MassUntangler: a novel alignment tool for label-free liquid chromatography-mass spectrometry proteomic data.

Liquid chromatography-mass spectrometry (LC-MS) has become an important analytical tool for quantitative proteomics and biomarker discovery. In the label-free differential LC-MS approach computational methods are required for an accurate alignment of peaks extrapolated from the experimental raw data accounting for retention time and m/z signals intensity, which are strongly affected by sample matrix and instrumental performance. A novel procedure "MassUntangler" for pairwise alignment has been developed, relying on a pattern-based matching algorithm integrated with filtering algorithms in a multi-step approach. The procedure has been optimized employing a two-step approach. Firstly, low-complexity LC-MS data derived from the enzymatic digestion of two standard proteins have been analyzed. Then, the algorithm's performance has been evaluated by comparing the results with other achieved using state-of-the-art alignment tools. In the second step, our algorithm has been used for the alignment of high-complexity LC-MS data consisting of peptides obtained by an Escherichia coli lysate available from a public repository previously used for the comparison of other alignment tools. MassUntangler gave excellent results in terms of precision scores (from 80% to 93%) and recall scores (from 68% to 89%), showing performances similar and even better than the previous developed tools. Considering the mass spectrometry sensitivity and accuracy, this approach allows the identification and quantification of peptides present in a biological sample at femtomole level with high confidence. The procedure's capability of aligning LC-MS data previously corrected for distortion in retention time has been studied through a hybrid approach, in which MassUntangler was interfaced with the OpenMS TOPP tool MapAligner. The hybrid aligner yielded better results, showing that an integration of different bioinformatic approaches for accurate label-free LC-MS data alignment should be used.

Photostability studies on the furosemide-triamterene drug association.

The photostability of the diuretic drugs triamterene and furosemide, individually and combined, was evaluated. Spectrophotometric, spectrofluorimetric and chromatographic (HPLC) methods were applied to monitor the drug photodegradation. Furosemide was confirmed to be highly photolable in both pH 7.4 solution and methanol. Differently triamterene proved to be highly fluorescent (emission quantum yield: 0.9 in methanol and 0.8 in pH 7.4 solution), but essentially photostable (photochemical reaction quantum yield: congruent with 5 x 10(-4)) under exposure at 365 and 313 nm radiations. When the combined drugs in pH 7.4 solutions were exposed to 365 nm radiations a significant photoprotective effect of triamterene on furosemide was observed. The photoreactivity of the drugs was exploited to develop an HPLC method involving a post-column on-line photochemical derivatization useful to confirm the analyte identity in a commercial dosage form (tablets). The commercial product, containing the combined drugs, proved to be photostable also after long (65 h) light exposure.

Artificial molecular-level machines: which energy to make them work?

The concept of machine can be extended to the molecular level by designing and synthesizing (supra)molecular species capable of performing mechanical movements. The energy needed to make a machine work can be supplied as chemical energy, electrical energy, or light. When a chemical "fuel" is used, waste products are formed, whereas this is not the case when suitable photochemical or electrochemical energy inputs are employed. A number of elementary functions performed by molecular-level machines are illustrated, and more complex ones are foreseen.

Studies on the photostability and in vitro phototoxicity of Labetalol.

The purpose of this study was to obtain information on the photochemical and phototoxic properties of Labetalol, a beta-blocker drug. Preliminary information on the drug photoreactivity was achieved using a flow system with a photochemical reactor on-line with a diode array detection system. Photophysical and photochemical investigations on the drug were performed in aqueous solutions at different pH values using spectrophotometric and fluorimetric methods; the photodegradation quantum yield was found to be 2.7 x 10(-3) at pH 5.8 and 1.5 x 10(-2) at pH 11.5. Forced photodegradation of labetalol solutions under exposure to UVA--UVB radiations (xenon arc lamp) was monitored by reversed-phase liquid chromatography. The main photodegradation products were isolated and characterized by NMR and mass spectrometry; labetalol was found to give 3-amino-1-phenylbutane and salicylamide-4-carboxaldehyde as the main photoproducts. Preliminary phototoxic testings on human keratinocyte cultures were performed evaluating the viability of the cells by the neutral-red uptake assay; mutagenic and photomutagenicity tests were also carried out based on Salmonella typhimurium strains. As a result, labetalol was found to be photolabile,mainly in alkaline medium, but evidences of significant phototoxic and photomutagenic effects by the drug were not observed.

A photochemically driven molecular-level abacus

A molecular-level abacus-like system driven by light inputs has been designed in the form of a [2]rotaxane, comprising the pi-electron-donating macrocyclic polyether bis-p-phenylene-34-crown-10 (BPP34C10) and a dumbbell-shaped component that contains 1) a Ru(II) polypyridine complex as one of its stoppers in the form of a photoactive unit, 2) a p-terphenyl-type ring system as a rigid spacer, 3) a 4,4'-bipyridinium unit and a 3,3'-dimethyl-4,4'-bipyridinium unit as pi-electron-accepting stations, and 4) a tetraarylmethane group as the second stopper. The synthesis of the [2]rotaxane was accomplished in four successive stages. First of all, the dumbbell-shaped component of the [2]rotaxane was constructed by using conventional synthetic methodology to make 1) the so-called "west-side" comprised of the Ru(II) polypyridine complex linked by a bismethylene spacer to the p-terphenyl-type ring system terminated by a benzylic bromomethyl function and 2) the so-called "east-side" comprised of the tetraarylmethane group, attached by a polyether linkage to the bipyridinium unit, itself joined in turn by a trismethylene spacer to an incipient 3,3'-dimethyl-4,4'-bipyridinium unit. Next, 3) the "west-side" and "east-side" were fused together by means of an alkylation to give the dumbbell-shaped compound, which was 4) finally subjected to a thermodynamically driven slippage reaction, with BPP34C10 as the ring, to afford the [2]rotaxane. The structure of this interlocked molecular compound was characterized by mass spectrometry and NMR spectroscopy, which also established, along with cyclic voltammetry, the co-conformational behavior of the molecular shuttle. The stable translational isomer is the one in which the BPP34C10 component encircles the 4,4'-bipyridinium unit, in keeping with the fact that this station is a better pi-electron acceptor than the other station. This observation raises the question- can the BPP34C10 macrocycle be made to shuttle between the two stations by a sequence of photoinduced electron transfer processes? In order to find an answer to this question, the electrochemical, photophysical, and photochemical (under continuous and pulsed excitation) properties of the [2]rotaxane, its dumbbell-shaped component, and some model compounds containing electro- and photoactive units have been investigated. In an attempt to obtain the photoinduced abacus-like movement of the BPP34C10 macrocycle between the two stations, two strategies have been employed-one was based fully on processes that involved only the rotaxane components (intramolecular mechanism), while the other one required the help of external reactants (sacrificial mechanism). Both mechanisms imply a sequence of four steps (destabilization of the stable translational isomer, macrocyclic ring displacement, electronic reset, and nuclear reset) that have to compete with energy-wasteful steps. The results have demonstrated that photochemically driven switching can be performed successfully by the sacrificial mechanism, whereas, in the case of the intramolecular mechanism, it would appear that the electronic reset of the system is faster than the ring displacement.

Tetrathiafulvalenenaphthalenophanes: planar chirality and cis/trans photoisomerization

A cyclophane incorporating one 1,5-dioxynaphthalene ring system and one tetrathiafulvalene (TTF) unit bridged by [SCH(2)CH(2)O] linkages has been synthesized. In this cyclophane, the TTF unit can adopt either cis or trans configurations. In addition, the 1, 5-dioxynaphthalene ring system imposes one element of planar chirality on this cyclophane. A second element of planar chirality is introduced by the trans form of the TTF unit. Thus, the cyclophane exists in diastereoisomeric forms as three pairs of enantiomers. The enantiomeric pairs associated with the cis form of the TTF unit, as well as one of those associated with the trans form, have been isolated by crystallization, and their structures assigned in the solid state by single-crystal X-ray analyses. In solution, cis/trans isomerization occurs when either the cis or the trans form of the cyclophane is exposed to light. The photoisomerization reaction can be followed by (1)H NMR and UV-vis spectroscopies, as well as by HPLC. The photoisomerization quantum yield has been measured at two different excitation wavelengths (406 and 313 nm). In both cases, the trans --> cis process (Phi = 0.20 at 406 nm) is much more efficient than the reverse cis --> trans process (Phi = 0.030 at 406 nm). Since the absorption spectra of the trans and cis isomers are different and the quantum yield of the trans --> cis photoisomerization reaction depends on the excitation wavelength, the mole fraction of the two diastereoisomers present at the photostationary state depends on the wavelength of the exciting light. No isomerization occurs when the solutions, regardless of the mole fraction of the two diastereoisomers, are stored in the dark.