An Integrated Mass Spectrometry-Based Glycomics-Driven Glycoproteomics Analytical Platform to Functionally Characterize Glycosylation Inhibitors

Cancer progression is linked to aberrant protein glycosylation due to the overexpression of several glycosylation enzymes. These enzymes are underexploited as potential anticancer drug targets and the development of rapid-screening methods and identification of glycosylation inhibitors are highly sought. An integrated bioinformatics and mass spectrometry-based glycomics-driven glycoproteomics analysis pipeline was performed to identify an N-glycan inhibitor against lung cancer cells. Combined network pharmacology and in silico screening approaches were used to identify a potential inhibitor, pictilisib, against several glycosylation-related proteins, such as Alpha1-6FucT, GlcNAcT-V, and Alpha2,6-ST-I. A glycomics assay of lung cancer cells treated with pictilisib showed a significant reduction in the fucosylation and sialylation of N-glycans, with an increase in high mannose-type glycans. Proteomics analysis and in vitro assays also showed significant upregulation of the proteins involved in apoptosis and cell adhesion, and the downregulation of proteins involved in cell cycle regulation, mRNA processing, and protein translation. Site-specific glycoproteomics analysis further showed that glycoproteins with reduced fucosylation and sialylation were involved in apoptosis, cell adhesion, DNA damage repair, and chemical response processes. To determine how the alterations in N-glycosylation impact glycoprotein dynamics, modeling of changes in glycan interactions of the ITGA5–ITGB1 (Integrin alpha 5-Integrin beta-1) complex revealed specific glycosites at the interface of these proteins that, when highly fucosylated and sialylated, such as in untreated A549 cells, form greater hydrogen bonding interactions compared to the high mannose-types in pictilisib-treated A549 cells. This study highlights the use of mass spectrometry to identify a potential glycosylation inhibitor and assessment of its impact on cell surface glycoprotein abundance and protein–protein interaction.     

Vectorspace categories immersed in directed components

It is known that, given a tame algebra Λ, the Tits form qΛ is weakly non negative

Moreover, the converse has been shown for some families of algebras, but it is not true in general. The purpose of this work is to show that for certain wild vectorspace categories K = Hom(M,B - mod) where B is tame and M is an indecomposable B-module, we have qB[M] strongly indefinite. This gives partial converses of the above theorem.     

An in vitro screen of bacterial lipopolysaccharide biosynthetic enzymes identifies an inhibitor of ADP-heptose biosynthesis

The lipopolysaccharide (LPS)-rich outer membrane of gram-negative bacteria provides a protective barrier that insulates these organisms from the action of numerous antibiotics. Breach of the LPS layer can therefore provide access to the cell interior to otherwise impermeant toxic molecules and can expose vulnerable binding sites for immune system components such as complement. Inhibition of LPS biosynthesis, leading to a truncated LPS molecule, is an alternative strategy for antibacterial drug development in which this vital cellular structure is weakened. A significant challenge for in vitro screens of small molecules for inhibition of LPS biosynthesis is the difficulty in accessing the complex carbohydrate substrates. We have optimized an assay of the enzymes required for LPS heptose biosynthesis that simultaneously surveys five enzyme activities by using commercially available substrates and report its use in a small-molecule screen that identifies an inhibitor of heptose synthesis.     

Selective recognition of pyrophosphate in water using a backbone modified cyclic peptide receptor

A cyclic peptide based receptor, bearing two dipicolylamino arms complexed to zinc(II) ions, binds pyrophosphate ions with high affinity and selectivity in aqueous solution as determined using an indicator displacement assay.     

The 5-deoxy-5-methylthio-xylofuranose residue in mycobacterial lipoarabinomannan. absolute stereochemistry, linkage position, conformation, and immunomodulatory activity

Mycobacteria produce a cell-surface glycoconjugate, lipoarabinomannan (LAM), which has been shown to be a potent modulator of the immune response that arises from infection by these organisms. Recently, LAM from the human pathogens Mycobacterium tuberculosis and M. kansasii has been shown to contain an unusual 5-deoxy-5-methylthio-xylofuranose (MTX) residue as well as its corresponding oxidized counterpart, 5-deoxy-5-methylsulfoxy-xylofuranose (MSX). To date, the absolute configuration of these residues and their linkage position to the polysaccharide are unknown, as is their biological role. Through the combined use of chemical synthesis and NMR spectroscopy, we have established that the MTX/MSX residues in these glycoconjugates are of the d-configuration and that they are linked alpha-(1-->4) to a mannopyranose residue in the mannan portion of the glycan. Conformational analysis of the MTX/MSX residue using NMR spectroscopy showed differences in ring conformation and as well as in the rotamer populations about the C-4-C-5 bond, as compared to the parent compound, methyl alpha-d-xylofuranoside. Two of the synthesized disaccharides, 3 and 34, were tested in cytokine induction assays, and neither led to the production of TNF-alpha or IL-12p70. In contrast, both demonstrated modest inhibitory properties when these same cytokines were induced using a preparation of Interferon-gamma and Staphylococcus aureus Cowan strain (SAC/IFN-gamma). These latter observations suggest that this motif may play a role in the immune response arising from mycobacterial infection.     

Experimental and Theoretical Determination of the Limiting Partial Molar Volume of Indole in CCl<Subscript>4</Subscript>, Tetrahydrofuran and Acetonitrile at 293.15 K: A Comparative Study with Benzimidazole and Benzothiophene

The partial molar volumes of indole(Ind) at infinite dilution (V₂^￥V_{2}^{\infty}) in carbon tetrachloride (CCl₄), acetonitrile (ACN) and tetrahydrofuran (THF) as solvents, were estimated from densitometry measurements at 293.15 K. The results indicate that $V_{2}^{\infty}\mbox{(ACN)}>V_{2}^{\infty}\mbox{(CCl$V_{2}^{\infty}\mbox{(ACN)}>V_{2}^{\infty}\mbox{(CCl $\approx V_{2}^{\infty}\mbox{(THF)}$\approx V_{2}^{\infty}\mbox{(THF)}. The values determined in this study are close to the values calculated from reported density for Ind in the solid state. In order to make a comparison the partial molecular volume of benzimidazole (Bim) and benzothiophene (BT) in solvents with appropriate solubility were measured too, and the results have revealed that $V_{2}^{\infty}\mbox{(BT)}>V_{2}^{\infty}\mbox{(Ind)}$V_{2}^{\infty}\mbox{(BT)}>V_{2}^{\infty}\mbox{(Ind)} in CCl₄ and $V_{2}^{\infty}\mbox{(Ind)}>V_{2}^{\infty}\mbox{(Bim)}$V_{2}^{\infty}\mbox{(Ind)}>V_{2}^{\infty}\mbox{(Bim)} in THF. In this work the role of solvent reorganization around to solute cavity, and specific and nonspecific interactions on the volumetric behavior of these molecules in solution are discussed using the Terasawa-Itsuki-Arakawa model, the Lee-Graziano model, molar volumes of solutes calculated at the DFT-B3LYP/cc-pVTZ and aug-cc-pVTZ level in the gas phase and considering solvent presence with the Onsager’s reaction field, and the van der Waals volume. This analysis suggests that the molecular volumes of solutes are overestimated by the quantum methods employed in this work and that the volumetric contribution from the van der Waals components to the limiting partial molecular volumes of solutes is important, with the exception of Ind in CCl₄ where the solvent reorganization is the dominant factor.     

Thermal decomposition of cyclic organic peroxides in pure solvents and binary solvent mixtures

The thermal decomposition reaction of acetone cyclic triperoxide, acetone cyclic diperoxide, 4‐heptanone cyclic diperoxide, and pinacolone cyclic diperoxide ca. 0.02 M was studied in pure solvents (acetone and 1‐propanol) and in binary mixtures of acetone/1‐propanol at 150°C. The kinetics of each system was explored by gas chromatography (GC) at different solvent compositions. The reactions showed a behavior accordingly with a pseudo‐first‐order kinetic law up to at least 90% peroxide decomposition. The main organic products derived from these thermolysis reactions were detected by GC analysis. Among them, the corresponding ketones, methane, ethane, and propane were the main identified products. The rates of decomposition of pinacolone diperoxide in the pure solvents were practically independent of the solvent characteristics, so it was of no interest to analyze its kinetic behavior in binary solvent mixtures. In acetone/1‐propanol mixtures, the solvation effect on the cyclic peroxides derived from 4‐heptanone and acetone molecules was slightly dominated by specific interactions between 1‐propanol and a diradical‐activated complex initially formed. This species was preferentially solvated by 1‐propanol instead of acetone. Specific interactions between the O atoms from the peroxidic bond and the H from the OH in 1‐propanol can be taken into account. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 347–353, 2010     

The synthesis of 4H-imidazo[5,1-c][1,4]benzothiazine derivatives

A facile synthesis of the 4H-imidazo[5,1-c][1,4]benzothiazine ring system is described. The synthesis utilized the annulation of an imidazole ring onto a 2H-1,4-benzothiazin-3(4H)-one via the addition of the anion of ethyl isocyanoacetate. Methods for the functionalization of the 1-, 3-, 4-, and 5-positions of the ring system are presented.     

Synthesis of polysubstituted benzothiophenes and sulfur-containing polycyclic aromatic compounds via samarium diiodide promoted three-component coupling reactions of thiophene-2-carboxylate

By the promotion of samarium diiodide, thiophene-2-carboxylate reacted with 2 equiv of ketones at the C-4 and C-5 positions to give diols such as 2 and 9. Because the intermediary organosamarium species were oxophilic but not too basic, the double hydroxyalkylations with various ketone substrates, including alkyl aryl ketones, acetylthiophenes, cyclohexanone, alpha-tetralone, and alpha-phenylacetophenones, were realized without complication of side reactions. The diol products underwent an acid-catalyzed dehydration to give dienes such as 3 and 10, which were treated with DDQ to give either polysubstituted thiophenes (e.g., 4 and 11) or benzothiophenes (e.g., 5, 13, and 14) depending on the reaction conditions. Oxidative annulations of 4,5-diarylthiophenes 11 and 4,5,6,7-tetraphenylbenzothiophenes 14 were carried out by photochemical or chemical methods to give the sulfur-containing polycyclic aromatic compounds, such as phenanthro[9,10-b]thiophene-2-carboxylate, piceno[13,14-b]thiophene-2-carboxylate, and tribenzo[fg,ij,rst]pentapheno[15,16-b]thiophene-2-carboxylates. This method is applicable to the preparation of polysubstituted thiophenes, benzothiophenes, and the related compounds possessing liquid crystalline, photochromic, and other functional properties.