Copper-free Sonogashira cross-coupling for functionalization of alkyne-encoded proteins in aqueous medium and in bacterial cells

Bioorthogonal reactions suitable for functionalization of genetically or metabolically encoded alkynes, for example, copper-catalyzed azide-alkyne cycloaddition reaction ("click chemistry"), have provided chemical tools to study biomolecular dynamics and function in living systems. Despite its prominence in organic synthesis, copper-free Sonogashira cross-coupling reaction suitable for biological applications has not been reported. In this work, we report the discovery of a robust aminopyrimidine-palladium(II) complex for copper-free Sonogashira cross-coupling that enables selective functionalization of a homopropargylglycine (HPG)-encoded ubiquitin protein in aqueous medium. A wide range of aromatic groups including fluorophores and fluorinated aromatic compounds can be readily introduced into the HPG-containing ubiquitin under mild conditions with good to excellent yields. The suitability of this reaction for functionalization of HPG-encoded ubiquitin in Escherichia coli was also demonstrated. The high efficiency of this new catalytic system should greatly enhance the utility of Sonogashira cross-coupling in bioorthogonal chemistry.     

Squaric acid N-hydroxylamides: synthesis, structure, and properties of vinylogous hydroxamic acid analogues

The synthesis of squaric acid N-hydroxylamide esters 5 and amides 6 from dimethyl squarate 2a is described. These derivatives are analogues of the naturally occurring iron(III) chelator hydroxamic acid. On the basis of a comparative reactivity study, a concerted retro-Cope mechanism for the formation of the N-hydroxylamide esters 5 by reaction of dimethyl squarate with hydroxylamines is proposed. A preliminary iron(III) binding study of these hydroxamic acid analogues is presented, demonstrating binding of iron(III) to amides 6 in aqueous solutions, while the esters 5 did not show any sign of metal ion binding. 13C NMR spectroscopic data (chemical shift and spin-lattice relaxation time determination) of these and related derivatives delineate the resonance structures predominant in these molecules. The resonance structures of the derivatives rationalize their spectroscopic data, chemical reactivity, and iron(III) binding properties. Single-crystal X-ray structure analyses of squaric acid N-hydroxylamide ester 5b and squaric acid N-hydroxylamide amide 6c confirm their connectivity and provide structural evidence supporting the spectroscopically derived conclusions. The squaric acid N-hydroxylamides are potentially useful in the construction of chemosensors for iron(III).     

Template‐free anion‐controlled synthesis of Pd (II) nano‐aggregates for the antifouling polymerization of CO and ethylene

The reaction of [(domppp) Pd (OAc)₂] [domppp = 1,3‐bis (di‐o‐methoxyphenylphosphino)propane] and imidazolium‐functionalized carboxylic acids containing various anions (Br^?, PF₆^?, SbF₆^? and BF₄^?) resulted in the formation of nano‐sized Pd (II) aggregates under template‐free conditions. The rate of formation of aggregates can be modulated by changing the anion, affecting the rate of polymerization of CO and olefins without fouling. Herein, we describe the analysis of Pd (II) catalysts by dynamic light scattering, atomic force microscopy, X‐ray photoelectron spectroscopy and X‐ray crystallography, and co‐ and terpolymerization results including the catalytic activity, and bulk density and molecular weight of polymers.     

Semi-empirical insertion probability for hard-spheres and hard-sphere chains

In spite of its simplicity and a well-defined theoretical basis, the Flory–Guggenheim approach is conventionally regarded as inapplicable to off-lattice system since the insertion probability of the approach does not account for the excluded region, existing in the off-lattice system. In this work, we propose the insertion probability accounting for the excluded region of off-lattice fluids and derive a new version of equation of state (EOS) for hard-sphere chains basing on the Flory–Guggenheim approach. To investigate the behavior of the excluded regions, a Monte Carlo sampling was performed for hard disks and the various excluded regions were found to have different density dependence. On the basis of the simulation result, we formulated the insertion probability for hard-sphere and that of hard-sphere chain which accounts for the effect of chain-connectivity on the monomer insertion. The proposed insertion probability was found to correctly predict the simulation data for monomer and correctly correlate the simulation data for chain fluids. The resulting EOS was found to meet closed-packed limit and predict the simulation data of compressibility factor for monomer and chains with a reasonable degree of accuracy. When compared with other off-lattice based EOS, it shows a comparable or better result. For second virial coefficient of chain molecules, the model was found to reasonably predict the simulation data.     

Interleukin-1beta stimulates matrix metalloproteinase-2 expression via a prostaglandin E2-dependent mechanism in human chondrocytes

IL-1beta is known promote cyclooxygenase-2 (COX- 2) and matrix metalloproteinase-2 (MMP-2) expression. This study focuses on the characterization of the signaling cascade associated with IL-1beta-induced matrix metalloproteinase-2 (MMP-2) regulation in human chondrocytes. The decrease in collagen levels in the conditioned media was prevented by a broad spectrum MMP inhibitor, suggesting that IL-1beta promotes the proteolytic process leading to MMP-2 activation. IL-1beta-related MMP-2 expression was found to be dependent on prostaglandin E2 (PGE2) production. In addition, the induction of COX-2 and MMP-2 was inhibited by the pretreatment of chondrocytes with a SB203580 or Ro 31-8220, indicating the involvement of protein kinase C (PKC) or p38 mitogen-activated protein kinase (MAPK). However, there is no cross-talk between PKC and p38 MAPK in the IL-1beta-induced MMP-2 activation. Taken together, these results demonstrated that IL-1beta induces MMP-2 expression through the PGE2-dependent mechanism in human chondrocytes.     

Preparation of block copolymer vesicles in solution

Block copolymer vesicles can be prepared in solution from a variety of different amphiphilic systems. Polystyrene‐block‐poly(acrylic acid), polystyrene‐block‐poly(ethylene oxide), and many other block copolymer systems can produce vesicles of a wide range of sizes; those in the range of 100–1000 nm have been explored extensively. Different factors, such as the absolute and relative block lengths, the presence of additives (ions, homopolymers, and surfactants), the water content in the solvent mixture, the nature and composition of the solvent, the temperature, and the polydispersity of the hydrophilic block, provide control over the types of vesicles produced. Their high stability, resistance to many external stimuli, and ability to package both hydrophilic and hydrophobic compounds make them excellent candidates for use in the medical, pharmaceutical, and environmental fields. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 923–938, 2004     

Photoactivation of pheophorbide a induces a mitochondrial-mediated apoptosis in Jurkat leukaemia cells

The mechanism of cell death by pheophorbide a (Pba) which has been established to be a potential photosensitizer was examined in experimental photodynamic therapy (PDT) on Jurkat cells, a human lymphoid tumor cell line. In 30-60 min after irradiation, Pba treated cells exhibited apoptotic features including membrane blebbing and DNA fragmentation. Pba/PDT caused a rapid release of cytochrome c from mitochondria into the cytosol. Sequentially, activation of caspase-3 and the cleavage of poly ADP-ribose polymerase (PARP) were followed. Meanwhile, no evidence of activation of caspase-8 was indicated in the cells. In experiments with caspase inhibitors, it was found that caspase-3 alone was sufficient initiator for the Pba-induced apoptosis of the cells. Pba specific emission spectra were confirmed in the mitochondrial fraction and the light irradiation caused a rapid change in its membrane potential. Thus, mitochondria were entailed as the crucial targets for Pba as well as a responsible component for the cytochrome c release to initiate apoptotic pathways. Taken together, it was concluded that the mode of Jurkat cell death by Pba/PDT is an apoptosis, which is initiated by mitochondrial cytochrome c release and caspase-3-pathways.     

A convenient synthesis of a selective gelatinase inhibitor as an antimetastatic agent

Compound 1, 2-(4-phenoxyphenylsulfonylmethyl)thiirane, is a potent and selective inhibitor for human gelatinases (J. Am. Chem. Soc. 2000, 122, 6799-6800), enzymes implicated in a number of diseases, including cancer. This compound is showing excellent promise in animal trials in a number of disease models. Large quantities of this compound were necessary for these studies. A convenient four-step synthetic route for compound 1 is described herein. The synthesis is amenable to scale-up to tens of grams and gives an overall yield of 57% for this important compound.     

Sample enrichment by using monolithic precolumns in microcolumn liquid chromatography

An on-line sample enrichment system was designed using monolithic precolumns in microcolumn LC. The monolithic ODS capillary columns were prepared via in situ sol-gel processes. The enrichment efficiency of the monolithic columns was tested by using phthalates as the analytes. The relative standard deviations (n = 6) for the retention time, peak area and peak height were between 0.4 and 1.2%, 0.9 and 5.5% and 0.4 and 3.9%, respectively. The system was linear (R2 > 0.99) within the working sample concentration and sample volume ranges. Comparing to 0.2 microl injection with a typical sample injector, the theoretical plate number of a same separation column was increased by 3-6-fold when the precolumn unit was used for sample injection. The recoveries of the analytes were between 88 and 120%, and the sample volume that could be injected into the system was increased up to 5000-fold. The limits of detection were improved by more than 2000-fold and were between 0.21 and 0.87 ng ml(-1) even with a UV absorbance detector. This system was applied to the determination of phthalates contained in laboratory distilled water and tap water samples.     

Electrochemical genosensing properties of gold nanoparticle–carbon nanotube hybrid

We have investigated the electrochemical genosensing properties of gold nanoparticle–carbon nanotube hybrid. Thiolated oligonucleotide probes and mercaptohexanol were self-assembled onto the Au–CNT hybrid. The hybridization events of target oligonucleotides are monitored using electrochemical impedance spectroscopy, cyclic voltammetry and a.c. voltammetry techniques. A redox-active mediator is used to detect the oxidation of guanine residues. The as-fabricated genosensor is able to differentiate between complementary and mismatched hybridizations, relying on the oxidation current of the guanine residues mediated via .