Discovery of a new Bcl-2 inhibitor through synthesis, anticancer activity, docking and MD simulations.

A database of 300 compounds was virtually screened and docked against Bcl-2 protein; the stability of the best-formed complex was evaluated through Molecular dynamics, the top ten compounds with the best in-silico complexation affinities were synthesized, and their In-vitro cytotoxic activity was examined. Thiazolidinone (4e) and isoxazoline (4a-d) were evaluated in-silico. For further evaluation and examination, we designed and synthesized from naturally occurring (R)-carvone and characterized it via spectroscopic analysis, as well as tested for their anticancer activities towards human cancer cell lines such as HT-1080 (fibrosarcome cancer), MCF-7 and MDA-MB-231 (breast cancer) and A-549 (lung cancer) by using MTT method with Doxorubicin as standard drug. Among them, compound 4d showed the most promising anticancer activity against HT-1080, A-549, MCF-7, and MDA-MB-231 cell lines with IC50 values of 15.59 ± 3.21 µM; 18.32 ± 2.73 µM; 17.28 ± 0.33 µM and 19.27 ± 2.73 µM respectively.Communicated by Ramaswamy H. Sarma.

In silico discovery of novel inhibitors from Northern African natural products database against main protease (Mpro) of SARS-CoV-2.

The recent outbreak of COVID-19 (Coronavirus Disease 2019), caused by a novel SARS-CoV-2 virus, has led to public health emergencies worldwide where time is as important as equipment to save lives. Antimalarial drugs such as hydroxychloroquine and chloroquine derivatives are used in emergencies but they are not suitable for patients with high blood pressure, diabetes and heart problems. Since there are no approved drugs for this disease, science is challenged to find vaccines and new drugs. Therefore, as part of our Silico drug design strategy, we identified drug-like compounds that inhibit replication of the main protease (Mpro) of SARS-CoV-2 based on receptor-based virtual database screening, molecular docking, molecular dynamics, and drug-similarity profiling from the NANPDB natural products database available at North African. The two resulting hit compounds named 5- Chloro-Omega-hydroxy-1-O-methylemodin and cystodion E showed the highest binding energy with Mpro of SARS-CoV-2 and strong inhibitory activity compared with the previously published N3 inhibitor. The complexes of these two compounds were validated by molecular dynamics analysis (RMSD, RMSF, Rg, total number of hydrogen bonds and secondary structure fractions of the protein in the complex) as the best method to evaluate the biological stability of the system. Therefore, these molecules deserve more attention in drug development compared to COVID-19. HighlightsA large database of natural compounds was screened against nCoV-2's Mpro.Molecular docking and Molecular dynamics were used as powerful methods.Two compounds were found are very attractive to inhibit Mpro of nCoV-2.ADME-Tox profiling is evaluated the active compounds are not cancerogenic.Communicated by Ramaswamy H. Sarma.

Synthesis of eugenol derivative by the ring opening of epoxide eugenol and its analysis through chemical reactivity: a DFT approach.

Eugenol, a plant bioactive component, is frequently found in a variety of medicinal plants with well-defined functional attributes. Essential oils containing eugenol were extracted from buds of Eugenia caryophyllata commonly named clove using hydrodistillation. Afterwards, the analysis of the essential oils using gas chromatography/mass spectrometry (GC/MS) shows that eugenol is the major constituent with 70.14% of it. The alkene group in eugenol was epoxidised using m-chloroperbenzoic acid leading to the synthesis of epoxide eugenol. The epoxide ring was cleaved to vanillyl glycol by mixed the epoxide eugenol with aluminum chloride hydrate in an ethanolic medium. A Density Functional Theory (DFT) study was investigated to understand the reactivity of the epoxide eugenol with the aluminum chloride hydrate. The results obtained from DFT based reactivity descriptors were in good agreement with the experiment results.

Insecticidal Activities of Atriplex halimus L., Salvia rosmarinus Spenn. and Cuminum cyminum L. against Dactylopius opuntiae (Cockerell) under Laboratory and Greenhouse Conditions.

The wild cochineal Dactylopius opuntiae (Hemiptera: Dactylopiidae) is one of the major insect pests of the prickly pear Opuntia ficus-indica (L.) in Morocco, a well-known fruit and vegetable crop of arid and semi-arid regions around the world. The present study investigated the insecticidal potential of six extracts (three aqueous and three hydroalcoholic (MeOH/H2O, 20/80 (v/v)) from Atriplex halimus (leaves), Salvia rosmarinus (leaves) and Cuminum cyminum (seeds) to control nymphs and adult females of D. opuntiae under laboratory and greenhouse conditions. Out of the tested samples, A. halimus aqueous extract showed the highest activity, inducing mortality rates of 67.04% (after 4 days) and 85% (after 8 days) on nymphs and adult females of D. opuntiae, respectively, at a concentration of 5% under laboratory conditions. It also showed the highest mortality rate of nymphs with 100% (4 days after application) and 83.75% of adult females (7 days after the second application) at a concentration of 5% when combined with black soap at 10 g/L under greenhouse conditions. The difference in the toxicity of plant species of the study was correlated with their saponin content. A total of 36 of these triterpene glucosides were suggested after a comprehensive LC-MSn profiling of the most active extract, A. halimus, in addition to phytoecdysones and glycosylated phenolic acids and flavonoids. These findings provided evidence that the aqueous leaf extract of A. halimus could be incorporated in the management of the wild cochineal as an alternative to chemical insecticides.

Crataegus oxyacantha Extract as a Biostimulant to Enhance Tolerance to Salinity in Tomato Plants.

Salinity is a severe abiotic problem that has harmful impacts on agriculture. Recently, biostimulants were defined as bioprotectant materials that promote plant growth and improve productivity under various stress conditions. In this study, we investigated the effect of Crataegus oxyacantha extract as a biostimulant on tomato plants (Solanum lycopersicum) grown under salt stress. Concentrations of 20 mg/L, 30 mg/L, and 70 mg/L of C. oxyacantha extract were applied to tomato plants that were grown under salt stress. The results indicated that plants that were treated with C. oxyacantha extract had a higher ability to tolerate salt stress, as demonstrated by a significant (p < 0.05) increase in plant growth and photosynthetic pigment contents, in addition to a significant increase in tomato soluble sugars and amino acids compared to the control plants. In the stressed tomato plants, malondialdehyde increased and then decreased significantly with the different concentrations of C. oxyacantha extract. Furthermore, there was a significant improvement in the antioxidant enzyme activities of superoxide dismutase (SOD), glutathione peroxidase (GPx), glutathione S-transferase (GST), and glutathione reductase (GR) in the stressed plants, especially after treatment with 70 mg/L of the extract. Overall, our results suggest that C. oxyacantha extract could be a promising biostimulant for treating tomato plants under salinity stress.

Newly synthesized (R)-carvone-derived 1,2,3-triazoles: structural, mechanistic, cytotoxic and molecular docking studies.

In the current study, natural (R)-carvone was used as starting material for the efficient synthesis of several 1,2,3-triazole derivatives. The produced products were obtained in good yields and characterized by 1H and 13C NMR and HRMS analysis. The newly synthesized monoterpenic 1,2,3-triazole 4 and derivatives were analyzed by viability tests (MTT) for their cytotoxic activity against three human cancer cells. Product 5 showed a medium antitumor activity, for which the IC50 values against selected cells HT-1080, A-549 and MCF-7 were 29.25 µM, 31.62 µM and 26.02 µM, respectively. The regioselectivity of the condensation reaction and the molecular structure of the title compounds were determined by Density Functional Theory (DFT) using B3LYP calculations at 6-311 + G(d,p) level. The orbitals HOMO and LUMO were studied to determine the electronic properties of the synthesized compounds. In addition, the global reactivity indices were used to explain the regioselectivity for the formation of compound 6, and the theoretical results agree well with the experimental results. Molecular docking and molecular dynamics confirmed the empirical test results and confirmed the stability of the complex during inhibition of the anti-apoptotic protein for killing cancer cells. Communicated by Ramaswamy H. Sarma.

Electronic investigation and spectroscopic analysis using DFT with the long-range dispersion correction on the six lowest conformers of 2.2.3-trimethyl pentane.

The conformational stability and internal rotation barriers, HOMO-LUMO gap and related properties, molecular static polarizability and hyperpolarizability parameters, and the NBO delocalization energies associated with the internal charge transfer (ICT) of 2.2.3-trimethylpentane in the ground state were carried out taking into account the long range dispersion correction through CAM-B3LYP and WB97XD levels at aug-cc-pvtz basis set. The six lowest conformations were differentiated by a deep and multiple spectroscopic investigation. The ultraviolet-visible (UV-Vis) absorption bands are assigned using molecular orbital data obtained by TD-WB97XD/aug-cc-pvtz calculations, and carbon 13C NMR signal peaks have been assigned using GIAO-WB97XD/aug-cc-pvtz method. In addition, the normal mode calculations of the most and less stable conformers using a scaled force field in terms of non-redundant local symmetry coordinates have been confronted to the experimental vibrational spectra temperature dependency.

Insights into evolutionary interaction patterns of the 'Phosphorylation Activation Segment' in kinase.

We are interested in studying the phosphorylation of the kinase activation loop, distinguishing the passage from the unphosphorylated to the phosphorylated form without allostery. We performed an interaction study to trace the change of interactions between the activation segment and the kinase catalytic core, before and after phosphorylation. Results show that the structural changes are mainly due to the attraction between the phosphate group and guanidine groups of the arginine side chains of RD-pocket, which are constituted mainly of guanidine groups of the catalytic loop, the ß9, and the αC helix. This attraction causes propagation of structural variation of the activation segment, principally towards the N-terminal. The structural variations are not made on all the amino acids of the activation segment; they are conditioned by the existence of two beta sheets stabilizing the loop during phosphorylation. The first,ß6-ß9 sheet is usually present in most of the kinases; the second, ß10-ß11 is formed due to the interaction between the main chain amino acids of the activation loop and the αEF/αF loop.

Ab initio study on the six lowest energy conformers of iso-octane: conformational stability, barriers to internal rotation, natural bond orbital and first-order hyperpolarizability analyses, UV and NMR predictions, spectral temperature sensitivity, and scaled vibrational assignment.

In this paper, we present the quantum electronic study of iso-octane, based on MP2 and B3LYP methods using the 6-311++G(d,p) basis set. In addition to conformational stability and internal rotation barriers studies, the delocalization energies associated with the internal charge transfer (ICT) within each of the six lowest energy conformers were evaluated using NBO analysis. With the aim to differentiate even more between these conformers, the energy gap between HOMO and LUMO orbitals, chemical softness, and first-order hyperpolarizability (nonlinear optics property) were evaluated. Similarly, their spectral behavior was investigated at different levels; the ultraviolet (UV) absorption bands were assigned using molecular orbitals data obtained by TD-B3LYP calculations with 6-311++G(d,p) basis set, while carbon 13C NMR and proton 1H signal peaks were assigned using the GIAO-B3LYP/6-311++G(d,p) method. In addition, the normal mode calculations of the most and least stable conformers using a scaled force field in terms of nonredundant local symmetry coordinates were carried out to approach the vibrational spectra temperature dependency.

Combining a QSAR Approach and Structural Analysis to Derive an SAR Map of Lyn Kinase Inhibition.

Lyn kinase, a member of the Src family of protein tyrosine kinases, is mainly expressed by various hematopoietic cells, neural and adipose tissues. Abnormal Lyn kinase regulation causes various diseases such as cancers. Thus, Lyn represents, a potential target to develop new antitumor drugs. In the present study, using 176 molecules (123 training set molecules and 53 test set molecules) known by their inhibitory activities (IC50) against Lyn kinase, we constructed predictive models by linking their physico-chemical parameters (descriptors) to their biological activity. The models were derived using two different methods: the generalized linear model (GLM) and the artificial neural network (ANN). The ANN Model provided the best prediction precisions with a Square Correlation coefficient R² = 0.92 and a Root of the Mean Square Error RMSE = 0.29. It was able to extrapolate to the test set successfully (R² = 0.91 and RMSE = 0.33). In a second step, we have analyzed the used descriptors within the models as well as the structural features of the molecules in the training set. This analysis resulted in a transparent and informative SAR map that can be very useful for medicinal chemists to design new Lyn kinase inhibitors.