Synthesis of 1-aryl-3H-[1,2,5]triazepino[5,4-a]benzimidazol-4(5H)-ones and quantum chemical investigation of the rotamers of the Boc-protected hydrazide key intermediate

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Structural impact of GTP binding on downstream KRAS signaling

Oncogenic RAS proteins, involved in ∼30% of human tumors, are molecular switches of various signal transduction pathways. Here we apply a new protocol for the NMR study of KRAS in its (inactive) GDP- and (activated) GTP-bound form, allowing a comprehensive analysis of the backbone dynamics of its WT-, G12C- and G12D variants. We found that Tyr32 shows opposite mobility with respect to the backbone of its surroundings: it is more flexible in the GDP-bound form while more rigid in GTP-complexes (especially in WT- and G12D-GTP). Using the G12C/Y32F double mutant, we showed that the presence of the hydroxyl group of Tyr32 has a marked effect on the G12C-KRAS-GTP system as well. Molecular dynamics simulations indicate that Tyr32 is linked to the γ-phosphate of GTP in the activated states – an arrangement shown, using QM/MM calculations, to support catalysis. Anchoring Tyr32 to the γ-phosphate contributes to the capture of the catalytic waters participating in the intrinsic hydrolysis of GTP and supports a simultaneous triple proton transfer step (catalytic water → assisting water → Tyr32 → O1G of the γ-phosphate) leading to straightforward product formation. The coupled flip of negatively charged residues of switch I toward the inside of the effector binding pocket potentiates ligand recognition, while positioning of Thr35 to enter the coordination sphere of the Mg²⁺ widens the pocket. Position 12 mutations do not disturb the capture of Tyr32 by the γ-phosphate, but (partially) displace Gln61, which opens up the catalytic pocket and destabilizes catalytic water molecules thus impairing intrinsic hydrolysis.

Nucleotide exchange to the physiological, activated, GTP-bound form of KRAS results in the anchoring of Tyr32 within the active site.     

Dimensional scaling of flame propagation in discrete particulate clouds

The critical dimension necessary for a flame to propagate in suspensions of fuel particles in oxidiser is studied analytically and numerically. Two types of models are considered: First, a continuum model, wherein the individual particulate sources are not resolved and the heat release is assumed spatially uniform, is solved via conventional finite difference techniques. Second, a discrete source model, wherein the heat diffusion from individual sources is modelled via superposition of the Green's function of each source, is employed to examine the influence of the random, discrete nature of the media. Heat transfer to cold, isothermal walls and to a layer of inert gas surrounding the reactive medium are considered as the loss mechanisms. Both cylindrical and rectangular (slab) geometries of the reactive medium are considered, and the flame speed is measured as a function of the diameter and thickness of the domains, respectively. In the continuum model with inert gas confinement, a universal scaling of critical diameter to critical thickness near 2:1 is found. In the discrete source model, as the time scale of heat release of the sources is made small compared to the interparticle diffusion time, the geometric scaling between cylinders and slabs exhibits values greater than 2:1. The ability of the flame in the discrete regime to propagate in thinner slabs than predicted by continuum scaling is attributed to the flame being able to exploit local fluctuations in concentration across the slab to sustain propagation. As the heat release time of the sources is increased, the discrete source model reverts back to results consistent with the continuum model. Implications of these results for experiments are discussed.     

Two Types of σ-Allenyl Complexes from Reactions of Silylenes and Germylenes with Chromium Fischer Alkynyl(alkoxy)carbenes

The reactivity of amidinatotetrylenes of the type E(tBu₂bzm)R¹ (E=Si, Ge; tBu₂bzm=N,N′-bis(tertbutyl)benzamidinate; R¹=alkyl or aryl) with the chromium Fischer alkynylcarbene complexes [Cr{C(OEt)C₂R²}(CO)₅] (R²=Ph; ferrocenyl, Fc) has been studied. At room temperature, two different reaction pathways have been identified: (a) attack of the amidinatotetrylene to the alkynyl C² atom (γ-attack), which leads to σ-allenyl complexes in which the original C_carbene atom maintains its attachment to the Cr(CO)₅ and OEt groups (compounds 3 ), and (b) attack of the amidinatotetrylene to the C_carbene atom (α-attack), which ends in σ-allenyl complexes in which the original C_carbene atom is not attached to the metal atom and has been inserted into an E−N bond of the amidinatotetrylene forming an E-C-N-C-N five-membered ring (compounds 4 ). It has been found that compounds 3 are thermodynamically less stable than their corresponding 4 isomers and that some of the former (E=Ge; R¹=CH₂SiMe₃) can be transformed into the latter upon heating. At high temperatures (>70 °C) the reactions involving bulky amidinatotetrylenes (R¹=Mes, tBu) end in the carbene-substitution products [Cr{E(tBu₂bzm)R¹}(CO)₅].     

Scaling law analysis of electrohydrodynamics and dielectrophoresis for isomotive dielectrophoresis microfluidic devices

Isomotive dielectrophoresis (isoDEP) is a unique DEP geometrical configuration where the gradient of the field-squared () is constant. IsoDEP analyzes polarizable particles based on their magnitude and direction of translation. Particle translation is a function of the polarizability of both the particles and suspending medium, the particles’ size and shape, and the frequency of the electric field. However, other electrokinetics act on the particles simultaneously, including electrothermal hydrodynamics. Hence, to maximize the DEP force relative to over electrokinetic forces, design parameters such as microchannel geometry, fabrication materials, and applied electric field must be properly tuned. In this work, scaling law analyses were developed to derive design rules, relative to particle diameter, to reduce unwanted electrothermal hydrodynamics relative to DEP-induced particle translation. For a particle suspended in 10 mS/m media, if the channel width and height are below ten particle diameters, the electrothermal-driven flow is reduced by ∼500 times compared to a channel that is 250 particles diameters in width and height. Replacing glass with silicon as the device's underlying substrate for an insulative-based isoDEP reduces the electrothermal induced flow approximately 20 times less.     

A Bis-Chelating / Ligand for the Synthesis of Heterobimetallic Platinum(II)/Rhenium(I) Complexes: Tools for the Optimization of a New Class of Platinum(II) Anticancer Agents

The two independent and coordination sites of a newly synthesized bis[2-(hydroxyphenyl)-1,2,4-triazole] platform have been exploited to prepare four monometallic neutral ()Pt^II complexes carrying DMSO, pyridine, triphenylphosphine, or N-heterocyclic carbene as the fourth ligand. Then, the second coordination site was used to introduce an IR-active rhenium tricarbonyl entity, affording the four corresponding heterobimetallic neutral Pt^II/Re^I complexes, as well as a cationic Pt^II/Re^I derivative. X-ray crystallographic studies showed that distortion of the organic platform occurred to accommodate the coordination geometry of both metal centers. No ligand exchange or transchelation occurred upon incubation of the Pt^II complexes in aqueous environment or in the presence of Fe^III, respectively. The antiproliferative activity of the ligand and complexes was first screened on the triple-negative breast cancer cell line MDA-MB-231. Then, the IC₅₀ values of the most active candidates were determined on a wider panel of human cancer cells (MDA-MB-231, MCF-7, and A2780), as well as on a nontumorigenic cell line (MCF-10A). Low micromolar activities were reached for the complexes carrying a DMSO ligand, making them the first examples of highly active, but hydrolytically stable, Pt^II complexes. Finally, the characteristic mid-IR signature of the {Re(CO)₃} fragment in the Pt/Re heterobimetallic complexes was used to quantify their uptake in breast cancer cells.     

Label-free immunosensor for monitoring vitellogenin as a biomarker for exogenous oestrogen compounds in amphibian species

A label-free, optical waveguide lightmode spectroscopy based immunosensor was developed for frog (Bombina orientalis) vitellogenin (Vtg) determination in biological samples as a biomarker for exogenous oestrogen compounds. Antibody against Vtg was produced in rabbits immunised with purified lipovitellin (Lpv), a precursor of Vtg, from the homogenised ovary of oriental fire-bellied toads (B. orientalis). The purified protein and Lpv/Vtg-specific serum were applied in both competitive and direct immunoassay formats using optical waveguide lightmode spectroscopy immunosensor. When measuring Vtg in direct manner, the Lpv antibody (1.76 µg mL^?1) was immobilised on the sensor surface, and the linear measuring range for Vtg was 0.1–10 µg mL^?1. During the competitive measurement, 100 ng mL^?1 Lpv was applied for the immobilisation. The linear measuring range for Vtg was 0.5–50 ng mL^?1. We studied the relative substrate specificity of the antibody, and it was concluded that the method is suitable for the sensitive and selective determination of Vtg levels in toads. Heart, liver and gonad samples from male animals were spiked with Vtg and were analysed using the newly developed method, and female toads and spawn samples were tested and compared to the calibration curve obtained by the spiked samples.