Extremely tough cyclic peptide nanopolymers

MRS Advances ◽  
2019 ◽  
Vol 4 (46-47) ◽  
pp. 2527-2532 ◽  
Author(s):  
Manoj K. Kolel-Veetil ◽  
LCDR Luis Estrella ◽  
Christopher R. So ◽  
Kenan P. Fears
Keyword(s):  
Self Assembly ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Molecular Architecture ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
New Class ◽  
Ca 50 ◽  
Bioinspired Nanomaterials ◽  
Linear Polymer Chain

ABSTRACTWe present a new class of bioinspired nanomaterials that are stabilized by a combination of covalent and hydrogen bonds. Prior work by others has shown that cyclic peptides can self-assemble to form supramolecular assemblies through backbone-backbone hydrogen bonding. To improve upon this molecular architecture, we develop a synthesis route to polymerize cyclic peptides and form a linear polymer chain that can transition between a rigid nanorod and an unfolded conformation. For a cyclic peptide polymer containing amine-terminated side chains on each ring, we demonstrate self-assembly can be triggered in aqueous solutions by varying the pH. We measure the elastic modulus of the rigid nanorods to be ca. 50 GPa, which is comparable to our molecular dynamics (MD) prediction (ca. 64 GPa). Our results highlight the uniqueness of our molecular architecture, namely their exemplary toughness (up to 3 GJ m-3), in comparison to other cyclic peptide-based assemblies. Finally, we demonstrate amphiphilic cyclic β-peptides are capable of inhibiting the growth of gram-negative and gram-positive bacteria.

scholarly journals Systematic study of the structural parameters affecting the self-assembly of cyclic peptide–poly(ethylene glycol) conjugates

Soft Matter ◽  
2018 ◽  
Vol 14 (30) ◽  
pp. 6320-6326 ◽  
Author(s):  
Edward D. H. Mansfield ◽  
Matthias Hartlieb ◽  
Sylvain Catrouillet ◽  
Julia Y. Rho ◽  
Sophie C. Larnaudie ◽  
...  
Keyword(s):  
Amino Acids ◽  
Self Assembly ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Hydrophobic Interactions ◽  
Structural Parameters ◽  
The Self ◽  
Poly Ethylene Glycol ◽  
Self Assembling ◽  
Poly Ethylene

Self-assembling cyclic peptides (CP) consisting of amino acids with alternating d- and l-chirality form nanotubes by hydrogen bonding, hydrophobic interactions, and π–π stacking in solution.

MODELLING ION, WATER AND ION–WATER CLUSTER ENTERING PEPTIDE NANOTUBES

2015 ◽  
Vol 57 (1) ◽  
pp. 62-78
Author(s):  
N. THAMWATTANA
Keyword(s):  
Self Assembly ◽  
Water Cluster ◽  
Cyclic Peptides ◽  
Simple Structure ◽  
Cyclic Peptide ◽  
Initial Energy ◽  
Jones Potential ◽  
Peptide Nanotubes ◽  
Organic Nanostructures ◽  
Peptide Nanotube

Recently, organic nanostructures have attracted much attention, and amongst them peptide nanotubes are of interest in many fields of application including medicine and nanobiotechnology. Peptide nanotubes are formed by self-assembly of cyclic peptides with alternating L- and D-amino acids. Due to their biodegradability, flexible design and easy synthesis, many applications have been proposed such as artificial transmembrane ion channels, templates for nanoparticles, mimicking pore structures, nanoscale testing tubes, biosensors and carriers for targeted drug delivery. The mechanisms of an ion, a water molecule and an ion–water cluster entering into a peptide nanotube of structure cyclo[(-D-Ala-L-Ala-)$_{4}$] are explored here. In particular, the Lennard-Jones potential and a continuum approach are employed to determine three entering mechanisms: (i) through the tube open end, (ii) through a region between each cyclic peptide ring and (iii) around the edge of the tube open end. The results show that while entering the nanotube by method (i) is possible, an ion or a molecule requires initial energy to overcome an energetic barrier to be able to enter the nanotube through positions (ii) and (iii). Due to its simple structure, the D-, L-Ala cyclopeptide nanotube is chosen in this model; however, it can be easily extended to include more complicated nanotubes.

scholarly journals Ambuic Acid Inhibits the Biosynthesis of Cyclic Peptide Quormones in Gram-Positive Bacteria

2008 ◽  
Vol 53 (2) ◽  
pp. 580-586 ◽  
Author(s):  
Jiro Nakayama ◽  
Yumi Uemura ◽  
Kenzo Nishiguchi ◽  
Norito Yoshimura ◽  
Yasuhiro Igarashi ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Regulatory System ◽  
Gram Positive ◽  
Communication Signals ◽  
Gram Positive Bacteria ◽  
A Cell ◽  
Secondary Fungal Metabolite ◽  
Potential Use

ABSTRACT Quorum sensing is a cell-density-dependent regulatory system in gram-positive bacteria and is often regulated by cyclic peptides called “quormones,” which function as extracellular communication signals. With an aim to discover an antipathogenic agent targeting quorum sensing in gram-positive bacteria, we screened 153 samples of fungal butanol extracts with the guidance of the inhibition of quorum-sensing-mediated gelatinase production in Enterococcus faecalis. Following the screenings, we found that ambuic acid, a known secondary fungal metabolite, inhibited the quorum-sensing-mediated gelatinase production without influencing the growth of E. faecalis. We further demonstrated that ambuic acid targeted the biosynthesis of a cyclic peptide quormone called gelatinase biosynthesis-activating pheromone. Furthermore, ambuic acid also inhibited the biosynthesis of the cyclic peptide quormones of Staphylococcus aureus and Listeria innocua. These results suggest the potential use of ambuic acid as a lead compound of antipathogenic drugs that target the quorum-sensing-mediated virulence expression of gram-positive bacteria.

scholarly journals Fluorinated nanotubes: synthesis and self-assembly of cyclic peptide–poly(vinylidene fluoride) conjugates

2021 ◽  
Author(s):  
Enrique Folgado ◽  
Qiao Song ◽  
Sebastien Perrier ◽  
Vincent Ladmiral ◽  
Mona Semsarilar
Keyword(s):  
Self Assembly ◽  
Cyclic Peptides ◽  
Vinylidene Fluoride ◽  
Cyclic Peptide ◽  
Poly Vinylidene Fluoride

Fluorinated hollow nanotubes were prepared from pre-assembled cyclic peptides bearing xanthate moieties by RAFT/MADIX of VDF.

Self-Assembly Effects of Cyclic Peptide Dimers: Molecular Modeling Study

2007 ◽  
Vol 353-358 ◽  
pp. 2257-2260
Author(s):  
Jing Chuan Zhu ◽  
Jie Cheng ◽  
Bo Liu
Keyword(s):  
Self Assembly ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
The Self ◽  
Transport Channel ◽  
Structure And Property ◽  
Self Assembling ◽  
Intermolecular Hydrogen Bonding Interaction ◽  
Bonding Interaction ◽  
Peptide Nanotube

The cyclic peptides can self-assemble into β-sheet like antiparallel tubular ensembles through intermolecular hydrogen-bonding interaction. Under the self-assembling effects of the dimer subunits, various aggregate properties may alter with the change of the structure. The relationship between the property and structure of ensembles is extremely important for designing new nanostructures. Molecular mechanics (MM) and molecular dynamics (MD) were employed to investigate the structure and property of single dimer and dimer-ensemble from cyclo-[D-Phe-(1R, 3S)-γ-Acc]3. Results reveal that the single dimer cannot adsorb CHCl3 molecule into its cavity, while the two-dimer ensemble can do. It suggests that the self-assembled cyclic peptide nanotube from the dimer-ensemble may act as the transport channel of CHCl3 molecules.

scholarly journals In vitro evaluation of ABT-719, a novel DNA gyrase inhibitor.

1995 ◽  
Vol 39 (4) ◽  
pp. 964-970 ◽  
Author(s):  
R K Flamm ◽  
C Vojtko ◽  
D T Chu ◽  
Q Li ◽  
J Beyer ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Active Compound ◽  
Dna Gyrase ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
New Class ◽  
Gram Negative Organisms ◽  
Gyrase Inhibitors

ABT-719 (A-86719.1) is the first compound of a new class of novel DNA gyrase inhibitors, the 2-pyridones, with potent antibacterial activity against gram-positive, gram-negative, and anaerobic organisms. ABT-719 was more active than ciprofloxacin, sparfloxacin, and clinafloxacin against gram-positive bacteria. ABT-719 was particularly active against Staphylococcus aureus (MIC at which 90% of the isolates were inhibited [MIC90] = 0.015 micrograms/ml) and Streptococcus pneumoniae (MIC90 = 0.03 micrograms/ml). ABT-719 was also the most active of the compounds tested against ciprofloxacin-resistant S. aureus isolates, with an MIC90 of 0.25 micrograms/ml, compared with 64 micrograms/ml for ciprofloxacin. Against gram-negative organisms, ABT-719 was as active as or slightly more active than ciprofloxacin and was the most active compound against ciprofloxacin-resistant Pseudomonas aeruginosa (MIC90 = 2.0 micrograms/ml). ABT-719 was also the most active compound against both gram-positive and gram-negative anaerobes, with MIC90s ranging from 0.12 to 0.25 micrograms/ml.

Microanatomy of the Periplasm of Bacillus Licheniformis

1971 ◽  
Vol 29 ◽  
pp. 262-263
Author(s):  
B.K. Ghosh
Keyword(s):  
Cell Wall ◽  
Plasma Membrane ◽  
Bacillus Licheniformis ◽  
External Environment ◽  
Permeability Barrier ◽  
Periplasmic Space ◽  
Modified Technique ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria

Periplasm of bacteria is the space outside the permeability barrier of plasma membrane but enclosed by the cell wall. The contents of this special milieu exterior could be regulated by the plasma membrane from the internal, and by the cell wall from the external environment of the cell. Unlike the gram-negative organism, the presence of this space in gram-positive bacteria is still controversial because it cannot be clearly demonstrated. We have shown the importance of some periplasmic bodies in the secretion of penicillinase from Bacillus licheniformis.In negatively stained specimens prepared by a modified technique (Figs. 1 and 2), periplasmic space (PS) contained two kinds of structures: (i) fibrils (F, 100 Å) running perpendicular to the cell wall from the protoplast and (ii) an array of vesicles of various sizes (V), which seem to have evaginated from the protoplast.

Rapid demonstration of septic or infectious arthritis due to Gram-negative bacteria

1992 ◽  
Vol 50 (1) ◽  
pp. 686-687
Author(s):  
Jacob S. Hanker ◽  
Paul R. Gross ◽  
Beverly L. Giammara
Keyword(s):  
Chronic Arthritis ◽  
Blood Cultures ◽  
Gram Negative Bacteria ◽  
Infectious Arthritis ◽  
Bacterial Arthritis ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria

Blood cultures are positive in approximately only 50 per cent of the patients with nongonococcal bacterial infectious arthritis and about 20 per cent of those with gonococcal arthritis. But the concept that gram-negative bacteria could be involved even in chronic arthritis is well-supported. Gram stains are more definitive in staphylococcal arthritis caused by gram-positive bacteria than in bacterial arthritis due to gram-negative bacteria. In the latter situation where gram-negative bacilli are the problem, Gram stains are helpful for 50% of the patients; they are only helpful for 25% of the patients, however, where gram-negative gonococci are the problem. In arthritis due to gram-positive Staphylococci. Gramstained smears are positive for 75% of the patients.

Antibacterial activity of magnesium oxide nanoparticles prepared by Calcination method

2019 ◽  
Vol 10 (03) ◽  
Author(s):  
Elaf Ayad Kadhem ◽  
Miaad Hamzah Zghair ◽  
Sarah , Hussam H. Tizkam, Shoeb Alahmad Salih Mahdi ◽  
Hussam H. Tizkam ◽  
Shoeb Alahmad
Keyword(s):  
Antibacterial Activity ◽  
Magnesium Oxide ◽  
Diffusion Method ◽  
Oxide Nanoparticles ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Magnesium Oxide Nanoparticles ◽  
Agar Disc

magnesium oxide nanoparticles (MgO NPs) were prepared by simple wet chemical method using different calcination temperatures. The prepared NPs were characterized by Electrostatic Discharge (ESD), Scanning Electron Microscope (SEM) and X-ray Diffraction (XRD). It demonstrates sharp intensive peak with the increase of crystallinty and increase of the size with varying morphologies with respect to increase of calcination temperature. Antibacterial studies were done on gram negative bacteria (E.coli) and gram positive bacteria (S.aureus) by agar disc diffusion method. The zones of inhibitions were found larger for gram positive bacteria than gram negative bacteria, this mean, antibacterial MgO NPs activity more active on gram positive bacteria than gram negative bacteria because of the structural differences. It was found that antibacterial activity of MgO NPs was found it has directly proportional with their concentration.

A Target-Based Method for Designing Heterochiral Cyclic Peptide Binders: De Novo Inhibitors of the PD-1/PD-L1 Interaction

2020 ◽  
Author(s):  
Salvador Guardiola ◽  
Monica Varese ◽  
Xavier Roig ◽  
Jesús Garcia ◽  
Ernest Giralt
Keyword(s):  
Protein Interactions ◽  
Cyclic Peptides ◽  
General Framework ◽  
Large Scale ◽  
Cyclic Peptide ◽  
De Novo ◽  
Inhibitory Effect ◽  
Original Text ◽  
Retraction Notice ◽  
Pharmaceutical Properties

<p>NOTE: This preprint has been retracted by consensus from all authors. See the retraction notice in place above; the original text can be found under "Version 1", accessible from the version selector above.</p><p><br></p><p>------------------------------------------------------------------------</p><p><br></p><p>Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-<i>i</i>3 and PD-<i>i</i>6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys. A comprehensive biophysical evaluation confirmed their binding mechanism to PD-1 and their inhibitory effect on the PD-1/PD-L1 interaction. Finally, elucidation of their solution structures by NMR served as validation of our <i>de novo </i>design approach. We anticipate that our results will provide a general framework for designing target-specific drug-like peptides.<i></i></p>

Sign in / Sign up

Export Citation Format

Share Document