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Menke FS, Mazzier D, Wicher B, Allmendinger L, Kauffmann B, Maurizot V, Huc I. Molecular torsion springs: alteration of helix curvature in frustrated tertiary folds. Org Biomol Chem 2023; 21:1275-1283. [PMID: 36645374 DOI: 10.1039/d2ob02109a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The first abiotic foldamer tertiary structures have been recently reported in the form of aromatic helix-turn-helix motifs based on oligo-quinolinecarboxamides held together by intramolecular hydrogen bonds. Tertiary folds were predicted by computational modelling of the hydrogen-bonding interfaces between helices and later verified by X-ray crystallography. However, the prognosis of how the conformational preference inherent to each helix influences the tertiary structure warranted further investigation. Several new helix-turn-helix sequences were synthesised in which some hydrogen bonds have been removed. Contrary to expectations, this change did not strongly destabilise the tertiary folds. On closer inspection, a new crystal structure revealed that helices adopt their natural curvature when some hydrogen bonds are missing and undergo some spring torsion upon forming the said hydrogen bonds, thus potentially giving rise to a conformational frustration. This phenomenon sheds light on the aggregation behaviour of the helices when they are not linked by a turn unit.
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Affiliation(s)
- Friedericke S Menke
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Daniela Mazzier
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Barbara Wicher
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan, Poland
| | - Lars Allmendinger
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie (UMS3011/US001), CNRS, Inserm, Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Victor Maurizot
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Ivan Huc
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
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2
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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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3
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Peng WC, Wang H, Zhang DW, Li ZT. Folding and Aggregation of Oligoviologens in Water and Cucurbit[ n]uril ( n=7, 8) Modulation. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202108025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
In this highlight, we describe the construction of supramolecular single/double/triple-helical assemblies from small di/tri/tetrapeptides and their applications.
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Affiliation(s)
- Rajat Subhra Giri
- Department of Chemistry, Laboratory of Peptide and Amyloid Research, Indian Institute of Technology Guwahati, Assam-781039, India
| | - Bhubaneswar Mandal
- Department of Chemistry, Laboratory of Peptide and Amyloid Research, Indian Institute of Technology Guwahati, Assam-781039, India
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5
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Roy S, Giri RS, Dolai G, Mandal B. Role of side-chain and chirality of the amino acids on the supramolecular assemblies of dipeptides. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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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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7
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Said Stålsmeden A, Paterson AJ, Szigyártó IC, Thunberg L, Johansson JR, Beke-Somfai T, Kann N. Chiral 1,5-disubstituted 1,2,3-triazoles - versatile tools for foldamers and peptidomimetic applications. Org Biomol Chem 2020; 18:1957-1967. [PMID: 32101244 DOI: 10.1039/d0ob00168f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1,4- and 1,5-Disubstituted triazole amino acid monomers have gained increasing interest among peptidic foldamers, as they are easily prepared via Cu- and Ru-catalyzed click reactions, with the potential for side chain variation. While the latter is key to their applicability, the synthesis and structural properties of the chiral mono- or disubstituted triazole amino acids have only been partially addressed. We here present the synthesis of all eight possible chiral derivatives of a triazole monomer prepared via a ruthenium-catalyzed azide alkyne cycloaddition (RuAAC). To evaluate the conformational properties of the individual building units, a systematic quantum chemical study was performed on all monomers, indicating their capacity to form several low energy conformers. This feature may be used to effect structural diversity when the monomers are inserted into various peptide sequences. We envisage that these results will facilitate new applications for these artificial oligomeric compounds in diverse areas, ranging from pharmaceutics to biotechnology.
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Affiliation(s)
- Anna Said Stålsmeden
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden.
| | - Andrew J Paterson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden.
| | - Imola Cs Szigyártó
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Linda Thunberg
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Johan R Johansson
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Nina Kann
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden.
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8
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Mazzier D, De S, Wicher B, Maurizot V, Huc I. Parallele homochirale und antiparallele heterochirale Wasserstoffbrücken‐Interaktionsflächen in multihelikalen abiotischen Foldameren. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniela Mazzier
- Department of Pharmacy and Centre for Integrated Protein Science Ludwig-Maximilians-Universität Butenandtstraße 5–13 81377 Munich Deutschland
- CBMN Laboratory Université de Bordeaux CNRS, IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Soumen De
- CBMN Laboratory Université de Bordeaux CNRS, IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Barbara Wicher
- Department of Chemical Technology of Drugs Poznan University of Medical Sciences Grunwaldzka 6 60–780 Poznan Polen
| | - Victor Maurizot
- CBMN Laboratory Université de Bordeaux CNRS, IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Ivan Huc
- Department of Pharmacy and Centre for Integrated Protein Science Ludwig-Maximilians-Universität Butenandtstraße 5–13 81377 Munich Deutschland
- CBMN Laboratory Université de Bordeaux CNRS, IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
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9
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Mazzier D, De S, Wicher B, Maurizot V, Huc I. Parallel Homochiral and Anti-Parallel Heterochiral Hydrogen-Bonding Interfaces in Multi-Helical Abiotic Foldamers. Angew Chem Int Ed Engl 2020; 59:1606-1610. [PMID: 31671236 PMCID: PMC7004161 DOI: 10.1002/anie.201912805] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Indexed: 11/25/2022]
Abstract
A hydrogen-bonding interface between helical aromatic oligoamide foldamers has been designed to promote the folding of a helix-turn-helix motif with a head-to-tail arrangement of two helices of opposite handedness. This design complements an earlier helix-turn-helix motif with a head-to-head arrangement of two helices of identical handedness interface. The two motifs were shown to have comparable stability and were combined in a unimolecular tetra-helix fold constituting the largest abiotic tertiary structure to date.
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Affiliation(s)
- Daniela Mazzier
- Department of Pharmacy and Centre for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstrasse 5–1381377MunichGermany
- CBMN LaboratoryUniversité de BordeauxCNRS, IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Soumen De
- CBMN LaboratoryUniversité de BordeauxCNRS, IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Barbara Wicher
- Department of Chemical Technology of DrugsPoznan University of Medical SciencesGrunwaldzka 660–780PoznanPoland
| | - Victor Maurizot
- CBMN LaboratoryUniversité de BordeauxCNRS, IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Ivan Huc
- Department of Pharmacy and Centre for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstrasse 5–1381377MunichGermany
- CBMN LaboratoryUniversité de BordeauxCNRS, IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
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10
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Mazzier D, De S, Wicher B, Maurizot V, Huc I. Interplay of secondary and tertiary folding in abiotic foldamers. Chem Sci 2019; 10:6984-6991. [PMID: 31588265 PMCID: PMC6676331 DOI: 10.1039/c9sc01322a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/08/2019] [Indexed: 12/30/2022] Open
Abstract
The first true abiotic tertiary folded structures, i.e. at the exclusion of any aliphatic amino acid, have recently been introduced under the form of aromatic oligoamide helix-turn-helix foldamers stabilized by hydrogen bonds in organic solvents. We present an investigation of the interplay of secondary and tertiary folding and of some cooperative effects in these systems. A solid phase synthesis approach to the preparation of these sequences was developed to facilitate systematic variation. Flexible pyridine-based units were introduced in various proportions in replacement of more rigid quinoline-based units. Conformational behaviour was assessed in solution by NMR, in the solid state by X-ray crystallography, and computationally through molecular dynamics simulations. Altogether, our results demonstrate that tertiary folding stabilizes otherwise flexible secondary structures, and that the disruption of tertiary folds upon adding polar solvents follows different mechanisms depending on whether secondary structures are inherently stable or not. These findings constitute a solid basis on which to further increase the size and complexity of abiotic folded structures and to eventually orchestrate folding dynamics and responsiveness.
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Affiliation(s)
- Daniela Mazzier
- Department of Pharmacy , Centre for Integrated Protein Science , Ludwig-Maximilians-Universität , Butenandtstraße 5-13 , D-81377 Munich , Germany .
- CBMN Laboratory , Université de Bordeaux , CNRS , IPB , Institut Européen de Chimie et Biologie , 2 rue Escarpit , 33600 Pessac , France
| | - Soumen De
- CBMN Laboratory , Université de Bordeaux , CNRS , IPB , Institut Européen de Chimie et Biologie , 2 rue Escarpit , 33600 Pessac , France
| | - Barbara Wicher
- Department of Chemical Technology of Drugs , Poznan University of Medical Sciences , Grunwaldzka 6 , 60-780 Poznan , Poland
| | - Victor Maurizot
- CBMN Laboratory , Université de Bordeaux , CNRS , IPB , Institut Européen de Chimie et Biologie , 2 rue Escarpit , 33600 Pessac , France
| | - Ivan Huc
- Department of Pharmacy , Centre for Integrated Protein Science , Ludwig-Maximilians-Universität , Butenandtstraße 5-13 , D-81377 Munich , Germany .
- CBMN Laboratory , Université de Bordeaux , CNRS , IPB , Institut Européen de Chimie et Biologie , 2 rue Escarpit , 33600 Pessac , France
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11
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Lee KJ, Sable GA, Shin MK, Lim HS. Oligomers of α-ABpeptoid/β 3 -peptide hybrid. Biopolymers 2019; 110:e23289. [PMID: 31150108 DOI: 10.1002/bip.23289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 12/20/2022]
Abstract
Peptoids, oligomers of N-substituted glycines, have been attracting increasing interest due to their advantageous properties as peptidomimetics. However, due to the lack of chiral centers and amide hydrogen atoms, peptoids, in general, do not form folding structures except that they have α-chiral side chains. We have recently developed "peptoids with backbone chirality" as a new class of peptoid foldamers called α-ABpeptoids and demonstrated that they could have folding conformations owing to the methyl groups on chiral α-carbons in the backbone structure. Here we report α-ABpeptoid/β3 -peptide oligomers as a unique peptidomimetic structure with a heterogeneous backbone. This hybrid structure contains a mixed α-ABpeptoid and β3 -peptide residues arranged in an alternate manner. These α-ABpeptoid/β3 -peptide oligomers could form intramolecular hydrogen bonding and have better cell permeability relative to pure peptide sequences. These oligomers were shown to adopt ordered folding structures based on circular dichroism studies. Overall, α-ABpeptoid/β3 -peptide oligomers may represent a novel class of peptidomimetic foldamers and will find a wide range of applications in biomedical and material sciences.
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Affiliation(s)
- Kang Ju Lee
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
| | - Ganesh A Sable
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
| | - Min-Kyung Shin
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
| | - Hyun-Suk Lim
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
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12
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Amabili P, Calvaresi M, Martelli G, Orena M, Rinaldi S, Sgolastra F. Imidazolidinone-Tethered α-Hydrazidopeptides - Synthesis and Conformational Investigation. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801427] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Paolo Amabili
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Via Brecce Bianche 60131 Ancona Italy
| | - Matteo Calvaresi
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Gianluca Martelli
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Via Brecce Bianche 60131 Ancona Italy
| | - Mario Orena
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Via Brecce Bianche 60131 Ancona Italy
| | - Samuele Rinaldi
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Via Brecce Bianche 60131 Ancona Italy
| | - Federica Sgolastra
- 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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Liu B, Pappas CG, Zangrando E, Demitri N, Chmielewski PJ, Otto S. Complex Molecules That Fold Like Proteins Can Emerge Spontaneously. J Am Chem Soc 2019; 141:1685-1689. [PMID: 30562021 PMCID: PMC6356852 DOI: 10.1021/jacs.8b11698] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Folding can bestow macromolecules with various properties, as evident from nature's proteins. Until now complex folded molecules are the product either of evolution or of an elaborate process of design and synthesis. We now show that molecules that fold in a well-defined architecture of substantial complexity can emerge autonomously and selectively from a simple precursor. Specifically, we have identified a self-synthesizing macrocyclic foldamer with a complex and unprecedented secondary and tertiary structure that constructs itself highly selectively from 15 identical peptide-nucleobase subunits, using a dynamic combinatorial chemistry approach. Folding of the structure drives its synthesis in 95% yield from a mixture of interconverting molecules of different ring sizes in a one-step process. Single-crystal X-ray crystallography and NMR reveal a folding pattern based on an intricate network of noncovalent interactions involving residues spaced apart widely in the linear sequence. These results establish dynamic combinatorial chemistry as a powerful approach to developing synthetic molecules with folding motifs of a complexity that goes well beyond that accessible with current design approaches. The fact that such molecules can form autonomously implies that they may have played a role in the origin of life at earlier stages than previously thought possible.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry , Stratingh Institute , Nijenborgh 4, 9747 AG Groningen , The Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry , Stratingh Institute , Nijenborgh 4, 9747 AG Groningen , The Netherlands
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences , University of Trieste , 34127 Trieste , Italy
| | - Nicola Demitri
- Elettra-Sincrotrone Trieste , S.S. 14 Km 163.5 in Area Science Park , 34149 Basovizza, Trieste , Italy
| | - Piotr J Chmielewski
- Department of Chemistry , University of Wrocław , F. Joliot-Curie 14, 50383 Wrocław , Poland
| | - Sijbren Otto
- Centre for Systems Chemistry , Stratingh Institute , Nijenborgh 4, 9747 AG Groningen , The Netherlands
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14
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Chinthakindi PK, Benediktsdottir A, Ibrahim A, Wared A, Aurell CJ, Pettersen A, Zamaratski E, Arvidsson PI, Chen Y, Sandström A. Synthesis of Sulfonimidamide-Based Amino Acid Building Blocks with Orthogonal Protecting Groups. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801541] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Praveen K. Chinthakindi
- Department of Medicinal Chemistry; Drug Design and Discovery; Uppsala University, Box 574, 75123; Uppsala Sweden
| | - Andrea Benediktsdottir
- Department of Medicinal Chemistry; Drug Design and Discovery; Uppsala University, Box 574, 75123; Uppsala Sweden
| | - Ayah Ibrahim
- Department of Medicinal Chemistry; Drug Design and Discovery; Uppsala University, Box 574, 75123; Uppsala Sweden
| | - Atta Wared
- Department of Medicinal Chemistry; Drug Design and Discovery; Uppsala University, Box 574, 75123; Uppsala Sweden
| | - Carl-Johan Aurell
- Large Scale Chemistry; Early Chemical Development; AstraZeneca; 83 Gothenburg Sweden
| | - Anna Pettersen
- Early Product Development; Pharmaceutical Sciences; IMED Biotech Unit; AstraZeneca; 83 Gothenburg Sweden
| | - Edouard Zamaratski
- Department of Medicinal Chemistry; Drug Design and Discovery; Uppsala University, Box 574, 75123; Uppsala Sweden
| | - Per I. Arvidsson
- Science for Life Laboratory; Drug Discovery and Development Platform and Division of Translational Medicine and Chemical Biology; Department of Medical Biochemistry and Biophysics; Karolinska Institutet; 171 77 Stockholm Sweden
- Catalysis and Peptide Research Unit; University of KwaZulu Natal; 4000 Durban South Africa
| | - Yantao Chen
- Medicinal Chemistry; Cardiovascular Renal and Metabolism; IMED Biotech Unit; AstraZeneca; 431 83 Gothenburg Sweden
| | - Anja Sandström
- Department of Medicinal Chemistry; Drug Design and Discovery; Uppsala University, Box 574, 75123; Uppsala Sweden
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15
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Dumonteil G, Bhattacharjee N, Angelici G, Roy O, Faure S, Jouffret L, Jolibois F, Perrin L, Taillefumier C. Exploring the Conformation of Mixed Cis–Trans α,β-Oligopeptoids: A Joint Experimental and Computational Study. J Org Chem 2018; 83:6382-6396. [DOI: 10.1021/acs.joc.8b00606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Geoffrey Dumonteil
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Nicholus Bhattacharjee
- Université de Toulouse-INSA-UPS, LPCNO, CNRS UMR 5215, 135 av Rangueil, F-31077, Toulouse, France
- Université de Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INSA Lyon, ICBMS, CNRS UMR 5246, Equipe ITEMM, Bât Curien, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
| | - Gaetano Angelici
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Olivier Roy
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Sophie Faure
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Laurent Jouffret
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Franck Jolibois
- Université de Toulouse-INSA-UPS, LPCNO, CNRS UMR 5215, 135 av Rangueil, F-31077, Toulouse, France
| | - Lionel Perrin
- Université de Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INSA Lyon, ICBMS, CNRS UMR 5246, Equipe ITEMM, Bât Curien, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France
| | - Claude Taillefumier
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
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16
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Jang HB, Choi YR, Jeong KS. Matched and Mismatched Phenomena in the Helix Orientation Bias Induced by Chiral Appendages at Multiple Positions of Indolocarbazole-Pyridine Hybrid Foldamers. J Org Chem 2018; 83:5123-5131. [PMID: 29693388 DOI: 10.1021/acs.joc.8b00482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of indolocarbazole-pyridine (IP) hybrid foldamers containing chiral residues at multiple different positions were prepared to reveal the matched and mismatched phenomena of local stereocenters on the induction of helical bias. These foldamers adopted stable helical conformations, thus affording well-resolved separate sets of 1H NMR signals for right- ( P) and left-handed ( M) helices in water saturated organic solvents such as toluene and dichloromethane. The ratios of P- and M-helices were determined by integrating the 1H NMR signals, in combination with the molar circular dichroism (Δε) and optical rotation ([α]D) values. The degree of helical bias was larger in the IP foldamer bearing chiral residues at the termini relative to those at the pyridine side chains, but the preferred helix orientation was opposite to each other. Foldamers 5( SS)t( SSS)py and 6( RR)t( SSS)py with chiral residues at five different positions demonstrated the matched and mismatched phenomena of local stereocenters in 6( RR)t( SSS)py and 5( SS)t( SSS)py, respectively.
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Affiliation(s)
- Han Bit Jang
- Department of Chemistry , Yonsei University , Seoul 03722 , Korea
| | - Ye Rin Choi
- Department of Chemistry , Yonsei University , Seoul 03722 , Korea
| | - Kyu-Sung Jeong
- Department of Chemistry , Yonsei University , Seoul 03722 , Korea
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17
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Kotmale AS, Sangtani E, Gonnade RG, Sarkar D, Burade S, Rajamohanan PR, Sanjayan GJ. Conformational studies of Ant–Pro motif-incorporated cyclic peptides: gramicidin S and avellanin. NEW J CHEM 2018. [DOI: 10.1039/c7nj03701e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conformational studies suggest that an AntDPro motif-incorporated synthetic gramicidin S analog retains β-sheet conformation, while its truncated analog avellanin disturbs the β-sheet conformation.
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Affiliation(s)
- Amol S. Kotmale
- Division of Organic Chemistry
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune 411 008
- India
- Central NMR Facility
| | - Ekta Sangtani
- Center for Materials Characterization
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune 411 008
- India
| | - Rajesh G. Gonnade
- Center for Materials Characterization
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune 411 008
- India
| | - Dhiman Sarkar
- Combichem-Bioresource Center
- Organic Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Sachin Burade
- Department of Chemistry
- Savitribai Phule Pune University
- Pune
- India
| | | | - Gangadhar J. Sanjayan
- Division of Organic Chemistry
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune 411 008
- India
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18
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Annala R, Suhonen A, Laakkonen H, Permi P, Nissinen M. Structural Tuning and Conformational Stability of Aromatic Oligoamide Foldamers. Chemistry 2017; 23:16671-16680. [PMID: 29105164 DOI: 10.1002/chem.201703985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Indexed: 11/09/2022]
Abstract
A series of aromatic oligoamide foldamers with two or three pyridine-2,6-dicarboxamide units as their main folding motifs and varying aromatic building blocks as linkers have been synthetized to study the effects of the structural variation on the folding properties and conformational stability. Crystallographic studies showed that in the solid state the central linker unit either elongates the helices and more open S-shaped conformations, compresses the helices to more compact conformations, or acts as a rigid spacer separating the pyridine-2,6-dicarboxamide units, which for their part add the predictability of the conformational properties. Multidimensional NMR studies showed that, even in solution, foldamers show conformational stability and folded conformations comparable to the solid-state structures.
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Affiliation(s)
- Riia Annala
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014 University of, Jyvaskyla, Finland
| | - Aku Suhonen
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014 University of, Jyvaskyla, Finland
| | - Heikki Laakkonen
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014 University of, Jyvaskyla, Finland
| | - Perttu Permi
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014 University of, Jyvaskyla, Finland.,Department of Chemistry and Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014 University of, Jyvaskyla, Finland
| | - Maija Nissinen
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, P.O. Box 35, 40014 University of, Jyvaskyla, Finland
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19
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De S, Chi B, Granier T, Qi T, Maurizot V, Huc I. Designing cooperatively folded abiotic uni- and multimolecular helix bundles. Nat Chem 2017; 10:51-57. [PMID: 29256508 DOI: 10.1038/nchem.2854] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/27/2017] [Indexed: 01/09/2023]
Abstract
Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.
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Affiliation(s)
- Soumen De
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Bo Chi
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Thierry Granier
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Ting Qi
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Victor Maurizot
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Ivan Huc
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
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20
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. New Modalities for Challenging Targets in Drug Discovery. Angew Chem Int Ed Engl 2017; 56:10294-10323. [PMID: 28186380 DOI: 10.1002/anie.201611914] [Citation(s) in RCA: 233] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/31/2017] [Indexed: 12/11/2022]
Abstract
Our ever-increasing understanding of biological systems is providing a range of exciting novel biological targets, whose modulation may enable novel therapeutic options for many diseases. These targets include protein-protein and protein-nucleic acid interactions, which are, however, often refractory to classical small-molecule approaches. Other types of molecules, or modalities, are therefore required to address these targets, which has led several academic research groups and pharmaceutical companies to increasingly use the concept of so-called "new modalities". This Review defines for the first time the scope of this term, which includes novel peptidic scaffolds, oligonucleotides, hybrids, molecular conjugates, as well as new uses of classical small molecules. We provide the most representative examples of these modalities to target large binding surface areas such as those found in protein-protein interactions and for biological processes at the center of cell regulation.
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Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Stéphanie M Guéret
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
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21
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. Neue Modalitäten für schwierige Zielstrukturen in der Wirkstoffentwicklung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611914] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Stéphanie M. Guéret
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
- Fakultät für Chemie and Chemische Biologie; Technische Universität Dortmund; Deutschland
| | - Tom N. Grossmann
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; Niederlande
| | - Alleyn T. Plowright
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
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22
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George KL, Horne WS. Heterogeneous-Backbone Foldamer Mimics of Zinc Finger Tertiary Structure. J Am Chem Soc 2017; 139:7931-7938. [PMID: 28509549 DOI: 10.1021/jacs.7b03114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A variety of oligomeric backbones with compositions deviating from biomacromolecules can fold in defined ways. Termed "foldamers," these agents have diverse potential applications. A number of protein-inspired secondary structures (e.g., helices, sheets) have been produced from unnatural backbones, yet examples of tertiary folds combining several secondary structural elements in a single entity are rare. One promising strategy to address this challenge is the systematic backbone alteration of natural protein sequences, through which a subset of the native side chains is displayed on an unnatural building block to generate a heterogeneous backbone. A drawback to this approach is that substitution at more than one or two sites often comes at a significant energetic cost to fold stability. Here we report heterogeneous-backbone foldamers that mimic the zinc finger domain, a ubiquitous and biologically important metal-binding tertiary motif, and do so with a folded stability that is superior to the natural protein on which their design is based. A combination of UV-vis spectroscopy, isothermal titration calorimetry, and multidimensional NMR reveals that suitably designed oligomers with >20% modified backbones can form native-like tertiary folds with metal-binding environments identical to the prototype sequence (the third finger of specificity factor 1) and enhanced thermodynamic stability. These results expand the scope of heterogeneous-backbone foldamer design to a new tertiary structure class and show that judiciously applied backbone modification can be accompanied by improvement to fold stability.
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Affiliation(s)
- Kelly L George
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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23
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Horeau M, Lautrette G, Wicher B, Blot V, Lebreton J, Pipelier M, Dubreuil D, Ferrand Y, Huc I. Metal-Coordination-Assisted Folding and Guest Binding in Helical Aromatic Oligoamide Molecular Capsules. Angew Chem Int Ed Engl 2017; 56:6823-6827. [PMID: 28471081 DOI: 10.1002/anie.201701693] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Indexed: 11/07/2022]
Abstract
The development of foldamer-based receptors is driven by the design of monomers with specific properties. Herein, we introduce a pyridazine-pyridine-pyridazine diacid monomer and its incorporation into helical aromatic oligoamide foldamer containers. This monomer codes for a wide helix diameter and can sequester metal ions on the inner wall of the helix cavity. Crystallographic studies and NMR titrations show that part of the metal coordination sphere remains available and may then promote the binding of a guest within the cavity. In addition to metal coordination, binding of the guest is assisted by cooperative interactions with the helix host, thereby resulting in significant enhancements depending on the foldamer sequence, and in slow guest capture and release on the NMR time scale. In the absence of metal ions, the pyridazine-pyridine-pyridazine monomer promotes an extended conformation of the foldamer that results in aggregation, including the formation of an intertwined duplex.
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Affiliation(s)
- Maxime Horeau
- UMR 6230-CEISAM, Univ. Nantes-CNRS, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France
| | - Guillaume Lautrette
- UMR 5248-CBMN, Univ. Bordeaux-CNRS-Institut Polytechnique de Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Barbara Wicher
- UMR 5248-CBMN, Univ. Bordeaux-CNRS-Institut Polytechnique de Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Virginie Blot
- UMR 6230-CEISAM, Univ. Nantes-CNRS, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France
| | - Jacques Lebreton
- UMR 6230-CEISAM, Univ. Nantes-CNRS, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France
| | - Muriel Pipelier
- UMR 6230-CEISAM, Univ. Nantes-CNRS, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France
| | - Didier Dubreuil
- UMR 6230-CEISAM, Univ. Nantes-CNRS, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France
| | - Yann Ferrand
- UMR 5248-CBMN, Univ. Bordeaux-CNRS-Institut Polytechnique de Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33600, Pessac, France
| | - Ivan Huc
- UMR 5248-CBMN, Univ. Bordeaux-CNRS-Institut Polytechnique de Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33600, Pessac, France
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24
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Horeau M, Lautrette G, Wicher B, Blot V, Lebreton J, Pipelier M, Dubreuil D, Ferrand Y, Huc I. Metal-Coordination-Assisted Folding and Guest Binding in Helical Aromatic Oligoamide Molecular Capsules. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701693] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Maxime Horeau
- UMR 6230-CEISAM; Univ. Nantes-CNRS; Faculté des Sciences et des Techniques; 2 rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Guillaume Lautrette
- UMR 5248-CBMN; Univ. Bordeaux-CNRS-Institut Polytechnique de Bordeaux; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33600 Pessac France
| | - Barbara Wicher
- UMR 5248-CBMN; Univ. Bordeaux-CNRS-Institut Polytechnique de Bordeaux; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33600 Pessac France
| | - Virginie Blot
- UMR 6230-CEISAM; Univ. Nantes-CNRS; Faculté des Sciences et des Techniques; 2 rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Jacques Lebreton
- UMR 6230-CEISAM; Univ. Nantes-CNRS; Faculté des Sciences et des Techniques; 2 rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Muriel Pipelier
- UMR 6230-CEISAM; Univ. Nantes-CNRS; Faculté des Sciences et des Techniques; 2 rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Didier Dubreuil
- UMR 6230-CEISAM; Univ. Nantes-CNRS; Faculté des Sciences et des Techniques; 2 rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Yann Ferrand
- UMR 5248-CBMN; Univ. Bordeaux-CNRS-Institut Polytechnique de Bordeaux; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33600 Pessac France
| | - Ivan Huc
- UMR 5248-CBMN; Univ. Bordeaux-CNRS-Institut Polytechnique de Bordeaux; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33600 Pessac France
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25
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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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26
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Abstract
Aromatic amide foldamers constitute a growing class of oligomers that adopt remarkably stable folded conformations. The folded structures possess largely predictable shapes and open the way toward the design of synthetic mimics of proteins. Important examples of aromatic amide foldamers include oligomers of 7- or 8-amino-2-quinoline carboxylic acid that have been shown to exist predominantly as well-defined helices, including when they are combined with α-amino acids to which they may impose their folding behavior. To rapidly iterate their synthesis, solid phase synthesis (SPS) protocols have been developed and optimized for overcoming synthetic difficulties inherent to these backbones such as low nucleophilicity of amine groups on electron poor aromatic rings and a strong propensity of even short sequences to fold on the solid phase during synthesis. For example, acid chloride activation and the use of microwaves are required to bring coupling at aromatic amines to completion. Here, we report detailed SPS protocols for the rapid production of: (1) oligomers of 8-amino-2-quinolinecarboxylic acid; (2) oligomers containing 7-amino-8-fluoro-2-quinolinecarboxylic acid; and (3) heteromeric oligomers of 8-amino-2-quinolinecarboxylic acid and α-amino acids. SPS brings the advantage to quickly produce sequences having varied main chain or side chain components without having to purify multiple intermediates as in solution phase synthesis. With these protocols, an octamer could easily be synthesized and purified within one to two weeks from Fmoc protected amino acid monomer precursors.
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27
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Kudo M, Carbajo López D, Maurizot V, Masu H, Tanatani A, Huc I. Synthesis and Conformational Analysis of Quinoline-Oxazole Peptides. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Hu X, Dawson SJ, Nagaoka Y, Tanatani A, Huc I. Solid-Phase Synthesis of Water-Soluble Helically Folded Hybrid α-Amino Acid/Quinoline Oligoamides. J Org Chem 2016; 81:1137-50. [PMID: 26703882 DOI: 10.1021/acs.joc.5b02671] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here a solid phase synthesis methodology that allows the incorporation of α-amino acids (X) into quinoline (Q) oligoamide foldamer sequences. Water-soluble hybrid oligoamides based on the XQ2 trimer repeat motif were shown to adopt helical conformations presenting α-amino acid side chains in a predictable linear array on one face of the helix. In contrast, sequences based on the XQ dimer motif expressed less well-defined behavior, most likely due to local conformational variability precluding long-range order. Also presented is a full structural investigation by NMR of a dodecameric XQ2-type foldamer containing four different amino acid residues (Lys, Ala, Asp, and Ser).
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Affiliation(s)
- Xiaobo Hu
- Université de Bordeaux, CBMN (UMR5248) , Institut Européen de Chimie et Biologie, 2 Rue Escarpit, 33600 Pessac, France
| | - Simon J Dawson
- CNRS, CBMN (UMR 5248) , Institut Européen de Chimie et Biologie, 2 Rue Escarpit, 33600 Pessac, France
| | - Yui Nagaoka
- Department of Chemistry, Faculty of Science, Ochanomizu University , 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Aya Tanatani
- Department of Chemistry, Faculty of Science, Ochanomizu University , 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Ivan Huc
- Université de Bordeaux, CBMN (UMR5248) , Institut Européen de Chimie et Biologie, 2 Rue Escarpit, 33600 Pessac, France
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29
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Vijayadas KN, Kotmale AS, Thorat SH, Gonnade RG, Nair RV, Rajamohanan PR, Sanjayan GJ. Reversal of H-bonding direction by N-sulfonation in a synthetic reverse-turn peptide motif. Org Biomol Chem 2015; 13:3064-9. [PMID: 25624112 DOI: 10.1039/c4ob02438a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This communication depicts an intriguing example of hydrogen-bonding reversal upon introduction of a sulfonamide linkage at the N-terminus of a synthetic reverse-turn peptide motif. The ready availability of two sulfonyl oxygen atoms, as hydrogen-bonding acceptors, combined with the inherent twisted conformation of sulfonamides are seen to act as switches that engage/disengage the hydrogen-bond at the sticky ends/termini.
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Affiliation(s)
- Kuruppanthara N Vijayadas
- Division of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
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30
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Priya G, Kotmale AS, Chakravarty D, Puranik VG, Rajamohanan PR, Sanjayan GJ. Conformational modulation of peptides using β-amino benzenesulfonic acid (SAnt). Org Biomol Chem 2015; 13:2087-91. [DOI: 10.1039/c4ob02421d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This communication describes the utility of the conformationally restricted aromatic β-amino acid (2-aminobenzenesulfonic acid, SAnt) for inducing various folding interactions in short peptides.
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Affiliation(s)
- Gowri Priya
- Division of Organic Chemistry
- National Chemical Laboratory
- Pune 411 008
- India
| | - Amol S. Kotmale
- Centre for Materials Characterisation
- National Chemical Laboratory
- Pune 411 008
- India
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31
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Kheria S, Nair RV, Kotmale AS, Rajamohanan PR, Sanjayan GJ. The role of N-terminal proline in stabilizing the Ant–Pro zipper motif. NEW J CHEM 2015. [DOI: 10.1039/c4nj02151g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper deals with the role of N-terminal proline in stabilizing the Ant–Pro zipper structure by the co-operative contribution of competing forces viz. hydrogen bonding, aromatic stacking and backbone chirality.
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Affiliation(s)
- Sanjeev Kheria
- Division of Organic Chemistry
- National Chemical Laboratory
- Pune 411 008
- India
| | - Roshna V. Nair
- Division of Organic Chemistry
- National Chemical Laboratory
- Pune 411 008
- India
| | - Amol S. Kotmale
- Central NMR Facility
- National Chemical Laboratory
- Pune 411 008
- India
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