Comparison of interactions between beta-hairpin decapeptides and SDS/DPC micelles from experimental and simulation data

Background  

We applied a combined experimental and computational approach to ascertain how peptides interact with host and microbial membrane surrogates, in order to validate simulation methodology we hope will enable the development of insights applicable to the design of novel antimicrobial peptides. We studied the interactions of two truncated versions of the potent, but cytotoxic, antimicrobial octadecapeptide protegrin-1, PC-72 [LCYCRRRFCVC] and PC-73 [CYCRRRFCVC].     

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction

Background  

Eps15 homology (EH) domains are protein interaction modules binding to peptides containing Asn-Pro-Phe (NPF) motifs and mediating critical events during endocytosis and signal transduction. The EH domain of POB1 associates with Eps15, a protein characterized by a striking string of DPF triplets, 15 in human and 13 in mouse Eps15, at the C-terminus and lacking the typical EH-binding NPF motif.     

Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces

Background  

Peptide-membrane interactions play a key role in the binding, partitioning and folding of membrane proteins, the activity of antimicrobial and fusion peptides, and a number of other processes. To gain a better understanding of the thermodynamics of such interactions, White and Wimley created an interfacial hydrophobicity scale based of the transfer free energy from water to octanol or lipid bilayers of a series of synthetic peptapeptides (Ace-WLXLL, with X being any of the twenty natural amino acids) (White and Wimley (1996) Nat. Struct. Biol. 3, 842–848). In this study, we performed molecular dynamics simulations of a representative set of ten of these peptides (X = D, K, R, N, A, T, S, I, F and W) in two membrane mimetic interfaces: water-cyclohexane (10 ns) and a fully solvated dioleoylphosphatidylcholine (DOPC) bilayer (50 ns) using both constant pressure and constant area ensembles. We focus on partitioning of the ten peptides at the cyclohexane/water and lipid/water interfaces.     

A strategy using NMR peptide structures of thromboxane A2 receptor as templates to construct ligand-recognition pocket of prostacyclin receptor

Background:  

Prostacyclin receptor (IP) and thromboxane A2 receptor (TP) belong to rhodopsin-type G protein-coupling receptors and respectively bind to prostacyclin and thromboxane A2 derived from arachidonic acid. Recently, we have determined the extracellular loop (eLP) structures of the human TP receptor by 2-D 1H NMR spectroscopy using constrained peptides mimicking the individual eLP segments. The studies have identified the segment along with several residues in the eLP domains important to ligand recognition, as well as proposed a ligand recognition pocket for the TP receptor.     

The acidic domains of the Toc159 chloroplast preprotein receptor family are intrinsically disordered protein domains

Background  

The Toc159 family of proteins serve as receptors for chloroplast-destined preproteins. They directly bind to transit peptides, and exhibit preprotein substrate selectivity conferred by an unknown mechanism. The Toc159 receptors each include three domains: C-terminal membrane, central GTPase, and N-terminal acidic (A-) domains. Although the function(s) of the A-domain remains largely unknown, the amino acid sequences are most variable within these domains, suggesting they may contribute to the functional specificity of the receptors.     

Calcium adsorption and displacement: characterization of lipid monolayers and their interaction with membrane-active peptides/proteins

Background  

The first target of antimicrobial peptides (AMPs) is the bacterial membrane. In the case of Gram-negative bacteria this is the outer membrane (OM), the lipid composition of which is extremely asymmetric: Whereas the inner leaflet is composed of a phospholipid mixture, the outer leaflet is made up solely from lipopolysaccharides (LPSs). LPS, therefore, represents the first target of AMPs. The binding and intercalation of polycationic AMPs is driven by the number and position of negatively charged groups of the LPS. Also, proteins other than cationic AMPs can interact with LPS, e.g. leading eventually to a neutralization of the endotoxic effects of LPS. We compared different biophysical techniques to gain insight into the properties of the electrical surface potentials of lipid monolayers and aggregates composed of LPSs and various phospholipids and their interaction with peptides and proteins.     

Peptidomic analysis of endogenous plasma peptides from patients with pancreatic neuroendocrine tumours

Rationale

Diagnosis of pancreatic neuroendocrine tumours requires the study of patient plasma with multiple immunoassays, using multiple aliquots of plasma. The application of mass spectrometry based techniques could reduce the cost and amount of plasma required for diagnosis.

Methods

Plasma samples from two patients with pancreatic neuroendocrine tumours were extracted using an established acetonitrile‐based plasma peptide enrichment strategy. The circulating peptidome was characterised using nano and high flow rate liquid chromatography/mass spectrometry (LC/MS) analyses. To assess the diagnostic potential of the analytical approach, a large sample batch (68 plasmas) from control subjects, and aliquots from subjects harbouring two different types of pancreatic neuroendocrine tumour (insulinoma and glucagonoma), were analysed using a 10‐min LC/MS peptide screen.

Results

The untargeted plasma peptidomics approach identified peptides derived from the glucagon prohormone, chromogranin A, chromogranin B and other peptide hormones and proteins related to control of peptide secretion. The glucagon prohormone derived peptides that were detected were compared against putative peptides that were identified using multiple antibody pairs against glucagon peptides. Comparison of the plasma samples for relative levels of selected peptides showed clear separation between the glucagonoma and the insulinoma and control samples.

Conclusions

The combination of the organic solvent extraction methodology with high flow rate analysis could potentially be used to aid diagnosis and monitor treatment of patients with functioning pancreatic neuroendocrine tumours. However, significant validation will be required before this approach can be clinically applied.

     

Prion protein self-peptides modulate prion interactions and conversion

Background  

Molecular mechanisms underlying prion agent replication, converting host-encoded cellular prion protein (PrP^C) into the scrapie associated isoform (PrP^Sc), are poorly understood. Selective self-interaction between PrP molecules forms a basis underlying the observed differences of the PrP^C into PrP^Sc conversion process (agent replication). The importance of previously peptide-scanning mapped ovine PrP self-interaction domains on this conversion was investigated by studying the ability of six of these ovine PrP based peptides to modulate two processes; PrP self-interaction and conversion.     

Aminopeptidase B,a glucagon-processing enzyme: site directed mutagenesis of the Zn<Superscript>2+</Superscript>-binding motif and molecular modelling

Background  

Aminopeptidase B (Ap-B; EC 3.4.11.6) catalyzes the cleavage of basic residues at the N-terminus of peptides and processes glucagon into miniglucagon. The enzyme exhibits, in vitro, a residual ability to hydrolyze leukotriene A₄ into the pro-inflammatory lipid mediator leukotriene B₄. The potential bi-functional nature of Ap-B is supported by close structural relationships with LTA₄ hydrolase (LTA₄H ; EC 3.3.2.6). A structure-function analysis is necessary for the detailed understanding of the enzymatic mechanisms of Ap-B and to design inhibitors, which could be used to determine the complete in vivo functions of the enzyme.     

Reactions of mercaptobenzimidazole with allenylphosphonates

Abstract  

Reactions of 2-mercaptobenzimidazole with 3-methylbuta-1,2-dienylphosphonates involve the mercapto group of the heterocyclic compound and the 1,2-double bond of allenylphosphonate.     

MyD88-dependent and independent pathways of Toll-Like Receptors are engaged in biological activity of Triptolide in ligand-stimulated macrophages

Background  

Triptolide is a diterpene triepoxide from the Chinese medicinal plant Tripterygium wilfordii Hook F., with known anti-inflammatory, immunosuppressive and anti-cancer properties.     

Enantioselective synthesis of 1-arylethanediols by rhodium-catalyzed transfer hydrogenation of α-tosyloxyarylketones

Abstract  

Catalytic transfer hydrogenation of α-tosyloxyarylketones mediated by a chiral rhodium complex using an azeotropic mixture of formic acid/triethylamine afforded the corresponding 1-arylethanediol monotosylates in excellent yield with high enantioselectivity.     

A one-pot synthesis of functionalized ethyl 1,3-thiazole-5-carboxylates from thioamides or thioureas and 2-chloro-1,3-dicarbonyl compounds in an ionic liquid

Abstract  

A simple one-pot synthesis of functionalized ethyl 1,3-thiazole-5-carboxylates from the reaction of 2-chloro-1,3-dicarbonyl compounds with thioureas or thioamides in the presence of 1-butyl-3-methylimidazolium trifluoromethanesulfonate is described.     

Highly efficient glucosylation of flavonoids

Abstract  

A highly efficient procedure for glucosylation of flavonoids by acetobromoglucose is described. Glucosylation is carried out in a two-phase system CHCl₃/H₂O over 96 h using tetrabutylammonium bromide as phase-transfer catalyst. A purification procedure can be performed without column chromatography, and the yields of the glucosylated flavonoids are mostly quantitative. Acetylated glucosides were deprotected with sodium methanolate to afford the desired glucosides of flavonoids.     

Chemoselective trimethylsilylation of alcohols catalyzed by saccharin sulfonic acid

Abstract  

Saccharin sulfonic acid was easily prepared by the reaction of saccharin with neat chlorosulfonic acid at room temperature. This reagent is efficiently able to catalyze the chemoselective trimethylsilylation of alcohols with hexamethyldisilazane in the presence of amines and thiols.     

Glycyl-alanyl-histidine protects PC12 cells against hydrogen peroxide toxicity

Background

Peptides with cytoprotective functions, including antioxidants and anti-infectives, could be useful therapeutics. Carnosine, β-alanine-histidine, is a dipeptide with anti-oxidant properties. Tripeptides of Ala-His-Lys, Pro-His-His, or Tyr-His-Tyr are also of interest in this respect.

Results

We synthesized several histidine-containing peptides including glycine or alanine, and tested their cytoprotective effects on hydrogen peroxide toxicity for PC12 cells. Of all these peptides (Gly-His-His, Ala-His-His, Ala-His-Ala, Ala-Ala-His, Ala-Gly-His, Gly-Ala-His (GAH), Ala-His-Gly, His-Ala-Gly, His-His-His, Gly-His-Ala, and Gly-Gly-His), GAH was found to have the strongest cytoprotective activity. GAH decreased lactate dehydrogenase (LDH) leakage, apoptosis, morphological changes, and nuclear membrane permeability changes against hydrogen peroxide toxicity in PC12 cells. The cytoprotective activity of GAH was superior to that of carnosine against hydrogen peroxide toxicity in PC12 cells. GAH also protected PC12 cells against damage caused by actinomycin D and staurosporine. Additionally, it was found that GAH also protected SH-SY5Y and Jurkat cells from damage caused by hydrogen peroxide, as assessed by LDH leakage.

Conclusion

Thus, a novel tripeptide, GAH, has been identified as having broad cytoprotective effects against hydrogen peroxide-induced cell damage.

     

Granulated copper oxide nano-catalyst: a novel and efficient catalyst for C–N cross-coupling of amines with iodobenzene

Abstract  

Nano-structured CuO granules catalyze the C–N cross-coupling of amines with iodobenzene in excellent yields. The reaction is simple, efficient, and operates in air under ligand-free conditions.     

Application of chloroaluminate ionic liquid as catalyst and medium for the dealkylation of esters

Abstract  

Dealkylation of esters to carboxylic acids was performed using chloroaluminate ionic liquids (PyHBr/AlCl₃, PyHCl/AlCl₃, Me₃NHCl/AlCl₃, Et₃NHCl/AlCl₃) as catalyst and medium. The catalytic activity of PyHBr/AlCl₃ (X(AlCl₃) = 0.67) proved to be superior to the other three ionic liquids for the dealkylation of methyl benzoate with a conversion of 97% after 3 h at 140 °C. After easy separation from the products the ionic liquid PyHBr/AlCl₃ could be reused six times without loss of its activity.     

Expedient one-pot synthesis of N-aryliminoethers via mild electrophilic activation of secondary amides

Abstract  

The direct transformation of various secondary amides into N-aryliminoethers via mild electrophilic activation with trifluoromethanesulfonic anhydride in the presence of 2-chloropyridine is described. Low temperature amide activation followed by warming to 0 °C and subsequent treatment with phenols provides the desired products with short overall reaction times and moderate to high reaction yields.     

Coiodination of styrene with commercial clays: a convenient preparation of styrene oxide

Abstract  

Styrene oxide is easily prepared in 82–91% yield by the reaction of styrene with iodine/water in the presence of commercial clays, followed by in situ addition of KOH in n-hexane/water.