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.     

Beobachtung des Stickstoffstoffwechsels bei Leguminosen mittels 15N

Es war Ziel dieser Arbeit, zu ermitteln, welchen Einfluß höhere Dosen von Stickstoffdüngemitteln in Form von KNO₃ auf die Menge des in der Pflanze fixierten Luftstickstoffs haben. Als Versuchspflanze wählten wir Pferdebohnen (Vicia faba, Chlumetzer Abart) wegen ihrer vielseitigen Verwendung in der Landwirtschaft und ihrer besonderen experimentellen Eignung.     

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.     

Instabilities in free-surface electroosmotic flows

Instability of a thin electrolyte film undergoing a direct current electroosmotic flow has been investigated. The film with a compliant electrolyte–air interface is flowing over a rigid charged substrate. Unlike previous studies, inclusion of the Maxwell stresses in the formulation shows the presence of a new finite wavenumber shear-flow mode of instability, alongside the more frequently observed long-wave interfacial mode. The shear mode is found to be the dominant mode of instability when the electrolyte–solid and electrolyte–air interfaces are of opposite charge or of same charge but have very large zeta-potential at the electrolyte–air interface. The conditions for mode-switch (interfacial to shear) and the direction of the travelling waves are discussed through stability diagrams. Interestingly, the analysis shows that when the interfaces are of nearly same zeta potential, the ‘free’ electrolyte–air interface behaves more like a ‘stationary’ wall because of the ion transport in the reverse direction of the flow.     

Refractive index profiles of LiNbO3: Ti waveguides

Eight LiNbO₃: Ti waveguides have been fabricated under differing conditions. The effective refractive indices of guided modes have been measured and successfully fitted to Gaussian index profiles. The change of refractive index and titanium concentration are related by a power law, the exponents being different for the extraordinary and the ordinary beam.     

Raman spectroscopy of halogen‐containing carbonates

Raman spectroscopy complemented with infrared spectroscopy has been used to study a series of selected natural halogenated carbonates from different origins, including bastnasite, parisite and northupite. The position of CO₃²⁻ symmetric stretching vibration varies with the mineral composition. An additional band for northupite at 1107 cm⁻¹ is observed. Raman spectra of bastnasite, parisite and northupite show single bands at 1433, 1420 and 1554 cm⁻¹, respectively, assigned to the ν₃ (CO₃)²⁻ asymmetric stretching mode. The observation of additional Raman bands for the ν₃ modes for some halogenated carbonates is significant in that it shows distortion of the CaO₆ octahedron. No ν₂ Raman bending modes are observed for these minerals. The band is observed in the infrared spectra, and multiple ν₂ modes at 844 and 867 cm⁻¹ are observed for parisite. A single intense infrared band is found at 879 cm⁻¹ for northupite. Raman bands are observed forthe carbonate ν₄ in‐phase bending modes at 722 cm⁻¹ for bastnasite, 736 and 684 cm⁻¹ for parisite and 714 cm⁻¹ for northupite. Multiple bands are observed in the OH stretching region for selected bastansites and parisites, indicating the presence of water and OH units in the mineral structure. The presence of such bands brings into question the actual formula of these halogenated carbonate minerals. Copyright © 2007 John Wiley & Sons, Ltd.