Synthesis and use of deuterated palmitic acids to decipher the cryptoregiochemistry of a Delta13 desaturation

The synthesis of two hexadeuterated palmitic acids differing in the position of the diagnostic labels, and their use to decipher the cryptoregiochemistry of a Delta13 desaturation are described. A dithiane and a triple bond functionalities were used to introduce the diagnostic (C13 or C14) and tagging (C8 and C9) labels, respectively, in the palmitic acid skeleton. Using these probes, the cryptoregiochemistry of the Delta13 desaturation involved in the biosynthesis of Thaumetopoea pityocampa sex pheromone was studied by means of kinetic isotope effect determinations. Transformation of both (Z)-11-hexadecenoic and 11-hexadecynoic acids into (Z, Z)-11,13-hexadecadienoic and (Z)-13-hexadecen-11-ynoic acids, respectively, is initiated by abstraction of the hydrogen atom at the C13 position, followed by the fast elimination of the C14 hydrogen to give the double bond.     

Using chemical probes to investigate the sub-inhibitory effects of azithromycin

The antibacterial drug azithromycin has clinically beneficial effects at sub-inhibitory concentrations for the treatment of conditions characterized by chronic Pseudomonas aeruginosa infection, such as cystic fibrosis. These effects are, in part, the result of inhibition of bacterial biofilm formation. Herein, the efficient synthesis of azithromycin in 4 steps from erythromycin and validation of the drug's ability to inhibit biofilm formation at sub-MIC (minimum inhibitory concentration) values are reported. Furthermore, the synthesis of immobilized and biotin-tagged azithromycin analogues is described. These chemical probes were used in pull-down assays in an effort to identify azithromycin's binding partners in vivo. Results from these assays revealed, as expected, mainly ribosomal-related protein binding partners, suggesting that this is the primary target of the drug. This was further confirmed by studies using a P. aeruginosa strain containing plasmid-encoded ermC, which expresses a protein that modifies 23S rRNA and so blocks macrolide entry to the ribosome. In this strain, no biofilm inhibition was observed. This work supports the hypothesis that the sub-inhibitory effects of azithromycin are mediated through the ribosome. Moreover, the synthesis of these chemical probes, and proof of their utility, is of value in global target identification in P. aeruginosa and other species.     

Hydrophobic nitroxide radicals as probes to investigate the hydrophobic interaction

The EPR spectrum of 2,2,6,6-tetramethylpiperidine-N-oxide (TEMPO) has been systematically investigated in several solvents and in aqueous solutions of glycerol,t-BuOH, Bu₄NBr,n-HexNH₃Br,n-OctNH₃Br, NaBPh₄, and Ph₄AsCl. Most of the results have been obtained at 25°C, though the temperature dependence of the linewidths has been examined in water and several organic solvents. Data on the spectrum of ditertiarybutylnitroxide in aqueous solutions of glycerol and Bu₄NBr are also presented. The spectrum was simulated to determine W_H, the linewidth after allowance for the unresolved proton hyperfine interaction, in each manifold of the triplet due to the nitrogen hyperfine interaction. The linewidth W_H is analyzed in terms of the reorientational correlation time Äθ and the angular velocity correlation time ÄJ. In most solutions Äθ is determined only by the bulk solution viscosity, except in situations where significant clustering of hydrophobic solute molecules occurs. In pure nonaqueous solvents the temperature dependence results are consistent with ÄJ being determined by the bulk viscosity, while in water or aqueous solutions, a very different behavior is found which is interpreted as a manifestation of clathrate-like hydration of the hydrophobic radical. This interpretation is incorporated in a two-state model developed to account for the W_H data of TEMPO in aqueous solutions of various hydrophobic solutes. The equilibrium parameters derived from the model, for the association of TEMPO with several hydrophobic solutes, support the concept of hydrophobic interactions as pictured from thermodynamic excess functions.     

Fluorescent caged phosphoserine peptides as probes to investigate phosphorylation-dependent protein associations

The development of chemical probes for the investigation of the complex phosphorylation signaling cascades that regulate biological events is crucial to understanding these processes. We describe herein a bifunctional probe that enables spatial and temporal release of a biologically active ligand while allowing simultaneous monitoring of its binding to the protein of interest. Substitution of Tyr(-2) for the enviromentally sensitive fluorescent amino acid DANA in the sequence RLYRpSLPA which is known to bind the 14-3-3 protein does not adversely affect binding affinity and allows monitoring of the binding process. The binding of the peptide to 14-3-3 places the fluorescent reporter unit into a hydrophobic pocket, which changes the fluorescent maximum emission intensity and wavelength. At the same time, the newly developed photolabile 1-(2-nitrophenyl)ethyl-caged phosphoserine allows control of the release of the biologically active ligand through unmasking of the key phosphoserine functionality upon UV irradiation.     

A review of the animal models used to investigate the health benefits of soy isoflavones

This review considers the recent literature in which animal models were used to investigate the purported health benefits of soy isoflavones. The main conclusions are that our animal models demonstrate minimal effects in breast, prostate, and colon cancer prevention, and that, while some cancers may respond to isoflavones, it would appear that isoflavones do not prevent further development once cancer has become established. Regarding cardiovascular health, the lipid-lowering effects of isoflavones have been established, but their efficacy may be less than original research purported. However, it may be considered a bonus of habitual soy consumption that blood cholesterol levels would be reduced somewhat. With respect to osteoporosis and menopausal symptoms, animal models do not show any consistent benefit of isoflavones in preventing osteoporosis, and calcium fortification or the use of prescribed medications are likely much better approaches to combat bone loss. However, our animal models of osteoporosis and menopausal symptoms may not be entirely representative of the human situation. Perhaps the benefit of isoflavones in cognitive skills and in delaying Alzheimer's disease is an area where they can be of some advantage. However, this field is very recent and requires much more research in both humans and animal models before any definitive benefit can be propounded. On the other hand, isoflavones in moderation are probably not dangerous, as few studies have indicated adverse effects. However, large doses have been shown to increase apoptosis and cell degeneration, and in some cancer regimes, once the cancer has progressed beyond the hormone-dependent stage, high doses of isoflavones may be contraindicated. The prospect of mega-dosing from isoflavone supplements opens a new chapter in the risk assessment of isoflavone consumption.     

Synthesis and use of stereospecifically deuterated analogues of palmitic Acid to investigate the stereochemical course of the delta11 desaturase of the processionary moth

Thaumetopoea pityocampa pheromone glands contain desaturases that, after several sequential reactions from palmitic acid, catalyze the formation of a unique enyne fatty acid, which is the immediate sex pheromone precursor. In this article, we describe the synthesis of different stereospecifically deuterium-labeled and isotopically tagged palmitic acid probes needed to decipher the stereochemical course of the T. pityocampa Delta(11) desaturase. The synthesis of probes has been carried out by a chemoenzymatic route, in which the key step is the kinetic lipase-catalyzed resolution of racemic mixtures of secondary propargyl alcohols. The presence of the acetylenic bond simplifies the absolute configuration determination of the resolved alcohols. Moreover, it allows the introduction of the isotopic tag by deuteration. By use of the probes thus prepared, experimental evidence is presented that the Delta(11) desaturase of T. pityocampa transforms palmitic acid into (Z)-11-hexadecenoic acid by removal of the pro-(R)-hydrogen atoms from both C11 and C12.     

The EPR study of dialkyl nitroxides as probes to investigate the exchange of solutes between micellar and water phases

An EPR investigation of the kinetics of the exit, k ^-, and entrance, k ⁺, processes in micelles of sodium dodecyl sulfate, hexadecyltrimethylammonium bromide and polyoxyethylene(6)decanol of a family of para-substituted benzyl tert -butyl nitroxides and para-substituted benzyl hydroxyalkyl nitroxides is reported. The inclusion of nitroxide probes in the hydrophobic environment of the micelle gives rise to a reduction of the value of both nitrogen and β-proton splittings, with the result that the resonance fields for the M_I(2H _β ) = ±1lines of the free and included species are significantly different. The rate constants were obtained by analyzing the EPR line shape variations as function of surfactant concentration and temperature. The experimental value of k ⁺ obtained from the study of benzyl tert-butyl nitroxide indicates that the association reaction is very close to being controlled by diffusion. The value of the exit rate, k ^-, instead, depends on the probe hydrocarbon chain length. A comparison of our results with those obtained by luminescence quenching techniques is also reported.     

Synthesis of HyBeacons and dual-labelled probes containing 2'-fluorescent groups for use in genetic analysis

An FMOC-protected 2'-hydroxyethyl uridine phosphoramidite has been used to synthesise fluorescein-labelled HyBeacon probes and "FAM-ROX" dual-labelled fluorogenic oligonucleotides.     

Synthesis of fluorophore and quencher monomers for use in scorpion primers and nucleic acid structural probes

We report the syntheses of monomers to incorporate fluorescein and methyl red within the sequence and at the termini of modified oligonucleotides. These monomers have been used in the solid-phase synthesis of fluorogenic oligonucleotides for genetic analysis and the study of multi-stranded nucleic acid structures.     

Synthesis and use of mechanism-based protein-profiling probes for retaining beta-D-glucosaminidases facilitate identification of Pseudomonas aeruginosa NagZ

The NagZ class of retaining exo-glucosaminidases play a critical role in peptidoglycan recycling in Gram-negative bacteria and the induction of resistance to beta-lactams. Here we describe the concise synthesis of 2-azidoacetyl-2-deoxy-5-fluoro-beta-d-glucopyranosyl fluoride as an activity-based proteomics probe for profiling these exo-glycosidases. This active-site directed reagent covalently inactivates this class of retaining N-acetylglucosaminidases with exquisite selectivity by stabilizing the glycosyl-enzyme intermediate. Inactivated Vibrio cholerae NagZ can be elaborated with biotin or a FLAG-peptide epitope using the Staudinger ligation or the Sharpless-Meldal click reaction and detected at nanogram levels. This ABPP enabled the profiling of the Pseudomonas aeruginosa proteome and identification at endogenous levels of a tagged protein with properties consistent with those of PA3005. Cloning of the gene encoding this hypothetical protein and biochemical characterization enabled unambiguous assignment of this hypothetical protein as a NagZ. The identification and cloning of this NagZ may facilitate the development of strategies to circumvent resistance to beta-lactams in this human pathogen. As well, this general strategy, involving such 5-fluoro inactivators, may prove to be of general use for profiling proteomes and identifying glycoside hydrolases of medical importance or having desirable properties for biotechnology.     

Synthesis and spectral properties of polymethine-cyanine dye-nitroxide radical hybrid compounds for use as fluorescence probes to monitor reducing species and radicals

Various hybrid compounds comprised of two types of nitroxide radicals and either a pentamethine (Cy5) or trimethine cyanine (Cy3) were synthesized. The nitroxide radicals were linked either via an ester-bond to one or two N-alkyl carboxyl-terminated groups of Cy5, or via two amido-bonds (aminocarbonyl or carbonylamino group) to the 5-position of the indolenine moieties of Cy5 and Cy3. Changes in fluorescence and ESR intensities of the hybrid compounds were measured before and after addition of Na ascorbate in PBS (pH 7.0) to reduce the radicals. Among the hybrid compounds synthesized, those that linked the nitroxide radicals via an aminocarbonyl residue at the 5-position of the indolenine moieties on Cy5 and Cy3 exhibited a 1.8- and 5.1-fold increase in fluorescence intensity with the reduction of the nitroxide segment by the addition of Na ascorbate, respectively. In contrast, fluorescence intensity was not enhanced in the other hybrid compounds. Thus, the hybrid compounds which exhibited an increase in fluorescent intensity with radical reduction can be used in the quantitative measurement of reducing species such as Fe(2+) and ascorbic acid, and hydroxyl radicals. Because these hybrid compounds have the advantage of fluorescing at longer wavelengths-661 (Cy5) or 568 (Cy3)nm, respectively, they can be used to measure radical-reducing species or radicals either in solution or in vivo.     

Synthesis of photoaffinity probes of tautomycin

Two types of photoaffinity probe, which possesses a benzophenone or a diazirine photophore on the 2-position of tautomycin, were prepared in order to prove the details of binding site to PP1. These photoaffinity probes were designed on the basis of the structure-activity relationship; thus, the diacid moiety is indispensable. The selective introduction of photolabeling units on the 2-position of tautomycin was achieved through the 2-oxime of tautomycin diacid.     

Synthesis and characterization of photolabeling probes of miltefosine

Miltefosine is an ether-phospholipid analogue showing remarkable anti-cancer and anti-leishmanial activity thanks to its cell membrane-targeting properties. In order to study the mechanisms responsible for the biological effects of miltefosine using a photolabeling approach, we designed, synthesized and characterized photolabeling probes for studying the effects of miltefosine. In these probes, the photoactivatable tetrafluorophenylazido group is incorporated either at the polar head or in the alkyl chain of miltefosine. The probes showed fast, clear-cut photochemical reactions, which suggests that they are promising tools for use in photolabeling studies.     

Synthesis of novel ginkgolide photoaffinity--biotin probes

Site-selective introduction of biotin and benzophenone probes onto ginkgolide scaffolds is described.     

Synthesis and characterization of the first metallacyclooctane

Ring closing metathesis (RCM) using Grubbs' 1st generation catalyst with cis-[L(2)Pt(CH(2)CH(2)CH[double bond, length as m-dash]CH(2))(CH(2)CH(2)CH(2)CH[double bond, length as m-dash]CH(2))] yields a platinacyclooctene which can be hydrogenated to the platinacyclooctane, L(2)Pt(CH(2))(7) [L(2) = Ph(2)PCH(2)CH(2)CH(2)PPh(2) (dppp) or Ph(2)PCH(2)CH(2)PPh(2) (dppe)] in high yield.     

Synthesis and metabolism of the first thia-bilirubin

A symmetrical C(10)-thiabilirubin analogue, 8,12-bis(2-carboxyethyl)-2,3,17,18-tetraethyl-7,13-dimethyl-10-thia-(21H,23H,24H)-bilin-1,19-dione (1), was synthesized from 8-(2-carboxyethyl)-2,3-diethyl-7-methyl-10H-dipyrrin-1-one in one step by reaction with sulfur dichloride. The thia-rubin exhibited the expected IR, UV-vis, and NMR spectroscopic properties, which are rather similar to those of mesobilirubin-XIIIalpha. Like bilirubin and mesobilirubin, 1 adopts an intramolecularly hydrogen-bonded conformation, shaped like a ridge-tile but with a steeper pitch. The longer C-S bond lengths and smaller bond angles at C-S-C, as compared to C-CH(2)-C, lead to an interplanar angle between the two dipyrrinones of only 74 degrees -or considerably less than that of bilirubin (approximately 100 degrees). On normal- and reversed-phase chromatography, 1 is substantially less polar than bilirubin. Despite this conformational distortion, 1 is metabolized in normal rats to acyl glucuronides, which are secreted into bile. In mutant (Gunn) rats lacking bilirubin glucuronosyl transferase, 1 (like bilirubin) was not excreted in bile.     

Synthesis of the second generation photoaffinity probes of tautomycin

Five photoaffinity probes of tautomycin, which possess an aromatic azide with linker attached to the 2-position of tautomycin, were prepared in order to study the binding site of tautomycin with protein phosphatase 1γ. The photoaffinity probes were synthesized by selectively introducing the photolabeling units onto the 2-position of tautomycin by using oxime chemistry.     

The use of fluorescent probes in immunochemistry

The limitations and advantages of particular dyes for labelling proteins and other biological materials are discussed. Methods available for conjugating dyes to proteins are outlined. Following a discussion of double labelling methods the use of photoactivatable fluorochromes and time resolved fluorescence methodologies are outlined. The reasons for the photoinstability of some fluorochromes are discussed and methods for overcoming the problem are described.