest Hungary
- Laboratory of Structural Chemistry and Biology; Institute of Chemistry; Eötvös University; Pázmány Péter sétány 1/A 1117 Budapest Hungary
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24
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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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25
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Chan MHY, Ng M, Leung SYL, Lam WH, Yam VWW. Synthesis of Luminescent Platinum(II) 2,6-Bis(N-dodecylbenzimidazol-2′-yl)pyridine Foldamers and Their Supramolecular Assembly and Metallogel Formation. J Am Chem Soc 2017. [DOI: 10.1021/jacs.7b03635] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Michael Ho-Yeung Chan
- Institute of Molecular Functional Materials (Areas of Excellence Scheme University Grants Committee (Hong Kong)) and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong, People’s Republic of China
| | - Maggie Ng
- Institute of Molecular Functional Materials (Areas of Excellence Scheme University Grants Committee (Hong Kong)) and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong, People’s Republic of China
| | - Sammual Yu-Lut Leung
- Institute of Molecular Functional Materials (Areas of Excellence Scheme University Grants Committee (Hong Kong)) and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong, People’s Republic of China
| | - Wai Han Lam
- Institute of Molecular Functional Materials (Areas of Excellence Scheme University Grants Committee (Hong Kong)) and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong, People’s Republic of China
| | - Vivian Wing-Wah Yam
- Institute of Molecular Functional Materials (Areas of Excellence Scheme University Grants Committee (Hong Kong)) and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong, People’s Republic of China
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26
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Thodupunuri P, Katukuri S, Ramakrishna KVS, Sharma GVM, Kunwar AC, Sarma AVS, Hofmann HJ. Solvent-Directed Switch of a Left-Handed 10/12-Helix into a Right-Handed 12/10-Helix in Mixed β-Peptides. J Org Chem 2017; 82:2018-2031. [DOI: 10.1021/acs.joc.6b02856] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Prashanth Thodupunuri
- Organic
and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Sirisha Katukuri
- Nuclear Magnetic Resonance & Structural Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Kallaganti V. S. Ramakrishna
- Nuclear Magnetic Resonance & Structural Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Gangavaram V. M. Sharma
- Organic
and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Ajit C. Kunwar
- Nuclear Magnetic Resonance & Structural Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Akella V. S. Sarma
- Nuclear Magnetic Resonance & Structural Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Hans-Jörg Hofmann
- Institute
of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
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27
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Del Borgo MP, Kulkarni K, Aguilar MI. Unique Functional Materials Derived from β-Amino Acid Oligomers. Aust J Chem 2017. [DOI: 10.1071/ch16511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The unique structures formed by β-amino acid oligomers, or β-peptide foldamers, have been studied for almost two decades, which has led to the discovery of several distinctive structures and bioactive molecules. Recently, this area of research has expanded from conventional peptide drug design to the formation of assemblies and nanomaterials by peptide self-assembly. The unique structures formed by β-peptides give rise to a set of new materials with altered properties that differ from conventional peptide-based materials; such new materials may be useful in several bio- and nanomaterial applications.
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28
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Clerici F, Erba E, Gelmi ML, Pellegrino S. Non-standard amino acids and peptides: From self-assembly to nanomaterials. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.11.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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29
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Shin S, Lee M, Guzei IA, Kang YK, Choi SH. 12/10-Helical β-Peptide with Dynamic Folding Propensity: Coexistence of Right- and Left-Handed Helices in an Enantiomeric Foldamer. J Am Chem Soc 2016; 138:13390-13395. [DOI: 10.1021/jacs.6b08235] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Seonho Shin
- Department
of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Mihye Lee
- Department
of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Ilia A. Guzei
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Young Kee Kang
- Department
of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Soo Hyuk Choi
- Department
of Chemistry, Yonsei University, Seoul 03722, Korea
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30
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Gopalakrishnan R, Frolov AI, Knerr L, Drury WJ, Valeur E. Therapeutic Potential of Foldamers: From Chemical Biology Tools To Drug Candidates? J Med Chem 2016; 59:9599-9621. [PMID: 27362955 DOI: 10.1021/acs.jmedchem.6b00376] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, foldamers have progressively emerged as useful architectures to mimic secondary structures of proteins. Peptidic foldamers, consisting of various amino acid based backbones, have been the most studied from a therapeutic perspective, while polyaromatic foldamers have barely evolved from their nascency and remain perplexing for medicinal chemists due to their poor drug-like nature. Despite these limitations, this compound class may still offer opportunities to study challenging targets or provide chemical biology tools. The potential of foldamer drug candidates reaching the clinic is still a stretch. Nevertheless, advances in the field have demonstrated their potential for the discovery of next generation therapeutics. In this perspective, the current knowledge of foldamers is reviewed in a drug discovery context. Recent advances in the early phases of drug discovery including hit finding, target validation, and optimization and molecular modeling are discussed. In addition, challenges and focus areas are debated and gaps highlighted.
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Affiliation(s)
- Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Department of Chemical Biology, Max Planck Institute of Molecular Physiology , Dortmund 44202, Germany
| | - Andrey I Frolov
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Laurent Knerr
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - William J Drury
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
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31
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Demizu Y, Okitsu K, Yamashita H, Doi M, Misawa T, Oba M, Tanaka M, Kurihara M. α-Helical Structures of Oligopeptides with an Alternating l-Leu-Aib Segment. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yosuke Demizu
- National Institute of Health Sciences; Setagaya 158-8501 Tokyo Japan
| | - Koyo Okitsu
- National Institute of Health Sciences; Setagaya 158-8501 Tokyo Japan
| | - Hiroko Yamashita
- National Institute of Health Sciences; Setagaya 158-8501 Tokyo Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences; 569-1094 Osaka Japan
| | - Takashi Misawa
- National Institute of Health Sciences; Setagaya 158-8501 Tokyo Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences; Nagasaki University; 852-8521 Nagasaki Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences; Nagasaki University; 852-8521 Nagasaki Japan
| | - Masaaki Kurihara
- National Institute of Health Sciences; Setagaya 158-8501 Tokyo Japan
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32
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Chin SL, Lu Q, Dane EL, Dominguez L, McKnight CJ, Straub JE, Grinstaff MW. Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides. J Am Chem Soc 2016; 138:6532-40. [DOI: 10.1021/jacs.6b01837] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
| | - Qing Lu
- Division
of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, United States
| | | | | | | | - John E. Straub
- Division
of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, United States
| | - Mark W. Grinstaff
- Division
of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, United States
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33
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Sharma GVM, Ravindranath H, Bhaskar A, Sirisha K, Ramakrishna KVS, Sarma AVS. Design and Synthesis of Diastereomeric β3-Peptides from (R,R)/(S,S)-APyC and (R)/(S)-β3-Caa: Determination of Enantiomeric Handedness. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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34
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Gopalan R, Del Borgo M, Mechler A, Perlmutter P, Aguilar MI. Geometrically Precise Building Blocks: the Self-Assembly of β-Peptides. ACTA ACUST UNITED AC 2015; 22:1417-1423. [DOI: 10.1016/j.chembiol.2015.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/30/2015] [Accepted: 10/03/2015] [Indexed: 12/23/2022]
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35
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Mándity IM, Fülöp F. An overview of peptide and peptoid foldamers in medicinal chemistry. Expert Opin Drug Discov 2015; 10:1163-77. [PMID: 26289578 DOI: 10.1517/17460441.2015.1076790] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Foldamers are artificial self-organizing systems with various critical properties: i) a stable and designable secondary structure; ii) a larger molecular surface as compared with ordinary organic drug molecules; iii) appropriate control of the orientation of the side-chain functional groups; iv) resistance against proteolytic degradation, which leads to potentially increased oral bioavailability and a longer serum half-life relative to ordinary α-peptides; and v) the lower conformational freedom may result in increased receptor binding in comparison with the natural analogs. AREAS COVERED This article covers the general properties and types of foldamers. This includes highlighted examples of medicinal chemical applications, including antibacterial and cargo molecules, anti-Alzheimer compounds and protein-protein interaction modifiers. EXPERT OPINION Various new foldamers have been created with a range of structures and biological applications. Membrane-acting antibacterial foldamers have been introduced. A general property of these structures is their amphiphilic nature. The amphiphilicity can be stationary or induced by the membrane binding. Cell-penetrating foldamers have been described which serve as cargo molecules, and foldamers have been used as autophagy inducers. Anti-Alzheimer compounds too have been created and the greatest breakthrough was attained via the modification of protein-protein interactions. This can serve as the chemical and pharmaceutical basis for the relevance of foldamers in the future.
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Affiliation(s)
| | - Ferenc Fülöp
- a University of Szeged Institute of Pharmaceutical Chemistry , H-6720 Szeged, Eötvös u. 6, Hungary +36 62 545 768 ; +36 62 545 564 ; +36 62 545 705 ; ;
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36
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Kann N, Johansson JR, Beke-Somfai T. Conformational properties of 1,4- and 1,5-substituted 1,2,3-triazole amino acids – building units for peptidic foldamers. Org Biomol Chem 2015; 13:2776-85. [PMID: 25605623 PMCID: PMC4718141 DOI: 10.1039/c4ob02359e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/02/2015] [Indexed: 01/22/2023]
Abstract
Peptidic foldamers have recently emerged as a novel class of artificial oligomers with properties and structural diversity similar to that of natural peptides, but possessing additional interesting features granting them great potential for applications in fields from nanotechnology to pharmaceuticals. Among these, foldamers containing 1,4- and 1,5-substitued triazole amino acids are easily prepared via the Cu- and Ru-catalyzed click reactions and may offer increased side chain variation, but their structural capabilities have not yet been widely explored. We here describe a systematic analysis of the conformational space of the two most important basic units, the 1,4-substitued (4Tzl) and the 1,5-substitued (5Tzl) 1,2,3-triazole amino acids, using quantum chemical calculations and NMR spectroscopy. Possible conformations of the two triazoles were scanned and their potential minima were located using several theoretical approaches (B3LYP/6-311++G(2d,2p), ωB97X-D/6-311++G(2d,2p), M06-2X/6-311++G(2d,2p) and MP2/6-311++G(2d,2p)) in different solvents. BOC-protected versions of 4Tzl and 5Tzl were also prepared via one step transformations and analyzed by 2D NOESY NMR. Theoretical results show 9 conformers for 5Tzl derivatives with relative energies lying close to each other, which may lead to a great structural diversity. NMR analysis also indicates that conformers preferring turn, helix and zig-zag secondary structures may coexist in solution. In contrast, 4Tzl has a much lower number of conformers, only 4, and these lack strong intraresidual interactions. This is again supported by NMR suggesting the presence of both extended and bent conformers. The structural information provided on these building units could be employed in future design of triazole foldamers.
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Affiliation(s)
- Nina Kann
- Department of Chemical and Biological Engineering , Chalmers University of Technology , SE-41296 Göteborg , Sweden . ; ; http://www.chalmers.se/chem/ ; Fax: +46-31-7723858 ; Tel: +46 (0)31 772 3029, +46 (0)31 772 3070
| | - Johan R. Johansson
- AstraZeneca R&D Mölndal , RIA IMED , Medicinal Chemistry , SE-43183 Mölndal , Sweden .
| | - Tamás Beke-Somfai
- Department of Chemical and Biological Engineering , Chalmers University of Technology , SE-41296 Göteborg , Sweden . ; ; http://www.chalmers.se/chem/ ; Fax: +46-31-7723858 ; Tel: +46 (0)31 772 3029, +46 (0)31 772 3070
- Research Centre for Natural Sciences , Hungarian Academy of Sciences , Pázmány Péter sétány 1 , H-1125 Budapest , Hungary
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37
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Olajos G, Hetényi A, Wéber E, Németh LJ, Szakonyi Z, Fülöp F, Martinek TA. Induced folding of protein-sized foldameric β-sandwich models with core β-amino acid residues. Chemistry 2015; 21:6173-80. [PMID: 25677195 DOI: 10.1002/chem.201405581] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 01/27/2023]
Abstract
The mimicry of protein-sized β-sheet structures with unnatural peptidic sequences (foldamers) is a considerable challenge. In this work, the de novo designed betabellin-14 β-sheet has been used as a template, and α→β residue mutations were carried out in the hydrophobic core (positions 12 and 19). β-Residues with diverse structural properties were utilized: Homologous β(3) -amino acids, (1R,2S)-2-aminocyclopentanecarboxylic acid (ACPC), (1R,2S)-2-aminocyclohexanecarboxylic acid (ACHC), (1R,2S)-2-aminocyclohex-3-enecarboxylic acid (ACEC), and (1S,2S,3R,5S)-2-amino-6,6-dimethylbicyclo[3.1.1]heptane-3-carboxylic acid (ABHC). Six α/β-peptidic chains were constructed in both monomeric and disulfide-linked dimeric forms. Structural studies based on circular dichroism spectroscopy, the analysis of NMR chemical shifts, and molecular dynamics simulations revealed that dimerization induced β-sheet formation in the 64-residue foldameric systems. Core replacement with (1R,2S)-ACHC was found to be unique among the β-amino acid building blocks studied because it was simultaneously able to maintain the interstrand hydrogen-bonding network and to fit sterically into the hydrophobic interior of the β-sandwich. The novel β-sandwich model containing 25 % unnatural building blocks afforded protein-like thermal denaturation behavior.
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Affiliation(s)
- Gábor Olajos
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, 6720 Szeged (Hungary)
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38
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Sarkar R, Debnath M, Maji K, Haldar D. Solvent assisted structural diversity: supramolecular sheet and double helix of a short aromatic γ-peptide. RSC Adv 2015. [DOI: 10.1039/c5ra12831e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Solvent interaction has a significant effect on the molecular motions, folding and self-assembly of short aromatic γ-peptides that leads to a change in initial helical conformation.
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Affiliation(s)
- Rajib Sarkar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
| | - Mintu Debnath
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
| | - Krishnendu Maji
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
| | - Debasish Haldar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- India
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39
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Kwon S, Kang P, Choi MG, Choi SH. cis-2-Aminocyclohex-4-enecarboxylic acid as a new building block of helical foldamers. NEW J CHEM 2015. [DOI: 10.1039/c4nj02056a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
cis-2-Aminocyclohex-4-enecarboxylic acid can promote the α/β-peptide 11/9-helix in solution and in the crystal state.
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Affiliation(s)
- Sunmi Kwon
- Department of Chemistry
- Yonsei University
- Seoul 120-749
- Republic of Korea
| | - Philjae Kang
- Department of Chemistry
- Yonsei University
- Seoul 120-749
- Republic of Korea
| | - Moon-Gun Choi
- Department of Chemistry
- Yonsei University
- Seoul 120-749
- Republic of Korea
| | - Soo Hyuk Choi
- Department of Chemistry
- Yonsei University
- Seoul 120-749
- Republic of Korea
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40
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Mándity IM, Olasz B, Ötvös SB, Fülöp F. Continuous-flow solid-phase peptide synthesis: a revolutionary reduction of the amino acid excess. CHEMSUSCHEM 2014; 7:3172-3176. [PMID: 25196512 DOI: 10.1002/cssc.201402436] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 06/03/2023]
Abstract
A highly efficient continuous-flow technique for the synthesis of peptides was developed. The method allows the application of only 1.5 equivalents of amino acids during coupling, while yielding virtually quantitative conversions. A mesoscale reactor was constructed which permits the use of high temperature and pressure during the synthesis. A complete reaction parameter optimization was carried out. Under the optimum conditions, the couplings of all 20 proteinogenic amino acids were achieved with 1.5 amino acid equivalents with quantitative conversions. As a demonstration of the efficiency of the methodology, difficult sequences and β-peptide foldamers with alicyclic side-chains were synthetized in excellent yields and with lower costs thanks to the lower amounts of amino acid and solvent used. By this the synthesis is highly economic and sustainable. Importantly, exotic and expensive artificial amino acids were incorporated into peptidic sequences by the utilization of a reasonable number of amino acid equivalents. The synthesis can be performed in quantities of microgram to gram in an automated way.
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Affiliation(s)
- István M Mándity
- Institute of Pharmaceutical Chemistry, University of Szeged, Eötvös u. 6, 6720 Szeged (Hungary)
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41
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Jadhav SV, Misra R, Gopi HN. Foldamers to Nanotubes: Influence of Amino Acid Side Chains in the Hierarchical Assembly of α,γ4-Hybrid Peptide Helices. Chemistry 2014; 20:16523-8. [DOI: 10.1002/chem.201404961] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Indexed: 12/28/2022]
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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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Sharma GVM, Yadav TA, Marumudi K, Thodupunuri P, Reddy PP, Kunwar AC. Three-Residue Turn in β-Peptides Nucleated by a 12/10 Helix. Chem Asian J 2014; 9:3153-62. [DOI: 10.1002/asia.201402465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Indexed: 01/07/2023]
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44
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Stidham S, Chin SL, Dane EL, Grinstaff MW. Carboxylated glucuronic poly-amido-saccharides as protein stabilizing agents. J Am Chem Soc 2014; 136:9544-7. [PMID: 24949521 PMCID: PMC4105061 DOI: 10.1021/ja5036804] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Indexed: 12/23/2022]
Abstract
The synthesis of novel carbohydrate-based polymers allows the structure to be tailored at the monomer level for a specific property and expands the range of available structures beyond those found in nature. Using a controlled anionic polymerization, a new type of carbohydrate polymer is synthesized in which glucose-derived monomers are joined by an α-1,2 amide linkage to give enantiopure poly-amido-saccharides (PASs). To investigate the effect of adding ionizable carboxylic acid groups, such as those found in natural polysaccharides containing glucuronic acid, the oxidation of the primary alcohol at the C6-position of the repeat unit to a carboxylic acid is reported. TEMPO-mediated oxidation provides control over the degree of oxidation in excellent yield. Based on circular dichroism, the oxidized polymers possess an ordered helical secondary structure in aqueous solution. Finally, oxidized PASs stabilize lysozyme toward dehydration and freezing stresses better than a current, widely used protein stabilizing agent, trehalose.
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Affiliation(s)
- Sarah
E. Stidham
- Departments of Chemistry
and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Stacy L. Chin
- Departments of Chemistry
and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Eric L. Dane
- Departments of Chemistry
and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Mark W. Grinstaff
- Departments of Chemistry
and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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45
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Sharma GVM, Ravindranath H, Bhaskar A, Jeelani Basha S, Gurava Reddy PRG, Sirisha K, Sarma AVS, Hofmann HJ. Design and Study of Peptides Containing 1:1 Left- and Right-Handed Helical Patterns from Aminopyrancarboxylic Acids. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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46
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Mándity IM, Monsignori A, Fülöp L, Forró E, Fülöp F. Exploiting aromatic interactions for β-peptide foldamer helix stabilization: a significant design element. Chemistry 2014; 20:4591-7. [PMID: 24664416 DOI: 10.1002/chem.201304448] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Indexed: 11/09/2022]
Abstract
Tetrameric H10/12 helix stabilization was achieved by the application of aromatic side-chains in β-peptide oligomers by intramolecular backbone-side chain CH-π interactions. Because of the enlarged hydrophobic surface of the oligomers, a further aim was the investigation of the self-assembly in a polar medium for the β-peptide H10/12 helices. NMR, ECD, and molecular modeling results indicated that the oligomers formed by cis-[1S,2S]- or cis-[1R,2R]-1-amino-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid (ATENAC) and cis-[1R,2S]- or cis-[1S,2R]-2-aminocyclohex-3-enecarboxylic acid (ACHEC) residues promote stable H10/12 helix formation with an alternating backbone configuration even at the tetrameric chain length. These results support the view that aromatic side-chains can be applied for helical structure stabilization. Importantly, this is the first observation of a stable H10/12 helix with tetrameric chain-length. The hydrophobically driven self-assembly was achieved for the helix-forming oligomers, seen as vesicles in transmission electron microscopy images. The self-association phenomenon, which supports the helical secondary structure of these oligomers, depends on the hydrophobic surface area, because a higher number of aromatic side-chains yielded larger vesicles. These results serve as an essential element for the design of helices relating to the H10/12 helix. Moreover, they open up a novel area for bioactive foldamer construction, while the hydrophobic area gained through the aromatic side-chains may yield important receptor-ligand interaction surfaces, which can provide amplified binding strength.
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Affiliation(s)
- István M Mándity
- Institute of Pharmaceutical Chemistry, University of Szeged, Eötvös u. 6, 6720 Szeged (Hungary), Fax: (+36) 62-545705
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47
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Johansson JR, Hermansson E, Nordén B, Kann N, Beke-Somfai T. δ-Peptides from RuAAC-Derived 1,5-Disubstituted Triazole Units. European J Org Chem 2014. [DOI: 10.1002/ejoc.201400018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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48
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Roy A, Kotmale AS, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. Probing the folding induction ability of orthanilic acid in peptides: some observations. RSC Adv 2014. [DOI: 10.1039/c3ra47039c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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49
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Lee W, Kwon S, Kang P, Guzei IA, Choi SH. Helical folding of α/β-peptides containing β-amino acids with an eight-membered ring constraint. Org Biomol Chem 2014; 12:2641-4. [DOI: 10.1039/c4ob00266k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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50
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Giuliano MW, Maynard SJ, Almeida AM, Reidenbach AG, Guo L, Ulrich EC, Guzei IA, Gellman SH. Evaluation of a cyclopentane-based γ-amino acid for the ability to promote α/γ-peptide secondary structure. J Org Chem 2013; 78:12351-61. [PMID: 24303945 PMCID: PMC4109159 DOI: 10.1021/jo401501g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the asymmetric synthesis of the γ-amino acid (1R,2R)-2-aminomethyl-1-cyclopentane carboxylic acid (AMCP) and an evaluation of this residue's potential to promote secondary structure in α/γ-peptides. Simulated annealing calculations using NMR-derived distance restraints obtained for α/γ-peptides in chloroform reveal that AMCP-containing oligomers are conformationally flexible. However, additional evidence suggests that an internally hydrogen-bonded helical conformation is partially populated in solution. From these data, we propose characteristic NOE patterns for the formation of the α/γ-peptide 12/10-helix and discuss the apparent conformational frustration of AMCP-containing oligomers.
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Affiliation(s)
| | - 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
| | - Andrew G. Reidenbach
- 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
| | - Emily C. Ulrich
- 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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