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.

A simple synthesis of α-Costic acid analogue with antibacterial potential, DFT and molecular docking

Natural products extracted from plants has been recognized as the most efficient starting materials to synthesize new derivatives of medicinal interest. Our research focuses on the isolation and characterization of sesquiterpene derivatives from Dittrichia Viscosa (L), as well as their hemisynthesis. To that end, a phytochemical study of Dittrichia viscosa leaves was conducted in order to obtain a sesquiterpenoid, α -Costic acid, which will be further transformed to γ -Costic acid with high yield using simple processes. Optimized molecular geometry and vibrational frequencies of both products were computed using the density functional theory. In addition, the antibacterial activity of isolated and hemisynthesized products were analyzed in vitro against Escherichia coli resistant to β-lactamase 616, Pseudomonas aeruginosa, and Staphylococcus aureus. The obtained compounds were investigated by in silico biological method to evaluate their potential inhibitory activity against same strains using FtsA, LasR proteins and DNA polymerase III enzyme.

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.

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.

Fingerprint-based 2D-QSAR Models for Predicting Bcl-2 Inhibitors Affinity

Background:

Bcl-2 family plays an essential role in the cell cycle events incorporating survival, proliferation, and differentiation in normal and neoplastic neuronal cells. Thus, it has been validated as a principal target for the treatment of cancer. For this reason, we will build a model based on a large number of Bcl-2 inhibitors to predict the activities of new compounds as future Bcl-2 inhibitors.

Methods:

In this study, QSAR models were successfully used to predict the inhibitory activity against Bcl-2 for a set of compounds collected from BDB (Binding database). The kPLS (kernelbased Partial Least-Square) method implemented in Schrodinger's Canvas, was used for searching the correlation between pIC50 and binary fingerprints for a set of known Bcl-2 inhibitors.

Results and Discussion:

Models based on binary fingerprints with two kPLS factors have been found with decent predictive power (q2 > 0.58), while the optimal number of factors is about 5. The enrichment study (148 actives, 5700 decoys) has shown excellent classification ability of our models (AUC > 0.90) for all cases).

Conclusion:

We found that the kPLS method, in combination with binary fingerprints, is useful for the affinity prediction and the Bcl-2 inhibitors classification. The obtained promising results, methods, and applications highlighted in this study will help us to design more selective Bcl-2 inhibitors with better structural characteristics and improved anti-cancer activity.

Towards a theoretical understanding of alkaloid-extract Cytisine derivatives of Retama monosperma (L.) Boiss. Seeds, as eco-friendly inhibitor for carbon steel corrosion in acidic 1M HCl solution

Because of their availability, lower cost, biodegradability, respect for health, environmental standards and their extremely high efficiency [Benmessaoud Left D, Zertoubi M, Irhzo A, Azzi M, Revue: Huiles et extraits de plantes comme inhibiteurs de corrosion pour différents métaux et alliages dans le milieu acide chlorhydrique, J Mater Environ Sci 4:855–866, 2013], the green corrosion inhibitors are currently the most sought after candidates. The ultimate aim of this work is to study the selectivity and reactivity of a series of three molecules, namely Cytisine, Dehydro-Cytisine and N-methyl Cytisine which are the major constituents of Retama monosperma seeds alkaloid extract (AERS) as eco-friendly inhibitors of corrosion of carbon steel in acidic medium HCl (1M), using the density functional theory (DFT) at B3LYP/aug-cc-pvdz levels. Indeed, this alkaloid extract AERS has proven experimentally its corrosion inhibitory power for carbon steel in 1 M HCl even at lower concentration (94.42% at 400[Formula: see text]mg/L). Besides, its adsorption on the steel surface in 1 M HCl solution followed Langmuir’s isotherm [El Hamdani N, Fdil R, Tourabi M, Jama C, Bentiss F, Alkaloids extract of Retama monosperma (L.) Boiss. seeds used as novel eco-friendly inhibitor for carbon steel corrosion in 1 M HCl solution: Electrochemical and surface studies, Appl Surf Sci 357:1294–1305, 2015, doi: 10.1016/j.apsusc.2015.09.159; El Hamdani N, Contribution a la valorisation des parties aériennes de Retama Monosperma, phytochimie, activités antimicrobiennes et propriétés anticorrosives, Universite Chouaib Doukkali Faculte des sciences El jadida, 2015]. Herein, the major aim of this work is to investigate the likelihood of the carbon steel corrosion being inhibited by the protonated species in the aqueous acidic solution. For this purpose, after proving that the most favorable protonation site for protonation was N9, we have evaluated the structural, global and local reactivity descriptors, partial atomic charge in terms of Natural bond orbital (NBO) of the three protonated inhibitors at the level of N9, which are the most stable in the aqueous acidic solution. NBO analysis and the thermodynamic properties such as entropy, enthalpy, heat capacity and Gibbs free energy were also done. In conclusion, it was observed that three protonated molecules showed a high propensity to adsorb to the mild steel surface with a priority of the molecule d-CytN9H+.

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 β9, 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,β6-β9 sheet is usually present in most of the kinases; the second, β10-β11 is formed due to the interaction between the main chain amino acids of the activation loop and the αEF/αF loop.

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.