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Šenica L, Grošelj U, Kasunič M, Kočar D, Stanovnik B, Svete J. Synthesis of Enaminone-Based Vinylogous Peptides. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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2
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A compendium of cyclic sugar amino acids and their carbocyclic and heterocyclic nitrogen analogues. Amino Acids 2013; 45:613-89. [DOI: 10.1007/s00726-013-1521-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/21/2013] [Indexed: 12/19/2022]
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3
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C-3 branched δ-3,5-cis- and trans-THF sugar amino acids: synthesis of the first generation of branched homooligomers. Amino Acids 2011; 41:643-61. [PMID: 21350854 DOI: 10.1007/s00726-011-0849-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 02/12/2011] [Indexed: 12/22/2022]
Abstract
This article describes the efficient synthesis of the first generation of branched sugar amino acid (SAA) oligomers in solution phase via two main routes: by the use of a standard coupling reagent and via the use of active ester intermediates. Benzyl-protected dimeric carbopeptoid and methyl-protected dimeric and tetrameric, hexameric and octameric carbopeptoids were obtained from a branched δ-3,5-trans-tetrahydrofuran (THF) SAA and methyl-protected dimeric and tetrameric carbopeptoids were synthesised from a branched δ-3,5-cis-THF SAA. These systems are of interest because of their potential to display foldameric properties reminiscent of those observed in α-peptides and proteins. Amongst their many uses, foldamers provide simpler models in the study of the factors which induce the folding and unfolding of proteins and, ultimately, potential insights into their functioning.
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Jiménez Blanco JL, Ortega-Caballero F, Ortiz Mellet C, García Fernández JM. (Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties. Beilstein J Org Chem 2010; 6:20. [PMID: 20485602 PMCID: PMC2870983 DOI: 10.3762/bjoc.6.20] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 02/11/2010] [Indexed: 01/04/2023] Open
Abstract
Oligosaccharides are currently recognised as having functions that influence the entire spectrum of cell activities. However, a distinct disadvantage of naturally occurring oligosaccharides is their metabolic instability in biological systems. Therefore, much effort has been spent in the past two decades on the development of feasible routes to carbohydrate mimetics which can compete with their O-glycosidic counterparts in cell surface adhesion, inhibit carbohydrate processing enzymes, and interfere in the biosynthesis of specific cell surface carbohydrates. Such oligosaccharide mimetics are potential therapeutic agents against HIV and other infections, against cancer, diabetes and other metabolic diseases. An efficient strategy to access this type of compounds is the replacement of the glycosidic linkage by amide or pseudoamide functions such as thiourea, urea and guanidine. In this review we summarise the advances over the last decade in the synthesis of oligosaccharide mimetics that possess amide and pseudoamide linkages, as well as studies focussing on their supramolecular and recognition properties.
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Affiliation(s)
- José L Jiménez Blanco
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, Prof. García González 1, Seville 41012, Spain.
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Edwards AA, Alexander BD, Fleet GWJ, Tranter GE. Spectroscopic studies of oligomers containing 2,5-trans furanoid sugar amino acids. Chirality 2008; 20:969-72. [PMID: 18311778 DOI: 10.1002/chir.20538] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Sugar amino acids and their oligomers, known as carbopeptoids, are commonly studied as foldamers. However, study of their conformational preference is often challenging when the adopted conformations are extended and/or disordered. This study is the first to explore the disordered nature of such carbopeptoids by utilizing a family of 2,5-trans carbopeptoids. An array of spectroscopic techniques has been used to investigate the conformational preference of these carbopeptoids. However, using this data alone it has not been possible to assign conformational preference as an ordered extended conformation or as a disordered family of closely related conformations. Computational methods need to be employed to achieve reliable interpretation of the spectroscopic data.
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Affiliation(s)
- Alison A Edwards
- Medway School of Pharmacy, Universities of Kent and Greenwich at Medway, Kent, United Kingdom.
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Synthesis of a bicyclic δ-amino acid as a constrained Gly-Asn dipeptide isostere. Amino Acids 2008; 35:37-44. [DOI: 10.1007/s00726-007-0636-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 11/06/2007] [Indexed: 10/22/2022]
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7
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Risseeuw MD, Overhand M, Fleet GW, Simone MI. A compendium of sugar amino acids (SAA): scaffolds, peptide- and glyco-mimetics. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.tetasy.2007.08.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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8
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Edwards AA, Fleet GWJ, Tranter GE. Classification of conformation for sugar amino acid systems using chiroptical spectroscopy. Chirality 2007; 18:265-72. [PMID: 16528733 DOI: 10.1002/chir.20248] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A number of structurally related sugar amino acid systems have been examined by chiroptical methods to aid interpretation of their conformational preference. The use of circular dichroism, in addition to NMR and solution IR, has enabled classification of the conformations adopted by sugar amino acid systems as hydrogen-bonded regular, non-hydrogen-bonded regular, and non-hydrogen-bonded irregular. A set of tetrameric SAAs are examined and the effect of change in primary structure related to conformation.
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Affiliation(s)
- Alison A Edwards
- Biological Chemistry, Division of Biomedical Sciences, Imperial College, London, United Kingdom.
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9
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Ingrid Velter, Barbara La Ferla, Francesco Nicotra. Carbohydrate‐Based Molecular Scaffolding. J Carbohydr Chem 2006. [DOI: 10.1080/07328300600733020] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Ingrid Velter
- a Dipartimento di Biotecnologie e Bioscienze , Università degli Studi di Milano‐Bicocca , Milano, Italy
| | - Barbara La Ferla
- a Dipartimento di Biotecnologie e Bioscienze , Università degli Studi di Milano‐Bicocca , Milano, Italy
| | - Francesco Nicotra
- a Dipartimento di Biotecnologie e Bioscienze , Università degli Studi di Milano‐Bicocca , Milano, Italy
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Temelkoff DP, Zeller M, Norris P. N-Glycoside neoglycotrimers from 2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl azide. Carbohydr Res 2006; 341:1081-90. [PMID: 16678807 DOI: 10.1016/j.carres.2006.04.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2006] [Revised: 04/06/2006] [Accepted: 04/10/2006] [Indexed: 11/15/2022]
Abstract
2,3,4,6-Tetra-O-acetyl-beta-D-glucopyranosyl azide is available on large scale from D-glucose by means of a three-step sequence involving acetylation, activation as the glycosyl bromide, and stereospecific displacement with azide anion. The azide functionality then serves as a convenient anchor upon which to introduce new functionality, usually with retention of the beta-stereochemistry. Here we report the synthesis of an amide-linked N-glycosyl trimer, by employing a Staudinger-aza-Wittig process on the azide, as well as a hybrid N-glycosyl triazole-amide-linked trimer in which the sugars are separated by 1,2,3-triazole heterocycles. Both of these neoglycotrimers are isolated in good yield with high beta-selectivity in each case.
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Affiliation(s)
- David P Temelkoff
- Department of Chemistry, Youngstown State University, 1 University Plaza, Youngstown, OH 44555-3663, USA
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12
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Edwards AA, Sanjayan GJ, Hachisu S, Soengas R, Stewart A, Tranter GE, Fleet GW. Synthesis of 4-aminomethyl-tetrahydrofuran-2-carboxylates with 2,4-cis and 2,4-trans relationships. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Grison C, Coutrot P, Genève S, Didierjean C, Marraud M. Structural Investigation of “cis” and “trans” Vinylogous Peptides: cis-Vinylog Turn in Folded cis-Vinylogous Peptides, an Excellent Mimic of the Natural β-Turn. J Org Chem 2005; 70:10753-64. [PMID: 16355997 DOI: 10.1021/jo051483y] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text] Various sequences of modified peptides including those containing a cis- or trans-vinylogous residue have been studied using X-ray diffraction in the solid state and 1H NMR and IR spectroscopy in solution. A cis-vinylogous residue promotes an NH to CO intramolecular H-bond, closing a nine-membered pseudocycle that stabilizes a folded moiety that we proposed to name the cis-vinylogous turn. A trans-vinylogous residue involves an extended conformation. Two consecutive vinylogous residues retain their own structural propensity: "Xaa(tr)"-"Xaa(cis)" or "Xaa(cis)"-"Xaa(tr)" sequence is singly folded, whereas "Xaa(cis)"-"Xaa(cis)" sequence is doubly folded. Oligo vinylogs with all-trans or all-cis or alternating cis-trans motifs could constitute new classes of foldamers.
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Affiliation(s)
- Claude Grison
- UMR 7565 CNRS-Université Henri Poincaré, Nancy 1, BP 239, 54506 Vandoeuvre-les-Nancy, France.
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Baron R, Bakowies D, van Gunsteren WF. Principles of carbopeptoid folding: a molecular dynamics simulation study. J Pept Sci 2005; 11:74-84. [PMID: 15635631 DOI: 10.1002/psc.597] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The conformational spaces of five oligomers of tetrahydrofuran-based carbopeptoids in chloroform and dimethyl sulfoxide were investigated through nine molecular dynamics simulations. Prompted by nuclear magnetic resonance experiments that indicated various stable folds for some but not all of these carbopeptoids, their folding behaviour was investigated as a function of stereochemistry, chain length and solvent. The conformational distributions of these molecules were analysed in terms of occurrence of hydrogen bonds, backbone torsional-angle distributions, conformational clustering and solute configurational entropy. While a cis-linkage across the tetrahydrofuran ring favours right-handed helical structures, a trans-linkage results in a larger conformational variability. Intra-solute hydrogen bonding is reduced with increasing chain length and with increasing solvent polarity. Solute configurational entropies confirm the picture obtained: they are smaller for cis- than for trans-linked peptides, for chloroform than for dimethyl sulfoxide as solvent and for shorter peptide chains. The simulations provide an atomic picture of molecular conformational variability that is consistent with the available experimental data.
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Affiliation(s)
- Riccardo Baron
- Laboratorium für Physikalische Chemie, ETH, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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15
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Chakraborty TK, Roy S, Kumar SK, Kunwar AC. Synthesis and structural studies of peptides containing a glucose-derived furanoid sugar amino acid. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Luppi G, Soffrè C, Tomasini C. Stabilizing effects in oxazolidin-2-ones-containing pseudopeptides. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.03.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Chakraborty TK, Srinivasu P, Sakunthala Madhavendra S, Kiran Kumar S, Kunwar AC. Conformational studies of the linear homooligomers of a glucose-derived furanoid sugar amino acid. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.03.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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van Well RM, Marinelli L, Altona C, Erkelens K, Siegal G, van Raaij M, Llamas-Saiz AL, Kessler H, Novellino E, Lavecchia A, van Boom JH, Overhand M. Conformational analysis of furanoid epsilon-sugar amino acid containing cyclic peptides by NMR spectroscopy, molecular dynamics simulation, and X-ray crystallography: evidence for a novel turn structure. J Am Chem Soc 2003; 125:10822-9. [PMID: 12952461 DOI: 10.1021/ja035461+] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sugar amino acids (SAAs) are useful building blocks for the design of peptidomimetics and peptide scaffolds. The three-dimensional structures of cyclic hybrid molecules containing the furanoid epsilon-SAA III and several amino acids were elucidated to study the preferred conformation of such an epsilon-SAA and its conformational influence on the backbone of cyclic peptides. NMR-based molecular dynamics simulations and empirical calculations of the cyclic tetramer 1, consisting of two copies of the SAA residue and two amino acids, revealed that it is conformationally restrained. The two SAA residues adopt different conformations. One of them forms an unusual turn, stabilized by an intraresidue nine-member hydrogen bond. The methylene functionalities of the other SAA residue are positioned in such a way that an intraresidue H bond is not possible. The X-ray crystal structure of 1 strongly resembles the solution conformation. Molecular dynamics calculations in combination with NMR analysis were also performed for compounds 2 and 3, which contain the RGD (Arg-Gly-Asp) consensus sequence and were previously shown to inhibit alpha(IIb)beta(3)-receptor-mediated platelet aggregation. The biologically most active compound 2 adopts a preferred conformation with the single SAA residue folded into the nine-member H bond-containing turn. Compound 3, containing an additional valine residue, as compared with compound 2, is conformational flexible. Our studies demonstrate that the furanoid epsilon-SAA III is able to introduce an unusual intraresidue hydrogen bond-stabilized beta-turn-like conformation in two of the three cyclic structures.
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Affiliation(s)
- Renate M van Well
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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van Well RM, Meijer ME, Overkleeft HS, van Boom JH, van der Marel GA, Overhand M. Synthesis of bridged sugar amino acids: a new entry into conformationally locked δ- and ε-amino acids. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00288-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Gruner SAW, Locardi E, Lohof E, Kessler H. Carbohydrate-based mimetics in drug design: sugar amino acids and carbohydrate scaffolds. Chem Rev 2002; 102:491-514. [PMID: 11841252 DOI: 10.1021/cr0004409] [Citation(s) in RCA: 329] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sibylle A W Gruner
- Institut für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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Schweizer F. Glycosaminosäuren und ihre Verwendung als Bausteine in der kombinatorischen Synthese sowie ihre Bedeutung für die Wirkstoff-Forschung. Angew Chem Int Ed Engl 2002. [DOI: 10.1002/1521-3757(20020118)114:2<240::aid-ange240>3.0.co;2-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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22
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Synthesis and structural studies of oligomers of 6-amino-2,5-anhydro-6-deoxy-d-mannonic acid. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)01425-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Smith MD, Fleet GW. Designing secondary structures: 5-azidomethyl tetrahydrofuran-2-carboxylates as carbohydrate-derived dipeptide isosteres. J Pept Sci 1999; 5:425-41. [PMID: 10580642 DOI: 10.1002/(sici)1099-1387(199910)5:10<425::aid-psc222>3.0.co;2-o] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The potential of carbohydrate-like tetrahydrofuran frameworks as building blocks with predictable conformational propensities useful in the design and synthesis of novel peptidomimetic materials which adopt well-defined secondary structures is discussed.
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Affiliation(s)
- M D Smith
- University of Oxford, The Dyson Perrins Laboratory, Oxford Centre for Molecular Sciences, UK
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Long DD, Hungerford NL, Smith MD, Brittain DE, Marquess DG, Claridge TD, Fleet GW. From sequencamers to foldamers? Tetrameric furanose carbopeptoids from cis- and trans-5-aminomethyl-tetrahydrofuran-2-carboxylates. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)00110-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Claridge TD, Long DD, Hungerford NL, Aplin RT, Smith MD, Marquess DG, Fleet GW. An octameric carbopeptoid; secondary structure in octameric and tetrameric 5-aminomethyl-tetrahydrofuran-2-carboxylates. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)00111-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Lohof E, Burkhart F, Born MA, Planker E, Kessler H. Sugar amino acids and carbohydrates as scaffolds and peptidomimetics. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1874-5113(99)80011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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