ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures

ProBiS-Database is a searchable repository of precalculated local structural alignments in proteins detected by the ProBiS algorithm in the Protein Data Bank. Identification of functionally important binding regions of the protein is facilitated by structural similarity scores mapped to the query protein structure. PDB structures that have been aligned with a query protein may be rapidly retrieved from the ProBiS-Database, which is thus able to generate hypotheses concerning the roles of uncharacterized proteins. Presented with uncharacterized protein structure, ProBiS-Database can discern relationships between such a query protein and other better known proteins in the PDB. Fast access and a user-friendly graphical interface promote easy exploration of this database of over 420 million local structural alignments. The ProBiS-Database is updated weekly and is freely available online at http://probis.cmm.ki.si/database.     

Identification of volatile lung cancer markers by gas chromatography–mass spectrometry: comparison with discrimination by canines

In this work, a chromatographic method for identification of volatile organic compounds was compared with canine recognition. Gas chromatography and mass spectrometry (GC-TOF MS) were used for determination of concentrations of trace gases present in human breath. The technique enables rapid determination of compounds in human breath, at the parts per billion level. Linear correlations were from 0.83-234.05 ppb, the limit of detection was the range 0.31-0.75 ppb, and precision, expressed as relative standard deviation (RSD), was less than 10.00 %. Moreover, trained dogs are able to discriminate breath samples of patients with diagnosed cancer. We found a positive correlation between dog indications and the ethyl acetate and 2-pentanone content of breath (r = 0.85 and r = 0.97, respectively). The methods presented for detection of lung cancer markers in exhaled air could be used as a potential non-invasive tool for screening. In addition, the canine method is relatively simple and inexpensive in comparison with chromatography.     

Photophysics of Schiff Bases: Theoretical Study of Salicylidene Methylamine

The proton‐transfer reaction in a model aromatic Schiff base, salicylidene methylamine (SMA), in the ground and in the lowest electronically‐excited singlet states, is theoretically analyzed with the aid of second‐order approximate coupled‐cluster model CC2, time‐dependent density functional theory (TD‐DFT) using the Becke, three‐parameter Lee–Yang–Parr (B3LYP) functional, and complete active space perturbation theory CASPT2 electronic structure methods. Computed vertical‐absorption spectra for the stable ground‐state isomers of SMA fully confirm the photochromism of SMA. The potential‐energy profiles of the ground and the lowest excited singlet state are calculated and four photophysically relevant isomeric forms of SMA; α, β, γ, and δ are discussed. The calculations indicate two S₁/S₀ conical intersections which provide non‐adiabatic gates for a radiationless decay to the ground state. The photophysical scheme which emerges from the theoretical study is related to recent experimental results obtained for SMA and its derivatives in the low‐temperature argon matrices (J. Grzegorzek, A. Filarowski, Z. Mielke, Phys. Chem. Chem. Phys. 2011 , 13, 16596–16605). Our results suggest that aromatic Schiff bases are potential candidates for optically driven molecular switches.     

Activity-based probes for studying the activity of flavin-dependent oxidases and for the protein target profiling of monoamine oxidase inhibitors

High profile: new activity-based protein profiling (ABPP) probes have been designed that target exclusively monoamine oxidases A and B within living cells (see picture; FAD=flavin adenine dinucleotide, FMN=flavin monodinucleotide). With these probes it could be shown that the MAO inhibitor deprenyl, which is in clinical use against Parkinson's disease, shows unique protein specificity despite its covalent mechanism of action.     

The oxidative degradation of dibenzoazepine derivatives by cerium(IV) complexes in acidic sulfate media

The kinetics of the oxidation of imipramine and desipramine using cerium(IV) complexes were studied in the presence of a large excess of azepine derivative (TCA) in acidic sulfate media using UV-Vis spectroscopy. The reaction proceeds via dibenzoazepine radical formation, identified by EPR measurements. The kinetics of the first degradation step were studied independently of the further slower degradation reactions. Linear dependences, with zero intercept, of the pseudo-first-order rate constants (k(obs)) on [TCA] were established for both dibenzoazepine radical formation processes. Rates of reactions decreased with increasing concentration of the H(+) ion indicating that cerium(IV) as well as both reductants exist in an equilibrium with their protolytic forms. The activation parameters for the degradation of dibenzoazepine derivatives in the first oxidation stage were as follows: ΔH(≠) = 39 ± 2 kJ mol(-1), ΔS(≠) = -28 ± 8 J K(-1) mol(-1) for imipramine and ΔH(≠) = 39 ± 2 kJ mol(-1), ΔS(≠) = -28 ± 6 J K(-1) mol(-1) for desipramine, respectively. Imipramine and desipramine radicals dimerized leading to an intermediate radical dimer, which decayed in a first-order consecutive decay process. These two further reactions proceed with rates which are characterized by non-linear dependences of the pseudo-first-order rate constants (k(obs)) on [TCA]. The degradation reaction of the intermediate radical dimer leads to an uncharged dimer as a final product. Mechanistic consequences of all the results are discussed.     

12-hydroxy-1-azaperylene-limiting case of the ESIPT system: enol-keto tautomerization in S0 and S1 states

Absorption, fluorescence, and fluorescence excitation spectra of 12-hydroxy-1-azaperylene (HAP) and 1-azaperylene were studied in n-alkane matrices at 5 K. Two stable tautomers of HAP, each of them in n-nonane embedded in two sites, were identified and attributed to the enol and keto forms. Theoretical calculations of the energy and vibrational structure of the spectra suggest that tautomer A, with the (0, 0) transition energy at 18,980 ± 10 cm(-1) (and 19,060 ± 10 cm(-1) in the high energy site), should be identified as the keto form, whereas tautomer B, with the (0, 0) energy at 19,200 ± 20 cm(-1) (19,290 ± 20 cm(-1)), as the enol form. Observation of absorption and fluorescence of both tautomeric forms and lack of large Stokes shift of fluorescence of the keto form classify HAP as the limiting case of the excited-state intramolecular proton transfer system.     

The application of an in vitro gastrointestinal extraction to assess the oral bioaccessibility of polycyclic aromatic hydrocarbons in soils from a former industrial site

The total and bioaccessible concentration of 16 polycyclic aromatic hydrocarbons (PAHs) in soil from a former industrial site was investigated. Typical total concentrations across the sampling sites ranged from 1.5 mg kg⁻¹ for acenaphthylene up to 243 mg kg⁻¹ for fluoranthene. The oral bioaccessibility of PAHs in soil was assessed using an in vitro gastrointestinal extraction (Fed Organic Estimation human Simulation Test, FOREhST method). The oral bioaccessibility data indicated that fluorene, phenanthrene, chrysene, indeno(1,2,3-cd)pyrene and dibenzo(a,h)anthracene had the highest % bioaccessible fraction (based on their upper 75th percentile values being >60%) while the other PAHs had lower % bioaccessible fractions (means ranging between 35 and 59%). Significantly lower bioaccessibilities were determined for naphthalene. With respect to method validation and inter-laboratory comparison, the total and bioaccessible concentrations of benzo(a)anthracene, benzo(b)anthracene, benzo(k)fluoranthene, benzo(a)pyrene, indeno(1,2,3-cd)pyrene and dibenzo(a,h)anthracene was compared to published data derived using the same samples. The total PAH concentrations at the site were compared with generic assessment criteria (GAC) using the residential land use scenario (with plant uptake at 6% soil organic matter). Concentrations of 7 of the PAHs investigated within the soils could lead to an unacceptable risk to human health at this site.     

Fluorescence-based active site probes for profiling deubiquitinating enzymes

Novel ubiquitin-based active site probes including a fluorescent tag have been developed and evaluated. A new, functionalizable electrophilic trap is utilized allowing for late stage diversification of the probe. Attachment of fluorescent dyes allowed direct detection of endogenous deubiquitinating enzyme (DUB) activities in cell extracts by in-gel fluorescence imaging.     

Design and synthesis of a bivalent ligand to explore the putative heterodimerization of the mu opioid receptor and the chemokine receptor CCR5

The bivalent ligand approach has been utilized not only to study the underlying mechanism of G protein-coupled receptors dimerization and/or oligomerization, but also to enhance ligand affinity and/or selectivity for potential treatment of a variety of diseases by targeting this process. Substance abuse and addiction have made both the prevention and the treatment of human immunodeficiency virus (HIV) infection more difficult to tackle. Morphine, a mu opioid receptor (MOR) agonist, can accelerate HIV infection through up-regulating the expression of the chemokine receptor CCR5, a well-known co-receptor for HIV invasion to the host cells and this has been extensively studied. Meanwhile, two research groups have described the putative MOR-CCR5 heterodimers in their independent studies. The purpose of this paper is to report the design and synthesis of a bivalent ligand to explore the biological and pharmacological process of the putative MOR-CCR5 dimerization phenomenon. The developed bivalent ligand thus contains two distinct pharmacophores linked through a spacer; ideally one of which will interact with the MOR and the other with the CCR5. Naltrexone and Maraviroc were selected as the pharmacophores to generate such a bivalent probe. The overall reaction route to prepare this bivalent ligand was convergent and efficient, and involved sixteen steps with moderate to good yields. The preliminary biological characterization showed that the bivalent compound 1 retained the pharmacological characteristics of both pharmacophores towards the MOR and the CCR5 respectively with relatively lower binding affinity, which tentatively validated our original molecular design.     

Multimodal Zr-Silicalite-1 zeolite nanocrystal aggregates with interconnected hierarchically micro-meso-macroporous architecture and enhanced mass transport property

Hierarchical porous architecture with interconnected trimodal micro-meso-macroporous systems constructed from uniform zeolite Zr-doped silicalite-1 nanocrystals has been prepared. The synthesis has been made by using glycerin as a reaction medium via a quasi-solid-state crystallization of hierarchically meso-macroporous zirconosilicate precursor under the effect of the structure directing agent TPAOH. The presence of glycerin is crucial in the synthesis systems to maintain the porous hierarchy. The pores inter-connectivity, Zr location in the framework, the acidity and the catalytic activity have been studied by laser-hyperpolarized (129)Xe NMR spectroscopy, UV-visible spectroscopy, temperature-programmed desorption of ammonia and the catalytic isopropylbenzene cracking probe reaction, respectively. The products possess well-defined macrochannels interconnected with mesopores located in the macropore walls, which in turn have been constructed from microporous MFI-type zeolite units. (129)Xe NMR study indicated that the hierarchically micro-, meso-, macro-pore systems are homogeneously distributed throughout the final materials and well interconnected, which is important for molecular diffusion. The TPD-NH(3) investigation revealed that the hierarchically micro-meso-macroporous materials constructed from zeolite Zr-Silicalite-1 nanocrystals present strong acidity.