Discovery of novel Agonists and antagonists of the free fatty acid receptor 1 (FFAR1) using virtual screening

The G-protein-coupled receptor free fatty acid receptor 1 (FFAR1), previously named GPR40, is a possible novel target for the treatment of type 2 diabetes. In an attempt to identify new ligands for this receptor, we performed virtual screening (VS) based on two-dimensional (2D) similarity, three-dimensional (3D) pharmacophore searches, and docking studies by using the structure of known agonists and our model of the ligand binding site, which was validated by mutagenesis. VS of a database of 2.6 million compounds followed by extraction of structural neighbors of functionally confirmed hits resulted in identification of 15 compounds active at FFAR1 either as full agonists, partial agonists, or pure antagonists. Site-directed mutagenesis and docking studies revealed different patterns of ligand-receptor interactions and provided important information on the role of specific amino acids in binding and activation of FFAR1.

Antioxidants in health and disease

Free radical production occurs continuously in all cells as part of normal cellular function. However, excess free radical production originating from endogenous or exogenous sources might play a role in many diseases. Antioxidants prevent free radical induced tissue damage by preventing the formation of radicals, scavenging them, or by promoting their decomposition. This article reviews the basic chemistry of free radical formation in the body, the consequences of free radical induced tissue damage, and the function of antioxidant defence systems, with particular reference to the development of atherosclerosis.

Template-free environmentally friendly synthesis and characterization of unsupported tungsten carbide with a controllable porous framework

Tungsten carbide (WC) with controlled pore size distribution was synthesized using a novel “precursor reassembly” method. The precursor crystal was assembled by mixing ammonium metatungstate (AMT) and ammonium carbonate (AC) in distilled water, followed by hydrothermal treatment. The mesostructure, crystal phase, and amount of deposited graphitic carbon can be conveniently tuned by controlling carburizing atmosphere (CO or a CO/H2 mixture). Moreover, the influence of precursor preparation (AMT/AC mass ratio and hydrothermal temperature) on the materials was also investigated. The resultant materials with low carbon content were mesoporous WCs, which showed high specific surface areas (11.3-20.4 m2 g-1) and adjustable pore-size distributions (average pore size: 15.3-22.3 nm). A mechanism for the formation of WC with a controllable porous framework is proposed. Finally, cyclic voltammetry was used to investigate the inference of different mesoporous structure.

An understanding of chemoselective hydrogenation on crotonaldehyde over Pt(111) in the free energy landscape: The microkinetics study based on first-principles calculations

Microkinetic model is developed in the free energy landscape based on density functional theory (DFT) to quantitatively investigate the reaction mechanism of chemoselective partial hydrogenation of crotonaldehyde to crotyl alcohol over Pt(1 1 1) at the temperature of 353 K. Three different methods (mobile, immobile and collision theory models) were carried out to obtain free energy barrier of adsorption/desorption processes. The results from mobile and collision theory models are similar. The calculated TOFs from both models are close to the experiment value. However, for the immobile model, in which the free energy barrier of desorption approaches the energy barrier, the calculated TOF is 2 orders of magnitude lower than the other models. The difficulty of adsorption/ desorption may be overestimated in the immobile model. In addition, detailed analyses show that for the surface hydrogenation elementary steps, the entropy and internal energy effects are small under the reaction condition, while the zero-point-energy (ZPE) correction is significant, especially for the multi-step hydrogenation reaction. The total energy with the ZPE correction approaches to the full free energy calculation for the surface reaction under the reaction condition. (c) 2011 Elsevier B.V. All rights reserved.

DNA Reorientation on Au Nanoparticles: Label-Free Detection of Hybridization by Surface Enhanced Raman Spectroscopy

DNA sequences attached to Au nanoparticles via thiol linkers stand up from the surface, giving preferential enhancement of the adenine ring breathing SERS band. Non-specific binding via the nucleobases reorients the DNA, reducing this effect. This change in intensity on reorientation was utilised for label-free detection of hybridization of a molecular beacon.

Label-Free Detection of Single-Base Mismatches in DNA by Surface-Enhanced Raman Spectroscopy

Singles only: DNA sequences can be induced to spontaneously adsorb to the surfaces of Ag colloids through their nucleotide side chains (see picture). The SERS spectra of these nonspecifically bound strands are sufficiently reproducible that they can be used to identify single-base mismatches in short (25-mer and 23-mer) strands. Subtracting the spectra of different DNA sequences results in difference spectra that contain features corresponding to the exchanged nucleotides.

RESONANCE RAMAN-SPECTRA OF THE TRIPLET-STATE OF FREE-BASE TETRAPHENYLPORPHYRIN AND 6 OF ITS ISOTOPOMERS

The resonance Raman spectra of the ground state and the lowest excited tripler state of free-base tetraphenylporphyrin and six of its isotopomers have been obtained using two-color time-resolved techniques. Ground-state spectra were recorded using low-energy 447 nm probe laser pulses, and triplet-state spectra were probed, with similar pulses, 30 ns after high-energy excitation with 532 nm pump pulses. Polarization data on both the ground and triplet states are also reported. The resonance Raman spectrum of the triplet is very different from that of the ground state but the combination of extensive isotope substitution with polarization data allows bands in the ground state to be assigned and corresponding bands in the tripler state to be located. Isotope shifts of the same bands in the S-0 and T-1 states are similar, implying that the compositions of the vibrational modes do not change significantly on excitation. Two of the strongest bands in the T-1 spectra are associated with phenyl ring substituents; these are shifted less than 5 cm(-1) between the S-0 and T-1 states so that bonding in the phenyl substituents is barely affected by excitation to the T-1 state. The changes in position of the porphyrin ring bands are larger, but still only tens of cm(-1) or less, the main changes in the spectra being due to differences in relative band intensities in the two states. The relatively small shifts in the porphyrin ring band positions which are observed show that the excitation energy is not localized on a single small region of the molecule but is delocalized over the entire porphyrin skeleton. This picture of an excited species with high chemical reactivity, but with individual bonds only slightly perturbed from the ground state, is contrasted with molecules, such as benzophenone, where excitation causes a large perturbation in the bonding within a single functional group.

TIME-RESOLVED RESONANCE RAMAN-SPECTROSCOPY OF EXCITED SINGLET AND TRIPLET-STATES OF FREE-BASE MESO-TETRAPHENYLPORPHYRIN

Two-color time-resolved resonance Raman spectroscopy has been used to probe the lowest excited singlet (S1) and triplet (T1) states of free-base meso-tetraphenylporphyrin and meso-tetrakis(4-sulphonatophenyl)porphyrin in solution at room temperature. The spectra were recorded using 532-nm excitation pulses and time-delayed probe pulses (DELTAT = 0-30 ns, 447 and 460 nm) near lambda(max) of the S1 and T1 states. Significant shifts in frequency of the porphyrin core vibrations were observed upon excitation to either the S1 or T1 state. Several of the strongest polarized bands in the spectra of both excited states, including nu1, nu2, nu4, nu6, and phi4, are assigned, and the information they give on the differences in electron distribution in the ground, S1, and T1 states is discussed.

Enantioselective formal total synthesis of the Dendrobatidae frog toxin, (+)-pumiliotoxin B, via O-directed alkyne free radical hydrostannation

Herein we describe our application of the O-directed free radical hydrostannation of disubstituted alkyl-acetylenes (with Ph3SnH and Et3B) to the (+)-pumiliotoxin B total synthesis problem. Specifically, we report on the use of this method in the synthesis of the Overman alkyne 8, and thereby demonstrate the great utility of this process in a complex natural product total synthesis setting for the very first time. We also report here on a new, stereocontrolled, and highly practical enantioselective pathway to Overman's pyrrolidine epoxide partner 9 for 8, which overcomes the previous requirement for use of preparative HPLC to separate the 1:1 mixture of diastereomeric epoxides that was obtained in the original synthesis of 9.

Cu-Based Nanoalloys in the Base-Free Ullmann Heterocyle-Aryl Ether Synthesis

We report the first liquid-liquid Ullmann etherification process mediated not only by oxidatively stable Cu but also by CuZn and CuSn nanoparticle catalysts in conjunction with microwave heating that also avoids the use of solid and expensive bases. Conditions have led to improved turnovers and excellent yields in heteroaromatic Ullmann-type coupling reactions. Further enhancement is achieved upon the addition of 18-crown-6 as a kinetic promoter.

A comparison of the chemical repair rates of free radical precursors of DNA damage and cell killing in Chinese hamster V79 cells.

One of the important temporal stages of radiation action in cellular systems is the chemical phase, where oxygen fixation reactions compete with chemical repair reactions involving reducing agents such as GSH. Using the gas explosion technique it is possible to follow the kinetics of these fast (> 1 ms) reactions in intact cells. We have compared the chemical repair kinetics of the oxygen-dependent free radical precursors leading to DNA single-strand and double-strand breaks, measured using filter elution techniques, with those leading to cell killing in V79 cells. The chemical repair rates for DNA dsb (670s-1 at pH 7.2 and 380s-1 at pH 9.6) and cell killing (530s-1) were similar. This is in agreement with the important role of DNA dsb in radiation induced cell lethality. The rate for DNA ssb precursors was significantly slower (210s-1). The difference in rate between DNA ssb and dsb precursors may be explained on the basis of a dsb free radical precursor consisting of a paired radical, one radical on each strand. The instantaneous probability of one or other of these radicals being chemically repaired and not proceeding to form a dsb will be twice that of a ssb radical precursor. This agrees well with the concept of locally multiply damaged sites (LMDS) produced from clusters of ionizations in DNA (Ward 1985).

Label-free detection of nanomolar unmodified single- and double-stranded dna by using surface-enhanced raman spectroscopy on Ag and Au colloids

Unlabelled single- and double-stranded DNA (ssDNA and dsDNA, respectively) has been detected at concentrations =10-9?M by surface-enhanced Raman spectroscopy. Under appropriate conditions the sequences spontaneously adsorbed to the surface of both Ag and Au colloids through their nucleobases; this allowed highly reproducible spectra with good signal-to-noise ratios to be recorded on completely unmodified samples. This eliminated the need to promote absorption by introducing external linkers, such as thiols. The spectra of model ssDNA sequences contained bands of all the bases present and showed systematic changes when the overall base composition was altered. Initial tests also showed that small but reproducible changes could be detected between oligonucleotides with the same bases arranged in a different order. The spectra of five ssDNA sequences that correspond to different strains of the Escherichia coli bacterium were found to be sufficiently composition-dependent so that they could be differentiated without the need for any advanced multivariate data analysis techniques.

A greener, halide-free approach to ionic liquid synthesis

Conventionally, ionic liquids with anions generated from simple organic acids are prepared following a metathetic procedure from a halide salt, usually a chloride. Here, we describe an efficient means of generating hydroxide solutions of the cations of interest, allowing many ionic liquids to be produced by simple acid-base reactions, completely avoiding the use of halides.

Selective Orthosteric Free Fatty Acid Receptor 2 (FFA2) Agonists IDENTIFICATION OF THE STRUCTURAL AND CHEMICAL REQUIREMENTS FOR SELECTIVE ACTIVATION OF FFA2 VERSUS FFA3

Free fatty acid receptor 2 (FFA2; GPR43) is a G protein-coupled seven-transmembrane receptor for short-chain fatty acids (SCFAs) that is implicated in inflammatory and metabolic disorders. The SCFA propionate has close to optimal ligand efficiency for FFA2 and can hence be considered as highly potent given its size. Propionate, however, does not discriminate between FFA2 and the closely related receptor FFA3 (GPR41). To identify FFA2-selective ligands and understand the molecular basis for FFA2 selectivity, a targeted library of small carboxylic acids was examined using holistic, label-free dynamic mass redistribution technology for primary screening and the receptor-proximal G protein [S-35] guanosine 5'-(3-O-thio) triphosphate activation, inositol phosphate, and cAMP accumulation assays for hit confirmation. Structure-activity relationship analysis allowed formulation of a general rule to predict selectivity for small carboxylic acids at the orthosteric binding site where ligands with substituted sp(3)-hybridized alpha-carbons preferentially activate FFA3, whereas ligands with sp(2)- or sp-hybridized alpha-carbons prefer FFA2. The orthosteric binding mode was verified by site-directed mutagenesis: replacement of orthosteric site arginine residues by alanine in FFA2 prevented ligand binding, and molecular modeling predicted the detailed mode of binding. Based on this, selective mutation of three residues to their non-conserved counterparts in FFA3 was sufficient to transfer FFA3 selectivity to FFA2. Thus, selective activation of FFA2 via the orthosteric site is achievable with rather small ligands, a finding with significant implications for the rational design of therapeutic compounds selectively targeting the SCFA receptors.

Dissociative electron attachment to C2F5 radicals

Dissociative electron attachment to the reactive C2F5 molecular radical has been investigated with two complimentary experimental methods; a single collision beam experiment and a new flowing afterglow Langmuir probe technique. The beam results show that F- is formed close to zero electron energy in dissociative electron attachment to C2F5. The afterglow measurements also show that F- is formed in collisions between electrons and C2F5 molecules with rate constants of 3.7 × 10-9 cm3 s-1 to 4.7 × 10-9 cm3 s-1 at temperatures of 300–600 K. The rate constant increases slowly with increasing temperature, but the rise observed is smaller than the experimental uncertainty of 35%.