Helix-Forming Carbohydrate Amino Acids

Helix-forming aliphatic homo-δ-peptide foldamers based on the conformational restriction effects of cyclopropane

Considerable effort has been directed toward developing artificial peptide-based foldamers. However, detailed structural analysis of δ-peptide foldamers consisting of only aliphatic δ-amino acids has not been reported. Herein, we rationally designed and stereoselectively synthesized aliphatic homo-δ-peptides forming a stable helical structure by using a chiral cyclopropane δ-amino acid as a monomer unit. Structural analysis of the homo-δ-peptides using circular dichroism, infrared, and NMR spectroscopy indicated that they form a stable 14-helical structure in solution. Furthermore, we successfully conducted X-ray crystallographic analysis of the homo-δ-peptides, demonstrating a right-handed 14-helical structure. This helical structure of the crystal was consistent with those predicted by theoretical calculations and those obtained based on NMR spectroscopy in solution. This stable helical structure is due to the effective restriction of the backbone conformation by the structural characteristics of cyclopropane. This work reports the first example of aliphatic homo-δ-peptide foldamers having a stable helical structure both in the solution and crystal states.

Developing an Effective Glycan-based Vaccine for Streptococcus Pyogenes

Streptococcus pyogenes is a primary infective agent that causes approximately 700 million human infections each year, resulting in more than 500,000 deaths. Carbohydrate-based vaccines are proven to be one of the most promising subunit vaccine candidates, as the bacterial glycan pattern(s) are different from mammalian cells and show increased pathogen serotype conservancy than the protein components. In this review we highlight reverse vaccinology for use in the development of subunit vaccines against S. pyogenes, and report reproducible methods of carbohydrate antigen production, in addition to the structure-immunogenicity correlation between group A carbohydrate epitopes and alternative vaccine antigen carrier systems. We also report recent advances used to overcome hurdles in carbohydrate-based vaccine development.

Conformation Analysis of GalNAc-Appended Sugar Amino Acid Foldamers as Glycopeptide Mimics

Sugar amino acid (SAA)-based foldamers with well-defined secondary structures were appended with N-acetylgalactosamine (GalNAc) sugars to access sequence-defined, multidentate glycoconjugates with full control over number, spacing and position. Conformation analysis of these glycopeptides by extensive NMR spectroscopic studies revealed that the appended GalNAc units had a profound influence on the native conformational behaviour of the SAA foldamers. Whereas the 2,5-cis glycoconjugate showed a helical structure in water, comprising of two consecutive 16-membered hydrogen bonds, its 2,5-trans congener displayed an unprecedented 16/10-mixed turn structure not seen before in any glycopeptide foldamer.

Synthesis of O-Amino Sugars and Nucleosides

Nucleic acids and carbohydrates are essential biomolecules involved in numerous biological and pathological processes. Development of multifunctional building blocks based on nucleosides and sugars is in high demand for the generation of novel oligonucleotide mimics and glycoconjugates for biomedical applications. Recently, aminooxyl-functionalized compounds have attracted increasing research interest because of their easy derivatization through oxime ligation or N-oxyamide formation reactions. Various biological applications have been reported for O-amino carbohydrate- and nucleoside-derived compounds. Here, we report our efforts in the design and synthesis of glyco-, glycosyl, nucleoside- and nucleo-aminooxy acid derivatives from readily available sugars and amino acids, and their use for the generation of N-oxyamide-linked oligosaccharides, glycopeptides, glycolipids, oligonucleosides and nucleopeptides as novel glycoconjugates or oligonucleotide mimics. Delicate and key points in the synthesis will be emphasized.

Residue dependent hydrogen-bonding preferences in orthanilic acid-based short peptide β-turn motifs

This communication describes the competition between native β-turn (C10) and 2-aminobenzenesulfonic acid (^SAnt)(orthanilic acid)-based pseudo β-turn (C11) in their hybrid peptides.

Molecular architecture with carbohydrate functionalized β-peptides adopting 314-helical conformation

Carbohydrate recognition is essential in cellular interactions and biological processes. It is characterized by structural diversity, multivalency and cooperative effects. To evaluate carbohydrate interaction and recognition, the structurally defined attachment of sugar units to a rigid template is highly desired. β-Peptide helices offer conformationally stable templates for the linear presentation of sugar units in defined distances. The synthesis and β-peptide incorporation of sugar-β-amino acids are described providing the saccharide units as amino acid side chain. The respective sugar-β-amino acids are accessible by Michael addition of ammonia to sugar units derivatized as α,β-unsaturated esters. Three sugar units were incorporated in β-peptide oligomers varying the sugar (glucose, galactose, xylose) and sugar protecting groups. The influence of sugar units and the configuration of sugar-β-amino acids on β-peptide secondary structure were investigated by CD spectroscopy.

Artificial supersecondary structures based on aromatic oligoamides

With an intelligent design of the monomers, considerable effort has so far focused on the creation of aromatic oligoamide foldamers which are able to mimic the secondary structures of biopolymers. Supersecondary structure is a growing set of known and classifiable protein folding patterns that provides an important organizational context to this complex endeavor. In this article, we highlight the design, chemical synthesis, and structural studies of artificial supersecondary structures based on aromatic oligoamide foldamers in recent years.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006

This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.

(Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties

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.

Spectroscopic studies of oligomers containing 2,5-trans furanoid sugar amino acids

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.

Classification of conformation for sugar amino acid systems using chiroptical spectroscopy

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.

Foldamers as versatile frameworks for the design and evolution of function

Foldamers are sequence-specific oligomers akin to peptides, proteins and oligonucleotides that fold into well-defined three-dimensional structures. They offer the chemical biologist a broad pallet of building blocks for the construction of molecules that test and extend our understanding of protein folding and function. Foldamers also provide templates for presenting complex arrays of functional groups in virtually unlimited geometrical patterns, thereby presenting attractive opportunities for the design of molecules that bind in a sequence- and structure-specific manner to oligosaccharides, nucleic acids, membranes and proteins. We summarize recent advances and highlight the future applications and challenges of this rapidly expanding field.

Promoting helicity in carbohydrate-containing foldamers through long-range hydrogen bonds

A sensor system to probe the propensity of carbohydrates to induce helical structures through long-range hydrogen bonds, based on a C(2)-symmetric xylylene bis(thiourea) arrangement, is reported; the formation of intermolecular complexes with benzoate anion promotes helix uncoiling, the free energy of the process being related to helix stability.

Structural Characterization of a Pentapeptide Derived from a Novel Carbohydrate α-Amino Acid

Subsequent to our previous report describing several novel carbohydrate α-amino acid dipeptides (and the structural characterization of one of those), and their extension to higher peptides, a synchrotron radiation study of one of those—a pentapeptide—showing its structure to be a well-defined helical array in each of two independent molecules, stabilized by internal hydrogen bonds, is reported.

Self-assembly of cyclic homo- and hetero-β-peptides with cis- furanoid sugar amino acid and β-hGly as building blocks

The design, synthesis and characterization of a new class of peptide nanotubes, self-assembled from cyclic homo- and hetero-beta-peptides based on cis-furanoid sugar amino acid and beta-hGly residues are described; these results represent the expansion of the conformational pool of cis beta-sugar amino acids in the design of peptide nanotubes.

Conformational studies of oligomeric oxetane-based dipeptide isosteres derived fromL-rhamnose orD-xylose

Conformational investigations have been undertaken on oligomers (dimers, tetramers, hexamers) of five closely related oxetane-based dipeptide isosteres. All the oligomers were subjected to a range of studies by NMR, FT-IR and CD spectroscopy. The oligomers derived from methyl 2,4-anhydro-5-azido-3-O-tert-butyldimethylsilyl-5-deoxy-L-rhamnonate 'monomer' all exhibited evidence of ordered conformations in chloroform and 2,2,2-trifluoroethanol (TFE) solution. 5-Acetamido and N-methylamide derivatives of the L-rhamnonate 'monomer', along with a 'dimer' lacking silyl protection at C-3, were synthesized to ascertain the role of intramolecular interactions. This led to the conclusion that, for the L-rhamnonate oligomers, steric interactions govern the conformational preference observed. The equivalent silyl-protected D-lyxonate oligomers gave ordered CD spectra in TFE solution, but NMR and FT-IR spectroscopy in chloroform solution suggested an irregular, non-hydrogen bonded system. The remaining silyl-protected 6-deoxy-L-altronate, 6-deoxy-D-gulonate and D-fuconate oligomers appear to be characterized by their lack of ordered conformation in TFE and chloroform solution.