Mass spectrometry-based glycoprofiling of biopharmaceuticals by using an automated data processing tool: SimGlycan®

The therapeutic and immunological properties of biopharmaceuticals are governed by the glycoforms contained in them. Thus, bioinformatics tools capable of performing comprehensive characterization of glycans are significantly important to the biopharma industry. The primary structural elucidation of glycans using mass spectrometry is tricky and tedious in terms of spectral interpretation. In this study, the biosimilars of a therapeutic monoclonal antibody and an Fc-fusion protein with moderate and heavy glycosylation, respectively, were employed as representative biopharmaceuticals for released glycan analysis using liquid chromatography–tandem mass spectrometry instead of conventional mass spectrometry-based analysis. SimGlycan® is a software with proven ability to process tandem MS data for released glycans could identify eight additional glycoforms in Fc-fusion protein biosimilar, which were not detected during mass spectrometry analysis of released glycans or glyco-peptide mapping of the same molecule. Thus, liquid chromatography–tandem mass spectrometry analysis of released glycans not only complements conventional liquid chromatography–mass spectrometry-based glycan profiling but can also identify additional glycan structures that may otherwise be omitted during conventional liquid chromatography–tandem mass spectrometry based analysis of mAbs. The mass spectrometry data processing tools, such as PMI Byos™, SimGlycan^®, etc., can display pivotal analytical capabilities in automated liquid chromatography–mass spectrometry and liquid chromatography–tandem mass spectrometry-based glycan analysis workflows, especially for high-throughput structural characterization of glycoforms in biopharmaceuticals.     

Time resolved fluorescence spectroscopy of Eu(III) complexation with alpha-hydroxy isobutyric acid

Complexation of Eu(III) with alpha-hydroxy isobutyric acid (HIBA), a model compound of humic acid, has been studied by time resolved fluorescence spectroscopy. The ratio of fluorescence intensity of the two peaks at 616 and 592 nm (I(616/592)) was found to increase with increasing ligand to metal ratio. The I(616/592) data was used to deduce the stability constant of Eu-HIBA complexes of the type ML(i) (i=1-3). The formation of multiple ligand complexes was also corroborated by lifetime data which was found to increase with increasing [HIBA]/[Eu] ratio thus indicating replacement of coordinated water molecules by HIBA.     

Immobilization of monomeric organometallic molybdenum oxo and carbonyl complexes and their application in epoxidation reactions

Various oxomolybdenum complexes are efficient and selective homogeneous catalysts in the presence of organic hydroperoxides. The increasing interest in the heterogenisation of such catalysts has led to an increased interest in finding suitable support materials for the complexes. These supports include ionic liquids, mesoporous materials and zeolites to name a few. Several methods are used to anchor the catalyst depending on the nature of the carrier material. The supported catalysts combine properties of homogeneous catalysts such as reactivity, control and selectivity with those of heterogeneous catalysts such as enhanced stability and recyclability.     

Accurate and interpretable computational modeling of chemical mutagenicity

We describe a method for modeling chemical mutagenicity in terms of simple rules based on molecular features. A classification model was built using a rule-based ensemble method called RuleFit, developed by Friedman and Popescu. We show how performance compares favorably against literature methods. Performance was measured through the use of cross-validation and testing on external test sets. All data sets used are publicly available. The method automatically generated transparent rules in terms of molecular structure that agree well with known toxicology. While we have focused on chemical mutagenicity in demonstrating this method, we anticipate that it may be more generally useful in modeling other molecular properties such as other types of chemical toxicity.     

Operator space tensor products of <Emphasis Type="Italic">C</Emphasis>*-algebras

For C*-algebras A and B, the identity map from into A _λ B is shown to be injective. Next, we deduce that the center of the completion of the tensor product A⊗B of two C*-algebras A and B with centers Z(A) and Z(B) under operator space projective norm is equal to . A characterization of isometric automorphisms of and A _h B is also obtained. Dedicated to Ajit Iqbal Singh on her 65th birthday.     

Prediction of anti-HIV activity and cytotoxicity of pyrimidinyl and triazinyl amines: A QSAR study

A QSAR study on a series of pyrimidinyl and triazinyl amines was performed to explore the physico-chemical parameters responsible for their anti-HIV activity and cytotoxicity. Physico-chemical parameters were calculated using WIN CAChe 6.1. Stepwise multiple linear regression analysis was carried out to derive QSAR models which were further evaluated for statistical significance and predictive power by internal and external validation. The selected best QSAR models showed correlation coefficient R of 0.914 and 0.901, and cross-validated squared correlation coefficient Q ² of 0.685 and 0.691 for anti-HIV activity and cytotoxicity, respectively. The developed significant QSAR model indicates that hydrophobicity of the whole molecule plays an important role in the anti-HIV activity and cytotoxicity of pyrimidinyl and triazinyl amine derivatives. When hydrophobicity is increased, anti-HIV activity of the present series of compounds is decreased leading to high cytotoxicity.     

1H and 13C assignments of five cembrenes from guggul

Chemical shift assignments of (1)H and (13)C of five cembrene compounds isolated from the hexane extract of guggul, the resin of Commiphora mukul, are reported. Using (1)H, (13)C, and 2D NMR methods their structures were determined as cembrene (1-isopropyl-4,8,12-trimethyl-cyclotetradeca-2,4,7,11-tetraene), cembrene A (1-isopropenyl-4,8,12-trimethyl-cyclotetradeca-4,8,12-triene), cembrenol (1-isopropyl-4,8,12-trimethyl-cyclotetradeca-3,7,11-trienol), mukulol (1-isopropyl-4,8,12-trimethyl- cyclotetradeca-3,7,11-trienol), and verticillol (4,8,12,15,15-pentamethyl-bicyclo[9.3.1]pentadeca-3,7-dien-12-ol).     

Customizing scoring functions for docking

Empirical scoring functions used in protein-ligand docking calculations are typically trained on a dataset of complexes with known affinities with the aim of generalizing across different docking applications. We report a novel method of scoring-function optimization that supports the use of additional information to constrain scoring function parameters, which can be used to focus a scoring function’s training towards a particular application, such as screening enrichment. The approach combines multiple instance learning, positive data in the form of ligands of protein binding sites of known and unknown affinity and binding geometry, and negative (decoy) data of ligands thought not to bind particular protein binding sites or known not to bind in particular geometries. Performance of the method for the Surflex-Dock scoring function is shown in cross-validation studies and in eight blind test cases. Tuned functions optimized with a sufficient amount of data exhibited either improved or undiminished screening performance relative to the original function across all eight complexes. Analysis of the changes to the scoring function suggest that modifications can be learned that are related to protein-specific features such as active-site mobility.     

A facial microwave-assisted synthesis, spectroscopic characterization and preliminary complexation studies of calix[4]pyrroles containing the hydroxamic-acid moiety

The synthesis, spectroscopic characterization and preliminary complexation properties of functionalized calix[4]pyrroles are described. To date, two generalized preparative approaches have been pursued (i) modifying the basic pyrrole-plus-ketone synthesis of calix[4]pyrrole by using microwave irradiation protocol, (ii) the basic meso-tetra(methyl) meso-tetra(p-nitrophenyl) calix[4]pyrrole skeleton was functionalized to give hydroxamic acids, especially in the meso-position of the macrocycles. The structures of novel calix[4]pyrrole hydroxamic acid derivatives were confirmed on the basis of various physico-chemical techniques such as elemental analysis, FT-IR, ¹H NMR and FAB-Mass. The results of preliminary studies on the extraction of vanadium (V) with the host calix[4]pyrrole hydroxamic acids were elucidated by significant examination of UV–Vis spectroscopy and ICP-AES. Single crystal structure of basic meso-tetra(methyl) meso-tetra (p-nitro phenyl) calix[4]pyrrole moiety has also been reported.