Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stabilising Peptoid Helices Using Non-Chiral Fluoroalkyl Monomers.

ABSTRACT: Stability towards protease degradation combined with modular synthesis has made peptoids of considerable interest in the fields of chemical biology, medicine, and biomaterials. Given their tertiary amide backbone, peptoids lack the capacity to hydrogen-bond, and as such, controlling secondary structure can be challenging. The incorporation of bulky, charged, or chiral aromatic monomers can be used to control conformation but such building blocks limit applications in many areas. Through NMR and X-ray analysis we demonstrate that non-chiral neutral fluoroalkyl monomers can be used to influence the Kcis/trans equilibria of peptoid amide bonds in model systems. The cis-isomer preference displayed is highly unprecedented given that neither chirality nor charge is used to control the peptoid amide conformation. The application of our fluoroalkyl monomers in the design of a series of linear peptoid oligomers that exhibit stable helical structures is also reported.

SUBMITTER: Gimenez D

PROVIDER: S-EPMC6099454 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Stabilising Peptoid Helices Using Non-Chiral Fluoroalkyl Monomers.

Gimenez Diana D Aguilar Juan A JA Bromley Elizabeth H C EHC Cobb Steven L SL

Angewandte Chemie (International ed. in English) 20180627 33

Stability towards protease degradation combined with modular synthesis has made peptoids of considerable interest in the fields of chemical biology, medicine, and biomaterials. Given their tertiary amide backbone, peptoids lack the capacity to hydrogen-bond, and as such, controlling secondary structure can be challenging. The incorporation of bulky, charged, or chiral aromatic monomers can be used to control conformation but such building blocks limit applications in many areas. Through NMR and ...[more]

PMID: 29846037

Similar Datasets

Acyl hydrazides as peptoid sub-monomers.

Project description:The use of acyl hydrazides as peptoid sub-monomers is investigated. We demonstrate here that azapeptoids derived entirely from acyl hydrazides can be made conveniently and efficiently using standard peptoid sub-monomer chemistry. Structural studies reveal that the main chain amide bond in these molecules predominantly adopts a trans conformation. A high-quality one bead one compound library of tetramers was made by split and pool synthesis and we found that the identity of the molecule on a single bead could be determined by tandem MALDI mass spectrometry.

| S-EPMC3882750 | biostudies-literature

Peptoid Residues Make Diverse, Hyperstable Collagen Triple-Helices.

Project description:As the only ribosomally encoded N-substituted amino acid, proline promotes distinct secondary protein structures. The high proline content in collagen, the most abundant protein in the human body, is crucial to forming its hallmark structure: the triple-helix. For over five decades, proline has been considered compulsory for synthetic designs aimed at recapitulating collagen's structure and properties. Here we describe that N-substituted glycines (N-glys), also known as peptoid residues, exhibit a general triple-helical propensity similar to or greater than proline, enabling synthesis of stable triple-helical collagen mimetic peptides (CMPs) with unprecedented side chain diversity. Supported by atomic-resolution crystal structures as well as circular dichroism and computational characterizations spanning over 30 N-gly-containing CMPs, we discovered that N-glys stabilize the triple-helix primarily by sterically preorganizing individual chains into the polyproline-II helix. We demonstrated that N-glys with exotic side chains including a "click"-able alkyne and a photosensitive side chain enable CMPs for functional applications including the spatiotemporal control of cell adhesion and migration. The structural principles uncovered in this study open up opportunities for a new generation of collagen-mimetic therapeutics and materials.

| S-EPMC9209468 | biostudies-literature

Extraordinarily robust polyproline type I peptoid helices generated via the incorporation of α-chiral aromatic N-1-naphthylethyl side chains.

Project description:Peptoids, or oligomers of N-substituted glycines, are a class of foldamers that have shown extraordinary functional potential since their inception nearly two decades ago. However, the generation of well-defined peptoid secondary structures remains a difficult task. This challenge is due, in part, to the lack of a thorough understanding of peptoid sequence-structure relationships and, consequently, an incomplete understanding of the peptoid folding process. We seek to delineate sequence-structure relationships through the systematic study of noncovalent interactions in peptoids and the design of novel amide side chains capable of such interactions. Herein, we report the synthesis and detailed structural analysis of a series of (S)-N-(1-naphthylethyl)glycine (Ns1npe) peptoid homo-oligomers by X-ray crystallography, NMR spectroscopy, and circular dichroism (CD) spectroscopy. Four of these peptoids were found to adopt well-defined structures in the solid state, with dihedral angles similar to those observed in polyproline type I (PPI) peptide helices and in peptoids with α-chiral side chains. The X-ray crystal structure of a representative Ns1npe tetramer revealed an all cis-amide helix, with approximately three residues per turn, and a helical pitch of approximately 6.0 Å. 2D-NMR analysis of the length-dependent Ns1npe series showed that these peptoids have very high overall backbone amide K(cis/trans) values in acetonitrile, indicative of conformationally homogeneous structures in solution. Additionally, CD spectroscopy studies of the Ns1npe homo-oligomers in acetonitrile and methanol revealed a striking length-dependent increase in ellipticity per amide. These Ns1npe helices represent the most robust peptoid helices to be reported, and the incorporation of (S)-N-(1-naphthylethyl)glycines provides a new approach for the generation of stable helical structure in this important class of foldamers.

| S-EPMC3186054 | biostudies-literature

Triangular prism-shaped β-peptoid helices as unique biomimetic scaffolds.

Project description:β-Peptoids are peptidomimetics based on N-alkylated β-aminopropionic acid residues (or N-alkyl-β-alanines). This type of peptide mimic has previously been incorporated in biologically active ligands and has been hypothesized to be able to exhibit foldamer properties. Here we show, for the first time, that β-peptoids can be tuned to fold into stable helical structures. We provide high-resolution X-ray crystal structures of homomeric β-peptoid hexamers, which reveal right-handed helical conformations with exactly three residues per turn and a helical pitch of 9.6-9.8 Å between turns. The presence of folded conformations in solution is supported by circular dichroism spectroscopy showing length- and solvent dependency, and molecular dynamics simulations provide further support for a stabilized helical secondary structure in organic solvent. We thus outline a framework for future design of novel biomimetics that display functional groups with high accuracy in three dimensions, which has potential for development of new functional materials.

| S-EPMC4432622 | biostudies-literature

Fluorinated Aromatic Monomers as Building Blocks To Control α-Peptoid Conformation and Structure.

Project description:Peptoids are peptidomimetics of interest in the fields of drug development and biomaterials. However, obtaining stable secondary structures is challenging, and designing these requires effective control of the peptoid tertiary amide cis/trans equilibrium. Herein, we report new fluorine-containing aromatic monomers that can control peptoid conformation. Specifically, we demonstrate that a fluoro-pyridine group can be used to circumvent the need for monomer chirality to control the cis/trans equilibrium. We also show that incorporation of a trifluoro-methyl group ( NCF3Rpe) rather than a methyl group ( NRpe) at the α-carbon of a monomer gives rise to a 5-fold increase in cis-isomer preference.

| S-EPMC6463299 | biostudies-literature

Enantioselective Cobalt-Catalyzed Hydroboration of Fluoroalkyl-Substituted Alkenes to Access Chiral Fluoroalkylboronates.

Project description:Selective defluoroborylation and asymmetric hydroboration reactions of fluoroalkyl-substituted terminal alkenes with pinacolborane (HBpin) have been developed with cobalt catalysts generated from Co(acac)2 and bisphosphine ligands. A variety of fluoroalkyl-substituted terminal alkenes undergo this enantioselective hydroboration, affording the corresponding chiral alkylboronates containing fluoroalkyl-substituted stereogenic carbon centers with high enantioselectivity (up to 98% ee). This asymmetric hydroboration provides a versatile foundation for the synthesis of a variety of chiral organofluorine compounds containing fluoroalkyl-substituted stereogenic carbon centers.

| S-EPMC9434995 | biostudies-literature

Two helices from one chiral centre - self organization of disc shaped chiral nanoparticles.

Project description:Gold nanoparticles (AuNPs) have been prepared and surface-functionalized with a mixture of 1-hexanethiol co-ligands and chiral discogen ligands separated from a disulfide function via a flexible spacer. Polarized optical microscopy together with differential scanning calorimetry showed that the organic corona of the nanocomposite forms a stable chiral discotic nematic phase with a wide thermal range. Synchrotron X-ray diffraction showed that gold NPs form a superlattice with p2 plane symmetry. Analysis indicated that the organic corona takes up the shape of a flexible macrodisk. Synchrotron radiation-based circular dichroism signals of thin films are significantly enhanced on the isotropic-LC transition, in line with the formation of a chiral nematic phase of the organic corona. At lower temperatures the appearance of CD signals at longer wavelengths is associated with the chiral organisation of the NPs and is indicative of the formation of a second helical structure. The decreased volume required and the chiral environment of the disc ligands drives the nanoparticles into columns that arrange helically, parallel to the shortest axis of the two dimensional lattice.

| S-EPMC8179125 | biostudies-literature

Dynamic multistimuli-responsive reversible chiral transformation in supramolecular helices.

Project description:The design of new chiral chromophores that allow tunable assembly of higher order helical structures by using natural stimuli offers promising avenue in understanding various biological processes. In particular, access to dynamic multistimuli-responsive systems can provide real-time monitoring of chiral transformation in chemical and biological systems. We report on the synthesis of naphthalenediimide appended L-glutamate (NDI-L-Glu) that self-assembles into chiral supramolecular structures under physiological conditions. Specifically, NDI-L-Glu shows a mixture of left- and right-handed helices under physiological conditions, and any deviation from the ambient biochemical environment has a remarkable influence on the chirality of these structures. For instance, acidic environments shift the helicity to left-handedness while the alkaline conditions reversed the helical structures to right-handedness, thereby mimicking the molecular virulence mechanism of tobacco mosaic virus (TMV). The chirality of these supramolecular assemblies can also be controllably tuned by using temperature as an external stimulus, allowing reversible flip of helicity.

| S-EPMC6060148 | biostudies-other

Metalloporphyrin Dimers Bridged by a Peptoid Helix: Host-Guest Interaction and Chiral Recognition.

Project description:Co-facial porphyrins have been designed to construct porphyrin tweezers with versatile molecular recognition capabilities. In this study, we synthesized metalloporphyrin⁻peptoid conjugates (MPPCs) displaying two metalloporphyrins on a peptoid scaffold with either achiral unfolded (1) or helical (2 and 3) secondary structures. Host⁻guest complexation of MPPCs was realized with various guests of different lengths and basicities, and the extent of complexation was measured by UV-vis and circular dichroism (CD) spectroscopic titration. Intermolecular and intramolecular chirality induction were observed on achiral and chiral peptoid backbones, respectively. Spectroscopic data indicated that a broad scope of achiral guests can be recognized by chiral 2; in particular, longer and more flexible guests were seen to bind more tightly on 2. In addition, chiral 2 provided a distinct CD couplet with dl-, d-, or l-Lys-OMe, which was a result of the diastereomeric host⁻guest complex formation. Our results indicated that MPPCs can recognize, contrast, and analyze various achiral, chiral, or racemic molecules. Based on co-facial metalloporphyrins present on peptoid scaffolds, we developed a novel class of porphyrin tweezers, which can be further utilized in asymmetric catalysis, molecular sensing, and drug delivery.

| S-EPMC6278558 | biostudies-literature

From Oligo(Phenyleneethynylene) Monomers to Supramolecular Helices: The Role of Intermolecular Interactions in Aggregation.

Project description:Supramolecular helices that arise from the self-assembly of small organic molecules via non-covalent interactions play an important role in the structure and properties of the corresponding materials. Here we study the supramolecular helical aggregation of oligo(phenyleneethynylene) monomers from a theoretical point of view, always guiding the studies with experimentally available data. In this way, by systematically increasing the number of monomer units, optimized n-mer geometries are obtained along with the corresponding absorption and circular dichroism spectra. For the geometry optimizations we use density functional theory together with the B3LYP-D3 functional and the 6-31G** basis set. For obtaining the spectra we resort to time-dependent density functional theory using the CAM-B3LYP functional and the 3-21G basis set. These combinations of density functional and basis set were selected after systematic convergence studies. The theoretical results are analyzed and compared to the experimentally available spectra, observing a good agreement.

| S-EPMC8228480 | biostudies-literature

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