Activity-based chemical proteomics accelerates inhibitor development for deubiquitylating enzymes

Converting lead compounds into drug candidates is a crucial step in drug development, requiring early assessment of potency, selectivity, and off-target effects. We have utilized activity-based chemical proteomics to determine the potency and selectivity of deubiquitylating enzyme (DUB) inhibitors in cell culture models. Importantly, we characterized the small molecule PR-619 as a broad-range DUB inhibitor, and P22077 as a USP7 inhibitor with potential for further development as a chemotherapeutic agent in cancer therapy. A striking accumulation of polyubiquitylated proteins was observed after both selective and general inhibition of cellular DUB activity without direct impairment of proteasomal proteolysis. The repertoire of ubiquitylated substrates was analyzed by tandem mass spectrometry, identifying distinct subsets for general or specific inhibition of DUBs. This enabled identification of previously unknown functional links between USP7 and enzymes involved in DNA repair.     

An extensive FPGA-based realization study about the Izhikevich neurons and their bio-inspired applications

This study is aimed at analysing damping and gyroscopic effects on the stability of parametrically excited continuous rotor systems, taking into account both external (non-rotating) and internal (rotating) damping distributions. As case-study giving rise to a set of coupled differential Mathieu–Hill equations with both damping and gyroscopic terms, a balanced shaft is considered, modelled as a spinning Timoshenko beam loaded by oscillating axial end thrust and twisting moment, with the possibility of carrying additional inertial elements like discs or flywheels. After discretization of the equations of motion into a set of coupled ordinary differential Mathieu–Hill equations, stability is studied via eigenproblem formulation, obtained by applying the harmonic balance method. The occurrence of simple and combination parametric resonances is analysed introducing the notion of characteristic circle on the complex plane and deriving analytical expressions for critical solutions, including combination parametric resonances, valid for a large class of rotors. A numerical algorithm is then developed for computing global stability thresholds in the presence of both damping and gyroscopic terms, also valid when closed-form expressions of critical solutions do not exist. The influence on stability of damping distributions and gyroscopic actions is then analysed with respect to frequency and amplitude of the external loads on stability charts in the form of Ince–Strutt diagrams.

     

The effects of low dose leukotriene receptor antagonist therapy on airway remodeling and cysteinyl leukotriene expression in a mouse asthma model

Airway structural changes that occur in patients with asthma in response to persistent inflammation are termed airway remodeling. The cysteinyl leukotrienes (LTC(4), D(4) and E(4)) are known to play important roles in the pathobiology of asthma. To evaluate the effect of low dose montelukast (MK) on the development of airway remodeling using a chronic murine model of allergic airway inflammation with subepithelial fibrosis, BALB/c mice, after intraperitoneal ovalbumin (OVA) sensitization on days 0 and 14, received intranasal OVA periodically on days 14-75. MK treated mice received montelukast sodium intraperitoneally on days 26-75. The OVA sensitized/challenged mice developed an extensive eosinophil cell inflammatory response, goblet cell hyperplasia, mucus occlusion, and smooth muscle hypertrophy of the airways. In addition, in OVA sensitized/challenged mice, dense collagen deposition/fibrosis was seen throughout the lung interstitium surrounding the airways, blood vessels, and alveolar septae. The cysteinyl leukotriene 1 (CysLT1) receptor antagonist, MK significantly reduced the airway eosinophil infiltration, goblet cell hyperplasia, mucus occlusion, and lung fibrosis except airway smooth muscle hypertrophy in the OVA sensitized/challenged mice. The OVA sensitized/challenged mice had significantly increased epithelial desquamation compared with control mice. MK markedly reduced epithelial desquamation of airways in OVA/MK treated animals compared with OVA sensitized/challenged mice. MK treatment did not affect the levels of CysLT in lung tissue. Our results show that the important role of cysteinyl leukotrienes in the pathogenesis of asthma. Lower dose of CysLT1 receptor antagonism has a significant anti-inflammatory effect on allergen-induced lung inflammation and fibrosis but not airway smooth muscle hypertrophy in an animal model of asthma.     

On some constacyclic codes over $$\mathbb {Z}_{4}\left[ u\right] /\left\langle u^{2}-1\right\rangle $$, their $$\mathbb {Z}_4$$Z4 images,and new codes

In this paper, we study \(\lambda \)-constacyclic codes over the ring \(R=\mathbb {Z}_4+u\mathbb {Z}_4\) where \(u^{2}=1\), for \(\lambda =3+2u\) and \(2+3u\). Two new Gray maps from R to \(\mathbb {Z}_4^{3}\) are defined with the goal of obtaining new linear codes over \(\mathbb {Z}_4\). The Gray images of \(\lambda \)-constacyclic codes over R are determined. We then conducted a computer search and obtained many \(\lambda \)-constacyclic codes over R whose \(\mathbb {Z}_4\)-images have better parameters than currently best-known linear codes over \(\mathbb {Z}_4\).     

Generalized Lucas polynomials and relationships between the Fibonacci polynomials and Lucas polynomials

In this article, we find elements of the Lucas polynomials by using two matrices. We extend the study to the n-step Lucas polynomials. Then the Lucas polynomials and their relationship are generalized in the paper. Furthermore, we give relationships between the Fibonacci polynomials and the Lucas polynomials.     

Light-Mediated Formal Radical Deoxyfluorination of Tertiary Alcohols through Selective Single-Electron Oxidation with TEDA2+.

The synthesis of tertiary alkyl fluorides through a formal radical deoxyfluorination process is described herein. This light-mediated, catalyst-free methodology is fast and broadly applicable allowing for the preparation of C−F bonds from (hetero)benzylic, propargylic, and non-activated tertiary alcohol derivatives. Preliminary mechanistic studies support that the key step of the reaction is the single-electron oxidation of cesium oxalates—which are readily available from the corresponding tertiary alcohols—with in situ generated TEDA^2+. (TEDA: N-(chloromethyl)triethylenediamine), a radical cation derived from Selectfluor®.     

Diethoxy‐azobis(pyridinium) Salt as Photoinitiator for Cationic Polymerization: Towards Wavelength Tunability by Cis–Trans Isomerization

N,N′‐diethoxy‐4,4′‐azobis(pyridinium) hexafluorophosphate (DEAP) has been synthesized by alkylation of the corresponding N‐oxide and characterized. DEAP exhibits UV induced cis–trans isomerization with absorptions at around λ = 459 and 360 nm, respectively. The ability of the DEAP ion to act as a photoinitiator for the cationic polymerization of cyclohexene oxide and N‐vinylcarbazole is demonstrated. The initiation step involves the decay of the excited state of the trans form of the salt with homolytic bond rupture of the nitrogen–oxygen bond. Its potential use as a photoinitiator for free radical polymerization is also demonstrated using methyl methacrylate monomer as the example.

     

Quantum mechanical/molecular mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins

The protein environments surrounding the retinal tune electronic absorption maximum from 350 to 630 nm. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods can be used in calculating excitation energies of retinal in its native protein environments and in studying the molecular basis of spectral tuning. We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants.     

Analysis of high molecular mass proteins larger than 150 kDa using cyanogen bromide cleavage and conventional 2-DE

Proteomic approaches including high-resolution 2-DE are providing the tools needed to discover disease-associated biomarkers in complex biological samples. Although 2-DE is an extremely powerful approach to analyze the proteome, the separation of proteins with extreme molecular masses still remains an issue requiring improvement. Because high molecular mass (HMM) proteins larger than 150 kDa have already been observed to be differentially expressed in several pathologies such as cancer, we developed an original strategy to analyze this part of the proteome that is not easily separated by 2-DE in polyacrylamide gels. This strategy is based on the 2-DE separation of cyanogen bromide (CNBr) fragments of purified HMM protein fractions, and combines techniques including SEC fractionation, TCA precipitation, CNBr cleavage, 2-DE and MS analysis. The method was first tested on a model protein, the BSA. Preliminary results obtained using colonic tissues led to the identification of six HMM proteins with M(r) comprised between 163 and 533 kDa in their reduced state. These results demonstrated that our CNBr/2-DE approach should provide a powerful tool for identification of new biomarkers larger than 150 kDa.