Electrospray tandem mass spectrometric analysis of zeaxanthin and its oxidation products

Carotenoids have been implicated in protection of the eye from light-mediated photo-toxicity caused by free radicals. Under conditions of normal oxidative stress the carotenoids serve as protective antioxidants; however, when the oxidative stress exceeds the antioxidant capacity, carotenoids can be oxidized into numerous cleavage products. The determination and identification of oxidized carotenoids in biological samples remains a major challenge due to the small sample size and low stability of these compounds. We investigated the reaction of various zeaxanthin cleavage products with O-ethyl hydroxylamine to evaluate their levels in a biological sample. For this, a sensitive and specific electrospray tandem mass spectrometry (ESI-MS/MS) was developed, avoiding the classical lower sensitive and specific HPLC-UV and fluorescence absorption methods. Protonated molecules [M + H](+) of carotenoids upon collision-induced dissociation produced a number of structurally characteristic product ions. A series of complicated clusters of product ions differing in 14 (CH(2))and 26 (C(2)H(2))Da was characteristic of the polyene chain of intact carotenoids. All carotenoid ethyl oximes of zeaxanthin cleavage products were characterized by the losses of 60 and 61 Da in their MS/MS spectra. Through the application of the LC/MS/MS method, we identified two oxime derivatives of 3-hydroxy-beta-ionone and 3-hydroxy-14'-apocarotenal with protonated molecules at m/z 252 and m/z 370 respectively, in a human eye sample.     

Studies directed toward synthesis of quassinoids. VI—mass spectral fragmentation of D-ring seco esters and δ-lactone derivatives of cholic acid

Analogy and deuterium labeling demonstrate that considerable remote group interaction occurs between functional groups at positions 7 and 16 in 16, 17-secosteroids. It is proposed that ion-dipole interact?ions separations of distances of 10 to 2 Å will involve energies of 1–30 kcal mol^?1 and can play a significant role in fragmentation processes. Successive loss of one, two and three HOAc molecules from a milecular or daughter ion increase progressively in relative intensity; irregularity in this pattern indicates the operation of special factors or multiple genesis of daughter ions having the same m/e. Evidence is presented which suggests that facile ketene ejection from the acetate functional group only occurs from a radical ion and must be preceded by transfer of a hydrogen radical from the acetate group to the site of charge localization.     

A coupled electron diffraction and rigid unit mode (RUM) study of the crystal chemistry of some zeotypic AlPO4 compounds

Electron diffraction and lattice dynamical calculations are used to investigate the unit cells, space group symmetries and inherent displacive flexibility of the room-temperature average structures of AlPO₄-8, AlPO₄-16 and AlPO₄-tridymite. The zero-frequency rigid unit modes (RUMs) of the idealized high-symmetry polymorphs thereof are also investigated along with their relationship to the lower-temperature polymorphism of these zeotypic aluminophosphates. The clear presence of satellite reflections in addition to the Bragg reflections (G) of the underlying Cmc2₁ parent structure in the case of AlPO₄-8 shows that the true unit cell of the room-temperature polymorph has a doubled c-axis due to a condensed RUM mode. Structured diffuse scattering is also observed which can be related to the thermal excitation of RUM modes. In the case of AlPO₄-tridymite, a complex F1 triclinic polymorph is observed and related to soft RUM modes while, in the case of AlPO₄-16, a soft q=0 RUM mode is shown to be responsible for an observed phase transition in the case of the all SiO₂ analogue of AlPO₄-16. A large number of additional zero-frequency RUM modes also exist in the case of AlPO₄-16.     

Non-isothermal studies of adduct molecules of metallic halides with oxo-compounds in solid state. V

Non-isothermal studies of some adduct molecules of metallic halides with tetrahydropyran as the type MX₂(THP)_y in solid state, were carried out with a Derivatograph, where M  Mn(II), Co(II), Ni(II), Cu(II) or Cd(II), XCl^- or Br^-, THPtetrahydropyran and y0.1–1. These adduct molecules lost tetrahydropyran in single or multiple steps upon heating. Thermally stable intermediate products were isolated and characterised by elemental analysis and IR spectral measurement. The activation energy for each step of decomposition of the adduct was evaluated from the analysis of TG, DTG and DTA curves of the respective derivatogram. The enthalpy change was evaluated from the DTA peak area and the order of reaction was found to be unity, for each step of decomposition. Thermal parameters for the above adducts were compared with the adducts of other oxocompounds like dioxan, tetrahydrofuran, ethylene glycol dimethyl ether and diisopropyl ether.     

Screening an In-House Isoquinoline Alkaloids Library for New Blockers of Voltage-Gated Na+ Channels Using Voltage Sensor Fluorescent Probes: Hits and Biases

Voltage-gated Na⁺ (Na_V) channels are significant therapeutic targets for the treatment of cardiac and neurological disorders, thus promoting the search for novel Na_V channel ligands. With the objective of discovering new blockers of Na_V channel ligands, we screened an In-House vegetal alkaloid library using fluorescence cell-based assays. We screened 62 isoquinoline alkaloids (IA) for their ability to decrease the FRET signal of voltage sensor probes (VSP), which were induced by the activation of Na_V channels with batrachotoxin (BTX) in GH3b6 cells. This led to the selection of five IA: liriodenine, oxostephanine, thalmiculine, protopine, and bebeerine, inhibiting the BTX-induced VSP signal with micromolar IC₅₀. These five alkaloids were then assayed using the Na⁺ fluorescent probe ANG-2 and the patch-clamp technique. Only oxostephanine and liriodenine were able to inhibit the BTX-induced ANG-2 signal in HEK293-hNa_V1.3 cells. Indeed, liriodenine and oxostephanine decreased the effects of BTX on Na⁺ currents elicited by the hNa_V1.3 channel, suggesting that conformation change induced by BTX binding could induce a bias in fluorescent assays. However, among the five IA selected in the VSP assay, only bebeerine exhibited strong inhibitory effects against Na⁺ currents elicited by the hNav1.2 and hNav1.6 channels, with IC₅₀ values below 10 µM. So far, bebeerine is the first BBIQ to have been reported to block Na_V channels, with promising therapeutical applications.     

Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies

Monoclonal antibodies are emerging as a viable treatment for the coronavirus disease 19 (COVID-19). However, newly evolved variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can reduce the efficacy of currently available antibodies and can diminish vaccine-induced immunity. Here, we demonstrate that the microscopic dynamics of neutralizing monoclonal antibodies can be profoundly modified by the mutations present in the spike proteins of the SARS-COV-2 variants currently circulating in the world population. The dynamical perturbations within the antibody structure, which alter the thermodynamics of antigen recognition, are diverse and can depend both on the nature of the antibody and on the spatial location of the spike mutation. The correlation between the motion of the antibody and that of the spike receptor binding domain (RBD) can also be changed, modulating binding affinity. Using protein-graph-connectivity networks, we delineated the mutant-induced modifications in the information-flow along allosteric pathway throughout the antibody. Changes in the collective dynamics were spatially distributed both locally and across long-range distances within the antibody. On the receptor side, we identified an anchor-like structural element that prevents the detachment of the antibodies; individual mutations there can significantly affect the antibody binding propensity. Our study provides insight into how virus neutralization by monoclonal antibodies can be impacted by local mutations in the epitope via a change in dynamics. This realization adds a new layer of sophistication to the efforts for rational design of monoclonal antibodies against new variants of SARS-CoV2, taking the allostery in the antibody into consideration.

Mutations in the new variants of SARS-CoV-2 spike protein modulates the dynamics of the neutralizing antibodies. Capturing such modulations from MD simulations and graph network model identifies the role of mutations in facilitating immune evasion.     

A CSP and tabulation-based adaptive chemistry model

We demonstrate the feasibility of a new strategy for the construction of an adaptive chemistry model that is based on an explicit integrator stabilized by an approximation of the Computational Singular Perturbation (CSP)-slow-manifold projector. We examine the effectiveness and accuracy of this technique first using a model problem with variable stiffness. We assess the effect of using an approximation of the CSP-slow-manifold by either reusing the CSP vectors calculated in previous steps or from a pre-built tabulation. We find that while accuracy is preserved, the associated CPU cost was reduced substantially by this method. We used two ignition simulations – hydrogen–air and heptane–air mixtures – to demonstrate the feasibility of using the new method to handle realistic kinetic mechanisms. We test the effect of utilizing an approximation of the CSP-slow-manifold and find that its use preserves the order of the explicit integrator, produces no degradation in accuracy, and results in a scheme that is competitive with traditional implicit integration. Further analysis on the performance data demonstrates that the tabulation of the CSP-slow-manifold provides an increasing level of efficiency as the size of the mechanism increases. From the software engineering perspective, all the machinery developed is Common Component Architecture compliant, giving the software a distinct advantage in the ease of maintainability and flexibility in its utilization. Extension of this algorithm is underway to implement an automated tabulation of the CSP-slow-manifold for a detailed chemical kinetic system either off-line, or on-line with a reactive flow simulation code.     

A comparison of quantitative nuclear magnetic resonance methods: internal,external, and electronic referencing

The performance of three quantitative NMR methods was compared in terms of short‐term and long‐term precision and accuracy, robustness, linear range, and general applicability. The Internal Reference method employs a reference material co‐dissolved with sample; the External Reference method employs a reference material contained in a separate solution; and the third method, known as Electronic REference To access In vivo Concentrations (ERETIC), employs an externally calibrated digital reference peak. The Internal Reference method results were the most precise and remained stable within 0.1% for at least 4 weeks. The results from the External Reference and ERETIC methods were practically equivalent to each other during this time. These methods exhibited small differences relative to the standard set by the Internal Reference method and slightly lower precision, establishing them as practical alternatives to the Internal Reference method. In contrast to the Internal Reference method, the External Reference and ERETIC methods possess several advantages that address peak overlap, flexibility of calibration, and duration of applicability. The study was designed such that each spectrum contained the information needed to compare the three methods while all other variables were kept constant. Applicability of pulse width compensation is addressed. ERETIC software compensation and minor adjustments to 90° pulse width were concluded to be unnecessary for this system. Although each of the methods was applied here to specifically calculate and compare chemical purity values, this evaluation applies generally to absolute quantitation by NMR. Copyright © 2013 John Wiley & Sons, Ltd.