Theoretical study of GSK−3<Emphasis Type="Italic">α</Emphasis>: neural networks QSAR studies for the design of new inhibitors using 2D descriptors

Glycogen synthase kinase-3 (GSK-3) targets encompass proteins implicated in AD and neurological disorders. The functions of GSK-3 and its implication in various human diseases have triggered an active search for potent and selective GSK-3 inhibitors. In this sense, QSAR could play an important role in studying these GSK-3 inhibitors. For this reason, we developed QSAR models for GSK−3α, linear discriminant analysis (LDA), and artificial neural networks (ANNs) from nearly 50,000 cases with more than 700 different GSK−3α inhibitors obtained from ChEMBL database server; in total we used more than 20,000 different molecules to develop the QSAR models. The model correctly classified 237 out of 275 active compounds (86.2%) and 14,870 out of 15,970 non-active compounds (93.2%) in the training series. The overall training performance was 93.0%. Validation of the model was carried out using an external predicting series. In these series, the model classified correctly 458 out of 549 (83.4%) compounds and 29,637 out of 31,927 non-active compounds (83.4%). The overall predictability performance was 92.7%. In this study, we propose three types of non-linear ANN as alternative to already existing models, such as LDA. Linear neural network: LNN: 236:236-1-1:1 which had an overall training performance of 96% proved to be the best model. In addition, we did a study of the different fragments of the molecules of the database to see which fragments had more influence in the activity. This can help design new inhibitors of GSK−3α. This study reports the attempts to calculate, within a unified framework probabilities of GSK−3α inhibitors against different molecules found in the literature.     

Pharmacophore-based screening and drug repurposing exemplified on glycogen synthase kinase-3 inhibitors

The current study was conducted to elaborate a novel pharmacophore model to accurately map selective glycogen synthase kinase-3 (GSK-3) inhibitors, and perform virtual screening and drug repurposing. Pharmacophore modeling was developed using PHASE on a data set of 203 maleimides. Two benchmarking validation data sets with focus on selectivity were assembled using ChEMBL and PubChem GSK-3 confirmatory assays. A drug repurposing experiment linking pharmacophore matching with drug information originating from multiple data sources was performed. A five-point pharmacophore model was built consisting of a hydrogen bond acceptor (A), hydrogen bond donor (D), hydrophobic (H), and two rings (RR). An atom-based 3D quantitative structure–activity relationship (QSAR) model showed good correlative and satisfactory predictive abilities (training set \({R}^{2}= 0.904\); test set: \({Q}^{2}= 0.676\); whole data set: stability \(s = 0.803\)). Virtual screening experiments revealed that selective GSK-3 inhibitors are ranked preferentially by Hypo-1, but fail to retrieve nonselective compounds. The pharmacophore and 3D QSAR models can provide assistance to design novel, potential GSK-3 inhibitors with high potency and selectivity pattern, with potential application for the treatment of GSK-3-driven diseases. A class of purine nucleoside antileukemic drugs was identified as potential inhibitor of GSK-3, suggesting the reassessment of the target range of these drugs.     

Biological activity of aldose reductase and lipophilicity of pyrrolyl-acetic acid derivatives

Quantitative Structure-Activity Relationship modeling is a powerful approach for correlating an organic compound to its lipophilicity. In this paper QSAR models are established for estimation of correlation of the lipophilicity of a series of pyrrolyl-acetic acid derivatives, inhibitors of the aldose reductase enzyme, in the n-octanol-water system with biological activity of aldose reductase. Lipophilicity, expressed by the logarithm of n-octnol-water partition coefficient log P and biological activity of aldose reductase inhibitory activity by log it. Result obtained by QSAR modeling of compound series reveal a definite trend in biological activity and a further improvement in quantitative relationships are established if, beside log P, Hammett electronic constant σ and connectivity index chi-3 (³ χ) term included in the regression equation.     

Docking and quantitative structure–activity relationship studies for sulfonyl hydrazides as inhibitors of cytosolic human branched-chain amino acid aminotransferase

We have performed the docking of sulfonyl hydrazides complexed with cytosolic branched-chain amino acid aminotransferase (BCATc) to study the orientations and preferred active conformations of these inhibitors. The study was conducted on a selected set of 20 compounds with variation in structure and activity. In addition, the predicted inhibitor concentration (IC₅₀) of the sulfonyl hydrazides as BCAT inhibitors were obtained by a quantitative structure–activity relationship (QSAR) method using three-dimensional (3D) vectors. We found that three-dimensional molecule representation of structures based on electron diffraction (3D-MoRSE) scheme contains the most relevant information related to the studied activity. The statistical parameters [cross-validate correlation coefficient (Q ² = 0.796) and fitted correlation coefficient (R ² = 0.899)] validated the quality of the 3D-MoRSE predictive model for 16 compounds. Additionally, this model adequately predicted four compounds that were not included in the training set.     

Chronic administration of R-flurbiprofen attenuates learning impairments in transgenic amyloid precursor protein mice

Background  

Long-term use of non-steroidal anti-inflammatory drugs (NSAIDs) is associated with a reduced incidence of Alzheimer's disease (AD). We and others have shown that certain NSAIDs reduce secretion of Aβ42 in cell culture and animal models, and that the effect of NSAIDs on Aβ42 is independent of the inhibition of cyclooxygenase by these compounds. Since Aβ42 is hypothesized to be the initiating pathologic molecule in AD, the ability of these compounds to lower Aβ42 selectively may be associated with their protective effect. We have previously identified R-flurbiprofen (tarenflurbil) as a selective Aβ42 lowering agent with greatly reduced cyclooxygenase activity that shows promise for testing this hypothesis. In this study we report the effect of chronic R-flurbiprofen treatment on cognition and Aβ loads in Tg2576 APP mice.     

Comparative molecular field analysis and comparative molecular similarity indices analysis of hydroxyethylamine derivatives as selective human BACE-1 inhibitor

Three-dimensional quantitative structure–activity relationship (3D-QSAR) models were developed based on comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), on a series of 43 hydroxyethylamine derivatives, acting as potent inhibitors of β-site amyloid precursor protein (APP) cleavage enzyme (BACE-1). The crystal structure of the BACE-1 enzyme (PDB ID: 2HM1) with one of the most active compound 28 was available, and we assumed it to be the bioactive conformation of the studied series, for 3D-QSAR analysis. Statistically significant 3D-QSAR model was established on a training set of 34 compounds, which were validated by a test set of 9 compounds. For the best CoMFA model, the statistics are, r ² =  0.998, r²_cv = 0.810{r^{2}_{\rm cv} = 0.810} , n =  34 for the training set and r²_pred = 0.934{r^{2}_{\rm pred} = 0.934} , n = 9 for the test set. For the best CoMSIA model (combined steric, electrostatic, hydrophobic, and hydrogen bond donor fields), the statistics are r ² =  0.978, r²_cv = 0.754{r^{2}_{\rm cv} = 0.754} , n =  34 for the training set and r²_pred = 0.750{r^{2}_{\rm pred} = 0.750} , n =  9 for the test set. The resulting contour maps, produced by the best CoMFA and CoMSIA models, were used to identify the structural features relevant to the biological activity in this series of analogs. The data generated from the present study will further help to design novel, potent, and selective BACE-1 inhibitors.     

QSAR for RNases and theoretic–experimental study of molecular diversity on peptide mass fingerprints of a new <Emphasis Type="Italic">Leishmania infantum</Emphasis> protein

The toxicity and low success of current treatments for Leishmaniosis determines the search of new peptide drugs and/or molecular targets in Leishmania pathogen species (L. infantum and L. major). For example, Ribonucleases (RNases) are enzymes relevant to several biologic processes; then, theoretical and experimental study of the molecular diversity of Peptide Mass Fingerprints (PMFs) of RNases is useful for drug design. This study introduces a methodology that combines QSAR models, 2D-Electrophoresis (2D-E), MALDI-TOF Mass Spectroscopy (MS), BLAST alignment, and Molecular Dynamics (MD) to explore PMFs of RNases. We illustrate this approach by investigating for the first time the PMFs of a new protein of L. infantum. Here we report and compare new versus old predictive models for RNases based on Topological Indices (TIs) of Markov Pseudo-Folding Lattices. These group of indices called Pseudo-folding Lattice 2D-TIs include: Spectral moments π _k (x,y), Mean Electrostatic potentials ξ _k (x,y), and Entropy measures θ _k (x,y). The accuracy of the models (training/cross-validation) was as follows: ξ _k (x,y)-model (96.0%/91.7%)>π _k (x,y)-model (84.7/83.3) > θ _k (x,y)-model (66.0/66.7). We also carried out a 2D-E analysis of biological samples of L. infantum promastigotes focusing on a 2D-E gel spot of one unknown protein with M<20, 100 and pI <7. MASCOT search identified 20 proteins with Mowse score >30, but not one >52 (threshold value), the higher value of 42 was for a probable DNA-directed RNA polymerase. However, we determined experimentally the sequence of more than 140 peptides. We used QSAR models to predict RNase scores for these peptides and BLAST alignment to confirm some results. We also calculated 3D-folding TIs based on MD experiments and compared 2D versus 3D-TIs on molecular phylogenetic analysis of the molecular diversity of these peptides. This combined strategy may be of interest in drug development or target identification.     

Efficient synthesis and free-radical scavenging capacity of new 2,4-substituted tetrahydroquinolines prepared via BiCl<Subscript>3</Subscript>-catalyzed three-component Povarov reaction,using <Emphasis Type="Italic">N</Emphasis>-vinylamides

Efficient synthesis of new structurally different 2-(het)aryl-4-amidyl-substituted tetrahydroquinolines 8–29 is reported. The synthesis based on BiCl₃-catalyzed three-component Povarov reaction between anilines, (het)aryl aldehydes and enamides offers a fast, safe, and cheap way for efficient tetrahydroquinoline libraries construction. Using N-vinylamides (N-vinylpyrrolidin-2-one and N-vinylacetamide) in this reaction, it was possible to obtain two series of different cis tetrahydroquinolines with antioxidant properties. Among 14 tested compounds, 7 tetrahydroquinolines revealed a prominent anti-radical capacity, equal or higher than that of the commercial antioxidants. Being the most active molecule, the N-[2-(α-furanyl)-6-methoxy-1,2,3,4-tetrahydroquinolin-4-yl] acetamide 21 was ca. 2.2-fold more potent than the well-known antioxidant, vitamin E (α-tocopherol).     

Spin-phonon coupling in multiferroic manganites RMnO3: comparison of pure (R = Eu, Gd, Tb) and substituted (R = Eu1-xYx) compounds

For rare-earth manganite RMnO₃ compounds spin-phonon coupling manifests itself as a phonon softening in the temperature range of the magnetically ordered phases. Within this class of materials, a continuous tuning of the lattice and thus also of the magnetic properties of multiferroic manganites is achieved by Y doping in substituted Eu_{1- x} Y _x MnO₃. We compare the impact on spin-phonon coupling within this partial-substitution approach in a series of Eu_{1- x} Y _x MnO₃ samples 0 ≤ x ≤ 0.5) with the effect of a complete exchange of the rare earth ions R³⁺ in a series of pure RMnO₃ compounds (R = Eu, Gd, Tb). For this purpose we employ polarized Raman scattering in the 10–300 K temperature range. The low-temperature results show phonon softening in all investigated compounds. For decreasing R³⁺ radius, i.e. an increasing orthorhombic distortion and magnetic frustration, we observe in both systems a weakening of the spin-phonon coupling. For known sublattice magnetization within the MnO₂-plane, quantitative results for the spin-phonon coupling constant are derived for both cases within a molecular field approximation. Our results show, that the spin-phonon coupling strength in the magnetically ordered phases of the various investigated manganites does not correlate with the magnetization pattern. Instead, the pure RMnO₃ compounds and the substituted Eu_{1- x} Y _x MnO₃ fit excellently within a common scheme, in which the weakening of the spin-phonon coupling reflects the degree of tilting of the MnO₆ octahedra due to the orthorhombic distortion of the crystal lattice.     

X-ray,electrical conductivity,magnetic and infrared studies of the system Co2−x Ge1−x Fe2x O4

X-ray, electrical conductivity, magnetic hysteresis and IR studies for the system Co_2−x Ge_1−x Fe_2x O₄ were carried out. All the compounds, 0⩽x⩽1, showed cubic symmetry. X-ray intensity calculations, magnetic hysteresis measurements and IR studies indicated the presence of Ge⁴⁺ at tetrahedral, Co²⁺ at octahedral and Fe³⁺ at both the sites. The activation energy and threshold frequency decreased with increasing value ofx. The compounds withx⩽0.5 arep-type and those withx⩾0.75 aren-type semiconductors. Magnetic hysteresis indicated that all the compounds are ferrimagnetic except forx=0 which is antiferromagnetic. The shapes of χ/χ _i vsT plots, highH _c values andJ _R/J_s ratios showed that all the compounds exceptx=0 exhibit single-domain behaviour. Curie temperature,T _c increased with increasing Fe³⁺ ions. The probable ionic configuration for the system is suggested as Ge _1−x ⁴⁺ Fe _x ³⁺ [co _2−x ²⁺ Fe _x ³⁺ ]O ₄ ²⁻ .     

Spectral-luminescent properties of condensation products of 8-aminoquinoline,aromatic aldehydes,and dimedone

Hydrobenzophenanthrolinone derivatives were synthesized by three-component condensation of 8-aminoquinoline, aromatic aldehydes, and dimedone. The structures of the obtained substances were confirmed by NMR and IR spectroscopy and mass spectrometry. Spectral-luminescent investigations of the synthesized compounds showed that they were characterized by high oscillator strengths for allowed electronic transitions S _n ← S ₀ (n = 1–3). Low fluorescence quantum yields in EtOH (Φ_fl ~ 10^–4–10^–3) and an increase of the Φfl values in toluene (~10^–2) at room temperature and with lowering the temperature to 77 K (Φ_fl ~ 10^–1) for a number of the compounds under study were satisfactorily explained within the framework of Marcus theory.     

Magnetic studies of colossal magnetoresistance perovskites on macroscopic,mesoscopic and microscopic length scales

We have investigated magnetic correlations in various CMR manganites on macroscopic, mesoscopic and microscopic length scales by carrying out DC magnetization, neutron depolarization, and neutron diffraction measurements. We present here the effect of substituting Mn with Fe and La with Dy in the ferromagnetic La_0.7−xCa_xMnO₃ (x ∼ 0.3–0.33) compounds. Neutron diffraction has been used in order to characterize the long-range magnetic order and its gradual suppression by the substitution. Neutron depolarization study has been carried out in order to bridge the gap in our understanding regarding the nature of magnetic correlation obtained from the macroscopic and microscopic measurements. In particular, our study on La_0.67Ca_0.33Mn_0.9Fe_0.1O₃ has established the fact that a true double exchange mediated spin-glass is insulating. In another study of La-site ionic size effect and its disorder in (La_1−x Dy _x )_0.7Ca_0.3MnO₃, we have investigated the evolution of the length scale of magnetic ordering with a possible microscopic explanation and the results have been compared with that for the light rare earth substituted compounds.     

Anisotropic Scattering in Accordance with Pomraning Phase Function

The emergent intensity I(0,μ) from the equation of transfer in anisotropically scattering medium with Pomraning phase function is derived in n ^th approximation by using Chandrasekhar’s discrete ordinate method. AMS classification: 85A25