Liquid chromatographic analysis of nucleosides and their mono-, di- and triphosphates using porous graphitic carbon stationary phase coupled with electrospray mass spectrometry

Analysis of nucleosides and nucleotides is desirable in many biological studies, but the task is analytically challenging due to the high polarity of the analytes. In this study, resolution of mixtures containing nucleosides and their mono-, di- and triphosphates was achieved using a porous graphitic carbon (PGC) stationary phase, Hypercarb, under conditions suitable for liquid chromatography/mass spectrometry (LC/MS). Different organic mobile phases and modifiers were evaluated and the separation of 16 nucleosides and nucleotides was optimized using gradient elution with a water/acetonitrile mobile phase containing ammonium acetate and diethylamine as modifiers. The ammonium acetate concentration proved to be critical for retention and diethylamine was found to improve the peak shapes of di- and triphosphates for mass spectrometric detection. A variety of silica-based columns designed for polar compound separation were also tested using optimized LC conditions and compared with results obtained with the Hypercarb column. Only the Hypercarb column provided separations suitable for accurate quantitation of mixed nucleosides and their phosphates.     

Fast Photochemical Oxidation of Proteins (FPOP) Maps the Epitope of EGFR Binding to Adnectin

Epitope mapping is an important tool for the development of monoclonal antibodies, mAbs, as therapeutic drugs. Recently, a class of therapeutic mAb alternatives, adnectins, has been developed as targeted biologics. They are derived from the 10th type III domain of human fibronectin (¹⁰Fn3). A common approach to map the epitope binding of these therapeutic proteins to their binding partners is X-ray crystallography. Although the crystal structure is known for Adnectin 1 binding to human epidermal growth factor receptor (EGFR), we seek to determine complementary binding in solution and to test the efficacy of footprinting for this purpose. As a relatively new tool in structural biology and complementary to X-ray crystallography, protein footprinting coupled with mass spectrometry is promising for protein–protein interaction studies. We report here the use of fast photochemical oxidation of proteins (FPOP) coupled with MS to map the epitope of EGFR-Adnectin 1 at both the peptide and amino-acid residue levels. The data correlate well with the previously determined epitopes from the crystal structure and are consistent with HDX MS data, which are presented in an accompanying paper. The FPOP-determined binding interface involves various amino-acid and peptide regions near the N terminus of EGFR. The outcome adds credibility to oxidative labeling by FPOP for epitope mapping and motivates more applications in the therapeutic protein area as a stand-alone method or in conjunction with X-ray crystallography, NMR, site-directed mutagenesis, and other orthogonal methods. Figure

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Optimal echo spacing for multi-echo imaging measurements of Bi-exponential T2 relaxation

Calculations, analytical solutions, and simulations were used to investigate the trade-off of echo spacing and receiver bandwidth for the characterization of bi-exponential transverse relaxation using a multi-echo imaging pulse sequence. The Cramer–Rao lower bound of the standard deviation of the four parameters of a two-pool model was computed for a wide range of component T₂ values and echo spacing. The results demonstrate that optimal echo spacing (TE_opt) is not generally the minimal available given other pulse sequence constraints. The TE_opt increases with increasing value of the short T₂ time constant and decreases as the ratio of the long and short time constant decreases. A simple model of TE_opt as a function of the two T₂ time constants and four empirically derived scalars is presented.     

Enantioseparations of non-benzenoid and oligo-Tröger’s bases by HPLC on Whelk O1 column

The separation of enantiomers of several ‘bis- and tris-Tröger’s bases’ by HPLC on commercially available chiral stationary phase Whelk O1 is described for the first time. The observed structure–enantioselectivity relationships are in agreement with the previously established molecular recognition model. For all ‘bis- and tris-Tröger’s bases’ studied, satisfactory to excellent enantioselectivities were observed.     

Optimum extraction process of polyphenols from Bridelia grandis stem bark using experimental design

Euphorbiaceae barks are known to contain an appreciable amount of polyphenolic compounds responsible for several biological activities. Preliminary extraction from Bridelia grandis stem bark afforded high content of polyphenols, determined by spectrophotometric methods such as Folin–Ciocalteu (for total phenols, TP) and n‐butanol‐HCl (for condensed tannins, CT). A preliminary Plackett–Burman screening design was used to identify the key factors that influence the TP and CT extraction. Between all the variables known to influence the extraction from vegetable matrixes, six were selected; maceration was chosen as traditional extraction methodology. To investigate the effect of solvents and extraction method, methanol, acetone 70% (v/v in water), centrifugation and ultrasound were chosen. A full factorial design 2³ was applied to optimize the extraction procedure. The responses were obtained analyzing the extracts for their TP and CT contents determined by the above‐mentioned spectrophotometric methods. The results confirm that, within the explored domain, the optimum solvent is methanol and the optimum method is one‐cycle centrifugation. Finally, it was also compared with the effect of maceration on the considered responses. It has never given results better than centrifugation, whereas in the case of CT it represents an advantage to employ a three‐cycle centrifugation instead of one.     

meta-Benzenotetratetrazolophanes

A route to meta-benzenocyclophanes containing four tetrazole rings in the macrocycle is described.     

Inductive effect: a quantum theory of atoms in molecules perspective

Substituent effects are ubiquitous in chemistry and the most fundamental is the inductive effect. In this study, the so-called inductive effect was probed in derivatives of bicyclo[1.1.1]pentane-1-carboxylic acid using the isodesmic reaction energy of the acid-base deprotonation, calculated at the PBE0/6-31++G(d,p) level of theory (used throughout). Although structure, molecular orbitals, and nuclear magnetic shielding parameters are discussed, the main focus of this study is the use of the quantum theory of atoms in molecules to analyze the electron density distribution. It was observed that the effect propagates via the manipulation of atomic dipole moments controlled by that of the substituent. As the dipole moment conforms to the principle of atomic transferability, it is found that the substituent dipole determined in simple systems (e.g., R-H) can be used to describe the effect upon the bicyclo[1.1.1]pentane-1-carboxylic acid system.