Research of new acetylcholinesterase inhibitors based on QSAR and molecular docking studies of benzene-based carbamate derivatives

Design and evaluation of novel triazole derivatives as potential anti-gout inhibitors: a comprehensive molecular modeling study

Introduction

Gout is the most common inflammatory arthritis, characterized by hyperuricemia, tophus formation, joint disease, and kidney stones. Uric acid, the final byproduct of purine catabolism, is eliminated via the kidneys and digestive system. Xanthine oxidase (XO) catalyzes the conversion of hypoxanthine and xanthine into uric acid, making XO inhibitors crucial for treating hyperuricemia and gout. Currently, three XO inhibitors are clinically used, showing significant efficacy. A molecular modeling study on triazole derivatives aims to identify novel XO inhibitors using 3D-QSAR, molecular docking, MD simulations, ADMET analysis, and DFT calculations. These computational approaches facilitate drug discovery while reducing research costs.

Methods

Our work focuses on a series of synthesized anti-xanthine oxidase inhibitors, aiming to develop new inhibitors. A computational study was carried out to identify the xanthine oxidase inhibitory structural features of a series of triazole inhibitors using computational method.

Results

A model based on CoMFA and CoMSIA/SEA has been built to predict new triazole derivatives.

Discussion

The optimal model established from CoMFA and CoMSIA/SEA was successfully evaluated for its predictive capability. Visualization of the contour maps of both models showed that modifying the substituents plays a key role in enhancing the biological activity of anti-gout inhibitors. Molecular docking results for complexes N°8-3NVY and N°22-3NVY showed scores of -7.22 kcal/mol and -8.36 kcal/mol, respectively, indicating substantial affinity for the enzyme. Complex N°8-3NVY forms two hydrogen bonds with SER 69 and ASN 71, three alkyl bonds with ALA 70, LEU 74, and ALA 75, and one Pi-Pi T-shaped bond with PHE 68. Complex N°22-3NVY forms three hydrogen bonds with HIS 99, ARG 29, and ILE 91, and one halogen bond with LEU 128 at 3.60 Å. A MD study revealed that the N°22-3NVY complex remained highly stable throughout the simulation. Therefore, we proposed six new molecules, their anti-gout inhibitory activities were predicted using two models, and they were evaluated for Lipinski's rule, and ADMET properties. The results show that both Pred 4 and Pred 5 have better pharmacokinetic properties than the height potent molecule in the studied series, making these two compounds valuable candidates for new anti-gout drugs. Subsequently, using DFT study to evaluate the chemical reactivity properties of these two proposed compounds, the energy gap results revealed that both molecules exhibit moderate chemical stability and reactivity.

Exploring Cannabidiol-TRPV3 Mediated Biological Activities-Findings From Molecular Docking, Simulation and Proteins Network Interactions

Transient receptor potential vanilloid 3 (TRPV3) is a thermosensitive calcium-permeable ion channel and has a function in sensory perception, epidermal barrier function, inflammation and keratinocyte proliferation. TRPV3 dysfunction is linked with chronic pain, atopic dermatitis and neurodegenerative disorders. This study compared the binding efficacy and molecular dynamics of cannabidiol- and eugenol-TRPV3 complex(s), elucidating their ligand-protein dynamics. Computational methods, including density functional theory, molecular docking and molecular dynamics simulations, assessed electronic properties, binding affinities and interaction stability, respectively. Cannabidiol showed a higher binding affinity (-7.73 ± 0.73 kcal/mol) than eugenol (-6.0 ± 0.05 kcal/mol), driven by denser hydrophilic and hydrophobic contacts. Molecular dynamics revealed the cannabidiol-TRPV3 complex stability, with steady atomic deviation and protein compactness. Furthermore, cannabidiol-induced diverse TRPV3 conformational states, while eugenol exhibited greater flexibility. These findings highlight cannabidiol's stable, dynamic interaction with TRPV3, suggesting its potential to exert TRPV3-mediated biological effects. In contrast, eugenol may serve in transient modulation. This study offers insights into ligand-ion channel interactions, guiding drug development for TRPV3-related conditions.

Exploration of natural products for the development of promising cholinesterase inhibitors in Alzheimer's disease treatment

Cholinesterase enzymes (BuChE and AChE) are privileged biological targets for the symptomatic treatment of Alzheimer's disease. Indeed, inhibition of cholinesterase enzymes has been proven to improve the neurotransmission mechanisms in Alzheimer's disease patients. In this investigation, we attempt to highlight new cholinesterase inhibitors from natural products. For this purpose, secondary metabolites (299 phytoconstituents) of twenty-eight Medicinal plants were virtually screened using molecular docking, pharmacokinetic and toxicological analysis. Ten phytoconstituents (L82, L86, L92, L121, L148, L187, L211, L221, L228) exhibited their high binding affinity with BuChE, and five phytoconstituents, namely L119, L147, L149, L192 and L193, exhibited their strong binding ability with AChE. Subsequently, these phytoconstituents were evaluated for their ADMET properties. As result, L221 is predicted to be highly bioavailable and readily absorbed by the human intestinal tract without significant toxicity concerns, making it suitable for oral administration. Crucially, it can penetrate the blood-brain barrier (BBB), allowing it to effectively reach the central nervous system. Molecular dynamics simulations and MM-PBSA analysis revealed that the best-screened phytoconstituent form thermodynamically favorable and stable complex with the BuChE binding site. The conducted investigations highlighted promising outcomes that can orient towards the rational development of effective Cholinesterase inhibitors.

ANN-QSAR, Molecular Docking, ADMET Predictions, and Molecular Dynamics Studies of Isothiazole Derivatives to Design New and Selective Inhibitors of HCV Polymerase NS5B

Background/Objectives: RNA polymerase (NS5B), serves as a crucial target for pharmaceutical interventions aimed at combating the hepatitis C virus (HCV), which poses significant health challenges worldwide. The present research endeavors to explore and implement a variety of advanced molecular modeling techniques that aim to create and identify innovative and highly effective inhibitors that specifically target the RNA polymerase enzyme. Methods: In this study, a QSAR investigation was carried out on a set of thirty-eight isothiazole derivatives targeting NS5B inhibition and thus hepatitis C virus (HCV) treatment. The research methodology made use of various statistical techniques including multiple linear regression (MLR) and artificial neural networks (ANNs) to develop satisfactory models in terms of internal and external validation parameters, indicating their reliability in predicting the activity of new inhibitors. Accordingly, a series of potent NS5B inhibitors is designed, and their inhibitory potential is confirmed through molecular docking simulations. Results: These simulations showed that the interactions between these inhibitors and the active site 221 binding pocket of the NS5B protein are hydrophobic and hydrogen bond interactions, as well as carbon-hydrogen bonds and electrostatic interactions. Additionally, these newly formulated compounds displayed favorable ADMET characteristics, with molecular dynamics investigations revealing a stable energetic state and dynamic equilibrium. Conclusions: Our work highlights the importance of NS5B inhibition for the treatment of HCV.

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.

Exploration of alpha-glucosidase inhibitors: A comprehensive in silico approach targeting a large set of triazole derivatives

BACKGROUND

The increasing prevalence of diabetes and the side effects associated with current medications necessitate the development of novel candidate drugs targeting alpha-glucosidase as a potential treatment option.

METHODS

This study employed computer-aided drug design techniques to identify potential alpha-glucosidase inhibitors from the PubChem database. Molecular docking was used to evaluate 81,197 compounds, narrowing the set for further analysis and providing insights into ligand-target interactions. An ADMET study assessed the pharmacokinetic properties of these compounds, including absorption, distribution, metabolism, excretion, and toxicity. Molecular dynamics simulations validated the docking results.

RESULTS

9 compounds were identified as potential candidate drugs based on their ability to form stable complexes with alpha-glucosidase and their favorable pharmacokinetic profiles, three of these compounds were subjected to the molecular dynamics, which showed stability throughout the entire 100 ns simulation.

CONCLUSION

These findings suggest promising new alpha-glucosidase inhibitors for diabetes treatment. Further validation through in vitro and in vivo studies is recommended to confirm their efficacy and safety.

An In Silico Study Based on QSAR and Molecular Docking and Molecular Dynamics Simulation for the Discovery of Novel Potent Inhibitor against AChE

Acetylcholinesterase (AChE) is one of the main drug targets for treating Alzheimer's disease. This current study relies on multiple molecular modeling approaches to develop new potent inhibitors of AChE. We explored a 2D QSAR study using the statistical method of multiple linear regression based on a set of substituted 5-phenyl-1,3,4-oxadiazole and N-benzylpiperidine analogs, which were recently synthesized and proved their inhibitory activities against acetylcholinesterase (AChE). The molecular descriptors, polar surface area, dipole moment, and molecular weight are the key structural properties governing AChE inhibition activity. The MLR model was selected based on its statistical parameters: R2 = 0.701, R2test = 0.76, Q2CV = 0.638, and RMSE = 0.336, demonstrating its predictive reliability. Randomization tests, VIF tests, and applicability domain tests were adopted to verify the model's robustness. As a result, 11 new molecules were designed with higher anti-Alzheimer's activities than the model molecule. We demonstrated their improved pharmacokinetic properties through an in silico ADMET study. A molecular docking study was conducted to explore their AChE inhibition mechanisms and binding affinities in the active site. The binding scores of compounds M1, M2, and M6 were (-12.6 kcal/mol), (-13 kcal/mol), and (-12.4 kcal/mol), respectively, which are higher than the standard inhibitor Donepezil with a binding score of (-10.8 kcal/mol). Molecular dynamics simulations over 100 ns were used to validate the molecular docking results, indicating that compounds M1 and M2 remain stable in the active site, confirming their potential as promising anti-AChE inhibitors.

Designing efficient materials for high-performance of non-fullerene organic solar cells through side-chain engineering on DBT-4F derivatives by non-fused-ring electron acceptors

CONTEXT

For the advancement in fields of organic and perovskite solar cells, various techniques of structural alterations are being employed on previously reported chromophores. In this study, the end-capped engineering is carried out on DBT-4F (R) by modifying terminal acceptors to improve optoelectronic and photovoltaic attributes. Seven molecules (AD1-AD7) are modeled using different push-pull acceptors. DFT/B3LYP/6-31G along with its time-dependent approach (TD-DFT) are on a payroll to investigate ground state geometries, absorption maxima (λmax), energy gap (Eg), excitation energy (Ex), internal reorganization energy, light harvesting efficiency (LHE), dielectric constant, open circuit voltage (VOC), fill factor (FF), etc. of OSCs. AD1 displayed the lowest band gap (1.76 eV), highest λmax (876 nm), lowest Ex (1.41 eV), and lowest binding energy (0.21 eV). Among various calculated parameters, all of the sketched molecules demonstrated greater dielectric constant when compared to R. The highest dielectric constant was exhibited by AD3 (56.26). AD5 exhibited maximum LHE (0.9980). Lower reorganization energies demonstrated improved charge mobility. AD5 and AD7 (1.63 and 1.68 eV) have higher values of VOC than R (1.51 eV). All novel molecules having outperforming attributes will be better candidates to enhance the efficacy of OSCs for future use.

METHODS

Precisely, a DFT and TD-DFT analysis on all of the proposed organic molecules were conducted, using the functional MPW1PW91 at 6-31G (d,p) basis set to examine their optoelectronic aspects, additionally the solvent-state computations were studied with a TD-SCF simulation. For all these simulations, Guassian 09 and GuassView 5.0 were employed. Moreover, the Origin 6.0, Multiwfn 3.8, and PyMOlyze 1.1 software were utilized for the visual depiction of the graphs of absorption, TDM, and DOS, respectively of the studied molecules. A number of crucial aspects such as FMOs, bandgaps, light-harvesting efficiency, electrostatic potential, dipole moment, ionization potential, open-circuit voltage, fill factor, binding energy, interaction coefficient, chemical hardness-softness, and electrophilicity index were also investigated for the studied molecules.

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; R adj 2 = 0.767; R cv 2 = 0.651) and its applicability domain was defined. It was predicted to possess high predictive power (R test 2   = 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.

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.

A combined in silico approaches of 2D-QSAR, molecular docking, molecular dynamics and ADMET prediction of anti-cancer inhibitor activity for actinonin derivatives

Inhibition of human mitochondrial peptide deformylase (HsPDF) plays a major role in reducing growth, proliferation, and cellular cancer survival. In this work, a series of 32 actinonin derivatives for HsPDF (PDB: 3G5K) inhibitor's anticancer activity was computationally analyzed for the first time, using an in silico study considering 2D-QSAR modeling, and molecular docking studies, and validated by molecular dynamics and ADMET properties. The results of multilinear regression (MLR) and artificial neural networks (ANN) statistical analysis reveal a good correlation between pIC50 activity and the seven (7) descriptors. The developed models were highly significant with cross-validation, the Y-randomization test and their applicability range. In addition, all considered data sets show that the AC30 compound, exhibits the best binding affinity (docking score = -212.074 kcal/mol and H-bonding energy = -15.879 kcal/mol). Furthermore, molecular dynamics simulations were performed at 500 ns, confirming the stability of the studied complexes under physiological conditions and validating the molecular docking results. Five selected actinonin derivatives (AC1, AC8, AC15, AC18 and AC30), exhibiting best docking score, were rationalized as potential leads for HsPDF inhibition, in well agreement with experimental outcomes. Furthermore, based on the in silico study, new six molecules (AC32, AC33, AC34, AC35, AC36 and AC37) were suggested as HsPDF inhibition candidates, which would be combined with in-vitro and in-vivo studies to perspective validation of their anticancer activity. Indeed, the ADMET predictions indicate that these six new ligands have demonstrated a fairly good drug-likeness profile.

Comparison of acetylcholinesterase among employees based on job positions and personal protective equipment in fuel station

The purpose of this study was to compare the levels of acetylcholinesterase (AChE) among employees based on job positions and the wearing of personal protective equipment (PPE) in fuel station areas. The sample group consisted of 200 people sorted into various groups, including (i) Inside fuel dispenser area (I-FDA) group consisting of 100 employees for refueling, cashier, and loading fuel into storage tanks, and (ii) Outside fuel dispenser area (O-FDA) group, consisting of 100 employees working in convenience stores, food stores, coffee shops, and offices, as well as general staff and car washers. Data were collected using interview questionnaires and blood samples were analyzed for AChE activity. The results showed that the I-FDA group had a significantly lower mean of serum AChE (7.38±1.73 U/ml) than the O-FDA group (7.85±1.49 U/ml) (p<0.05). The I-FDA group had a 2.43 times higher risk of abnormal serum AChE than the O-FDA group (OR=2.43, 95%CI=1.05-5.60). When considering the risk factors for job positions, it was found that refueling and cashier positions had lower AChE activity levels than those who did not (p<0.05). In the part, employees for food sales in a closed building and those wearing PPE masks had significantly higher AChE activity levels than those who did not or who wore them (p<0.05). Based on the aforementioned, employers at fuel stations should strictly determine the appropriate measures for wearing a PPE mask. Further, employees should be provided accommodation away from oil supply or enclosed buildings during breaks to reduce the effects on the neurotransmitter.

Synthesis, Characterization, DFT Mechanistic Study, Antimicrobial Activity, Molecular Modeling, and ADMET Properties of Novel Pyrazole-isoxazoline Hybrids

A series of new heterocycle hybrids incorporating pyrazole and isoxazoline rings was successfully synthesized, characterized, and evaluated for their antimicrobial responses. The synthesized compounds were obtained utilizing N-alkylation and 1,3-dipolar cycloaddition reactions, as well as their structures were established through spectroscopic methods and confirmed by mass spectrometry. To get more light on the regioselective synthesis of new hybrid compounds, mechanistic studies were performed using DFT calculations with B3LYP/6-31G(d,p) basis set. Additionally, the results of the preliminary screening indicate that some of the examined hybrids showed potent antimicrobial activity, compared to standard drugs. The results confirm that the antimicrobial activity is strongly dependent on the nature of the substituents linked pyrazole and isoxazoline rings. Furthermore, molecular docking studies were conducted to highlight the interaction modes between the investigated hybrid compounds and the Escherichia coli and Candida albicans receptors. Notably, the results demonstrate that the investigated compounds have strong protein binding affinities. The stability of the formed complexes by the binding between the hybrid compound 6c, and the target proteins was also confirmed using a 100 ns molecular dynamics simulation. Finally, the prediction of ADMET properties suggests that almost all hybrid compounds possess good pharmacokinetic profiles and no signs of observed toxicity, except for compounds 6e, 6f, and 6g.