On Entropy-Based Molecular Descriptors: Statistical Analysis of Real and Synthetic Chemical Structures

This paper presents an analysis of entropy-based molecular descriptors. Specifically, we use real chemical structures, as well as synthetic isomeric structures, and investigate properties of and among descriptors with respect to the used data set by a statistical analysis. Our numerical results provide evidence that synthetic chemical structures are notably different to real chemical structures and, hence, should not be used to investigate molecular descriptors. Instead, an analysis based on real chemical structures is favorable. Further, we find strong hints that molecular descriptors can be partitioned into distinct classes capturing complementary information.

PARP inhibition induces BAX/BAK-independent synthetic lethality of BRCA1-deficient non-small cell lung cancer

Evasion of apoptosis contributes to both tumourigenesis and drug resistance in non-small cell lung carcinoma (NSCLC). The pro-apoptotic BCL-2 family proteins BAX and BAK are critical regulators of mitochondrial apoptosis. New strategies for targeting NSCLC in a mitochondria-independent manner should bypass this common mechanism of apoptosis block. BRCA1 mutation frequency in lung cancer is low; however, decreased BRCA1 mRNA and protein expression levels have been reported in a significant proportion of lung adenocarcinomas. BRCA1 mutation/deficiency confers a defect in homologous recombination DNA repair that has been exploited by synthetic lethality through inhibition of PARP (PARPi) in breast and ovarian cells; however, it is not known whether this same synthetic lethal mechanism exists in NSCLC cells. Additionally, it is unknown whether the mitochondrial apoptotic pathway is required for BRCA1/PARPi-mediated synthetic lethality. Here we demonstrate that silencing of BRCA1 expression by RNA interference sensitizes NSCLC cells to PARP inhibition. Importantly, this sensitivity was not attenuated in cells harbouring mitochondrial apoptosis block induced by co-depletion of BAX and BAK. Furthermore, we demonstrate that BRCA1 inhibition cannot override platinum resistance, which is often mediated by loss of mitochondrial apoptosis signalling, but can still sensitize to PARP inhibition. Finally we demonstrate the existence of a BRCA1-deficient subgroup (11-19%) of NSCLC patients by analysing BRCA1 protein levels using immunohistochemistry in two independent primary NSCLC cohorts. Taken together, the existence of BRCA1-immunodeficient NSCLC suggests that this molecular subgroup could be effectively targeted by PARP inhibitors in the clinic and that PARP inhibitors could be used for the treatment of BRCA1-immunodeficient, platinum-resistant tumours. Copyright (C) 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Use of synthetic peptides to locate novel integrin alpha(2)beta(1)-binding motifs in human collagen III

A set of 57 synthetic peptides encompassing the entire triple-helical domain of human collagen III was used to locate binding sites for the collagen-binding integrin alpha(2)beta(1). The capacity of the peptides to support Mg2+-dependent binding of several integrin preparations was examined. Wild-type integrins (recombinant alpha(2) I-domain, alpha(2)beta(1) purified from platelet membranes, and recombinant soluble alpha(2)beta(1) expressed as an alpha(2)-Fos/beta(1)-Jun heterodimer) bound well to only three peptides, two containing GXX'GER motifs (GROGER and GMOGER, where O is hydroxyproline) and one containing two adjacent GXX'GEN motifs (GLKGEN and GLOGEN). Two mutant alpha(2) I-domains were tested: the inactive T221A mutant, which recognized no peptides, and the constitutively active E318W mutant, which bound a larger subset of peptides. Adhesion of activated human platelets to GER-containing peptides was greater than that of resting platelets, and HT1080 cells bound well to more of the peptides compared with platelets. Binding of cells and recombinant proteins was abolished by anti-alpha(2) monoclonal antibody 6F1 and by chelation of Mg2+. We describe two novel high affinity integrin-binding motifs in human collagen III (GROGER and GLOGEN) and a third motif (GLKGEN) that displays intermediate activity. Each motif was verified using shorter synthetic peptides.

Developments in the production of biological and synthetic binders for immunoassay and sensor-based detection of small molecules

The need for chemical and biological entities of predetermined selectivity and affinity towards target analytes is greater than ever, in applications such as environmental monitoring, bioterrorism detection and analysis of natural toxin contaminants in the food chain.

Protein surface recognition using geometrically pure Ru(II) tris(bipyridine) derivatives

This manuscript illustrates that the geometric arrangement of protein-binding groups around a ruthenium(II) core leads to dramatic differences in cytochrome c (cyt c) binding highlighting that it is possible to define synthetic receptors with shape complementarity to protein surfaces.

Receptor binding and biologic activity of synthetic ET-1 peptides in the retinal pericyte

Purpose. The purpose of this study was to examine the effect of synthetic endothelin (ET)-1 peptides with antigenic potential for binding and biologic activity using an in vitro model of microvascular pericytes.

Confirmation of synthetic glucocorticoids with liquid chromatography/mass spectrometry: Organization and results of an international interlaboratory comparison test

Within the framework of a European Union (EU) research project entitled

Performance and characteristics of platinum, palladium/rhodium and palladium automotive catalysts when subjected to ethanol, acetaldehyde and a synthetic E85 exhaust gas mixture

The performance optimisation of automotive catalysts has been the focus of a great deal of research for many years as the automotive industry has endeavored to reduce the emission of toxic and pollutant gases generated from internal combustion engines. Just as the emissions from diesel and gasoline combustion vary so do the emissions from combustion of alternative fuels such as ethanol; the variation is in both quantity and chemical composition. In particular, when ethanol is contained in the fuel, ethanol and acetaldehyde are present in the exhaust gas stream and these are two compounds which the catalytic converter has not traditionally been designed to manage. The aim of the study outlined in this paper was to assess the performance of various catalyst formulations when subjected to a representative ethanol exhaust gas mixture. Three automotive catalytic converter formulations were tested including a fully Pt sample, a PdRh three-way catalyst sample and a fully Pd sample. Initially the samples were tested using single component hydrocarbon light-off tests followed by a set of tests with carbon monoxide included as an inlet gas to observe its effect on each individual hydrocarbon oxidation. Finally, each formulation was tested using a full E85 exhaust gas mixture. The study was carried out using a synthetic gas reactor along with FTIR and FID exhaust gas analysers. All formulations showed selectivity toward acetaldehyde formation from ethanol dehydrogenation which resulted in negative acetaldehyde conversion across each of the samples during the mixture tests. The fully Pt sample was the most detrimentally affected by the introduction of carbon monoxide into the gas feed. The Pd and PdRh samples exhibited a tendency toward acetaldehyde decomposition resulting in methane and carbon monoxide formation. The Pt sample did not form methane but did form ethylene as a result of ethanol dehydration.

Comparative Characterisation of 3-D Hydroxyapatite Scaffolds Developed via Replication of Synthetic Polymer Foams and Natural Marine Sponges

The production of complex inorganic forms, based on naturally occurring scaffolds offers an exciting avenue for the construction of a new generation of ceramic-based bone substitute scaffolds. The following study reports an investigation into the architecture (porosity, pore size distribution, pore interconnectivity and permeability), mechanical properties and cytotoxic response of hydroxyapatite bone substitutes produced using synthetic polymer foam and natural marine sponge performs. Infiltration of polyurethane foam (60 pores/in2) using a high solid content (80wt %), low viscosity (0.126Pas) hydroxyapatite slurry yielded 84-91% porous replica scaffolds with pore sizes ranging from 50µm - 1000µm (average pore size 577µm), 99.99% pore interconnectivity and a permeability value of 46.4 x10-10m2. Infiltration of the natural marine sponge, Spongia agaricina, yielded scaffolds with 56- 61% porosity, with 40% of pores between 0-50µm, 60% of pores between 50-500µm (average pore size 349 µm), 99.9% pore interconnectivity and a permeability value of 16.8 x10-10m2. The average compressive strengths and compressive moduli of the natural polymer foam and marine sponge replicas were 2.46±1.43MPa/0.099±0.014GPa and 8.4±0.83MPa /0.16±0.016GPa respectively. Cytotoxic response proved encouraging for the HA Spongia agaricina scaffolds; after 7 days in culture medium the scaffolds exhibited endothelial cells (HUVEC and HDMEC) and osteoblast (MG63) attachment, proliferation on the scaffold surface and penetration into the pores. It is proposed that the use of Spongia agaricina as a precursor material allows for the reliable and repeatable production of ceramic-based 3-D tissue engineered scaffolds exhibiting the desired architectural and mechanical characteristics for use as a bone 3 scaffold material. Moreover, the Spongia agaricina scaffolds produced exhibit no adverse cytotoxic response.