Glycosylated Foldamers To Probe the Carbohydrate−Carbohydrate Interaction

Self-Assembly of Glycolipid Epimers: Their Supramolecular Morphology Control and Immunoactivation Function

Although advances have been made in carbohydrate-based macromolecular self-assembly, harnessing epimers of carbohydrates to perform molecular assembly and further investigating the properties of supramolecular materials remain little explored. Herein, two classes of stereoisomeric glycolipid amphiphiles based on d-N-acetylgalactosamine (GalNAc) are reported, and they can aggregate into ribbon-like structures in the aqueous solution due to amphiphilic property, which allow to obtain glycocalyx-mimicking supramolecular materials. The subtle distinction in glycoside configuration of GalNAc-α-SSA and GalNAc-β-SSA dictates the different molecular packing in self-assembled structures. Since driven by the distinguishing carbohydrate-carbohydrate interactions, the ribbon-like architectures transform into spherical nanostructures via mixing GalNAc-α-SSA and GalNAc-β-SSA. The resulting spherical micelles fabricated by blending glycolipid epimers can potentiate the macrophage- and dendritic cell-mediated immune responses in vitro. Such glycolipid epimers will pave the way to create glycocalyx-mimicking immune modulators by incorporating stereochemistry into supramolecular self-assembly.

Coexistence of Left- and Right-Handed 12/10-Mixed Helices in Cyclically Constrained β-Peptides and Directed Formation of Single-Handed Helices upon Site-Specific Methylation

The inherent conformational preferences of the neutral β-peptide foldamer series, Ac-(ACHC)_n-NHBn, n = 2-4, are studied in the gas phase using conformation-specific IR-UV double resonance methods. The cyclically constrained chiral β-amino acid cis-2-aminocyclohexane carboxylic acid (ACHC) is designed to bring both right- and left-handed helices into close energetic proximity. Comparison of the infrared spectra in the NH stretch and amide I/II regions with the predictions of DFT calculations lead to the unambiguous assignment of four out of the six observed conformations of the molecules in this series, while corroborating computational and spectral evidence, affords tentative assignments of the remaining two conformers for which IR data were not recorded. The observed structures fall into one of two conformational families: a right-handed 12/10-mixed helix or its "cap-disrupted" left-handed helical analogue, which coexist with significant populations. Site-specific and stereospecific methylation on the cyclohexane backbone at the dipeptide (n = 2) level is also tested as a means to sterically lock in a predetermined cyclohexane chair conformation. These substitutions are proven to be a means of selectively driving formation of one helical screw sense or the other. Calculated relative energies and free energies of all possible structures for the molecules provide strong supporting evidence that the rigid nature of the ACHC residue confers unusual stability to the 12/10-mixed helix conformation, regardless of local environment, temperature, or C-terminal capping unit. The simultaneous presence of both handed helices offers unique opportunities for future studies of their interconversion.

Self-assembly of bacteria cellulose hydrogels carrying multiple carbohydrate appendages to visualize carbohydrate-carbohydrate interactions

Nata de coco was chemically modified to afford the bacterial cellulose hydrogels carrying terminal alkynes. The resultant hydrogels were then converted into hydrogels carrying lactosides or those carrying α-2,3-sialyllactosides by the Cu⁺-catalyzed alkyne-azide cyclization. The stable homo association of the hydrogels carrying lactosides was observed in an aqueous solution containing Ca²⁺, thereby demonstrating the Ca²⁺-mediated lactoside-lactoside interactions. Ca²⁺ also stabilized the hetero associations among the hydrogels carrying lactosides and those carrying α-2,3-sialyllactosides, thereby also demonstrating the Ca²⁺-induced interactions between the lactosides and the α-2,3-sialyllactosides. The sizes of these hydrogels were of the order of ca. 5 mm, and their associations could thus be readily monitored with the naked eye.

Synthesis of Glycosylated Metal Complexes for Probing Carbohydrate-Carbohydrate Interactions

Densely packed carbohydrate clusters on cell surfaces play essential roles in varieties of bioprocesses. Little information has been, however, accumulated so far concerning their structural/functional details. In this chapter, we discuss artificial systems to investigate carbohydrate-carbohydrate interactions within/between the carbohydrate cluster(s). Among such artificial systems, much attention will be especially placed on glycosylated tris-bipyridine ferrous complexes for monitoring not only carbohydrate-carbohydrate interactions within the glycocluster but also their resultant conformational changes.

Synthesis and conformational analysis of poly(phenylacetylene)s with serinol-tethered carbohydrate appendages

We synthesized phenylacetylenes containing β-lactoside, β-cellobioside, or β-maltoside, and polymerized them to produce the corresponding poly (phenylacetylene)s. In these poly (phenylacetylene)s, the pendent carbohydrates were tethered to the mainchains by serinol spacers. Because similar glycosyl serinol units are found in the natural glycosphingolipids in cell membranes, the densely packed carbohydrate clusters along the poly (phenylacetylene) mainchains act as molecular mimics of cell surface glycoclusters. We analyzed the conformation of the glycosylated poly (phenylacetylene)s using circular dichroism spectroscopy, and found that the spatial carbohydrate packing within the glycoclusters changed on the addition of salts.

Can Heterocyclic γ-Peptides Provide Polyfunctional Platforms for Synthetic Glycocluster Construction?

Sugars play key roles in many molecular and cellular communication processes involving a family of proteins named lectins. The low affinity associated with sugar recognition is generally counterbalanced by the multivalent nature of the interaction. While many polyglycosylated architectures have been described, only a few studies focused on the impact of topology variations of the multivalent structures on the interaction with lectin proteins. One major interest of our group concerns the design of new highly predictable and stable molecular pseudo-peptide architectures for therapeutic applications. In such a context, we described a class of constrained heterocyclic γ-amino acids built around a thiazole ring, named ATCs. ATC oligomers are helical molecules resulting from the formation of a highly stable C₉ hydrogen-bonding pattern. Following our program, we herein address the potential of ATC oligomers as tunable scaffolds for the development of original multivalent glycoclusters.

( S)-2-Amino-3-(5-methyl-3-hydroxyisoxazol-4-yl)propanoic Acid (AMPA) and Kainate Receptor Ligands: Further Exploration of Bioisosteric Replacements and Structural and Biological Investigation

Starting from 1-4 and 7 structural templates, analogues based on bioisosteric replacements (5a-c vs 1, 2 and 6 vs 7) were synthesized for completing the SAR analysis. Interesting binding properties at GluA2, GluK1, and GluK3 receptors were discovered. The requirements for GluK3 interaction were elucidated by determining the X-ray structures of the GluK3-LBD with 2 and 5c and by computational studies. Antinociceptive potential was demonstrated for GluK1 partial agonist 3 and antagonist 7 (2 mg/kg ip).

Interplay Of Stereochemistry, Conformational Rigidity, And Ease Of Synthesis For 13-Membered Cyclic Peptidomimetics Containing APC Residues

As part of a program to design small molecules that bind proteins, we require cyclic peptides (or peptidomimetics) that are severely constrained such that they adopt one predominant conformation in solution. This paper describes syntheses of the 13-membered cyclic tetrapeptides 1 containing aminopyrrolidine carboxyl (APC) residues. A linear precursor was prepared and used to determine optimal conditions for cyclization of that substrate. A special linker was prepared to enable cyclization of similar linear peptidomimetics on a solid phase, and the solution-phase cyclization conditions were shown to be appropriate for this too. Stereochemical variations were then used to determine the ideal APC configuration for cyclization of the linear precursors (on a solid phase, using the conditions identified previously). Consequently, a series of compounds were prepared that are representative of compounds 1. Conformational studies of representative compounds in DMSO solution were performed primarily using (i) NOE studies, (ii) quenched molecular dynamics simulations using no constraints from experiment, and (iii) MacroModel calculations with NMR constraints. All three strategies converged to the same conclusion: the backbone of molecules based on 1 tends to adopt one preferential conformation in solution and that conformation can be predicted from the stereochemistries of the α-amino acids involved.

Multivalent presentation of carbohydrates by 314-helical peptide templates: synthesis, conformational analysis using CD spectroscopy and saccharide recognition

A tetrameric glycoconjugate template, SSFT 1, was coupled with a variety of six aminooxy sugars to achieve multivalent glycoconjugates 2–7.

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.

Crystallographic characterization of 12-helical secondary structure in β-peptides containing side chain groups

Helices are the most extensively studied secondary structures formed by β-peptide foldamers. Among the five known β-peptide helices, the 12-helix is particularly interesting because the internal hydrogen bond orientation and macrodipole are analogous to those of α-peptide helices (α-helix and 3(10)-helix). The β-peptide 12-helix is defined by i, i+3 C═O···H-N backbone hydrogen bonds and promoted by β-residues with a five-membered ring constraint. The 12-helical scaffold has been used to generate β-peptides with specific biological functions, for which diverse side chains must be properly placed along the backbone and, upon folding, properly arranged in space. Only two crystal structures of 12-helical β-peptides have previously been reported, both for homooligomers of trans-2-aminocyclopentanecarboxylic acid (ACPC). Here we report five additional crystal structures of 12-helical β-peptides, all containing residues that bear side chains. Four of the crystallized β-peptides include trans-4,4-dimethyl-2-aminocyclopentanecarboxylic acid (dm-ACPC) residues, and the fifth contains a β(3)-hPhe residue. These five β-peptides adopt fully folded 12-helical conformations in the solid state. The new crystal structures, along with previously reported data, allow a detailed characterization of the 12-helical conformation; average backbone torsion angles of β-residues and helical parameters are derived. These structural parameters are found to be similar to those for i, i+3 C═O···H-N hydrogen-bonded helices formed by other peptide backbones generated from α- and/or β-amino acids. The similarity between the conformational behavior of dm-ACPC and ACPC is consistent with previous NMR-based conclusions that 4,4-disubstituted ACPC derivatives are compatible with 12-helical folding. In addition, our data show how a β(3)-residue is accommodated in the 12-helix, thus enhancing understanding of the diverse conformational behavior of this flexible class of β-amino acids.

Structure-based design of potent and selective 2-(quinazolin-2-yl)phenol inhibitors of checkpoint kinase 2

Structure-based design was applied to the optimization of a series of 2-(quinazolin-2-yl)phenols to generate potent and selective ATP-competitive inhibitors of the DNA damage response signaling enzyme checkpoint kinase 2 (CHK2). Structure-activity relationships for multiple substituent positions were optimized separately and in combination leading to the 2-(quinazolin-2-yl)phenol 46 (IC(50) 3 nM) with good selectivity for CHK2 against CHK1 and a wider panel of kinases and with promising in vitro ADMET properties. Off-target activity at hERG ion channels shown by the core scaffold was successfully reduced by the addition of peripheral polar substitution. In addition to showing mechanistic inhibition of CHK2 in HT29 human colon cancer cells, a concentration dependent radioprotective effect in mouse thymocytes was demonstrated for the potent inhibitor 46 (CCT241533).

Contiguous O-galactosylation of 4(R)-hydroxy-l-proline residues forms very stable polyproline II helices

The hydroxyproline-rich glycoproteins (HRGPs) are the major structural proteins of the extracellular matrix of algae and land plants. They are characterized by a rigid polyproline type II (PPII) conformation and extensive O-glycosylation of 4(R)-hydroxy-l-proline (Hyp) residues, which is a unique post-translational modification of proteins. The functional consequences of HRGP glycosylation remains unclear, but they have been implicated in contributing to their structural rigidity. Here, we have investigated the effects of naturally occurring beta-O-galactosylation of Hyp residues on the conformational stability of the PPII helix. In a series of well-defined model peptides Ac-(l-proline)(9)-NH(2) (1), Ac-(Hyp)(9)-NH(2) (2), and Ac-[Hyp(beta-d-galactose)](9)-NH(2) (3) we demonstrate that contiguous O-glycosylation of Hyp residues causes a dramatic increase in the thermal stability of the PPII helix according to analysis of thermal melting curves. This represents the first quantitative data on the contributions of glycosylation to stabilizing the PPII conformation. Molecular modeling indicates the increase in conformational stability may be due to a regular network of interglycan and glycan-peptide hydrogen bonds, in which the carbohydrate residues form a hydrophilic "overcoat" of the PPII helix. Evidence of this shielding effect of the amide backbone may be provided by analysis of the circular dichroism bands, which indicates an increase in the rho value of 3 relative to 1 and 2. This study gives further insight into the effects of naturally occurring Hyp beta-O-linked glycans on the PPII conformation as found in HRGPs in plant cell walls and also indicates that polyproline sequences may be suitable for the development of molecular scaffolds for the presentation of glycan structures.

[Study of the interactions between oligosaccharides involved in the cell adhesion. Example of the Lewis(x) trisaccharide]

Nature often chooses weak molecular interactions for playing important role in cellular recognition and adhesion. These interactions involve particularly oligosaccharides, which are the structural elements present at the most exterior surface of the cell. Three oligosaccharides were prepared for study of the interaction by vesicle micromanipulation technique. This study allowed us to measure directly, for the first time, a carbohydrate-carbohydrate interaction.

Synthesis and structural characterisation as 12-helix of the hexamer of a β-amino acid tethered to a pyrrolidin-2-one ring

Starting from (3S,4R,1'S)-3-amino-2-oxo-1-[1'-(4-methoxyphenylethyl)]pyrrolidine carboxylic acid (2), the first synthesis of a beta-foldamer containing pyrrolidin-2-one rings is described, whose 12-helix conformation is assigned by NMR analysis and confirmed by molecular dynamics (MD) simulations.