Binding interaction of protoberberine alkaloids against acetylcholinesterase (AChE) using molecular dynamics simulations and QM/MM calculations

Binding interactions and in silico ADME prediction of isoconessimine derivatives as potent acetylcholinesterase inhibitors

In pursuit of new acetylcholinesterase (AChE) inhibitors for treating Alzheimer's disease (AD), a series of ten previously synthesized isoconessimine compounds (7a-7j) was in silico investigated for their binding interactions with AChE and pharmacokinetics based on absorption, distribution, metabolism, and excretion (ADME) properties using molecular docking, ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) method and SwissADME tools. Docking experiments showed that all compounds bind within the active site gorge of AChE (PDB entry 1C2B), posing its aryloxy-substitutional ethyl group to catalytic site and conessine skeleton to peripheral anionic site. ONIOM interaction energy was used as an ONIOM score to improve docking score, and it ranked 7b as the most potent AChE inhibitor, in agreement with previous experiment. Residues, ASP74, TRP86, GLY122, GLU202, TRP286, GLU292, SER293, ILE294, TYR337, TYR341, and HIS447 were identified as important for the binding of the AChE-isoconessimine complex. The SwissADME investigation suggested that four compounds (7a, 7c, 7d and 7f) agree with the rules of drug-likeness. The steric and electronic effects on the aryloxy-substitutional ethyl group as important factors in the AChE inhibition were also discussed, which brings a better understanding of Alzheimer's disease drug development.

Inhibition mechanism of fisetin on acetylcholinesterase and its synergistic effect with galantamine

The search for acetylcholinesterase (AChE) inhibitors produced by natural sources is of great significance for the prevention and therapy of Alzheimer's disease and has been widely concerned. In this study, fisetin, a flavonoid compound of plant origin, displayed a mixed inhibition mode on AChE (IC50 = 8.88 ± 0.14 μM). Fluorescence spectra analysis revealed that fisetin statically quenched AChE fluorescence, and the ground state complex was formed by hydrogen bonds and hydrophobic interactions. Circular dichroism assays showed that fisetin induced AChE structure loosened with a decrease in α-helix structure (from 20.6 % to 19.5 %). Computer simulation exhibited that fisetin bound to both the peripheral anionic site (PAS) and the catalytic active site (CAS) and increased the stability of the AChE. Interestingly, the combination of fisetin and galantamine enhanced the binding affinity between AChE and galantamine and induced AChE structure further loosened, while the inhibition mode was still the mixed type. The heatmap analysis indicated that galantamine (0.2 μM) combined with fisetin (2.25 μM) had a significant synergy on AChE inhibition, probably because fisetin binding at the PAS-AChE induced conformation changes of the gorge and CAS, which enhanced galantamine binding affinity with CAS, and a further loose structure of AChE was induced by the mixture, so finally the interaction between the substrate and AChE was strongly affected. This work may offer a theoretical reference for the functional research of fisetin as a potential AChE inhibitor and an enhanced supplement for galantamine.

Palmatine attenuates LPS-induced neuroinflammation through the PI3K/Akt/NF-κB pathway

To investigate the key molecular mechanisms of palmatine for the treatment of neuroinflammation through modulation of a pathway using molecular docking, molecular dynamics (MD) simulation combined with network pharmacology, and animal experiments. Five alkaloid components were obtained from the traditional Chinese medicine Huangteng through literature mining. Molecular docking and MD simulation with acetylcholinesterase were used to screen palmatine. At the animal level, mice were injected with LPS intracerebrally to cause a neuroinflammatory model, and the Morris water maze experiment was performed to examine the learning memory of mice. Anxiety levels were tested using the autonomous activity behavior experiment with the open field and elevated behavior experiments. HE staining and Niss staining were performed on brain tissue sections to observe morphological lesions and apoptosis; serum was examined for inflammatory factors TNF-α, IL-6, and IL-1β; Western blot was performed to detect the protein expression. The expression of PI3K/AKT/NFkB signaling pathway-related proteins was examined by Western blot. The results of network pharmacology showed that the screening of palmatine activation containing the PI3K/Akt/NFkB signaling pathway exerts antineuroinflammatory effects. Results from behavioral experiments showed that Pal enhanced learning memory in model mice, improved anxiety behavior, and significantly improved brain damage caused by neuroinflammation. The results of HE staining and Niss staining of brain tissue sections showed that palmatine could alleviate morphological lesions and nucleus damage in brain tissue. Palmatine improved the levels of serum inflammatory factors TNF-α, IL-6, and IL-1β. SOD, MDA, CAT, ACH, and ACHE in the hippocampus were improved. Western blot results showed that palmatine administration ameliorated LPS-induced neuroinflammation through the PI3K/Akt/NFkB pathway.

Inhibition mechanisms of four ellagitannins from terminalia chebula fruits on acetylcholinesterase by inhibition kinetics, spectroscopy and molecular docking analyses

Acetylcholinesterase (AChE) is an important therapeutic target for the treatment of Alzheimer's disease (AD), and the development of natural AChE inhibitors as candidates has played a significant role in drug discovery. In this study, the inhibition mechanisms of four ellagitannins, punicalagin, chebulinic acid, geraniin and corilagin, from Terminalia chebula fruits on AChE were investigated systematically by a combination of inhibition kinetics, multi-spectroscopic methods and molecular docking. The kinetic results showed that punicalagin, chebulinic acid and geraniin exhibited strong reversible inhibitory effects on AChE in an uncompetitive manner with the IC50 values of 0.43, 0.50, and 0.51 mM, respectively, while corilagin inhibited AChE activity in a mixed type with the IC50 value of 0.72 mM. The results of fluorescence and UV-vis spectra and fluorescence resonance energy transfer (FRET) revealed that four ellagitannins could significantly quenched the intrinsic fluorescence of AChE though a static quenching along with non-radiative energy transfer. Thermodynamic analyses showed that values of ΔG, ΔH and ΔS were negative, indicating that all binding processes were spontaneous, and the hydrogen bonding and Van der Waals forces might make a great contribution to the formation of inhibitor-AChE complexes. The synchronous fluorescence, three-dimensional (3D) fluorescence, UV-vis, and FT-IR spectra studies suggested that four ellagitannins could lead to alterations in the micro-environment and secondary structure of AChE, and thus the conformational change of AChE. Moreover, molecular docking demonstrated that four ellagitannins could interacted with main amino acid residues of AChE with affinity energies ranging from -9.9 to -8.7 kJ/mol, and further confirmed the above experimental results. This study provided valuable findings for the potential application of four ellagitannins as promising candidates in the exploration of natural AChE inhibitors for the treatment of AD.

Elucidation of benzene sulfonamide derivative binding at a novel interprotomer pocket of wild type and mutants of coxsackievirus B3 viral capsid using molecular dynamics simulations and density functional theory

Coxsackievirus B3 (CVB3), a serotype of enterovirus B, causes hand, foot, and mouth disease; pericarditis; and myocarditis. A benzene sulfonamide derivative is reported to have inhibitory activity against wild-type (WT) and eight mutants of the viral capsid of CVB3. Furthermore, the crystal structure of the complex formed between WT viral capsid of CVB3 and the derivative revealed binding at a novel druggable interprotomer pocket. We investigated how the compound could be a potent inhibitor of both WT and some mutants of CVB3 by determining binding to the viral capsid and the interaction energy with the binding pocket based on molecular dynamics simulations and density functional theory. We found that hydrogen bonds, pi-pi interactions, and electrostatic interactions are the key interactions with a protomer unit of CVB3 viral capsid. The residual interaction energy determined using density functional theory revealed key binding with VP1:Arg234 and a residue in the nearby VP1 unit (VP1':Arg219). These results explain why the compound is still a potent inhibitor against eight mutants. Moreover, the decreased inhibitory activity for some mutants could be explained by the calculated binding energy and the highest occupied molecular orbital and lowest unoccupied molecular orbital energy. The results will be helpful for the development of drugs resistant to CVB3.

The composition, pharmacological effects, related mechanisms and drug delivery of alkaloids from Corydalis yanhusuo

Corydalis yanhusuo W. T. Wang, also known as yanhusuo, yuanhu, yanhu and xuanhu, is one of the herb components of many Chinese Traditional Medicine prescriptions such as Jin Ling Zi San and Yuanhu-Zhitong priscription. C. yanhusuo was traditionally used to relieve pain and motivate blood and Qi circulation. Now there has been growing interest in pharmacological effects of alkaloids, the main bioactive components of C. yanhusuo. Eighty-four alkaloids isolated from C. yanhusuo are its important bioactive components and can be characterized into protoberberine alkaloids, aporphine alkaloids, opiate alkaloids and others and proper extraction or co-administration methods modulate their contents and efficacy. Alkaloids from C. yanhusuo have various pharmacological effects on the nervous system, cardiovascular system, cancer and others through multiple molecular mechanisms such as modulating neurotransmitters, ion channels, gut microbiota, HPA axis and signaling pathways and are potential treatments for many diseases. Plenty of novel drug delivery methods such as autologous red blood cells, self-microemulsifying drug delivery systems, nanoparticles and others have also been investigated to better exert the effects of alkaloids from C. yanhusuo. This review summarized the alkaloid components of C. yanhusuo, their pharmacological effects and mechanisms, and methods of drug delivery to lay a foundation for future investigations.

Evaluation of berberine nanoparticles as a strategy to modulate acetylcholinesterase activity

Researchers have concentrated efforts in the search for natural-based reversible inhibitors for cholinesterase enzymes as they may play a key role in the treatment of degenerative diseases. Diverse plant alkaloids can inhibit the action of acetylcholinesterase and, among them, berberine is a promising bioactive. However, berberine has poor water solubility and low bioavailability, which makes it difficult to use in treatment. The solid dispersion technique can improve the water affinity of hydrophobic substances, but berberine solid dispersions have not been extensively studied. Safety testing is also essential to ensure that the berberine-loaded solid dispersions are safe for use. This study investigated the effectiveness of berberine-loaded solid dispersions (SD) as inhibitors of acetylcholinesterase enzyme (AChE). Docking simulation was used to investigate the influence of berberine on AChE, and in vitro assays were conducted to confirm the enzymatic kinetics of AChE in the presence of berberine. Berberine SD also showed improved cytotoxic effects on tumoral cells when dispersed in aqueous media. In vivo assays using Allium cepa were implemented, and no cytotoxicity/genotoxicity was found for the berberine solid dispersion. These results suggest that berberine SD could be a significant step towards safe nanostructures for use in the treatment of neurodegenerative diseases.

Two new dilactonized glycerol glycosides of the dual anticholinesterase active extract from Ocotea daphnifolia using bioguided fractionation and molecular docking studies

The dual inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) is considered as an important strategy for the treatment of Alzheimer's disease. In this study, we applied the bioguided fractionations of Ocotea daphinifolia ethyl acetate active extract to furnish a fraction with high inhibitory activity for AChE and BuChE (82% and 92%, respectively). High-performance liquid chromatography semipreparative purification of this fraction provided two new natural products: 1-β-D-galactopyranosyl-glycerol-2,3-heptanedionate, (1) whose complete chemical structural elucidation was made with spectrometric analysis (MS, 1D, and 2D NMR) and its minor derivative 1-β-D-gulopyranosyl-glycerol-2,3-heptanedionate; (2) which could be characterized by 2D ¹ H-¹³ C heteronuclear single-quantum correlation spectra analysis. Investigation of the intermolecular interactions with cholinesterases was carried out by molecular docking studies, and results suggested that both compounds are capable to interact with the catalytic site of both enzymes. Compounds 1 and 2 interact with residues of catalytic domains and the peripheral anionic binding site of AChE and BuChE. The results are comparable to those achieved with rivastigmine and galantamine. Thus, this study provides evidence for consideration of the glycosylglycerol from O. daphnifolia as new valuable dual cholinesterases inhibitor.