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

Exploring the anti-diabetic potential of bis-Schiff base derivatives of benzimidazole: In-Vitro α-amylase, α-glucosidase inhibition, molecular docking, ADMET and DFT studies

This work explores the anti-diabetic activities of some synthesized benzimidazole based bis-Schiff base derivatives. The synthesized products were screened for their in vitro α-amylase and α-glucosidase inhibitory activities. In the synthetic derivatives, seven compounds attributed excellent anti-diabetic potential in the range of IC50 values from (IC50 = 2.84 ± 0.12 and 3.16 ± 0.05 µM) to (IC50 = 15.83 ± 1.11 and 16.70 ± 1.23 µM), while the remaining derivatives were found significant to less active when compared with the standard acarbose. The docking study correlates well with the α-glucosidase inhibitory activity, particularly for compounds 2 g and 2k, which showing strong binding affinity and hydrogen bonding. Compound 2 g, with the strongest binding affinity, also demonstrates potent inhibition (IC50 = 6.94 ± 0.07 μM). The synthesized compounds exhibit promising inhibitory activity against α-amylase and α-glucosidase, but their predicted ADMET profile presents significant challenges for their development as oral drugs. The poor absorption, high PPB, potential for CYP inhibition, and moderate toxicity risks highlight the need for further structural optimization. The frontier molecular orbitals (FMOs) analysis provides the LUMO delocalized on the benzylidene ring, influenced by the substitution pattern, appears to be a key factor influencing inhibitory activity. The higher reactivity (smaller energy gap) observed for some compounds, particularly 2k, might contribute to their enhanced activity. The molecular topology of the synthesized bis-Schiff bases showed a strong intramolecular hydrogen bond between the hydroxyl group at the 2-position of the benzylidene ring and the carbonyl oxygen of the linker. These interactions could pre-organize the molecule for better binding to the enzyme.

Potential Azo-8-hydroxyquinoline derivatives as multi-target lead candidates for Alzheimer's disease: An in-depth in silico study of monoamine oxidase and cholinesterase inhibitors

Cognitive dysfunction in Alzheimer's disease results from a complex interplay of various pathological processes, including the dysregulation of key enzymes such as acetylcholinesterase (AChE), butyrylcholinesterase (BuChE), and monoamine oxidase B (MAO-B). This study proposes and designs a series of novel molecules derived from 8-hydroxyquinoline (Azo-8HQ) as potential multi-target lead candidates for treating AD. An exhaustive in silico analysis was conducted, encompassing docking studies, ADMET analysis, density functional theory (DFT) studies, molecular dynamics simulations, and subsequent MM-GBSA calculations to examine the pharmacological potential of these molecules with the specific targets of interest. Out of the 63 Azo-8HQ derivatives analysed, two molecules, 14c and 17c, demonstrated strong affinities for AChE, BuChE, and MAO-B, along with favourable pharmacokinetic profiles and electronic properties. Molecular dynamics simulations confirmed the stability of these molecules within the active sites of the targets, and MM-GBSA calculations revealed low binding energies, indicating robust interactions. These findings identify molecules 14c and 17c as promising multi-target candidates for the treatment of AD, based on an in-depth computational study aimed at minimizing drug development costs and time. Future work will include the synthesis of these molecules followed by in-depth in vitro and in vivo testing to validate their potential therapeutic efficacy.

An experimental and computational approach to evaluate the antidiabetic activity of Commiphora wightii gum extract

BACKGROUND

Plant formulations with antidiabetic and antioxidant properties have recently gained popularity due to their lower cost and lesser side effects. Guggul gum is one such formulation that is extensively being used to cure various ailments.

OBJECTIVE

The present study was designed to explore the antioxidant and antidiabetic properties of the aqua-ethanolic Guggul gum extract (GE) from Commiphora wightii using in silico studies and in vitro assays.

METHODS

Gas Chromatography Mass Spectroscopy (GCMS) identified compounds were docked to the Human pancreatic α-amylase (HPA, PDB ID: 1HNY) for in silico studies to predict the inhibition. Molecular dynamics simulations (MDS) were performed using GROMACS for 100 ns. The inhibition of the enzyme was further evaluated at in vitro level to show the compounds' hypoglycemic role.

RESULTS

The extract showed a good amount of phenolic (5.14 ± 0.011 mg), flavonoid (0.66 ± 0.023 mg) and terpenoid (1.08 ± 0.018 mg) content along with a promising free radical scavenging activity of 41.96 ± 4.02%. In the in silico studies, 3 out of 6 GCMS-identified bioactive compounds showed permissible values of bioavailability properties suggesting them as a potential candidate for antidiabetic drugs. Similarly, in molecular docking studies, 3 compounds showed more binding energy than the standard drug acarbose indicating better inhibition. MDS studies showed Compound 4 (Diisooctyl phthalate), was the most stable with the lowest root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values, a consistent radius of gyration (Rg), and stable solvent accessible surface area (SASA). This was further confirmed by in vitro analysis where the pancreatic α-amylase inhibitory activity of the extract and the standard drug (acarbose) were comparable at an IC50 value of 4.17 ± 1.26 mg/mL and 3.69 ± 0.89 mg/mL respectively.

CONCLUSION

The results demonstrated GE as a potential alternative to commercial antidiabetic drugs. Out of the major 6 GCMS-identified compounds, Compound 4 showed the most stable conformation during MDS studies. However, the isolation of the identified compounds could be done in the future for in vivo studies.

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.

Repurposing of sericin combined with dactolisib or vitamin D to combat non-small lung cancer cells through computational and biological investigations

This study aims to repurpose sericin in combating non-small lung cancer cells (A549 and H460) by combining it with dactolisib or vitamin D to reduce the dose of dactolisib and boost the anticancer effectiveness of dactolisib and vitamin D. Therefore, the binding affinities of individual and combined drugs were examined using in silico and protein-protein interaction studies, targeting NF-κB, Cyclin D1, p-AKT, and VEGF1 proteins. The findings manifested remarkable affinities for combinatorial drugs compared to individual compounds. To substantiate these findings, the combined IC50 for each combination (sericin + dactolisib and sericin + vitamin D) were determined, reporting 31.9 and 41.8 µg/ml, respectively, against A549 cells and 47.9 and 55.3 µg/ml, respectively, against H460 cells. Furthermore, combination indices were assessed to lower the doses of each drug. Interestingly, in vitro results exhibited marked diminutions in NF-κB, Cyclin D1, p-AKT, and VEGF1 after treatment with sericin + dactolisib and sericin + vitamin D compared to control lung cancer cells and those treated with a single drug. Moreover, A549 and H460 cells treated with both combinations demonstrated augmented caspase-3 levels, implying substantial apoptotic activity. Altogether, these results accentuated the prospective implementation of sericin in combination with dactolisib and vitamin D at low doses to preclude lung cancer cell proliferation.

Thiadiazine-thiones as inhibitors of leishmania pteridine reductase (PTR1) target: investigations and in silico approach

Leishmaniasis is a widespread parasitic disease and is one of the major public health concerns in developing countries. Many drugs have been identified for leishmania as targets, but the potential toxicity and long-term treatment remain the most significant problems in terms of further development. The present study employed physicochemical investigations, structure-based virtual screening, ADMET analysis, molecular dynamics simulation, and MM-PBSA, to identify potential compounds for Leishmania. We evaluated 30,926 natural products from the NPASS database, and four potentials passed the pharmacokinetic ADMET studies and were verified using the molecular docking approach. Molecular docking results showed good binding interaction of the compounds with the active site of leishmania pteridine reductase enzyme PTR1, with compound TTC1 showing FRED and Autodock binding energies of -10.33 and -10.94, respectively, which were comparable with the antileishmania drugs of Allopurinol, Miltefosine and the original ligand, methotrexate. TTC1 compound was found to be favorable for hydrophobic interaction with PTR1. In addition, the physicochemical properties of the compounds were studied using the SwissADME web server. All compounds followed Lipinski's rule of five and can be considered as good oral candidates. The analysis of the 100 ns molecular dynamics simulation results based on the best-docked TTC1 with PTR1 receptor demonstrates stable interactions, and the complex undergoes low conformational fluctuations. The average of the calculated binding free energy of the TTC1-1e7w complex is (-68.67 kJ/mol), and the result demonstrated that the TTC1 promoted stability to the Leishmania-PTR1 complex. The potential compounds can be further explored for their antileishmanial activity.Communicated by Ramaswamy H. Sarma.

Pharmacological evaluations of amide carboxylates as potential anti-Alzheimer agents: anti-radicals, enzyme inhibition, simulation and behavioral studies in animal models

Alzheimer's disease (AD) is a neurological disorder that progresses gradually but irreversibly leading to dementia and is difficult to prevent and treat. There is a considerable time window in which the progression of the disease can be intervened. Scientific advances were required to help the researchers to identify the effective methods for the prevention and treatment of disease. This research was designed to investigate potential mediators for the remedy of AD, five new carboxylate amide zinc complexes (AAZ9-AAZ13) were synthesized and characterized by spectroscopic and physicochemical techniques. The biological evaluation was carried out based on the cholinesterase inhibitory mechanism. The preparation methodology provided the effective synthesis of targeted moieties. The in vitro pharmacological activities were evaluated involving AChE/BChE inhibition and antioxidant potential. All synthesized compounds displayed activity against both enzymes in higher or comparable to the standard drug Galantamine, a reversible inhibitor but the results displayed by compound AAZ10 indicated IC50 of 0.0013 µM (AChE) and 0.061 µM (BChE) as high values for dual AChE/BChE inhibition with potent anti-oxidant results. Structure activity relationship (SAR) indicated that the potent activity of compound AAZ10 appeared due to the presence of nitro clusters at the ortho position of an aromatic ring. The potent synthesized compound AAZ10 was also explored for the in-vivo Anti-Alzheimer activity and anti-oxidant activity. Binding approaches of all synthesized compounds were revealed through molecular docking studies concerning binding pockets of enzymes that analyzed the best posture interaction with amino acid (AA) residues providing an appreciable understanding of enzyme inhibitory mechanisms. Results indicate that synthesized zinc (II) amide carboxylates can behave as an effective remedy in the treatment of Alzheimer's disease.Communicated by Ramaswamy H. Sarma.

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.

Synthesis, Antimicrobial, Molecular Docking Against Bacterial and Fungal Proteins and In Silico Studies of Glucopyranoside Derivatives as Potent Antimicrobial Agents

Carbohydrate derivatives play a crucial roles in biochemical and medicinal research, especially in the fields of chemistry and biochemistry. From this perspective, the present study was designed to explore the synthesis of methyl α-D-glucopyranoside derivatives (1-8), focusing on their efficacy against bacterial and fungal inhibition. The structure of the synthesized compounds was ascertained using FTIR, 1H-NMR, 13C-NMR, mass and elemental analyses. Antimicrobial screening revealed strong antifungal properties, with compound 7 exhibiting minimum inhibitory concentrations (MICs) ranging from 16-32 μg/L and minimum bactericidal concentrations (MBCs) ranging from 64-128 μg/L. Incorporating decanoyl acyl groups at C-2 and C-3 of (7) significantly improved the efficacy against bacteria and fungi. Structure-activity relationship (SAR) analysis indicated that adding nonanoyl and decanoyl groups to the ribose moiety enhanced potency against both bacterial and fungal strains. Computational methods, including molecular docking, density functional theory (DFT), Petra, Osiris, Molinspiration (POM) evaluation, and molecular dynamics (MD) simulations, were used to assess the efficacy of these derivatives. Compounds 6 and 7, which presented nonanoyl and decanoyl substituents, demonstrated greater efficacy. In addition, DFT studies identified compound 8 as possessing ideal electronic properties. Molecular docking revealed that compound 8 exhibits exceptional binding affinities to bacterial proteins, conferring potent antibacterial and antifungal activities. In addition, pharmacokinetic optimization via POM analysis highlighted compounds 1 and 2 as promising bioavailable drugs with minimal toxicity. Molecular dynamics simulations confirmed the stability of the 2-S. aureus complex, revealing the therapeutic potential of compounds 2 and 8. Future experiments are required to validate their efficacy for pharmaceutical development. The integration of in vitro and in silico methods, including DFT anchoring dynamics and molecular dynamics simulations, provides a solid framework for the advancement of effective anti-infective drugs.

Chromone-isoxazole hybrids molecules: synthesis, spectroscopic, MEDT, ELF, antibacterial, ADME-Tox, molecular docking and MD simulation investigations

A mechanistic study was performed within the molecular electron density theory at the B3LYP/6-311G (d,p) computational level to explain the regioselectivity observed. An electron localization function analysis was also performed, and the results confirm the zwitterionic-type (zw-type) mechanism of the cycloaddition reactions between nitrile oxide and alkylated 4H-chromene-2-carboxylate derivatives and shed more light on the obtained regioselectivity experimentally. In silico studies on the pharmacokinetics, ADME and toxicity tests of the compounds were also performed, and it was projected that compounds 5a, 5b, 5c and 5d are pharmacokinetic and have favorable ADME profiles. Moreover, docking and molecular dynamics investigations were conducted to evaluate the interactions, orientation and conformation of the target compounds on the active sites of four distinct enzymes. The results of this investigation showed that two compounds, 5a and 5c, interacted effectively with the S. aureus active site while maintaining acceptable binding energy.Communicated by Ramaswamy H. Sarma.

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.

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.

Finding structural requirements of structurally diverse α-glucosidase and α-amylase inhibitors through validated and predictive 2D-QSAR and 3D-QSAR analyses

Diabetes mellitus (DM) is a chronic metabolic disorder characterized by hyperglycemic state. The α-glucosidase and α-amylase are considered two major targets for the management of Type 2 DM due to their ability of metabolizing carbohydrates into simpler sugars. In the current study, cheminformatics analyses were performed to develop validated and predictive models with a dataset of 187 α-glucosidase and α-amylase dual inhibitors. Separate linear, interpretable and statistically robust 2D-QSAR models were constructed with datasets containing the activities of α-glucosidase and α-amylase inhibitors with an aim to explain the crucial structural and physicochemical attributes responsible for higher activity towards these targets. Consequently, some descriptors of the models pointed out the importance of specific structural moieties responsible for the higher activities for these targets and on the other hand, properties such as ionization potential and mass of the compounds as well as number of hydrogen bond donors in molecules were found to be crucial in determining the binding potentials of the dataset compounds. Statistically significant 3D-QSAR models were developed with both α-glucosidase and α-amylase inhibition datapoints to estimate the importance of 3D electrostatic and steric fields for improved potentials towards these two targets. Molecular docking performed with selected compounds with homology model of α-glucosidase and X-ray crystal structure of α-amylase largely supported the interpretations obtained from the cheminformatic analyses. The current investigation should serve as important guidelines for the design of future α-glucosidase and α-amylase inhibitors. Besides, the current investigation is entirely performed by using non-commercial open-access tools to ensure easy accessibility and reproducibility of the investigation which may help researchers throughout the world to work more on drug design and discovery.

2-Amino Thiazole Derivatives as Prospective Aurora Kinase Inhibitors against Breast Cancer: QSAR, ADMET Prediction, Molecular Docking, and Molecular Dynamic Simulation Studies

The aurora kinase is a key enzyme that is implicated in tumor growth. Research revealed that small molecules that target aurora kinase have beneficial effects as anticancer agents. In the present study, in order to identify potential antibreast cancer agents with aurora kinase inhibitory activity, we employed QSARINS software to perform the quantitative structure-activity relationship (QSAR). The statistical values resulted from the study include R2 = 0.8902, CCCtr = 0.7580, Q2 LOO = 0.7875, Q2LMO = 0.7624, CCCcv = 0.7535, R2ext = 0.8735, and CCCext = 0.8783. Among the four generated models, the two best models encompass five important variables, including PSA, EstateVSA5, MoRSEP3, MATSp5, and RDFC24. The parameters including the atomic volume, atomic charges, and Sanderson's electronegativity played an important role in designing newer lead compounds. Based on the above data, we have designed six series of compounds including 1a-e, 2a-e, 3a-e, 4a-e, 5a-e, and 6a-e. All these compounds were subjected to molecular docking studies by using AutoDock v4.2.6 against the aurora kinase protein (1MQ4). Among the above 30 compounds, the 2-amino thiazole derivatives 1a, 2a, 3e, 4d, 5d, and 6d have excellent binding interactions with the active site of 1MQ4. Compound 1a had the highest docking score (-9.67) and hence was additionally subjected to molecular dynamic simulation investigations for 100 ns. The stable binding of compound 1a with 1MQ4 was verified by RMSD, RMSF, RoG, H-bond, molecular mechanics-generalized Born surface area (MM-GBSA), free binding energy calculations, and solvent-accessible surface area (SASA) analyses. Furthermore, newly designed compound 1a exhibited excellent ADMET properties. Based on the above findings, we propose that the designed compound 1a may be utilized as the best theoretical lead for future experimental research of selective inhibition of aurora kinase, therefore assisting in the creation of new antibreast cancer drugs.

In Silico and In Vitro Analyses to Repurpose Quercetin as a Human Pancreatic α-Amylase Inhibitor

Human pancreatic α-amylase (HPA), situated at the apex of the starch digestion hierarchy, is an attractive therapeutic approach to precisely regulate blood glucose levels, thereby efficiently managing diabetes. Polyphenols offer a natural and multifaceted approach to moderate postprandial sugar spikes, with their slight modulation in carbohydrate digestion and potential secondary benefits, such as antioxidant and anti-inflammatory effects. Taking into consideration the unfavorable side effects of currently available commercial medications, we aimed to study a library of polyphenols attributed to their remarkable antidiabetic properties and screened the most potent HPA inhibitor via a comprehensive in silico study encompassing molecular docking, molecular mechanics with generalized Born and surface area solvation (MM/GBSA) calculation, molecular dynamics (MD) simulation, density functional theory (DFT) study, and pharmacokinetic properties followed by an in vitro assay. Significant hydrogen bonding with the catalytic triad residues of HPA, prominent MM/GBSA binding energy of -27.03 kcal/mol, and the stable nature of the protein-ligand complex with regard to 100 ns MD simulation screened quercetin as the best HPA inhibitor. Additionally, quercetin showed strong reactivity in the substrate-binding pocket of HPA and exhibited favorable pharmacokinetic properties with a considerable inhibitory concentration (IC50) of 57.37 ± 0.9 μg/mL against α-amylase. This study holds prospects for HPA inhibition and suggests quercetin as an approach to therapy for diabetes; however, it is imperative to conduct further research.

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 effect of increasing temperature on simulated nanocomposites reinforced with SWBNNs and its effect on characteristics related to mechanics and the physical attributes using the MDs approach

This study examines the effect of increasing temperature (300, 350, 400, 450 and 500 K) on simulated nanocomposites reinforced with exploration of the impact of single-walled boron nitride nanotubes (SWBNNTs) on both the mechanical properties (including Young's modulus, Poisson's ratio, shear modulus, and bulk modulus) and the physical property of density, achieved through molecular dynamics (MDs) simulations. MDs utilized to simulate nanocomposite models consisting of five case studies of SWBNNs with different chiralities (5, 0), (10, 0), (15, 0), (20, 0), and (25, 0) as the reinforcement and using thermoplastic polyurethane (TPU) as the common matrix. The results reveal that with increasing temperature and chiralities of SWBNNTs, the density and Poisson's ratio increase dramatically, and Young's, shear, and bulk moduli decrease continuously. At a consistent temperature, there is a noteworthy trend in the mechanical properties of SWBNNTs with various chiralities. This includes the increase in Young's modulus, Poisson's ratio, shear modulus, and bulk modulus in the simulated nanocomposite, ranging from SWBNNTs (5, 0) to (25, 0). Similarly, the physical property of density exhibits an increasing trend from SWBNNTs (5, 0) to (20, 0) and then decreases at SWBNNTs (25, 0). To validate the accuracy of these findings, a Radial Distribution Function (RDF) diagram is generated using Materials Studio software.

The Synergistic Influence of Polyflavonoids from Citrus aurantifolia on Diabetes Treatment and Their Modulation of the PI3K/AKT/FOXO1 Signaling Pathways: Molecular Docking Analyses and In Vivo Investigations

This study was aimed at probing the modulatory influence of polyflavonoids extracted from Citrus aurantifolia, lemon peel extract (LPE-polyflavonoids), on attenuating diabetes mellitus (DM) and its complications. HPLC investigations of the LPE exhibited the incidence of five flavonoids, including diosmin, biochanin A, hesperidin, quercetin, and hesperetin. The in silico impact on ligand-phosphatidylinositol 3-kinase (PI3K) interaction was investigated in terms of polyflavonoid class to explore the non-covalent intakes and binding affinity to the known protein active site. The drug likeness properties and pharmacokinetic parameters of the LPE-polyflavonoids were investigated to assess their bioavailability in relation to Myricetin as a control. Remarkably, the molecular docking studies demonstrated a prominent affinity score of all these agents together with PI3K, implying the potency of the extract to orchestrate PI3K, which is the predominant signal for lessening the level of blood glucose. To verify these findings, in vivo studies were conducted, utilizing diabetic male albino rats treated with LPE-polyflavonoids and other groups treated with hesperidin and diosmin as single flavonoids. Our findings demonstrated that the LPE-polyflavonoids significantly ameliorated the levels of glucose, insulin, glycogen, liver function, carbohydrate metabolizing enzymes, G6Pd, and AGEs compared to the diabetic rats and those exposed to hesperidin and diosmin. Furthermore, the LPE-polyflavonoids regulated the TBARS, GSH, CAT, TNF-α, IL-1β, IL-6, and AFP levels in the pancreatic and hepatic tissues, suggesting their antioxidant and anti-inflammatory properties. In addition, the pancreatic and hepatic GLUT4 and GLUT2 were noticeably increased in addition to the pancreatic p-AKT in the rats administered with the LPE-polyflavonoids compared to the other diabetic rats. Remarkably, the administration of LPE-polyflavonoids upregulated the expression of the pancreatic and hepatic PI3K, AMPK, and FOXO1 genes, emphasizing the efficiency of the LPE in orchestrating all the signaling pathways necessitated to reduce the diabetes mellitus. Notably, the histopathological examinations of the pancreatic and hepatic tissues corroborated the biochemical results. Altogether, our findings accentuated the potential therapeutic role of LPE-polyflavonoids in controlling diabetes mellitus.

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.

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.

α-amylase inhibition and in silico studies of novel naphtho[2,3-d]imidazole-4,9-dione linked N-acyl hydrazones

Aim: To enrich the pool of α-amylase inhibitors to manage Type 2 diabetes. Methods: Synthesis, conformational study, α-amylase inhibitory action and various in silico studies of novel N'-(arylbenzylidene)-2-(4,9-dioxo-4,9-dihydro-1H-naphtho[2,3-d]imidazol-1-yl)acetohydrazides carried out. Results: Compound H6 demonstrated the highest activity (IC50 = 0.0437 μmol mL-1) among the tested compounds. Structure-activity relationship study suggested that variable substitution at the aryl ring has a pivotal role in determining the inhibitory action of tested compounds. Docking simulations of the most active compound (H6) confirmed its interaction potential with active site residues of A. oryzae α-amylase. The root-mean-square deviation fluctuations substantiated the stability of protein-ligand complex. Absorption, distribution, metabolism and excretion prediction revealed optimal values for absorption, distribution, metabolism and excretion parameters. Conclusion: The developed molecules could be beneficial for the development of novel α-amylase inhibitors to treat Type 2 diabetes.

Structure‐Based Virtual Screening, ADMET analysis, and Molecular Dynamics Simulation of Moroccan Natural Compounds as Candidates α‐Amylase Inhibitors

Current treatments for diabetes mellitus are ineffective, as evidenced by the rise in diabetes cases. This has forced researchers to develop novel chemicals as drugs to block the enzyme alpha‐amylase as the severe way to treat diabetes disease. Many previous studies were done to determine the biological activity of a set of molecules isolated from medicinal plants. Morocco is renowned for the abundance of plants it has and for the traditional medical uses of these plants, which drives us to employ our cultural heritage and the variety of our nation‘s natural resources in the therapeutic area. In the current study, extensive research was conducted to compile a group of phytoconstituents derived from Moroccan plants and used in conventional Moroccan medicine to treat local illnesses. To assess the stability of the generated complexes, molecular docking of the investigated compounds was carried out in the active site of 4 distinct alpha‐amylase proteins. The remaining compounds with a high negative binding affinity were then subjected to the ADMET analysis to determine their pharmacological characteristics. The findings showed that two drugs have strong binding affinity for the target proteins and may be used orally as potential alpha‐amylase inhibitors. The results of molecular dynamics analysis and MMGBSA calculation were used to validate the optimal stability of created complexes (L97 with studied proteins 1HNY, 1OSE, 1UA7 and 1BAG).

Inhibition of albendazole and 2-(2-aminophenyl)-1H-benzimidazole against tyrosinase: mechanism, structure-activity relationship, and anti-browning effect

BACKGROUND

Tyrosinase is the key enzyme involved in enzymatic browning of plant-derived foods. Inhibition of tyrosinase activity contributes to the control of food browning. Due to safety regulations or other issues, most identified tyrosinase inhibitors are not suitable for practical use. Therefore, it is necessary to search for novel tyrosinase inhibitors. In this study, the anti-tyrosinase activity and mechanism of albendazole and 2-(2-aminophenyl)-1H-benzimidazole (2-2-A-1HB) were investigated through ultraviolet-visible absorption spectroscopy, fluorescence spectra, molecular docking, and molecular dynamic (MD) simulation. The anti-browning effect of albendazole on fresh-cut apples was then elucidated.

RESULTS

Albendazole and 2-2-A-1HB were both efficient tyrosinase inhibitors with IC₅₀ of 51 ± 1.5 and 128 ± 1.3 μmol L^-1 , respectively. Albendazole suppressed tyrosinase non-competitively and formed tyrosinase-albendazole complex statically. Hydrogen bond and hydrophobic interaction were major driving forces in stabilizing the tyrosinase-albendazole complex. While 2-2-A-1HB inhibited the enzyme competitively and quenched its intrinsic fluorescence through a static mechanism, it generated strong binding affinity with tyrosinase through hydrophobic interaction. MD simulations further validated that albendazole/2-2-A-1HB could form stable complexes with tyrosinase and loosened its basic framework structure, leading to a change in secondary structure and conformation. In addition, albendazole could delay the browning of fresh-cut apples by inhibiting the activity of polyphenol oxidase, peroxidase and phenylalanine ammonia-lyase, and reducing the oxidation of phenolic compounds.

CONCLUSION

This research might provide a deep view of tyrosinase inhibition by benzimidazole derivatives and a theoretical basis for developing albendazole as a potential fresh-keeping agent. © 2023 Society of Chemical Industry.

Design, synthesis, spectroscopic characterization, single crystal X-ray analysis, in vitro α-amylase inhibition assay, DPPH free radical evaluation and computational studies of naphtho[2,3-d]imidazole-4,9-dione appended 1,2,3-triazoles

In our quest to design and develop N/O-containing inhibitors of α-amylase, we have tried to synergize the inhibitory action of 1,4-naphthoquinone, imidazole and 1,2,3-triazole motifs by incorporating these structures into a single matrix. For this, a series of novel naphtho[2,3-d]imidazole-4,9-dione appended 1,2,3-triazoles is synthesized by a sequential approach involving [3 + 2] cycloaddition of 2-aryl-1-(prop-2-yn-1-yl)-1H-naphtho[2,3-d]imidazole-4,9-diones with substituted azides. The chemical structures of all the compounds are established with the help of 1D-NMR, 2D-NMR, IR, mass and X-ray studies. The developed molecular hybrids are screened for their inhibitory action on the α-amylase enzyme using the reference drug, acarbose. Different substituents present on the attached aryl part of the target compounds show amazing variations in inhibitory action against the α-amylase enzyme. Based on the type of substituents and their respective positions, it is observed that compounds containing -OCH₃ and -NO₂ groups show more inhibition potential than others. All the tested derivatives display α-amylase inhibitory activity with IC₅₀ values in the range of 17.83 ± 0.14 to 26.00 ± 0.17 μg/mL. Compound 2-(2,3,4-trimethoxyphenyl)-1-{[1-(4-methoxyphenyl)-1H-1,2,3-triazol-4-yl]methyl}-1H-naphtho[2,3-d]imidazole-4,9-dione (10y) show maximum inhibition of amylase activity with IC₅₀ value 17.83 ± 0.14 μg/mL as compared to reference drug acarbose (18.81 ± 0.05 μg/mL). A molecular docking study of the most active derivative (10y) is performed with A. oryzae α-amylase (PDB ID: 7TAA) and it unveils favourable binding interactions within the active site of the receptor molecule. The dynamic studies reveal that the receptor-ligand complex is stable as the RMSD of less than 2 is observed in 100 ns molecular dynamic simulation. Also, the designed derivatives are assayed for their DPPH free radical scavenging ability and all of them exhibit comparable radical scavenging activity with the standard, BHT. Further, to assess their drug-likeness properties, ADME properties are also evaluated and all of them demonstrate worthy in silico ADME results.

Cyclohexane-1,3-dione Derivatives as Future Therapeutic Agents for NSCLC: QSAR Modeling, In Silico ADME-Tox Properties, and Structure-Based Drug Designing Approach

The abnormal expression of the c-Met tyrosine kinase has been linked to the proliferation of several human cancer cell lines, including non-small-cell lung cancer (NSCLC). In this context, the identification of new c-Met inhibitors based on heterocyclic small molecules could pave the way for the development of a new cancer therapeutic pathway. Using multiple linear regression (MLR)-quantitative structure-activity relationship (QSAR) and artificial neural network (ANN)-QSAR modeling techniques, we look at the quantitative relationship between the biological inhibitory activity of 40 small molecules derived from cyclohexane-1,3-dione and their topological, physicochemical, and electronic properties against NSCLC cells. In this regard, screening methods based on QSAR modeling with density-functional theory (DFT) computations, in silico pharmacokinetic/pharmacodynamic (ADME-Tox) modeling, and molecular docking with molecular electrostatic potential (MEP) and molecular mechanics-generalized Born surface area (MM-GBSA) computations were used. Using physicochemical (stretch-bend, hydrogen bond acceptor, Connolly molecular area, polar surface area, total connectivity) and electronic (total energy, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels) molecular descriptors, compound 6d is identified as the optimal scaffold for drug design based on in silico screening tests. The computer-aided modeling developed in this study allowed us to design, optimize, and screen a new class of 36 small molecules based on cyclohexane-1,3-dione as potential c-Met inhibitors against NSCLC cell growth. The in silico rational drug design approach used in this study led to the identification of nine lead compounds for NSCLC therapy via c-Met protein targeting. Finally, the findings are validated using a 100 ns series of molecular dynamics simulations in an aqueous environment on c-Met free and complexed with samples of the proposed lead compounds and Foretinib drug.

Insight into the Interaction Mechanism of HSA with Aztreonam: A Multispectroscopic and Computational Approach

Aztreonam is a Gram-negative bacteria-targeting synthetic monobactam antibiotic. Human serum albumin (HSA) plays an important role in the transference of pharmaceuticals, hormones, and fatty acids, along with other compounds, determining their biodistribution and physiological fate. Using several biophysical and in silico approaches, we studied the interaction of aztreonam with HSA under physiological environments in this study. Results confirm the formation of HSA-aztreonam complex where aztreonam showed moderate affinity towards HSA. A static mode of quenching was confirmed from the steady state fluorescence data. FRET findings also showed that there was a significant feasibility of energy transfer between HSA and aztreonam. Site marker displacement experimental conclusion suggested the binding site of aztreonam was the sub-domain IB of HSA. Circular dichroic spectroscopic analysis suggested that aztreonam interaction decreases the α-helical content of HSA. Changes in microenvironment were studied through synchronous fluorescence data. According to molecular docking results, the HSA-aztreonam complex is mostly maintained by non-covalent forces, with a binding energy of 7.7 kcal mol^-1. The presence of a hydrogen bond, van der Waal interaction, and pi-anion interaction in the binding process, as well as conformational changes in HSA after binding with aztreonam, are all confirmed by molecular dynamic simulation.

Rational identification of small molecules derived from 9,10-dihydrophenanthrene as potential inhibitors of 3CLpro enzyme for COVID-19 therapy: a computer-aided drug design approach

Small molecules such as 9,10-dihydrophenanthrene derivatives have remarkable activity toward inhibition of SARS-CoV-2 3CLpro and COVID-19 proliferation, which show a strong correlation between their structures and bioactivity. Therefore, these small compounds could be suitable for clinical pharmaceutical use against COVID-19. The objective of this study was to remodel the structures of 9,10-dihydrophenanthrene derivatives to achieve a powerful biological activity against 3CLpro and favorable pharmacokinetic properties for drug design and discovery. Therefore, by the use of bioinformatics techniques, we developed robust 3D-QSAR models that are capable of describing the structure-activity relationship for 46 molecules based on 9,10-dihydrophenanthrene derivatives using CoMFA/SE (R 2 = 0.97, Q 2 = 0.81, R 2 pred = 0.95, c R 2 p = 0.71) and CoMSIA/SEHDA (R 2 = 0.94, Q 2 = 0.76, R 2 pred = 0.91, c R 2 p = 0.65) techniques. Accordingly, 96 lead compounds were generated based on a template molecule that showed the highest observed activity in vitro (T40, pIC50 = 5.81) and predicted their activities and bioavailability in silico. The rational screening outputs of 3D-QSAR, Molecular docking, ADMET, and MM-GBSA led to the identification of 9 novel modeled molecules as potent noncovalent drugs against SARS-CoV-2-3CLpro. Finally, by molecular dynamics simulations, the stability and structural dynamics of 3CLpro free and complex (PDB code: 6LU7) were discussed in the presence of samples of 9,10-dihydrophenanthrene derivative in an aqueous environment. Overall, the retrosynthesis of the proposed drug compounds in this study and the evaluation of their bioactivity in vitro and in vivo may be interesting for designing and discovering a new drug effective against COVID-19.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11224-022-02004-z.

Discovery of Phenylcarbamoylazinane-1,2,4-Triazole Amides Derivatives as the Potential Inhibitors of Aldo-Keto Reductases (AKR1B1 & AKRB10): Potential Lead Molecules for Treatment of Colon Cancer

Both members of the aldo-keto reductases (AKRs) family, AKR1B1 and AKR1B10, are over-expressed in various type of cancer, making them potential targets for inflammation-mediated cancers such as colon, lung, breast, and prostate cancers. This is the first comprehensive study which focused on the identification of phenylcarbamoylazinane-1, 2,4-triazole amides (7a−o) as the inhibitors of aldo-keto reductases (AKR1B1, AKR1B10) via detailed computational analysis. Firstly, the stability and reactivity of compounds were determined by using the Guassian09 programme in which the density functional theory (DFT) calculations were performed by using the B3LYP/SVP level. Among all the derivatives, the 7d, 7e, 7f, 7h, 7j, 7k, and 7m were found chemically reactive. Then the binding interactions of the optimized compounds within the active pocket of the selected targets were carried out by using molecular docking software: AutoDock tools and Molecular operation environment (MOE) software, and during analysis, the Autodock (academic software) results were found to be reproducible, suggesting this software is best over the MOE (commercial software). The results were found in correlation with the DFT results, suggesting 7d as the best inhibitor of AKR1B1 with the energy value of −49.40 kJ/mol and 7f as the best inhibitor of AKR1B10 with the energy value of −52.84 kJ/mol. The other potent compounds also showed comparable binding energies. The best inhibitors of both targets were validated by the molecular dynamics simulation studies where the root mean square value of <2 along with the other physicochemical properties, hydrogen bond interactions, and binding energies were observed. Furthermore, the anticancer potential of the potent compounds was confirmed by cell viability (MTT) assay. The studied compounds fall into the category of drug-like properties and also supported by physicochemical and pharmacological ADMET properties. It can be suggested that the further synthesis of derivatives of 7d and 7f may lead to the potential drug-like molecules for the treatment of colon cancer associated with the aberrant expression of either AKR1B1 or AKR1B10 and other associated malignancies.