Discovery of antagonist peptides against bacterial helicase-primase interaction in B. stearothermophilus by reverse yeast three-hybrid

Developing small-molecule antagonists against protein-protein interactions will provide powerful tools for mechanistic/functional studies and the discovery of new antibacterials. We have developed a reverse yeast three-hybrid approach that allows high-throughput screening for antagonist peptides against essential protein-protein interactions. We have applied our methodology to the essential bacterial helicase-primase interaction in Bacillus stearothermophilus and isolated a unique antagonist peptide. This peptide binds to the primase, thus excluding the helicase and inhibiting an essential interaction in bacterial DNA replication. We provide proof of principle that our reverse yeast three-hybrid method is a powerful "one-step" screen tool for direct high-throughput antagonist peptide selection against any protein-protein interaction detectable by traditional yeast two-hybrid systems. Such peptides will provide useful "leads" for the development of new antibacterials.     

Discovery of novel cathepsin S inhibitors by pharmacophore-based virtual high-throughput screening

The cysteine protease cathepsin S (CatS) is involved in the pathogenesis of autoimmune disorders, atherosclerosis, and obesity. Therefore, it represents a promising pharmacological target for drug development. We generated ligand-based and structure-based pharmacophore models for noncovalent and covalent CatS inhibitors to perform virtual high-throughput screening of chemical databases in order to discover novel scaffolds for CatS inhibitors. An in vitro evaluation of the resulting 15 structures revealed seven CatS inhibitors with kinetic constants in the low micromolar range. These compounds can be subjected to further chemical modifications to obtain drugs for the treatment of autoimmune disorders and atherosclerosis.     

Discovery of novel checkpoint kinase 1 inhibitors by virtual screening based on multiple crystal structures

Incorporating receptor flexibility is considered crucial for improvement of docking-based virtual screening. With an abundance of crystallographic structures freely available, docking with multiple crystal structures is believed to be a practical approach to cope with protein flexibility. Here we describe a successful application of the docking of multiple structures to discover novel and potent Chk1 inhibitors. Forty-six Chk1 structures were first compared in single structure docking by predicting the binding mode and recovering known ligands. Combinations of different protein structures were then compared by recovery of known ligands and an optimal ensemble of Chk1 structures were selected. The chosen structures were used in the virtual screening of over 60?000 diverse compounds for Chk1 inhibitors. Six novel compounds ranked at the top of the hits list were tested experimentally, and two of these compounds inhibited Chk1 activity-the best with an IC(50) value of 9.6 μM. Further study indicated that achieving a better enrichment and identifying more diverse compounds was more likely using multiple structures than using only a single structure even when protein structures were randomly selected. Taking into account conformational energy difference did not help to improve enrichment in the top ranked list.     

A novel method of surface modification on thin-film-composite reverse osmosis membrane by grafting hydantoin derivative

Membrane degradations by biofouling and free chlorine oxidation are the major obstacles for aromatic polyamide thin-film-composite (TFC) reverse osmosis (RO) membranes to realize high performance over a long period of operation. In this work, a hydantoin derivative, 3-monomethylol-5,5-dimethylhydantoin (MDMH), was grafted onto the nascent aromatic polyamide membrane surfaces by the reactions with active groups (e.g., acyl chloride groups) in the surfaces. The grafted MDMH moieties with high reaction activity and free chlorine could play as sacrificial pendant groups when membranes suffer from chlorine attacks, and the chlorination products N-halamines with strong antimicrobial function could sterilize microorganisms on membrane surfaces and then regenerate to MDMH. This was designed as a novel means to improve both chlorine resistances and anti-biofouling properties of the aromatic polyamide TFC RO membranes.Attenuated total reflectance mode Fourier transform infrared spectroscopy (ATR-FTIR) revealed that the MDMH-modified membranes had two characteristic bands at 1772 and 1709 cm⁻¹ corresponding to two carbonyl groups in hydantoin ring. This suggested the successful grafting of MDMH onto the membrane surfaces, which was further confirmed and quantified by X-ray photoelectron spectroscopy (XPS) analysis. After modification with MDMH, the membrane surface hydrophilicity increased obviously as contact angles decreased from 57.7° to 50.4–31.5°. But, there was no obvious change in membrane surface roughness after modification. The MDMH-modified membranes were shown to possess high chlorine resistances with small changes in water fluxes and salt rejections after chlorination with 100–2000 ppm h chlorine at pH 4. The chlorinated MDMH-modified membranes demonstrated obvious sterilization effects on Escherchia coli and substantial preventions against microbial fouling. Therefore, the MDMH-modified membranes offer a potential use as a new type of chlorine resistance and anti-biofouling TFC RO membranes.     

Synthesis and characterization of one-dimensional CdSe by a novel reverse micelle assisted hydrothermal method

Nanocrystalline cadmium selenide (CdSe) is a low bandgap material (E(g)=1.75 eV, at room temperature) with potential applications in photoelectronic devices. Its electronic properties are dependent on the dimensions of the crystals. In this study, one-dimensional wurtzite CdSe nanoparticles with a diameter of 43+/-6 nm and an aspect ratio of 3.7+/-0.6 were synthesized through a novel reverse micelle assisted hydrothermal method at a relatively low temperature. This method combines the advantages of the hydrothermal method's ability to achieve good crystallinity with the well-controlled growth offered by the reverse micelle method. The morphology of the nanoparticles can be controlled by the amount of sodium bis(2-ethylhexyl) sulfosuccinate (AOT), the amount of hydrazine hydrate and the reaction temperature. It is proposed that AOT controls the length while hydrazine hydrate controls the diameter of the growing nanocrystals. The photoluminescence (PL) of individual nanorods and the longitudinal-optical phonon properties were mapped using confocal microscopy. Raman spectroscopy showed a blue-shift of both the LO and 2LO phonon peaks which may be due to a lattice contraction of the CdSe nanorods. A nucleation and growth mechanism for these nanoparticles is also proposed based on time-dependent studies.     

Discovery of novel polyamine analogs with anti-protozoal activity by computer guided drug repositioning

Chagas disease is a parasitic infection caused by the protozoa Trypanosoma cruzi that affects about 6 million people in Latin America. Despite its sanitary importance, there are currently only two drugs available for treatment: benznidazole and nifurtimox, both exhibiting serious adverse effects and limited efficacy in the chronic stage of the disease. Polyamines are ubiquitous to all living organisms where they participate in multiple basic functions such as biosynthesis of nucleic acids and proteins, proliferation and cell differentiation. T. cruzi is auxotroph for polyamines, which are taken up from the extracellular medium by efficient transporters and, to a large extent, incorporated into trypanothione (bis-glutathionylspermidine), the major redox cosubstrate of trypanosomatids. From a 268-compound database containing polyamine analogs with and without inhibitory effect on T. cruzi we have inferred classificatory models that were later applied in a virtual screening campaign to identify anti-trypanosomal compounds among drugs already used for other therapeutic indications (i.e. computer-guided drug repositioning) compiled in the DrugBank and Sweetlead databases. Five of the candidates identified with this strategy were evaluated in cellular models from different pathogenic trypanosomatids (T. cruzi wt, T. cruzi PAT12, T. brucei and Leishmania infantum), and in vitro models of aminoacid/polyamine transport assays and trypanothione synthetase inhibition assay. Triclabendazole, sertaconazole and paroxetine displayed inhibitory effects on the proliferation of T. cruzi (epimastigotes) and the uptake of putrescine by the parasite. They also interfered with the uptake of others aminoacids and the proliferation of infective T. brucei and L. infantum (promastigotes). Trypanothione synthetase was ruled out as molecular target for the anti-parasitic activity of these compounds.     

Folding control in cyclic peptides through N-methylation pattern selection: formation of antiparallel beta-sheet dimers, double reverse turns and supramolecular helices by 3alpha,gamma cyclic peptides

Peptide foldamers constitute a growing class of nanomaterials with potential applications in a wide variety of chemical, medical and technological fields. Here we describe the preparation and structural characteristics of a new class of cyclic peptide foldamers (3alpha,gamma-CPs) that, depending on their backbone N-methylation patterns and the medium, can either remain as flat rings that dimerize through arrays of hydrogen bonds of antiparallel beta-sheet type, or can fold into twisted double reverse turns that, in the case of double gamma-turns, associate in nonpolar solvents to form helical supramolecular structures. A 3alpha,gamma-CP consists of a number of multiples of a repeat unit made up of four amino acid residues of alternating chirality: three corresponding to alpha-amino acids and one to a gamma-amino acid (a cis-3-aminocycloalkanecarboxylic acid).     

A novel and efficient approach for the amidation of C-terminal peptides

A highly efficient and practical synthesis of C-terminal amidated peptides has been developed. According to this approach, amidation of the C-terminus of peptides was carried out using NH₄Cl, alkylammonium chloride (RNH₃Cl) and semicarbazide hydrochloride in the presence of TBTU as a coupling reagent and a tertiary amine as the base at room temperature in good to high yields. Some opioid peptides such as enkephalin derivatives were synthesized according to this novel method.     

Identification of novel angiotensin-converting enzyme-inhibitory peptides from ovine milk proteins by CE-MS and chromatographic techniques

In this report, we present the use of CE-MS as complement to RP separation for the identification of novel angiotensin-converting enzyme-inhibitory (ACEI) peptides from a complex milk protein hydrolysate. As preliminary step, fast protein LC (FPLC) was used to isolate the different casein fractions from raw ovine milk. Enzymatic hydrolysis of these fractions was performed by using proteolytic enzymes of gastrointestinal origin. The most active hydrolysate, corresponding to kappa-casein hydrolyzed with pepsin, chymotrypsin, and trypsin, was fractionated by RP-HPLC and the peptides contained in the active fractions were sequenced by CE coupled to IT-MS (CE-MS). The use of CE-MS allowed the identification of short peptides with ACEI activity included in the scarcely retained fraction obtained by semipreparative RP-HPLC. Among the identified peptides, those with hydrophobic or positively charged residues at the C-terminal tripeptide were chemically synthesized to determine their ACEI activity. This procedure allowed us to identify four novel potent ACEI peptides from kappa-casein with sequences IAK, YQQRPVA, WQVLPNAVPAK, and HPHPHLSF. These active sequences could be obtained by enzymatic hydrolysis either of the individual kappa-casein fraction or the total casein fraction from ovine milk.     

Synthesis of novel fullerene amino acids and their multifullerene peptides

[60]-Fullerene functionalized amino acids with 4-6 methylene spacers from α-carbon to the nitrogen atom of fulleropyrolidine and corresponding multifullerene peptides have been synthesized.     

Two-dimensional reverse phase-reverse phase chromatography: A simple and robust platform for sensitive quantitative analysis of peptides by LC/MS. Hardware design

We have revised current two-dimensional RP-RP approaches and developed a new robust 2-D RP-RP platform. This platform was implemented on an Agilent 1100 2-D liquid chromatography system and is based on high pressure switching between two high-resolution RP columns. An independent binary gradient was implemented for each dimension. The powerful combination of dual analytical columns with independent gradient elution achieves high analyte purity, effectively eliminates matrix effects, and maximizes MS sensitivity in Q1 SIM comparable to the sensitivity enhancements of MS/MS-based methods. Implementation of dual simultaneous gradient profiles (overlapped gradients) reduces 2-D method run-time to the scale of 1-D method run-times. This robust and sensitive approach is particularly suitable for hydrophobic peptides and small proteins and can be used as a routine standard technique for enhanced on-line peptide purification coupled with mass spectrometric detection.     

A novel and efficient synthesis of DOPA and DOPA peptides by oxidation of tyrosine residues with IBX

An efficient route to 3,4-dihydroxylphenylalanine (DOPA) and DOPA peptides was described by oxidation of l-tyrosine and l-tyrosine derivatives with 2-iodoxybenzoic acid (IBX). DOPA was obtained after an situ reduction of the corresponding ortho-quinone with sodium dithionite. Oxidation reactions proceeded in good yields and high chemo- and regio-selectivity. The chirality of the DOPA residue was retained under the reaction conditions. The efficiency and the selectivity of the reaction were successfully tested using recyclable polymer-supported IBX.     

A novel artificial loop scaffold for the noncovalent constraint of peptides

BACKGROUND: Few examples exist of peptides of < 35 residues that form a stable tertiary structure without disulfide bonds. A method for stabilization and noncovalent constraint of relatively short peptides may allow the construction and use of intracellular peptide libraries containing protein minidomains. RESULTS: We have examined a novel method for the noncovalent constraint of peptides by attaching the peptide EFLIVKS (single-letter amino acid code), which forms dimers, to the amino and carboxyl termini of different peptide inserts. An 18 residue random coil taken from the inhibitor loop of barley chymotrypsin inhibitor 2 was inserted between the peptides to produce a 32-mer minidomain that is attacked only slowly by elastase, has numerous slowly exchanging protons, contains a high beta-structure content and has a T(m) above 37 degrees C. A point mutation disrupting the hydrophobic interior in both dimerizing peptides causes a loss of all slowly exchanging protons and of secondary structure. Adding specific charged residues to each terminus substantially increased the T(m), as did point mutants designed to add interdimerizer ion pairs. Three flexible epitope tag inserts and a nonamer insert do not appear to be folded in a stable structure by EFLIVKS. The properties of two peptides selected for expression in HeLa cells suggest they do form a stable tertiary structure. CONCLUSIONS: Attaching short dimerizing peptides to both the amino and carboxyl termini of several 18-mer peptides appears to create stable monomeric tertiary structures. Mutations in the dimerizers can either destabilize or significantly stabilize a standard 18-mer insert. Dimerizing peptides flanking random insert sequences could be used as a strategy to generate heterogeneous peptide libraries with both extended and folded members.     

Discovery and characterization of novel oxide anodes for solid oxide fuel cells

The search for alternative anode materials for solid oxide fuel cells (SOFCs) has been reviewed in the light of structure, stability, conductivity, chemical and thermal compatibility with electrolyte YSZ. In this review, we have presented the advantages and disadvantages of the traditional Ni-YSZ anode for SOFCs. The development of alternative anode for SOFCs with fluorite, rutile, tungsten bronze, pyrochlore, perovskite and spinel structures has been reviewed and discussed in detail. Among the reported materials systems, materials with perovskite structure are promising particularly where two ions with complimentary function are present on the B-site at high concentration. We have recently found a good redox stable anode (La(0.75)Sr(0.25))(1-x)Cr(0.5)Mn(0.5)O(3) (0 相似文献   

Design and synthesis of N-terminal cyclic motilin partial peptides: a novel pure motilin antagonist

Motilin antagonist was designed and synthesized on the basis of the structure-activity relationship analysis of porcine motilin that we reported recently. The drug design was performed on a specific concept to reduce a flexibility of peptide conformation of porcine motilin partial peptide by its cyclization. The cyclic peptide was synthesized using Boc (tert-butyloxycarbonyl) solid phase methodology, followed by cyclization using the azide procedure, and tested for the binding activity to motilin receptor and smooth muscle contractile activity. The cyclic peptides 3, 4, and 5 showed antagonistic property on contraction assay (pA2 [the negative logarithm of molar concentration of antagonist causing a 2-hold shift to the right of the concentration-response curve for motilin]: 4.5, 4.34, and 4.04, respectively, in rabbit duodenum) and no contractile activity even at high concentration.     

Molecular mechanisms of membrane perturbation by antimicrobial peptides and the use of biophysical studies in the design of novel peptide antibiotics

Antibiotic resistant bacterial strains represent a global health problem with a strong social and economic impact. Thus, there is an urgent need for the development of antibiotics with novel mechanisms of action. There is currently an extensive effort to understand the mode of action of antimicrobial peptides which are considered as one alternative to classical antibiotics. The main advantage of this class of substances, when considering bacterial resistance, is that they rapidly, within minutes, kill bacteria. Antimicrobial peptides can be found in every organism and display a wide spectrum of activity. Hence, the goal is to engineer peptides with an improved therapeutic index, i.e. high efficacy and target specificity. For the rational design of such novel antibiotics it is essential to elucidate the molecular mechanism of action. Biophysical studies have been performed using to a large extent membrane model systems demonstrating that there are distinctive different mechanisms of bacterial killing by antimicrobial peptides. One can distinguish between peptides that permeabilize and/or disrupt the bacterial cell membrane and peptides that translocate through the cell membrane and interact with a cytosolic target. Lantibiotics exhibit specific mechanisms, e.g. binding to lipid II, a precursor of the peptidoglycan layer, either resulting in membrane rupture by pore formation or preventing cell wall biosynthesis. The classical models of membrane perturbation, pore formation and carpet mechanism, are discussed and related to other mechanisms that may lead to membrane dysfunction such as formation of lipid-peptide domains or membrane disruption by formation of non-lamellar phases. Emphasis is on the role of membrane lipid composition in these processes and in the translocation of antimicrobial peptides.     

Synthesis and reactivity of enediynyl amino acids and peptides: a novel concept in lowering the activation energy of Bergman cyclisation by H-bonding and electrostatic interactions

Novel enediynyl amino acids and peptides 3 and 5-8 were synthesized and their thermal reactivity towards Bergman cyclization studied and compared with the earlier reported amino acid 4, which demonstrated, for the first time, the effect of H-bonding and electrostatic interactions in lowering the activation energy of Bergman cyclization.     

Discovery of novel promising targets for anti-AIDS drug developments by computer modeling: application to the HIV-1 gp120 V3 loop

The V3 loop on gp120 from HIV-1 is a focus of many research groups involved in anti-AIDS drug studies, because this region of the protein determines the preference of the virus for T-lymphocytes or primary macrophages. Although the V3 loop governs cell tropism and, for this reason, exhibits one of the most attractive targets for anti-HIV-1 drug developments, its high sequence variability is a major complicating factor. Nevertheless, the data on the spatial arrangement of V3 obtained here for different HIV-1 subtypes by computer modeling clearly show that, despite a wide range of 3D folds, this functionally important site of gp120 forms at least three structurally invariant segments, which contain residues critical for cell tropism. It is evident that these conserved V3 segments represent potential HIV-1 vulnerable spots and, therefore, provide a blueprint for the design of novel, potent and broad antiviral agents able to stop the HIV's spread.     

Highly regio-, chemo- and diastereoselective synthesis of oxa-bridged spirocycles: a novel observation of reverse selectivity

The reverse regio- and diastereoselectivities are observed between the reactions involving 5- and 6-membered-ring cyclic carbonyl ylide dipoles with alpha-methylene ketones. A mild catalytic route to synthesize spirocyclic systems with high regio-, chemo- and diastereoselectivities is described.