Benzimidazole Derivatives in Identifying Novel Acetylcholinesterase Inhibitors: A Combination of 3D-QSAR, Docking and Molecular Dynamics Simulation

Acetylcholinesterase (AChE) is a potential target for the development of small molecules as inhibitors for the therapy of Alzheimer's disease (AD). To design highly active acetylcholinesterase inhibitors, a three-dimensional quantitative structure-activity relationship (3D-QSAR) approach was performed on a series of N-benzylpyrrolidine derivatives previously evaluated for acetylcholinesterase inhibitory activity. The developed two models, CoMFA and CoMSIA, were statistically validated, and good predictability was achieved for both models. The information generated from 3D-QSAR contour maps may provide a better understanding of the structural features required for acetylcholinesterase inhibition and help to design new potential anti-acetylcholinesterase molecules. Consequently, six novel acetylcholinesterase inhibitors were designed, among which compound A1 with the highest predicted activity was subjected to detailed molecular docking and compared to the most active compound. Extra-precision molecular dynamics (MD) simulation of 50ns and binding free energy calculations using MM-GBSA were performed for the selected compounds to validate the stability. These results may afford important structural insights needed to identify novel acetylcholinesterase inhibitors and other promising strategies in drug discovery.

Major histocompatibility complex class I (MHC-I), a key element of the acquired immune system, plays essential roles in activating CD8+ T cells by recognizing intracellular antigens derived from pa...

Background:Alpinia officinarum, a member of the Zingiberaceae family, is native to East Asia. It possesses various properties, including antineoplastic effects, but the molecular mechanism underlying its inhibition of acute myeloid leukemia (AML) remains unclear. This study explored the biological mechanisms and pharmacological effects of Alpinia officinarum in AML through network pharmacology, molecular docking and molecular dynamics (MD) simulation. Methods: Active compounds were identified through a literature review and Dr. Duke’s database. Compounds were screened based on solubility, oral bioavailability (OB) and drug-likeness (DL) using SwissADME and Molsoft tools. Targets related to the identified compounds were acquired using SwissTargetPrediction, and AML targets were extracted from DisGeNET, OMIM and GeneCards. Common targets of the active compounds and AML were further analyzed via gene ontology (GO) and pathway enrichment using ShinyGO, followed by the protein–protein interaction (PPI) through STRING and Cytoscape to elucidate key targets. Molecular docking and dynamics simulation were employed to find a lead compound. Results: Eleven potential active compounds and six key targets were identified. The targets were enriched in pathways such as central carbon metabolism in cancer and the PI3K-Akt signaling pathway. Molecular docking revealed that Alpinin A had a high affinity for the six key targets (BCL2, AKT1, PIK3CA, ABL1, TERT and FLT3). Furthermore, MD simulation demonstrated the stability of the AKT1-Alpinin A complex which showed the best docking score among other active compounds. Conclusion: Our study indicates that Alpinin A may serve as a promising agent against AML, highlighting its potential for further pharmacological investigation.

Alzheimer’s disease (AD) is a multifactorial and polygenic disease. It is the most prevalent reason for dementia in the aging population. A dataset of twenty-six 1,2,3-triazole-based derivatives previously synthetized and evaluated for acetylcholinesterase inhibitory activity were subjected to the three-dimensional quantitative structure-activity relationship (3D-QSAR) study. Good predictability was achieved for comparative molecular field analysis (CoMFA) (Q2 = 0.604, R2 = 0.863, rext2 = 0.701) and comparative molecular similarity indices analysis (CoMSIA) (Q2 = 0.606, R2 = 0.854, rext2 = 0.647). The molecular features characteristics provided by the 3D-QSAR contour plots were quite useful for designing and improving the activity of acetylcholinesterase of this class. Based on these findings, a new series of 1,2,3-triazole based derivatives were designed, among which compound A1 with the highest predictive activity was subjected to detailed molecular docking and compared to the most active compound. The selected compounds were further subjected to 20 ns molecular dynamics (MD) simulations to study the comparative conformation dynamics of the protein after ligand binding, revealing promising results for the designed molecule. Therefore, this study could provide worthy guidance for further experimental analysis of highly effective acetylcholinesterase inhibitors.

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

Licorice flavonoids (LCFs) are natural flavonoids isolated from Glycyrrhiza which are known to have anti-melanoma activities in vitro. However, the molecular mechanism of LCF anti-melanoma has not been fully understood. In this study, network pharmacology, 3D/2D-QSAR, molecular docking, and molecular dynamics (MD) simulation were used to explore the molecular mechanism of LCF anti-melanoma. First of all, we screened the key active components and targets of LCF anti-melanoma by network pharmacology. Then, the logIC50 values of the top 20 compounds were predicted by the 2D-QSAR pharmacophore model, and seven highly active compounds were screened successfully. An optimal 3D-QSAR pharmacophore model for predicting the activity of LCF compounds was established by the HipHop method. The effectiveness of the 3D-QSAR pharmacophore was verified by a training set of compounds with known activity, and the possible decisive therapeutic effect of the potency group was inferred. Finally, molecular docking and MD simulation were used to verify the effective pharmacophore. In conclusion, this study established the structure–activity relationship of LCF and provided theoretical guidance for the research of LCF anti-melanoma.

Calcium-dependent lectin I from Pseudomonas aeruginosa (PA-IL) binds specifically to oligosaccharides presenting an alpha-galactose residue at their nonreducing end, such as the disaccharides alphaGal1-2betaGalOMe, alphaGal1-3betaGalOMe, and alphaGal1-4betaGalOMe. This provides a unique model for studying the effect of the glycosidic linkage of the ligands on structure and thermodynamics of the complexes by means of experimental and theoretical tools. The structural features of PA-IL in complex with the three disaccharides were established by docking and molecular dynamics simulations and compared with those observed in available crystal structures, including PA-IL.alphaGal1-2betaGalOMe complex, which was solved at 2.4 A resolution and reported herein. The role of a structural bridge water molecule in the binding site of PA-IL was also elucidated through molecular dynamics simulations and free energy calculations. This water molecule establishes three very stable hydrogen bonds with O6 of nonreducing galactose, oxygen from Pro-51 main chain, and nitrogen from Gln-53 main chain of the lectin binding site. Binding free energies for PA-IL in complex with the three disaccharides were investigated, and the results were compared with the experimental data determined by titration microcalorimetry. When the bridge water molecule was included in the free energy calculations, the simulations predicted the correct binding affinity trends with the 1-2-linked disaccharide presenting three times stronger affinity ligand than the other two. These results highlight the role of the water molecule in the binding site of PA-IL and indicate that it should be taken into account when designing glycoderivatives active against P. aeruginosa adhesion.

Phospholemman (PLM) is a 72-residue bitopic cardiac transmembrane protein, which acts as a modulator of the Na(+)/K(+)-ATPase and the Na(+)/Ca(2+) exchanger and possibly forms taurine channels in nonheart tissue. This work presents a high resolution structural model obtained from a combination of site-specific infrared spectroscopy and experimentally constrained high throughput molecular dynamics (MD) simulations. Altogether, 37 experimental constraints, including nine long range orientational constraints, have been used during MD simulations in an explicit lipid bilayer/water system. The resulting tetrameric alpha-helical bundle has an average helix tilt of 7.3 degrees and a crossing angle close to 0 degrees . It does not reveal a hydrophilic pore, but instead strong interactions between various residues occlude any pore. The helix-helix packing is unusual, with Gly(19) and Gly(20) pointing to the outside of the helical bundle, facilitating potential interaction with other transmembrane proteins, thus providing a structural basis for the modulatory effect of PLM on the Na(+)/K(+)-ATPase. A two-stage model of interaction between PLM and the Na(+)/K(+)-ATPase is discussed involving PLM-ATPase interaction and subsequent formation of an unstable PLM trimer, which readily interacts with surrounding ATPase molecules. Further unconstrained MD simulations identified other packing models of PLM, one of which could potentially undergo a conformational transition to an open pore.

Acetylcholinesterase (AChE) is a critical enzyme involved in neurotransmission by hydrolyzing acetylcholine at the synaptic cleft, making it a key target for drug discovery, particularly in the treatment of neurodegenerative disorders such as Alzheimer's disease. Computational approaches, particularly molecular docking and molecular dynamics (MD) simulations, have become indispensable tools for identifying and optimizing AChE inhibitors by predicting ligand-binding affinities, interaction mechanisms, and conformational dynamics. This review serves as a comprehensive guide for future research on AChE using molecular docking and MD simulations. It compiles and analyzes studies conducted over the past five years, providing a critical evaluation of the most widely used computational tools, including AutoDock, AutoDock Vina, and GROMACS, which have significantly contributed to the advancement of AChE inhibitor screening. Furthermore, we identify PDB ID: 4EY7, the most frequently used AChE crystal structure in docking studies, and highlight Donepezil, a well-established reference molecule widely employed as a control in computational screening for novel inhibitors. By examining these key aspects, this review aims to enhance the accuracy and reliability of virtual screening approaches and guide researchers in selecting the most appropriate computational methodologies. The integration of docking and MD simulations not only improves hit identification and lead optimization but also provides deeper mechanistic insights into AChE-ligand interactions, contributing to the rational design of more effective AChE inhibitors.

The sarco-plasmic reticulum calcium pump (SERCA) plays a critical role in the contraction-relaxation cycle of muscle. In cardiac muscle, SERCA is regulated by the inhibitor phospholamban. A new regulator, dwarf open reading frame (DWORF), has been reported to displace phospholamban from SERCA. Here, we show that DWORF is a direct activator of SERCA, increasing its turnover rate in the absence of phospholamban. Measurement of in-cell calcium dynamics supports this observation and demonstrates that DWORF increases SERCA-dependent calcium reuptake. These functional observations reveal opposing effects of DWORF activation and phospholamban inhibition of SERCA. To gain mechanistic insight into SERCA activation, fluorescence resonance energy transfer experiments revealed that DWORF has a higher affinity for SERCA in the presence of calcium. Molecular modeling and molecular dynamics simulations provide a model for DWORF activation of SERCA, where DWORF modulates the membrane bilayer and stabilizes the conformations of SERCA that predominate during elevated cytosolic calcium.

Modeling Macromolecular Motions by X-Ray-Scattering-Constrained Molecular Dynamics

Bioactive natural products have been extensively investigated for the discovery of alternative Alzheimer’s disease (AD) treatments. Recently, our structure-based virtual screening (SBVS) campaigns on natural products served in the LOTUS database exhibited the potency of isoliquiritigenin as an acetylcholinesterase (AChE) inhibitor, which propelled us to investigate it further. This study aimed to evaluate the acetylcholinesterase (AChE) inhibitory activity of isoliquiritigenin compared to commonly known inhibitors i.e., donepezil through in vitro and in silico studies. The AChE inhibitory activity of isoliquiritigenin and donepezil was evaluated using the improved Ellman method and the molecular mechanism in inhibiting AChE was identified using molecular docking and dynamics simulations. Our findings verified the AChE inhibitory activity of isoliquiritigenin, possessing an IC50 value of 126.22 µM compared to donepezil with an IC50 value of 36.98 µM. In silico studies revealed that five best-docked poses from 100 redocking and molecular docking simulations established interactions in the AChE active site in 5 ns after 5-ns equilibration run. Further dynamics interactions were explored to 50 ns, showing interactions of isoliquiritigenin and donepezil which were still in the AChE active site. These simulations also revealed the pivotality of the aromatic ring and hydroxyl moiety of isoliquiritigenin reinforcing the receptor-ligand stabilization. Our studies hence exhibited the potency of isoliquiritigenin acting as an AChE inhibitor and might be explored in isoliquiritigenin-containing bioactive natural products as AD alternative treatments.

In this study, a series of NSAID 1-acyl-4-cycloalkyl/arylsemicarbazides and 1-acyl-5-benzyloxy/hydroxy carbamoylcarbazides possess anti-cancer activity against three human cancer cell lines L1210, CEM, and HeLa have been investigated using a combined approach including quantitative structure activity relationship (QSAR) study, molecular docking, and molecular dynamics (MD) simulations. First, different molecular descriptors were calculated for these compounds. Stepwise multiple linear regression (MLR) method was performed for selecting some common descriptors, including VEA1, hydration energy (HE), log P, and binding energy for all three cell lines. Then, other QSAR models were constructed using support vector regression (SVR) method. According to the results, SVR models were more efficient in predicting the anti-cancer activity. To better understand the mechanism of the binding interactions of NSAID 1-acyl-4-cycloalkyl/arylsemicarbazide and 1-acyl-5-benzyloxy/hydroxy carbamoylcarbazide derivatives with 5-lipoxygenase (5-LOX) protein, molecular docking studies were conducted. These studies have also been used to explore the effects of HE, log P, and binding energy on anti-cancer activity of the studied compounds. The results of molecular docking suggest that hydrophobic interactions of ligands with the active site of 5-LOX are responsible for their anti-cancer activities. Finally, molecular dynamics (MD) simulations using GROMACS package were used for evaluating the stability of 5-LOX in complex with NSAID 1-acyl-4-cycloalkyl/arylsemicarbazide and 1-acyl-5-benzyloxy/hydroxy carbamoylcarbazide derivatives. The results of MD simulations demonstrate stability of protein structure in complex with active compounds, 12 and 27.

Alzheimer’s disease (AD), a progressive neurodegenerative disorder, poses a significant global health burden due to its intricate pathology and the absence of curative treatments. Current therapies primarily offer symptomatic relief, often with limited efficacy and complications, thereby underscoring the urgent need for innovative, safer, and more effective interventions. Stigmasterol, a plant-derived phytosterol, has demonstrated neuroprotective properties, including anti-inflammatory and antioxidant effects, which positions this sterol as a compelling candidate for further investigation in AD treatment. In this investigation, high-throughput virtual screening of 972 stigmasterol analogs (SAs) was conducted to identify potential acetylcholinesterase (AChE) inhibitors, followed by ADMET filtering, molecular dynamics (MD) simulations, MM/GBSA free binding energy estimations, and DFT calculations. Three lead compounds, including SA4 (-10.9 kcal/mol), SA12 (-10.6 kcal/mol), and SA15 (-10.5 kcal/mol), demonstrated superior binding affinities compared to stigmasterol (-9.6 kcal/mol) and the control drug donepezil (-8.6 kcal/mol). Docking interaction analysis revealed strong binding by hydrogen bonds and hydrophobic interactions, whereas pharmacokinetic, pharmacodynamic, and toxicity assessments confirmed the favorable characteristics of these compounds. MD simulations (200 ns) demonstrated the structural compactness of the compounds, which was further supported by principal component analysis and Gibbs free energy landscape experiments. MM/GBSA identified SA4 as the most potent analog (-82.21 kcal/mol), followed by SA15 (-80.40 kcal/mol) and SA12 (-69.72 kcal/mol). A DFT-based molecular reactivity analysis revealed decreased reactivity and increased kinetic stability of the lead candidates in their transition from free to bound states. These findings provide insights into the therapeutic potential of stigmasterol analogs as AChE inhibitors, thus offering the groundwork for in vivo and in vitro validation for advancing AD treatment.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-20527-3.

Rational design of peptide ligand for affinity chromatography of tissue-type plasminogen activator by the combination of docking and molecular dynamics simulations