Catalyst- and excess reagent recycling in aza-Michael additions.

16α-Azolyl-pregnenolone derivatives were prepared via 2-butyl-1,1,3,3-tetramethylguanidine (n-Bu-TMG) catalysed aza-Michael addition of 16-dehydropregnenolone (16-DHP) carried out in [bmim][BF4]. The application of the guanidine base and the imidazolium ionic liquid made it possible to recycle not only the catalyst/solvent mixture but also the excess of the N-heterocyclic reagent. By the introduction of CO2 at the end of the reaction, both the guanidine base and the unreacted (excess) reagent could be converted into ionic species that remained dissolved in the ionic liquid phase, while the steroid components were extracted with an apolar solvent. After the removal of CO2, the experiment could be repeated by the addition of the steroid substrate and only an equimolar amount of the N-heterocycle. The methodology was successfully applied to a number of N-heterocycles, such as imidazole, pyrazole, 1,2,3- and 1,2,4-triazoles, and benzimidazole. Indazole and indole could also be converted into the corresponding products, but a stronger base had to be used to obtain a recyclable system.

Very Low-Pressure CID Experiments: High Energy Transfer and Fragmentation Pattern at the Single Collision Regime.

We have performed CID experiments on a triple quadrupole instrument, lowering the collision gas pressure by 50 times compared to its conventional value. The results show that at very low-collision gas pressure, single collisions dominate the spectra. Indirectly, these results suggest that under conventional conditions, 20-50 collisions may be typical in CID experiments. The results show a marked difference between low- and high-pressure CID spectra, the latter being characterized in terms of 'slow heating' and predominance of consecutive reactions. The results indicate that under single collision conditions, the collisional energy transfer efficiency is very high: nearly 100% of the center of mass kinetic energy is converted to internal energy.

Fragment-Sized and Bidentate (Immuno)Proteasome Inhibitors Derived from Cysteine and Threonine Targeting Warheads.

Constitutive- and immunoproteasomes are part of the ubiquitin-proteasome system (UPS), which is responsible for the protein homeostasis. Selective inhibition of the immunoproteasome offers opportunities for the treatment of numerous diseases, including inflammation, autoimmune diseases, and hematologic malignancies. Although several inhibitors have been reported, selective nonpeptidic inhibitors are sparse. Here, we describe two series of compounds that target both proteasomes. First, benzoxazole-2-carbonitriles as fragment-sized covalent immunoproteasome inhibitors are reported. Systematic substituent scans around the fragment core of benzoxazole-2-carbonitrile led to compounds with single digit micromolar inhibition of the ß5i subunit. Experimental and computational reactivity studies revealed that the substituents do not affect the covalent reactivity of the carbonitrile warhead, but mainly influence the non-covalent recognition. Considering the small size of the inhibitors, this finding emphasizes the importance of the non-covalent recognition step in the covalent mechanism of action. As a follow-up series, bidentate inhibitors are disclosed, in which electrophilic heterocyclic fragments, i.e., 2-vinylthiazole, benzoxazole-2-carbonitrile, and benzimidazole-2-carbonitrile were linked to threonine-targeting (R)-boroleucine moieties. These compounds were designed to bind both the Thr1 and ß5i-subunit-specific residue Cys48. However, inhibitory activities against (immuno)proteasome subunits showed that bidentate compounds inhibit the ß5, ß5i, ß1, and ß1i subunits with submicromolar to low-micromolar IC50 values. Inhibitory assays against unrelated enzymes showed that compounds from both series are selective for proteasomes. The presented nonpeptidic and covalent derivatives are suitable hit compounds for the development of either ß5i-selective immunoproteasome inhibitors or compounds targeting multiple subunits of both proteasomes.

Cysteine specific bioconjugation with benzyl isothiocyanates.

Protein labelling has a wide variety of applications in medicinal chemistry and chemical biology. In addition to covalent inhibition, specific labelling of biomolecules with fluorescent dyes is important in both target discovery, validation and diagnostics. Our research was conducted through the fragment-based development of a new benzyl-isothiocyanate-activated fluorescent dye based on the fluorescein scaffold. This molecule was evaluated against fluorescein isothiocyanate, a prevalent labelling agent. The reactivity and selectivity of phenyl- and benzyl isothiocyanate were compared at different pHs, and their activity was tested on several protein targets. Finally, the clinically approved antibody trastuzumab (and it's Fab fragment) were specifically labelled through reaction with free cysteines reductively liberated from their interchain disulfide bonds. The newly developed benzyl-fluorescein isothiocyanate and its optimized labelling protocol stands to be a valuable addition to the tool kit of chemical biology.

Site-specific N-glycosylation of HeLa cell glycoproteins.

We have characterized site-specific N-glycosylation of the HeLa cell line glycoproteins, using a complex workflow based on high and low energy tandem mass spectrometry of glycopeptides. The objective was to obtain highly reliable data on common glycoforms, so rigorous data evaluation was performed. The analysis revealed the presence of a high amount of bovine serum contaminants originating from the cell culture media - nearly 50% of all glycans were of bovine origin. Unaccounted, the presence of bovine serum components causes major bias in the human cellular glycosylation pattern; as is shown when literature results using released glycan analysis are compared. We have reliably identified 43 (human) glycoproteins, 69 N-glycosylation sites, and 178 glycoforms. HeLa glycoproteins were found to be highly (68.7%) fucosylated. A medium degree of sialylation was observed, on average 46.8% of possible sialylation sites were occupied. High-mannose sugars were expressed in large amounts, as expected in the case of a cancer cell line. Glycosylation in HeLa cells is highly variable. It is markedly different not only on various proteins but also at the different glycosylation sites of the same protein. Our method enabled the detailed characterization of site-specific N-glycosylation of several glycoproteins expressed in HeLa cell line.

Isolation and structural elucidation of a novel brunnein-type antioxidant ß-carboline alkaloid from Cyclocybe cylindracea.

Effect-directed isolation of free radical scavengers from the methanol extract of the freeze-dried fruiting bodies of the cultivated basidiomycetous mushroom, black poplar (Cyclocybe cylindracea), yielded a ß-carboline alkaloid. Its structure was determined based on ESI-TOF-MS/MS, NMR and circular dichroism spectra by comparison with published data. The compound, identified as the C1-S diastereomer of brunnein B, exhibited explicit radical scavenging activity (EC50 = 119.1 ±â€¯1.2 µg/mL). The quantity of the active component was determined with HPLC-MS in the fruiting body (36.2 ±â€¯2.8 ng/g DW, dry weight) and its different tissues such as peel (94.7 ±â€¯1.9 ng/g DW), inner cap (90.5 ±â€¯1.3 ng/g DW), gills (71.5 ±â€¯0.6 ng/g DW), and stipe (162.2 ±â€¯1.7 ng/g DW). It is a ß-carboline alkaloid that was not reported previously.

Mapping the tandem mass spectrometric characteristics of citrulline-containing peptides.

RATIONALE: Protein citrullination (deimination) is a post-translational modification of proteins converting arginine(s) into citrulline(s). "Overcitrullination" could be associated with severe pathological conditions. Mass spectrometric analysis of modified proteins is hindered by several problems. A comprehensive study of the fragmentation of deiminated peptides is not yet available. In this paper we have made an attempt to describe the characteristics of these processes, based on the studies of epitope model oligopeptides derived from clinically relevant proteins. METHODS: Solutions of purified model peptides containing either one or two citrulline residues as well as their native variants were injected directly into the electrospray source of a high accuracy and resolution quadrupole-time-of-flight instrument and were analysed by tandem mass spectrometry using low-energy collision-induced dissociation. RESULTS: Loss of isocyanic acid from citrulline residues is a preferred fragmentation route for deiminated peptides, which yields ornithine residues in the sequence. However, simultaneous detection of both the isocyanic acid loss and sequence fragments is often compromised. A preferential cleavage site was observed between citrulline and any other following amino acids yielding intensive complementary b- and y-type ions. Also, citrulline positioned at the C-termini displays a preferential cleavage N-terminal to this residue yielding characteristic y1 ions. These phenomena are described here for the first time and are referred to as the "citrulline effect". CONCLUSIONS: We found that the citrulline effect is very pronounced and could be used as a complementary tool for the confirmation of modification sites in addition to losses of isocyanic acids from the protonated molecules or from fragment ions. Low collision energy applied to peptide ions having partially mobile protons reveals the site of modification by generating specific and intensive fragments of the sequence. On the other hand, fragmenting precursor ions with mobile protons usually allows full sequence coverage, although citrulline-specific fragments may exhibit lower intensities compared to other fragments.

Synthesis of 16α-amino-pregnenolone derivatives via ionic liquid-catalyzed aza-Michael addition and their evaluation as C17,20-lyase inhibitors.

Aza-Michael addition of 16-dehydropregnenolone was studied in the presence of a basic ionic liquid, [DBU][OAc] as catalyst and solvent. The reaction was carried out using different primary and secondary amines as N-nucleophiles. The products were obtained in moderate to good yields and were characterized by 1H and 13C NMR, MS and IR. The ionic liquid was found to be an efficient and recyclable catalyst that was reused five times. The products were investigated for the inhibition of in vitro C17,20-lyase activity and displayed moderate inhibitory effect.

Synthesis of novel 13α-18-norandrostane-ferrocene conjugates via homogeneous catalytic methods and their investigation on TRPV1 receptor activation.

13α-Steroid-ferrocene derivatives were synthesized via two reaction pathways starting from an unnatural 16-keto-18-nor-13α-steroid. The unnatural steroid was converted to ferrocene derivatives via copper-catalyzed azide-alkyne cycloaddition or palladium-catalyzed aminocarbonylation. 16-Azido- and 16-N-(prop-2-ynyl)-carboxamido-steroids were synthesized as starting materials for azide-alkyne cycloaddition with the appropriate ferrocene derivatives. Based on our earlier work, aminocarbonylation of 16-iodo-16-ene and 16-iodo-15-ene derivatives was studied with ferrocenylmethylamine. The new products were obtained in moderate to good yields and were characterized by (1)H and (13)C NMR, IR and MS. The solid state structure of the starting material 13α-18-norandrostan-16-one and two carboxamide products were determined by X-ray crystallography. Evidences were provided that the N-propargyl-carboxamide compound as well as its ferrocenylmethyltriazole derivative are able to decrease the activation of TRPV1 receptor on TRG neurons.

HPLC enrichment/isolation of proteins for post-translational modification studies from complex mixtures.

The paper describes a macroporous RP-HPLC method for separation and isolation/enrichment of proteins from complex mixtures. The method is robust and efficient; using 2.1 or 4.6mm diameter columns provides sufficient material for subsequent proteomic analysis. The main advantage of the method is that most protein variants are isolated in the same fraction, as separation is not based on differences in isoelectric point. This is highly advantageous for studying complex mixtures and post-translational modifications. Examples related to glycosylation analysis are discussed in detail.

Determination of energy metabolites in cancer cells by porous graphitic carbon liquid chromatography electrospray ionization mass spectrometry for the assessment of energy metabolism.

A high performance liquid chromatography (HPLC) tandem mass spectrometric (MS/MS) method has been developed for the simultaneous determination of fifteen glucose, or acetate derived metabolites isolated from tumor cells. Glycolytic and tricarboxylic acid (TCA) cycle metabolites as well as acidic amino acids were separated on a HPLC porous graphitic carbon (PGC) column and simultaneously determined by means of triple quadrupole MS/MS using multiple reaction monitoring (MRM). Target compounds were eluted within 10 min with 8% v/v formic acid as an electronic modifier added to a 4:1 v/v methanol water mobile phase. The calibration is linear in the 1-100 µM concentration range for each analyte. The limit of detection ranges between 0.39 and 2.78 µM for the analytes concerned. To test the PGC-HPLC-MS/MS method in metabolomic studies, ZR-75.1 human mammary adenocarcinoma cells were labeled with U-(13)C glucose or 1-(13)C acetate. Applying the MRM mode, the incorporation of (13)C into metabolites, isolated from the tumor cells, and derived from glucose or acetate, could be properly identified.

Interactions of oligomers of organic polyethers with histidine amino acid.

RATIONALE: Knowledge on noncovalent intermolecular interactions of organic polyethers with amino acids is essential to gain a better understanding on how polymers assemble in organic nanoparticles which are promising for drug delivery and cryoprotection. The main objective of the present study was to determine how polyethers assemble around ionizable amino acids such as histidine. METHODS: Electrospray mass spectrometry was applied to probe the interactions in model systems consisting of polyethylene glycol PEG-400 or oxyethylated glycerol OEG-5 and amino acid histidine hydrochloride. Molecular dynamics simulation was utilized to visualize the structure of complexes of polyether oligomers with histidine in different charge states. RESULTS: Stable gas-phase clusters composed of polyether oligomers (PEG(n), OEG(n)) with protonated histidine--PEG(n)•His•H(+), OEG(n)•His•H(+), OEG(n)•OEG(m)•His•H(+) and chlorine counterion--PEG(n)•Cl(-), OEG(n)•Cl(-), were observed under electrospray conditions. Molecular dynamics simulation of representative polyether-histidine complexes revealed the stabilization of oligomers by multiple hydrogen and coordination bonds whereby charged groups are wrapped by the polymeric chains. CONCLUSIONS: The self-organization of polyether chains around the protonated imidazole group of histidine was revealed. This finding should be considered when modelling a pegylated protein structure and polyether-based organic nanoparticles.

Synthesis of steroid-ferrocene conjugates of steroidal 17-carboxamides via a palladium-catalyzed aminocarbonylation--copper-catalyzed azide-alkyne cycloaddition reaction sequence.

Steroids with the 17-iodo-16-ene functionality were converted to ferrocene labeled steroidal 17-carboxamides via a two step reaction sequence. The first step involved the palladium-catalyzed aminocarbonylation of the alkenyl iodides with prop-2-yn-1-amine as the nucleophile in the presence of the Pd(OAc)(2)/PPh(3) catalyst system. In the second step, the product N-(prop-2-ynyl)-carboxamides underwent a facile azide-alkyne cycloaddition with ferrocenyl azides in the presence of CuSO(4)/sodium ascorbate to produce the steroid-ferrocene conjugates. The new compounds were obtained in good yield and were characterized by (1)H and (13)C NMR, IR, MS and elemental analysis.

Sterically-directed consecutive and size-selective self-assembly of palladium diphosphane complexes with an Ar-BIAN ligand: unexpected formation of pentameric and hexameric aggregates.

The coordination properties of N,N'-bis[4-(4-pyridyl)phenyl]acenaphthenequinonediimine (L(1)) and N,N'-bis[4-(2-pyridyl)phenyl]acenaphthenequinonediimine (L(2)) were investigated in self-assembly with palladium diphosphane complexes [Pd(P;P)(H(2)O)(2)](OTf)(2) (OTf = triflate) by using various analytical techniques, including multinuclear ((1)H, (15)N, and (31)P) NMR spectroscopy and mass spectrometry (P;P = dppp, dppf, dppe; dppp = bis(diphenylphosphanyl)propane, dppf = bis(diphenylphosphanyl)ferrocene, and dppe = bis(diphenylphosphanyl)ethane). Beside the expected trimeric and tetrameric species, the interaction of an equimolar mixture of [Pd(dppp)](2+) ions and L(1) also generates pentameric aggregates. Due to the E/Z isomerism of L(1), a dimeric product was also observed. In all of these species, which correspond to the general formula [Pd(dppp)L(1)](n)(OTf)(2n) (n = 2-5), the L(1) ligand is coordinated to the Pd center only through the terminal pyridyl groups. Introduction of a second equivalent of the [Pd(dppp)](2+) tecton results in coordination to the internal, sterically more encumbered chelating site and induces enhancement of the higher nuclearity components. The presence of higher-order aggregates (n = 5, 6), which were unexpected for the interaction of cis-protected palladium corners with linear ditopic bridging ligands, has been demonstrated both by mass-spectrometric and DOSY NMR spectroscopic analysis. The sequential coordination of the [Pd(dppp)](2+) ion is attributed to the dissimilar steric properties of the two coordination sites. In the self-assembled species formed in a 1:1:1 mixture of [Pd(dppp)](2+)/[Pd(dppe)](2+)/L(1), the sterically more demanding [Pd(dppp)](2+) tectons are attached selectively to the pyridyl groups, whereas the more hindered imino nitrogen atoms coordinate the less bulky dppe complexes, thus resulting in a sterically directed, size-selective sorting of the metal tectons. The propensity of the new ligands to incorporate hydrogen-bonded solvent molecules at the chelating site was confirmed by X-ray diffraction studies.

Sensitivity of redox reactions of dyes to variations of conditions created in mass spectrometric experiments.

Redox behaviour of four imidazophenazine dye derivatives under mass spectrometric conditions of matrix-assisted laser desorption/ionization (MALDI), laser desorption/ionization (LDI) from metal and graphite surface, electrospray, low temperature secondary ion mass spectrometry (LT SIMS) and fast atom bombardment (FAB) was studied and distinctions in the reduction-dependent spectral patterns were analyzed from the point of view of different quantities of protons and electrons available for reduction in different techniques. The reduction products [M + 2H](+*), [M + 3H](+) and M(-*), [M + H](-) were observed in the positive and negative ion modes, respectively, which permitted to suggest independent occurrence of reduction and protonation/deprotonation processes. LDI from graphite substrate was the only technique that allowed us to obtain abundant negative ions of all dye derivatives. The yield of field ionization (FI) or field desorption (FD) mechanism to ion formation under LDI from rough graphite surface has been addressed. The sensitivity of reduction of the dyes to variation of reduction-initiating agents confirms high redox activity of the dyes essential for their functioning in natural and artificial systems.

A new cyclization to fused pyrazoles tunable for pericyclic or pseudopericyclic route: an experimental and theoretical study.

2-Pyrazinyl (2) and 3-pyridazinylketone arylhydrazones (6) and their benzologues undergo a ring closure reaction to yield pyrazolo[3,4- b]pyrazines (4) and pyrazolo[4,3- c]pyridazines (7), respectively, in acceptable to good yields. The reaction was found to be accelerated by using acidic or basic conditions. Quantum chemical calculations suggest the key step of the mechanism to be a direct cyclization; analysis of aromaticity based on computed magnetic properties revealed its medium-dependent pericyclic or pseudopericyclic character. The cyclization reaction has also been extended for the synthesis of related ring systems ( 9, 12, 14).

Synthesis and application of a fluorous Lawesson's reagent: convenient chromatography-free product purification.

[reaction: see text] A fluorous analogue of Lawesson's reagent for thionation of carbonyl compounds has been developed and its use demonstrated on a series of amides, esters, and ketones. The separation of the Lawesson's reagent-derived byproducts can be achieved by a simple fluorous solid-phase extraction.

Recoverable fluorous CBS methodology for asymmetric reduction of ketones.

[reaction: see text]. An operationally simple and recoverable fluorous CBS methodology was developed. The in situ-generated fluorous oxazaborolidine efficiently catalyzed the reduction of ketones with high enantioselectivity and reactivity. The subsequent recycling of the fluorous prolinol precatalyst was achieved by fluorous solid-phase extraction.

Mass spectrometric and quantum-chemical study on the structure, stability, and chirality of protonated serine dimers.

Stability and structure of homo- and heterochiral protonated serine (Ser) dimers were investigated by a combination of mass spectrometry and ab initio quantum chemical calculations. This established that the energy difference between the most stable homo- and heterochiral forms is very small: tandem mass spectrometry with Cooks' kinetic method yielded a negligible difference in Gibbs free energy (0.2+/-0.2 kJ mol(-1)). The various isomeric forms of (Ser)2 H+ and their energetics were determined by extensive electronic-structure calculations, which yielded homo- and heterochiral forms of the isomers with distinctly different relative energies. The most stable homochiral isomer is stabilized by two hydrogen bonds and is far more stable than any other homochiral isomer. The most stable heterochiral isomer has completely different features, and it is characterized by a salt-bridge structure. This clearly shows that salt-bridge structures do exist in the gas phase even in comparatively small molecules and in the absence of particularly basic or acidic functional groups.

On the stability of the organic dication of the bisquaternary ammonium salt decamethoxinum under liquid secondary ion mass spectrometry.

In the course of a liquid secondary ion mass spectrometric (SIMS) investigation on a bisquaternary ammonium antimicrobial agent, decamethoxinum, unusual pathways of fragmentation of the organic dication M2+ of this bisquaternary salt, with preservation of the doubly charged state of the fragments, were observed. To reveal the structural and electronic parameters of decamethoxinum, which are responsible for the stabilization of its organic dication in the gas phase, a comprehensive SIMS study using metastable decay, collision-induced dissociation and kinetic energy release techniques complemented by ab initio quantum chemical calculations was performed. Pathways of fragmentation of two main precursors originating from decamethoxinum-organic dication M2+ and its cluster with a Cl- counterion [M.Cl]+-and a number of their primary fragments were established and systematized. Differences in the pathways of fragmentation of M2+ and [M.Cl]+ were revealed: the main directions of [M.Cl]+ decay involve dequaternization similar to thermal degradation of this compound, while in M2+ fragmentation via loss of one and two terminal radicals with preservation of the doubly charged state of the fragments dominates over charge separation processes. It was shown that pairing of the dication with a Cl- anion does not preserve the complex from fragmentation via separation of two positively charged centers or neutralization (dequaternization) of one such center. At the same time the low abundance of M2+ in the SIMS spectra is to a larger extent controlled by a probability of M2+ association with an anion than by the decay of the dication per se. Quantum chemical calculations of the structural and electronic parameters of the decamethoxinum dication have revealed at least three features which can provide stabilization of the doubly charged state. Firstly, in the most energetically favorable stretch conformation the distance between the quaternary nitrogens (rN1-N2=1.39 nm) is relatively large. Secondly, an intramolecular solvation of quaternary groups by carbonyl oxygens of the adjacent groups of the dication occurs, which contribute to structural stabilization. Thirdly, an important feature of the electronic structure of the dication is the presence of a partial negative charge on the nitrogen atoms and smearing of a positive charge mainly over the hydrogens of alkyl groups attached to the quaternary nitrogens, which reduces the net repulsion between the quaternary groups. The possible influence of charge smearing on the kinetic energy released on the dication fragmentation is discussed.