Integrative Approach for Designing Novel Triazole Derivatives as α-Glucosidase Inhibitors: QSAR, Molecular Docking, ADMET, and Molecular Dynamics Investigations.

In response to the increasing prevalence of diabetes mellitus and the limitations associated with the current treatments, there is a growing need to develop novel medications for this disease. This study is focused on creating new compounds that exhibit a strong inhibition of alpha-glucosidase, which is a pivotal enzyme in diabetes control. A set of 33 triazole derivatives underwent an extensive QSAR analysis, aiming to identify the key factors influencing their inhibitory activity against α-glucosidase. Using the multiple linear regression (MLR) model, seven promising compounds were designed as potential drugs. Molecular docking and dynamics simulations were employed to shed light on the mode of interaction between the ligands and the target, and the stability of the obtained complexes. Furthermore, the pharmacokinetic properties of the designed compounds were assessed to predict their behavior in the human body. The binding free energy was also calculated using MMGBSA method and revealed favorable thermodynamic properties. The results highlighted three novel compounds with high biological activity, strong binding affinity to the target enzyme, and suitability for oral administration. These results offer interesting prospects for the development of effective and well-tolerated medications against diabetes mellitus.

Insights into the inhibitory potential of novel hydrazinyl thiazole-linked indenoquinoxaline against alpha-amylase: a comprehensive QSAR, pharmacokinetic, and molecular modeling study.

The rising prevalence of diabetes necessitates the development of novel drugs, especially given the side effects associated with current medications like Acarbose and Voglibose. A series of 36 Hydrazinyl thiazole-linked indenoquinoxaline derivatives with notable activity against alpha-amylase were studied. To create a molecular model predicting alpha-amylase activity, a QSAR study was performed on these compounds. Molecular descriptors were calculated using Chem3D and Gaussian software and then correlated with their IC50 biological activities to form a dataset. This model data was refined using PCA and modeled with MLR. The model's performance was statistically verified (R2 =0.800; Radj2 = 0.767; Rcv2 = 0.651) and its applicability domain was defined. It was predicted to possess high predictive power (Rtest2  = 0.872). Based on this, new compounds were proposed, and their activities were predicted using the developed model. Additionally, their binding ability to the biological target was studied through molecular docking and dynamics. Their pharmacokinetics were also evaluated using ADMET predictions. Two designed compounds named AE and AB emerged as particularly promising, displaying properties that suggest substantial therapeutic potential and they can form stable complexes into the binding pocket of alpha-amylase enzyme.Communicated by Ramaswamy H. Sarma.

Genotoxic effects and mitosis aberrations of chromium (VI) on root cells of Vicia faba and its molecular docking analysis.

Like other heavy metals, Cr (VI) is a powerful carcinogen and mutagen agent. Its toxic effects on plants are well considered. In order to elucidate its adverse effects, the present work aims to study the mitosis aberrations of Cr (VI) on the Vicia faba root-cells and its molecular docking analysis to understand the genotoxicity mechanisms. In-vivo, Vicia faba plants were exposed to 50 and 100 µM Cr (VI) for 48 h. In-silico, molecular docking and molecular dynamics simulation were used to study the interactions between dichromate and tubulin tyrosine ligase T2R-TTL (PDBID: 5XIW) with reference to Colchicine (microtubule inhibitor). According to our results, Cr (VI) affects growth and cell division and also induces many mitosis aberrations such as chromosome sticking, anaphase/telophase bridges, lagging chromosomes and fragmentation during all phases of mitosis. On the one hand, Cr (VI) reduces mitotic index and promotes micronuclei induction. The in-silico results showed that dichromate establishes very strong bonds at the binding site of the tubulin tyrosine ligase T2R-TTL, with a binding affinity of -5.17 Kcal/Mol and an inhibition constant of 163.59 µM. These interactions are similar to those of colchicine with this protein, so dichromate could be a very potent inhibitor of this protein's activity. TTL plays a fundamental role in the tyrosination/detyrosination of tubulin, which is crucial to the regulation of the microtubule cytoskeleton. Its inhibition leads to the appearance of many morphogenic abnormalities such as mitosis aberrations. In conclusion, our data confirm the highest genotoxicity effects of Cr (VI) on Vicia faba root-cells.

Design, synthesis, In-vitro, In-silico and DFT studies of novel functionalized isoxazoles as antibacterial and antioxidant agents.

A series of new isoxazolederivatives incorporating the sulfonate ester function has been synthesized from 2-benzylidenebenzofuran-3(2 H)-one, known as aurone. The synthesis of the target compounds was carried out following an efficient methodology that allows access to the desired products in a reproducible way and with good yield. The structures of the synthesized compounds were established using NMR (1H and 13C) spectroscopy and mass spectrometry. A theoretical study was performed to optimize the geometrical structures and to calculate the structural and electronic parameters of the synthesized compounds. The calculations were also carried out to understand the influence and the effect of substitutions on the chemical reactivity of the studied compounds. The synthesized isoxazoles were screened for their antioxidant and antibacterial activities. The findings demonstrate that the studied compounds exhibit good to moderate antibacterial activity against the tested bacteria (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli). Moreover, a number of the tested isoxazole derivatives exhibit high effectiveness against DPPH free radicals. Besides that, molecular docking studies were carried out to predict binding affinity and identify the most likely binding interactions between the active molecules and the target microorganisms' proteins. A 100 ns molecular dynamics study was then conducted to examine the dynamic behavior and stability of the highly potent isoxazole 4e in complex with the target bacterial proteins. Finally, the ADMET analyses suggest that all the synthesized isoxazoles have good pharmacokinetic profiles and non-toxicity and non-carcinogenicity in biological systems.

Structure-based virtual screening, ADMET analysis, and molecular dynamics simulation of Moroccan natural compounds as candidates for the SARS-CoV-2 inhibitors.

The lack of treatments and vaccines effective against SARS-CoV-2 has forced us to explore natural compounds that could potentially inhibit this virus. Additionally, Morocco is renowned for its rich plant diversity and traditional medicinal uses, which inspires us to leverage our cultural heritage and the abundance of natural resources in our country for therapeutic purposes. In this study, an extensive investigation was conducted to gather a collection of phytoconstituents extracted from Moroccan plants, aiming to evaluate their ability to inhibit the proliferation of the SARS-CoV-2 virus. Molecular docking of the studied compounds was performed at the active sites of the main protease (6lu7) and spike (6m0j) proteins to assess their binding affinity to these target proteins. Compounds exhibiting high affinity to the proteins underwent further evaluation based on Lipinski's rule and ADME-Tox analysis to gain insights into their oral bioavailability and safety. The results revealed that the two compounds demonstrated strong binding affinity to the target proteins, making them potential candidates for oral antiviral drugs against SARS-CoV-2. The molecular dynamics results from this computational analysis supported the overall stability of the resulting complex.

Synthesis, biological evaluation and molecular modelling of 3-Formyl-6-isopropylchromone derived thiosemicarbazones as α-glucosidase inhibitors.

Type-2 Diabetes Mellitus (T2DM) is one of the most common metabolic disorders in the world and over the past three decades its incidence has increased drastically. α-Glucosidase inhibitors are used to control the hyperglycemic affect of T2DM. Herein, we report the synthesis, α-glucosidase inhibition, structure activity relationship, pharmacokinetics and docking analysis of various novel chromone based thiosemicarbazones 3(a-r). The derivatives displayed potent activity against α-glucosidase with IC50 in range of 0.11 ± 0.01-79.37 ± 0.71 µM. Among all the synthesized compounds, 3a (IC50 = 0.17 ± 0.026 µM), 3 g (IC50 = 0.11 ± 0.01 µM), 3n (IC50 = 0.55 ± 0.02 µM), and 3p (IC50 = 0.43 ± 0.025 µM) displayed higher inhibitory activity as compared to the standard, acarbose. Moreover, we have developed a statistically significant 2D-QSAR model (R2tr:0.9693; F: 50.4647 and Q2LOO:0.9190), which can be used in future to further design potent thiosemicarbazones as inhibitors of α-glucosidase.

The anti-SARS-CoV-2 activity of novel 9, 10-dihydrophenanthrene derivatives: an insight into molecular docking, ADMET analysis, and molecular dynamics simulation.

Originating in Wuhan, the COVID-19 pandemic wave has had a profound impact on the global healthcare system. In this study, we used a 2D QSAR technique, ADMET analysis, molecular docking, and dynamic simulations to sort and evaluate the performance of thirty-nine bioactive analogues of 9,10-dihydrophenanthrene. The primary goal of the study is to use computational approaches to create a greater variety of structural references for the creation of more potent SARS-CoV-2 3Clpro inhibitors. This strategy is to speed up the process of finding active chemicals. Molecular descriptors were calculated using 'PaDEL' and 'ChemDes' software, and then redundant and non-significant descriptors were eliminated by a module in 'QSARINS ver. 2.2.2'. Subsequently, two statistically robust QSAR models were developed by applying multiple linear regression (MLR) methods. The correlation coefficients obtained by the two models are 0.89 and 0.82, respectively. These models were then subjected to internal and external validation tests, Y-randomization, and applicability domain analysis. The best model developed is applied to designate new molecules with good inhibitory activity values against severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). We also examined various pharmacokinetic properties using ADMET analysis. Then, through molecular docking simulations, we used the crystal structure of the main protease of SARS-CoV-2 (3CLpro/Mpro) in a complex with the covalent inhibitor "Narlaprevir" (PDB ID: 7JYC). We also supported our molecular docking predictions with an extended molecular dynamics simulation of a docked ligand-protein complex. We hope that the results obtained in this study can be used as good anti-SARS-CoV-2 inhibitors.

In vitro and in silico analysis for elucidation of antioxidant potential of Djiboutian Avicennia Marina (Forsk.) Vierh. phytochemicals.

The present work aims to study the phytochemical composition, the antioxidant capacity of the crude extracts, and the fraction of extract giving the best antioxidant activity of Avicennia marina. The leaves contain high TFC compared to other parts of the plant, whereas fruits have the highest amount of TPC. Fat-soluble pigments are strongly present in the leaves of Avicennia marina i.e. ß-carotene, lycopene, chlorophyll a, and chlorophyll b. The crude methanolic flower extracts showed strong DPPH and ABTS radical scavenging activity with IC50 values of 0.30 and 0.33 mg/mL respectively compared to the leaf and stem methanolic extracts for the DPPH and ABTS models with a value IC50 greater than 1 mg/mL. The crude fruit extract shows good activity with the ABTS model, unlike the DPPH model whose IC50 values are 0.95 and 0.38 mg/mL, respectively. Fractionation improved the antioxidant effect of crude flower extract. The ethyl acetate fraction exhibits the best antioxidant activity for both DPPH and ABTS methods with IC50 values of 0.125 and 0.16 mg/mL. The HR-LCMS/MS led to the identification of 13 compounds: 6 flavonoids and 7 iridoid glycoside compounds in the different parts of the plant. A bioinformatics study was performed to evaluate the antioxidant activity of the three major Iridoid glycosides towards the target protein Catalase compound II through free binding energy. Out of these three iridoid glycosides, compound C10 does not represent any toxicity, unlike C8 and C9 which showed an irritancy effect. Furthermore, molecular dynamics shows good stability of the C10-2CAG complex. HighlightsExtraction and fractionation of different part (leaf, stem, flower and fruit) of Avicennia marina.Botanical description and phytochemical analysis of crude extract methanolic. Investigation by HR-LCMS characterization of polyphenols and iridoid glycosides.Evaluation the antioxidant activity of crudes extracts methanolics by two methods in vitro DPPH and ABTS.Antioxidant activity of the fraction of the crude flower extracts presenting the best biological response.Evaluate the contribution of three major compounds 2'-Cinnamoylmussaenosidic acid, 10-O-[E-Cinnamoyl]-geniposidic acid and 10-O-[(E)-p-Coumaroyl]-geniposidic acid in the ethyl acetate fraction on the antioxidant activity through docking and dynamic molecular.Communicated by Ramaswamy H. Sarma.

A computer-aided drug design approach to explore novel type II inhibitors of c-Met receptor tyrosine kinase for cancer therapy: QSAR, molecular docking, ADMET and molecular dynamics simulations.

Small molecules such as 4-phenoxypyridine derivatives have remarkable inhibitory activity against c-Met enzymatic activity and proliferation of cancer cell lines. Since there is a relationship between structure and biological activity of these molecules, these little compounds may have great potential for clinical pharmaceutical use against various types of cancer caused by c-Met activity. The purpose of this study was to remodel the structures of 4-phenoxypyridine derivatives to achieve strong inhibitory activity against c-Met and provide favorable pharmacokinetic properties for drug design and discovery. Therefore, this paper describes the structure-activity relationship and the rationalization of appropriate pharmacophore sites to improve the biological activity of the investigated molecules, based on bioinformatics techniques represented by a computer-aided drug design approach. Accordingly, robust and reliable 3D-QSAR models were developed based on CoMFA and CoMSIA techniques. As a result, 46 lead molecules were designed and their biological and pharmacokinetic activities were predicted in silico. Screening filters by 3D-QSAR, Molecular Docking, drug-like and ADME-Tox identified the computer-designed compounds P54 and P55 as the best candidates to achieve high inhibition of c-Met enzymatic activity compared to the synthesized template compound T14. Finally, through molecular dynamics simulations, the structural properties and dynamics of c-Met free and complex (PDB code: 3LQ8) in the presence of 4-phenoxypyridine-derived compounds in an aqueous environment are discussed. Overall, the rectosynthesis of the designed drug inhibitors (P54 and P55) and their in vitro and in vivo bioactivity evaluation may be attractive for design and discovery of novel drug effective to inhibit c-Met enzymatic activity.Communicated by Ramaswamy H. Sarma.

Combined computational approaches for developing new anti-Alzheimer drug candidates: 3D-QSAR, molecular docking and molecular dynamics studies of liquiritigenin derivatives.

Butyrylcholinesterase is an acetylcholine-degrading enzyme involved in the memorization process, which is becoming an interesting target for the symptomatic treatment of Alzheimer's disease. In the present investigation, the structure-activity relationship of a set of Liquiritigenin derivatives recently revealed to be Butyrylcholinesterase inhibitors was studied basing on comparative field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMISA). As a result, performant models with high predictive capability have been developed (CoMFA model: R2 = 0.91, Q2 = 0.62, R2 pred = 0.85; CoMISA model: R2 = 0.92, Q2 = 0.59, R2 pred = 0.83) and implemented to design new Liquiritigenin derivatives with improved activity. Besides, the affinity of the designed derivatives towards the active site of Butyrylcholinesterase, was confirmed by molecular docking and molecular dynamics studies. Moreover, they exhibited good pharmacokinetics properties. Accordingly, the outcomes of the present investigations can provide important direction for the development of new anti-Alzheimer's drug candidates.

Design of novel benzimidazole derivatives as potential α-amylase inhibitors using QSAR, pharmacokinetics, molecular docking, and molecular dynamics simulation studies.

In the present study, a quantitative relationship between the biological inhibitory activity of alpha-amylase and molecular structures of novel benzimidazole derivatives is analyzed in silico. The best QSAR model screened via MLR technique indicated that the exact mass, topological diameter and numerical rotational bonding structural properties of benzimidazole derivatives highly affect the bioactivity of these compounds against α-amylase. Based on the structural properties identified via linear QSAR model favorable for improving pIC50 of benzimidazole derivatives, fourteen new molecules bearing benzimidazole radicals were designed and their biological inhibitory activity against α-amylase was improved. QSAR model predictions showed that the designed molecules exhibited a higher potential biological level activity IC50 than acarbose used in positive control (IC50= 1.46 µM). Screening of drug-like properties, pharmacokinetics and toxicity of the proposed molecules led to select three molecules as candidates for use as drug aid to ingest starch and glycogen. As a result, using molecular docking simulations, the docking poses of the three molecules inside the α-amylase receptor pocket (PDB code: 1HNY) were predicted. Also, the most important potential interactions between the active amino acid sites in α-amylase protein pocket and the proposed drug molecules were described. The obtained hypotheses regarding the stability of the proposed molecules inside α-amylase pocket were validated by carrying out molecular dynamic simulations in aqueous background similar to the ones of proteins. The DM results confirmed the optimal stability of the α-amylase backbone with the drug molecules proposed in this computational investigation.