Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Synthesis of aromatic glycoconjugates. Building blocks for the construction of combinatorial glycopeptide libraries.

ABSTRACT: New aromatic glycoconjugate building blocks based on the trifunctional 3-aminomethyl-5-aminobenzoic acid backbone and sugars linked to the backbone by a malonyl moiety were prepared via peptide coupling. The orthogonally protected glycoconjugates, bearing an acetyl-protected glycoside, were converted into their corresponding acids which are suitable building blocks for combinatorial glycopeptide synthesis.

SUBMITTER: Norrlinger M

PROVIDER: S-EPMC4222372 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Synthesis of aromatic glycoconjugates. Building blocks for the construction of combinatorial glycopeptide libraries.

Nörrlinger Markus M Ziegler Thomas T

Beilstein journal of organic chemistry 20141022

New aromatic glycoconjugate building blocks based on the trifunctional 3-aminomethyl-5-aminobenzoic acid backbone and sugars linked to the backbone by a malonyl moiety were prepared via peptide coupling. The orthogonally protected glycoconjugates, bearing an acetyl-protected glycoside, were converted into their corresponding acids which are suitable building blocks for combinatorial glycopeptide synthesis. ...[more]

PMID: 25383116

Similar Datasets

Synthesis and NMR studies of malonyl-linked glycoconjugates of <i>N</i>-(2-aminoethyl)glycine. Building blocks for the construction of combinatorial glycopeptide libraries.

Project description:Four glycoconjugate building blocks for the construction of combinatorial PNA like glycopeptide libraries were prepared in 75-79% yield by condensing tert-butyl N-[2-(N-9-fluorenylmethoxycarbonylamino)ethyl]glycinate (AEG) 5 with 3-oxo-3-(2,3,4,6-tetra-O-acetyl-?-D-glucopyranosylamino)- (6a), 3-oxo-3-(?-D-galactopyranosylamino)- (6b), 3-oxo-3-(2-acetamido-2-deoxy-3,4,6-tetra-O-acetyl-?-D-glucopyranosylamino)- (6c) and 3-oxo-3-(2-acetamido-2-deoxy-3,4,6-tetra-O-acetyl-?-D-galactopyranosylamino)propanoic acid (6d), respectively. The resulting AEG glycoconjugates 1a-d were converted into the corresponding free acids 2a-d in 97-98% yield by treatment with aqueous formic acid. The Fmoc group of compound 1c was removed and the intermediate amine 9 was condensed with 2a to afford the corresponding glycosylated AEG dipeptide 4 in 58% yield. All glycoconjugate building blocks showed the presence of cis and trans rotamers. Compounds 1a, 1b and 4 were subjected to temperature dependent 1H NMR spectroscopy in order to determine the coalescence temperature which resulted in calculated rotation barriers of 17.9-18.3 kcal/mol for the rotamers.

| S-EPMC5082468 | biostudies-literature

Novel peptoid building blocks: synthesis of functionalized aromatic helix-inducing submonomers.

Project description:Peptoids, oligo-N-substituted glycines, can fold into well-defined helical secondary structures. The design and synthesis of new peptoid building blocks that are capable of both (a) inducing a helical secondary structure and (b) decorating the helices with chemical functionalities are reported. Peptoid heptamers containing carboxamide, carboxylic acid or thiol functionalities were synthesized, and the resulting peptoids were shown to form stable helices. A thiol-containing peptoid readily formed the homodisulfide, providing a convenient route to prepare peptoid helix homodimers.

| S-EPMC2814525 | biostudies-literature

Parallel Glyco-SPOT Synthesis of Glycopeptide Libraries.

Project description:Glycan recognition is typically studied using free glycans, but glycopeptide presentations represent more physiological conditions for glycoproteins. To facilitate studies of glycopeptide recognition, we developed Glyco-SPOT synthesis, which enables the parallel production of diverse glycopeptide libraries at microgram scales. The method uses a closed system for prolonged reactions required for coupling Fmoc-protected glycoamino acids, including O-, N-, and S-linked glycosides, and release conditions to prevent side reactions. To optimize reaction conditions and sample reaction progress, we devised a biopsy testing method. We demonstrate the efficient utilization of such microscale glycopeptide libraries to determine the specificity of glycan-recognizing antibodies (e.g., CTD110.6) using microarrays, enzyme specificity on-array and in-solution (e.g., ST6GalNAc1, GCNT1, and T-synthase), and binding kinetics using fluorescence polarization. We demonstrated that the glycosylation on these peptides can be expanded using glycosyltransferases both in-solution and on-array. This technology will promote the discovery of biological functions of peptide modifications by glycans.

| S-EPMC7556346 | biostudies-literature

Conjugated polymers based on metalla-aromatic building blocks.

Project description:Conjugated polymers usually require strategies to expand the range of wavelengths absorbed and increase solubility. Developing effective strategies to enhance both properties remains challenging. Herein, we report syntheses of conjugated polymers based on a family of metalla-aromatic building blocks via a polymerization method involving consecutive carbyne shuttling processes. The involvement of metal d orbitals in aromatic systems efficiently reduces band gaps and enriches the electron transition pathways of the chromogenic repeat unit. These enable metalla-aromatic conjugated polymers to exhibit broad and strong ultraviolet-visible (UV-Vis) absorption bands. Bulky ligands on the metal suppress π-π stacking of polymer chains and thus increase solubility. These conjugated polymers show robust stability toward light, heat, water, and air. Kinetic studies using NMR experiments and UV-Vis spectroscopy, coupled with the isolation of well-defined model oligomers, revealed the polymerization mechanism.

| S-EPMC9303910 | biostudies-literature

Encoded combinatorial libraries for the construction of cyclic peptoid microarrays.

Project description:A "one bead two compound" approach to the synthesis of encoded cyclic peptoid libraries is reported.

| S-EPMC4467580 | biostudies-literature

Synthesis of Modular Building Blocks using Glycosyl Phosphate Donors for the Construction of Asymmetric N-Glycans.

Project description:Glycosyl phosphates are known as versatile donors for the synthesis of complex oligosaccharides both chemically and enzymatically. Herein, we report the stereoselective construction of modular building blocks for the synthesis of N-glycan using glycosyl phosphates as donors. We have synthesized four trisaccharide building blocks with orthogonal protecting groups, namely, Manβ2GlcNAc(OAc)3β6GlcNAc (9), Manβ2GlcNAc-β6GlcNAc(OAc)3 (15), Manβ2GlcNAc(OAc)3β4GlcNAc (18) and Manβ2GlcNAcβ4GlcNAc(OAc) (22) for further selective elongation using glycosyltransferases. The glycosylation reaction using glycosyl phosphate was found to be high yielding with shorter reaction time. Initially, The phthalimide protected glucosamine donor was exploited to ensure the formation of β-glycosidic linkage and later converted to the N-acetyl group before the enzymatic synthesis. The selective deprotection of O-benzyl group was performed prior to enzymatic synthesis to avoid its negative interference.

| S-EPMC6456066 | biostudies-literature

In silico protein design by combinatorial assembly of protein building blocks.

Project description:Utilizing concepts of protein building blocks, we propose a de novo computational algorithm that is similar to combinatorial shuffling experiments. Our goal is to engineer new naturally occurring folds with low homology to existing proteins. A selected protein is first partitioned into its building blocks based on their compactness, degree of isolation from the rest of the structure, and hydrophobicity. Next, the protein building blocks are substituted by fragments taken from other proteins with overall low sequence identity, but with a similar hydrophobic/hydrophilic pattern and a high structural similarity. These criteria ensure that the designed protein has a similar fold, low sequence identity, and a good hydrophobic core compared with its native counterpart. Here, we have selected two proteins for engineering, protein G B1 domain and ubiquitin. The two engineered proteins share approximately 20% and approximately 25% amino acid sequence identities with their native counterparts, respectively. The stabilities of the engineered proteins are tested by explicit water molecular dynamics simulations. The algorithm implements a strategy of designing a protein using relatively stable fragments, with a high population time. Here, we have selected the fragments by searching for local minima along the polypeptide chain using the protein building block model. Such an approach provides a new method for engineering new proteins with similar folds and low homology.

| S-EPMC2286547 | biostudies-literature

Origami-based Building Blocks for Modular Construction of Foldable Structures.

Project description:Origami, widely known as the ancient Japanese art of paper folding, has recently inspired a new paradigm of design for mechanical metamaterials and deployable structural systems. However, lack of rationalized design guidelines and scalable manufacturing methods has hindered their applications. To address this limitation, we present analytical methods for designing origami-based closed-loop units with inherent foldability, and for predicting their folding response (e.g., folding force, bistability, and area and volume change by folding). These units can be employed as building blocks for application-driven design and modular construction of foldable structures with desired performance and manufacturing scalability.

| S-EPMC5665935 | biostudies-literature

Synthesis of Fmoc-Gly-Ile Phosphinic Pseudodipeptide: Residue Specific Conditions for Construction of Matrix Metalloproteinase Inhibitor Building Blocks.

Project description:The efficient synthesis of an Fmoc-Gly-Ile phosphinic pseudodipeptide was desired as an eventual building block for construction of matrix metalloproteinase inhibitors. A Michael-type addition reaction of bis(tri-methylsilyl) phosphonite with the appropriate acrylate generated the pseudodipeptide bond. Additional of adamantyl (Ad) protection by our prior route (reaction of in situ generated phosphinic acid chloride with the sodium salt of adamantanol) was surprisingly inefficient. Adamantyl protection was achieved in high yield by refluxing the phosphinic acid, Ag2O, and 1-AdBr in chloroform. Subsequently a concise one-pot three-step reaction comprising a double deprotection of the N- and C-termini under catalytic hydrogenation conditions followed by selective protection of the N-terminus with an Fmoc group yielded Fmoc-NHCH2PO(OAd)CH2CH(2-butyl)CO2H in 41 % overall yield. These results indicate that, as the diversity of phosphinic pseudodipeptides is increased to create selective matrix metalloproteinase inhibitors, different synthetic pathways may be required for efficient building block preparation.

| S-EPMC3564550 | biostudies-literature

Culture's building blocks: investigating cultural evolution in a LEGO construction task.

Project description:ONE OF THE MOST ESSENTIAL BUT THEORETICALLY VEXING ISSUES REGARDING THE NOTION OF CULTURE IS THAT OF CULTURAL EVOLUTION AND TRANSMISSION: how a group's accumulated solutions to invariant challenges develop and persevere over time. But at the moment, the notion of applying evolutionary theory to culture remains little more than a suggestive trope. Whereas the modern synthesis of evolutionary theory has provided an encompassing scientific framework for the selection and transmission of biological adaptations, a convincing theory of cultural evolution has yet to emerge. One of the greatest challenges for theorists is identifying the appropriate time scales and units of analysis in order to reduce the intractably large and complex phenomenon of "culture" into its component "building blocks." In this paper, we present a model for scientifically investigating cultural processes by analyzing the ways people develop conventions in a series of LEGO construction tasks. The data revealed a surprising pattern in the selection of building bricks as well as features of car design across consecutive building sessions. Our findings support a novel methodology for studying the development and transmission of culture through the microcosm of interactive LEGO design and assembly.

| S-EPMC4162372 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data