EGCG inhibits the oligomerization of amyloid beta (16-22) hexamer: Theoretical studies

Understanding the mechanisms of green tea EGCG against amyloid β oligomer neurotoxicity through computational studies

Oligomeric species of amyloid β peptide (Aβ) are pivotal in Alzheimer's disease (AD) pathogenesis, making them valuable therapeutic targets. Currently, there is no cure or preventive therapy available for AD, with only a few therapeutics offering temporary alleviation of symptoms. Natural products (NPs) are now considered promising anti-amyloid agents. Green tea catechins have garnered considerable attention due to their ability to remodel the toxic amyloid β peptide oligomers (AβOs) into non-toxic assemblies. Nevertheless, the precise molecular mechanism underlying their effects on AβOs remains unclear. In this study, we employ a combination of binding site prediction, molecular docking, and dynamics simulations to gain mechanistic insights into the binding of the potent anti-amyloid epigallocatechin-3-gallate (EGCG) and the less effective catechin, epicatechin (EC), on the structure of pore-forming Aβ tetramers (PDB ID 6RHY). This recently elucidated structure represents AβO(1-42) with two faces of the hydrophobic β-sheet core and hydrophilic edges. Our simulations revealed three potential druggable binding sites within the AβO: two in hydrophilic edges and one in the β-sheet core. Although both catechins bind via hydrogen bond (H-bond) and aromatic interactions to the three potential binding sites, EGCG interacted with key residues more efficiently than EC. We propose that EGCG may remodel AβOs preventing pore formation by binding to the hydrophilic edge binding sites. Additionally, EGCG interacts with key residues in the oligomer's β-sheet core binding site, crucial for fibrillar aggregation. A better understanding of how anti-amyloid compounds remodelling AβOs could be valuable for the development of new therapeutic strategies targeting Aβ in AD. Further experimental validation using point mutations involving key residues could be useful to define whether the establishment of these interactions is crucial for the EGCG remodelling effect.

Conformational Properties of Aβ Peptide Oligomers in Aqueous Ionic Liquid Solution: Insights from Molecular Simulation Studies

Alzheimer's disease is a progressive irreversible neurological disorder with abnormal extracellular deposition of amyloid β (Aβ) peptides in the brain. We have carried out atomistic molecular dynamics simulations to investigate the size-dependent conformational properties of aggregated Aβ oligomers of different orders, namely, pentamer [O(5)], decamer [O(10)], and hexadecamer [O(16)] in aqueous solutions containing the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]). The calculations revealed reduced peptide conformational fluctuations in O(5) and O(10) in the presence of the IL. In contrast, the higher order oligomer [O(16)] has been found to exhibit greater structural distortion due to enhanced flexibilities of its peptide units in the presence of the IL. Based on the distributions of the solvent (water) and the cosolvent (IL) components, it is demonstrated that exchange of water by the IL ion pairs at the exterior surface of the oligomers primarily occurs beyond the first layer of surface-bound water molecules. Importantly, a reduced number of relatively weaker peptide salt bridges have been found in O(16) in binary water-IL solution as compared to the other two smaller-sized oligomers [O(5) and O(10)]. Such differential influence of the IL on peptide salt bridges results in less favorable binding free energies of peptide monomers to O(16), which leads to its greater structural distortion and reduced stability compared to those of O(5) and O(10).

Combined Treatment with Curcumin and Ferulic Acid Suppressed the Aβ-Induced Neurotoxicity More than Curcumin and Ferulic Acid Alone

Alzheimer’s disease (AD) is a neurodegenerative disease that leads to progressive cognitive decline. Several effective natural components have been identified for the treatment of AD. However, it is difficult to obtain conclusive evidence on the safety and effectiveness of natural components, because a variety of factors are associated with the progression of AD pathology. We hypothesized that a therapeutic effect could be achieved by combining multiple ingredients with different efficacies. The purpose of this study was thus to evaluate a combination treatment of curcumin (Cur) and ferulic acid (FA) for amyloid-β (Aβ)-induced neuronal cytotoxicity. The effect of Cur or FA on Aβ aggregation using thioflavin T assay was confirmed to be inhibited in a concentration-dependent manner by Cur single or Cur + FA combination treatment. The effects of Cur + FA on the cytotoxicity of human neuroblastoma (SH-SY5Y) cells induced by Aβ exposure were an increase in cell viability, a decrease in ROS and mitochondrial ROS, and repair of membrane damage. Combination treatment showed an overall higher protective effect than treatment with Cur or FA alone. These results suggest that the combined action mechanisms of Cur and FA may be effective in preventing and suppressing the progression of AD.

Identifying Possible AChE Inhibitors from Drug-like Molecules via Machine Learning and Experimental Studies

Acetylcholinesterase (AChE) is one of the most important drug targets for Alzheimer's disease (AD) treatment. In this work, a machine learning model was trained to rapidly and accurately screen large chemical databases for the potential inhibitors of AChE. The obtained results were then validated via in vitro enzyme assay. Moreover, atomistic simulations including molecular docking and molecular dynamics simulations were then used to understand molecular insights into the binding process of ligands to AChE. In particular, two compounds including benzyl trifluoromethyl ketone and trifluoromethylstyryl ketone were indicated as highly potent inhibitors of AChE because they established IC₅₀ values of 0.51 and 0.33 μM, respectively. The obtained IC₅₀ of two compounds is significantly lower than that of galantamine (2.10 μM). The predicted log(BB) suggests that the compounds may be able to traverse the blood-brain barrier. A good agreement between computational and experimental studies was observed, indicating that the hybrid approach can enhance AD therapy.

(-)-Epigallocatechin-3-Gallate Diminishes Intra-and Extracellular Amyloid-Induced Cytotoxic Effects on Cholinergic-like Neurons from Familial Alzheimer's Disease PSEN1 E280A

Alzheimer’s disease (AD) is a complex neurodegenerative disease characterized by functional disruption, death of cholinergic neurons (ChNs) because of intracellular and extracellular Aβ aggregates, and hyperphosphorylation of protein TAU (p-TAU). To date, there are no efficient therapies against AD. Therefore, new therapies for its treatment are in need. The goal of this investigation was to evaluate the effect of the polyphenol epigallocatechin-3-gallate (EGCG) on cholinergic-like neurons (ChLNs) bearing the mutation E280A in PRESENILIN 1 (PSEN1 E280A). To this aim, wild-type (WT) and PSEN1 E280A ChLNs were exposed to EGCG (5–50 μM) for 4 days. Untreated or treated neurons were assessed for biochemical and functional analysis. We found that EGCG (50 μM) significantly inhibited the aggregation of (i)sAPPβf, blocked p-TAU, increased ∆Ψm, decreased oxidation of DJ-1 at residue Cys106-SH, and inhibited the activation of transcription factor c-JUN and P53, PUMA, and CASPASE-3 in mutant ChLNs compared to WT. Although EGCG did not reduce (e)Aβ42, the polyphenol reversed Ca²⁺ influx dysregulation as a response to acetylcholine (ACh) stimuli in PSEN1 E280A ChLNs, inhibited the activation of transcription factor NF-κB, and reduced the secretion of pro-inflammatory IL-6 in wild-type astrocyte-like cells (ALCs) when exposed to mutant ChLNs culture supernatant. Taken together, our findings suggest that the EGCG might be a promising therapeutic approach for the treatment of FAD.

Interplay between epigallocatechin-3-gallate and ionic strength during amyloid aggregation

The formation and accumulation of protein amyloid aggregates is linked with multiple amyloidoses, including neurodegenerative Alzheimer's or Parkinson's disease. The mechanism of such fibril formation is impacted by various environmental conditions, which greatly complicates the search for potential anti-amyloid compounds. One of these factors is solution ionic strength, which varies between different aggregation protocols during in vitro drug screenings. In this work, we examine the interplay between ionic strength and a well-known protein aggregation inhibitor-epigallocatechin-3-gallate. We show that changes in solution ionic strength have a major impact on the compound's inhibitory effect, reflected in both aggregation times and final fibril structure. We also observe that this effect is unique to different amyloid-forming proteins, such as insulin, alpha-synuclein and amyloid-beta.

Marine derivatives prevent wMUS81 in silico studies

The winged-helix domain of the methyl methanesulfonate and ultraviolet-sensitive 81 (wMUS81) is a potential cancer drug target. In this context, marine fungi compounds were indicated to be able to prevent wMUS81 structure via atomistic simulations. Eight compounds such as D197 (Tryptoquivaline U), D220 (Epiremisporine B), D67 (Aspergiolide A), D153 (Preussomerin G), D547 (12,13-dihydroxyfumitremorgin C), D152 (Preussomerin K), D20 (Marinopyrrole B) and D559 (Fumuquinazoline K) were indicated that they are able to prevent the conformation of wMUS81 via forming a strong binding affinity to the enzyme via perturbation approach. The electrostatic interaction is the dominant factor in the binding process of ligands to wMUS81. The residues Trp55, Arg59, Leu62, His63 and Arg69 were found to frequently form non-bonded contacts and hydrogen bonds to inhibitors. Moreover, the influence of the ligand D197, which formed the lowest binding free energy to wMUS81, on the structural change of enzyme was investigated using replica exchange molecular dynamics simulations. The obtained results indicated that D197, which forms a strong binding affinity, can modify the structure of wMUS81. Overall, the marine compounds probably inhibit wMUS81 due to forming a strong binding affinity to the enzyme as well as altering the enzymic conformation.

Inhibition of Aβ peptide aggregation by ruthenium(II) polypyridyl complexes through copper chelation

Alzheimer's disease (AD) is known as a complex multifactorial syndrome and both metal chelators and amyloid β peptide (Aβ) inhibitors show promise against AD. Herein, four small hybrid compounds have been designed and synthesized utilizing 8-hydroxyquinoline, pyridine or imidazole as chelators and benzimidazole as the recognition moiety for AD treatment. These conjugates can capture Cu²⁺ from Aβ and become dimers upon Cu²⁺ coordination and show high efficiency for both Cu²⁺ elimination and Aβ assembly inhibition. Besides, these designed complexes can inhibit the production of Aβ-induced reactive oxygen species (ROS), protect mitochondria from damage, and improve the survival rate of neuron cells. Our work provides a new strategy to combine hydrophobic interaction and metal ion chelation to design amyloid inhibitors.

The F19W mutation reduces the binding affinity of the transmembrane Aβ11-40 trimer to the membrane bilayer

Alzheimer's disease is linked to the aggregation of the amyloid-β protein (Aβ) of 40 or 42 amino acids. Lipid membranes are known to modulate the rate and mechanisms of the Aβ aggregation. Point mutations in Aβ can alter these rates and mechanisms. In particular, experiments show that F19 mutations influence the aggregation rate, but maintain the fibril structures. Here, we used molecular dynamics simulations to examine the effect of the F19W mutation in the 3Aβ11-40 trimer immersed in DPPC lipid bilayers submerged in aqueous solution. Substituting Phe by its closest (non-polar) aromatic amino acid Trp has a dramatic reduction in binding affinity to the phospholipid membrane (measured with respect to the solvated protein) compared to the wild type: the binding free energy of the protein-DPPC lipid bilayer increases by 40-50 kcal mol-1 over the wild-type. This is accompanied by conformational changes and loss of salt bridges, as well as a more complex free energy surface, all indicative of a more flexible and less stable mutated trimer. These results suggest that the impact of mutations can be assessed, at least partially, by evaluating the interaction of the mutated peptides with the lipid membranes.

Thermodynamics and kinetics in antibody resistance of the 501Y.V2 SARS-CoV-2 variant

Understanding the thermodynamics and kinetics of the binding process of an antibody to the SARS-CoV-2 receptor-binding domain (RBD) of the spike protein is very important for the development of COVID-19 vaccines. In particular, it is essential to understand how the binding mechanism may change under the effects of RBD mutations. In this context, we have demonstrated that the South African variant (B1.351 or 501Y.V2) can resist the neutralizing antibody (NAb). Three substitutions in the RBD including K417N, E484K, and N501Y alter the free energy landscape, binding pose, binding free energy, binding kinetics, hydrogen bonding, nonbonded contacts, and unbinding pathway of RBD + NAb complexes. The low binding affinity of NAb to 501Y.V2 RBD confirms the antibody resistance of the South African variant. Moreover, the fragment of NAb + RBD can be used as an affordable model to investigate changes in the binding process between the mutated RBD and antibodies.

Increasing FEL minima of 501Y.V2 RBD + antibody in comparison with the WT RBD systems imply that the complex 501Y.V2 RBD + antibody is more unstable than the WT one.

Curcumin and Its Derivatives as Theranostic Agents in Alzheimer's Disease: The Implication of Nanotechnology

Curcumin is a polyphenolic natural compound with diverse and attractive biological properties, which may prevent or ameliorate pathological processes underlying age-related cognitive decline, Alzheimer's disease (AD), dementia, or mode disorders. AD is a chronic neurodegenerative disorder that is known as one of the rapidly growing diseases, especially in the elderly population. Moreover, being the eminent cause of dementia, posing problems for families, societies as well a severe burden on the economy. There are no effective drugs to cure AD. Although curcumin and its derivatives have shown properties that can be considered useful in inhibiting the hallmarks of AD, however, they have low bioavailability. Furthermore, to combat diagnostic and therapeutic limitations, various nanoformulations have also been recognized as theranostic agents that can also enhance the pharmacokinetic properties of curcumin and other bioactive compounds. Nanocarriers have shown beneficial properties to deliver curcumin and other nutritional compounds against the blood-brain barrier to efficiently distribute them in the brain. This review spotlights the role and effectiveness of curcumin and its derivatives in AD. Besides, the gut metabolism of curcumin and the effects of nanoparticles and their possible activity as diagnostic and therapeutic agents in AD also discussed.

Hydroxycinnamic Acid from Corncob and Its Structural Analogues Inhibit Aβ40 Fibrillation and Attenuate Aβ40-Induced Cytotoxicity

The aggregation of amyloid-β protein (Aβ) is deemed a vital pathological feature of Alzheimer's disease (AD). Hence, inhibiting Aβ aggregation is noticed as a major tactic for the prevention and therapy of AD. Hydroxycinnamic acid, as a natural phenolic compound, is widely present in plant foods and has several biological activities including anti-inflammation, antioxidation, and neuroprotective effects. Here, it was found that hydroxycinnamic acid and its structural analogues (3-hydroxycinnamic acid, 2-hydroxycinnamic acid, cinnamic acid, 3,4-dihydroxycinnamic acid, 2,4-dihydroxycinnamic acid, and 3,4,5-trihydroxycinnamic acid) could inhibit Aβ40 fibrillogenesis and reduce Aβ40-induced cytotoxicity in a dose-dependent manner. Among these small molecules investigated, 3,4,5-trihydroxycinnamic acid is considered to be the most effective inhibitor, which reduces the ThT fluorescence intensity to 30.79% and increases cell viability from 49.47 to 84.78% at 200 μM. Also, the results with Caenorhabditis elegans verified that these small molecules can ameliorate AD-like symptoms of worm paralysis. Moreover, molecular docking studies showed that these small molecules interact with the Aβ40 mainly via hydrogen bonding. These results suggest that hydroxycinnamic acid and its structural analogues could inhibit Aβ40 fibrillogenesis and the inhibition activity is enhanced with the increase of phenolic hydroxyl groups of inhibitors. These small molecules have huge potential to be developed into novel aggregation inhibitors in neurodegenerative disorders.

Insights into the Effect of Curcumin and (-)-Epigallocatechin-3-Gallate on the Aggregation of Aβ(1-40) Monomers by Means of Molecular Dynamics

In this study, we compared the effects of two well-known natural compounds on the early step of the fibrillation process of amyloid-β (1–40), responsible for the formation of plaques in the brains of patients affected by Alzheimer’s disease (AD). The use of extensive replica exchange simulations up to the µs scale allowed us to characterize the inhibition activity of (–)-epigallocatechin-3-gallate (EGCG) and curcumin (CUR) on unfolded amyloid fibrils. A reduced number of β-strands, characteristic of amyloid fibrils, and an increased distance between the amino acids that are responsible for the intra- and interprotein aggregations are observed. The central core region of the amyloid-β (Aβ(1–40)) fibril is found to have a high affinity to EGCG and CUR due to the presence of hydrophobic residues. Lastly, the free binding energy computed using the Poisson Boltzmann Surface Ares suggests that EGCG is more likely to bind to unfolded Aβ(1–40) fibrils and that this molecule can be a good candidate to develop new and more effective congeners to treat AD.

Studies on the structure and conformational flexibility of secondary structures in amyloid beta — A quantum chemical study

Density functional theory (DFT) calculations are performed to study the conformational flexibility of secondary structures in amyloid beta (A[Formula: see text]) polypeptide. In DFT, M06-2X/6-31[Formula: see text]G(d, p) method is used to optimize the secondary structures of 2LFM and 2BEG in gas phase and in solution phase. Our calculations show that the secondary structures are energetically more stable in solution phase than in gas phase. This is due to the presence of strong solvent interaction with the secondary structures considered in this study. Among the backbone [Formula: see text] and [Formula: see text] dihedral angles, [Formula: see text] varies significantly in sheet structure. This is due to the absence of intermolecular hydrogen bond (H-bond) interactions in sheets considered in this study. Our calculations show that the conformational transition of helix/coil to sheet or vice-versa is due to the floppiness of the amino acid residues. This is observed from the Ramachandran map of the studied secondary structures. Further, it is noted that the intramolecular H-bond interactions play a significant role in the conformational transition of secondary structures of A[Formula: see text].

Polyphenols with Anti-Amyloid β Aggregation Show Potential Risk of Toxicity Via Pro-Oxidant Properties

Alzheimer's disease (AD) is the most common form of dementia among older people. Amyloid β (Aβ) aggregation has been the focus for a therapeutic target for the treatment of AD. Naturally occurring polyphenols have an inhibitory effect on Aβ aggregation and have attracted a lot of attention for the development of treatment strategies which could mitigate the symptoms of AD. However, considerable evidence has shown that the pro-oxidant mechanisms of polyphenols could have a deleterious effect. Our group has established an assay system to evaluate the pro-oxidant characteristics of chemical compounds, based on their reactivity with DNA. In this review, we have summarized the anti-Aβ aggregation and pro-oxidant properties of polyphenols. These findings could contribute to understanding the mechanism underlying the potential risk of polyphenols. We would like to emphasize the importance of assessing the pro-oxidant properties of polyphenols from a safety point of view.

Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ40 Peptide

There is experimental evidence that the astaxanthin, betanin, and epigallocatechin-3-gallate (EGCG) compounds slow down the aggregation kinetics and the toxicity of the amyloid-β (Aβ) peptide. How these inhibitors affect the self-assembly at the atomic level remains elusive. To address this issue, we have performed for each ligand atomistic replica exchange molecular dynamic (REMD) simulations in an explicit solvent of the Aβ_11-40 trimer from the U-shape conformation and MD simulations starting from Aβ_1-40 dimer and tetramer structures characterized by different intra- and interpeptide conformations. We find that the three ligands have similar binding free energies on small Aβ₄₀ oligomers but very distinct transient binding sites that will affect the aggregation of larger assemblies and fibril elongation of the Aβ₄₀ peptide.

Mitigating Alzheimer’s Disease with Natural Polyphenols: A Review

:

According to Alzheimer’s Disease International (ADI), nearly 50 million people worldwide were living with dementia in 2017, and this number is expected to triple by 2050. Despite years of research in this field, the root cause and mechanisms responsible for Alzheimer’s disease (AD) have not been fully elucidated yet. Moreover, promising preclinical results have repeatedly failed to translate into patient treatments. Until now, none of the molecules targeting AD has successfully passed the Phase III trial. Although natural molecules have been extensively studied, they normally require high concentrations to be effective; alternately, they are too large to cross the blood-brain barrier (BBB).

:

In this review, we report AD treatment strategies, with a virtually exclusive focus on green chemistry (natural phenolic molecules). These include therapeutic strategies for decreasing amyloid-β (Aβ) production, preventing and/or altering Aβ aggregation, and reducing oligomers cytotoxicity such as curcumin, (-)-epigallocatechin-3-gallate (EGCG), morin, resveratrol, tannic acid, and other natural green molecules. We also examine whether consideration should be given to potential candidates used outside of medicine and nutrition, through a discussion of two intermediate-sized green molecules, with very similar molecular structures and key properties, which exhibit potential in mitigating Alzheimer’s disease.

C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ11-42 Tetramer in Solution: Intensive MD Study

Amyloid beta (Aβ) peptides are characterized as the major factors associated with neuron death in Alzheimer's disease, which is listed as the most common form of neurodegeneration. Disordered Aβ peptides are released from proteolysis of the amyloid precursor protein. The Aβ self-assembly process roughly takes place via five steps: disordered forms → oligomers → photofibrils → mature fibrils → plaques. Although Aβ fibrils are often observed in patient brains, oligomers were recently indicated to be major neurotoxic elements. In this work, the neurotoxic compound S-shape Aβ11-42 tetramer (S4Aβ11-42) was investigated over 10 μs of unbiased MD simulations. In particular, the S4Aβ11-42 oligomer adopted a high dynamics structure, resulting in unsuccessful determination of their structures in experiments. The C-terminal was suggested as the possible nucleation of the Aβ42 aggregation. The sequences 27-35 and 39-40 formed rich β-content, whereas other residues mostly adopted coil structures. The mean value of the β-content over the equilibrium interval is ∼42 ± 3%. Furthermore, the dissociation free energy of the S4Aβ11-42 peptide was predicted using a biased sampling method. The obtained free energy is ΔG US = -58.44 kcal/mol which is roughly the same level as the corresponding value of the U-shape Aβ17-42 peptide. We anticipate that the obtained S4Aβ11-42 structures could be used as targets for AD inhibitor screening over the in silico study.

Adequate prediction for inhibitor affinity of Aβ40 protofibril using the linear interaction energy method

The search for efficient inhibitors targeting Aβ oligomers and fibrils is an important issue in Alzheimer's disease treatment. As a consequence, an accurate and computationally cheap approach to estimate the binding affinity for many ligands interacting with Aβ peptides is very important. Here, the calculated binding free energies of 30 ligands interacting with 12Aβ11-40 peptides using the linear interaction energy (LIE) approach are found to be in good correlation with experimental data (R = 0.79). The binding affinities of these complexes are also calculated by using free energy perturbation (FEP) and molecular mechanic/Poisson-Boltzmann surface area (MM/PBSA) methods. The time-consuming FEP method provides results with similar correlation (R = 0.72), whereas MM/PBSA calculations show very low correlation with experimental data (R = 0.27). In all complexes, van der Waals interactions contribute much more than electrostatic interactions. The LIE model, which is much less time-consuming than both the FEP and MM/PBSA methods, opens the door to accurate and rapid affinity prediction of ligands with Aβ peptides and the design of new ligands.

Correction of diffusion calculations when using two types of non-rectangular simulation boxes in molecular simulations

Although simulation boxes used in molecular dynamics are normally chosen to be cubic or rectangular, two other cell shapes that are very familiar to crystallographers-the truncated octahedron and the rhombic dodecahedron-could also be used because they are also space-filling cells. Due to their spherical nature, these boxes have been intentionally applied in simulations of biomolecular solutions and liquid structures. Indeed, due to the advantages of running many molecular dynamic codes in parallel, simulations based on these non-rectangular boxes have been growing in popularity in recent years. In this work, the effects of using these two types of boxes on diffusion are explored for the first time, and an appropriate correction formula is derived theoretically within the framework of hydrodynamics. In addition, the range of validity for the correction formula is evaluated by performing molecular dynamic simulations on argon at three different densities.

In vitroandin silicodetermination of glutaminyl cyclase inhibitors

Alzheimer's disease (AD) is the most common form of neurodegenerative disease currently. It is widely accepted that AD is characterized by the self-assembly of amyloid beta (Aβ) peptides. The human glutaminyl cyclase (hQC) enzyme is characterized by association with Aβ peptide generation. The development of hQC inhibitors could prevent the self-aggregation of Aβ peptides, resulting in impeding AD. Utilizing structural knowledge of the hQC substrates and known hQC inhibitors, new heterocyclic and peptidomimetic derivatives were synthesized and were able to inhibit the hQC enzyme. The inhibiting abilities of these compounds were evaluated using a fluorometric assay. The binding mechanism at the atomic level was estimated using molecular docking, free energy perturbation, and quantum chemical calculation methods. The predicted log(BBB) and human intestinal absorption values indicated that these compounds are able to permeate the blood–brain barrier and be well-absorbed through the gastrointestinal tract. Overall, 5,6-dimethoxy-N-(3-(5-methyl-1H-imidazol-1-yl)propyl)-1H-benzo[d]imidazol-2-amine (1_2) was indicated as a potential drug for AD treatment.

Rational design of new hQC inhibitors.

Etersalate prevents the formations of 6Aβ16-22 oligomer: An in silico study

Oligomerization of amyloid beta (Aβ) peptides has been considered as the crucially causative agent in the development of Alzheimer's disease. Etersalate, a nonsteroidal anti-inflammatory oral drug (United State Food and Drug Administration—Unique Ingredient Identifier: 653GN04T2G) was previously suggested to bind well to proto-fibrils of Aβ peptides in silico. Here, the effect of etersalate on the oligomerization of soluble Aβ_16–22 hexamer (6Aβ_16–22) were extensively investigated using temperature replica exchange molecular dynamics (REMD) simulations over ~16.8 μs in total for 48 replicas (350 ns per replica). The results reveal that etersalate can enter the inner space or bind on the surface of 6Aβ_16–22 conformations, which destabilizes the hexamer. Etersalate was predicted to able to cross the blood brain barrier using prediction of absorption, distribution, metabolism, and excretion—toxicity (preADMET) tools. Overall, although the investigation was performed with the low concentration of trial inhibitor, the obtained results indicate that etersalate is a potential drug candidate for AD through inhibiting formation of Aβ oligomers with the average binding free energy of -11.7 kcal/mol.

Neuroprotective effect of epigallocatechin-3-gallate (EGCG) on radiation-induced damage and apoptosis in the rat hippocampus

PURPOSE

This study investigated the potential neuroprotective effect of epigallocatechin-3-gallate (EGCG) on radiation-induced cell death and damage in the hippocampus.

MATERIALS AND METHODS

Adult male Wister rats received oral treatment with EGCG at doses of 2.5 and 5 mg/kg/d for 3 d before 4 Gy γ irradiation.

RESULTS

The pretreatment of irradiated rats with EGCG significantly ameliorated the increased plasma levels of homocysteine, amyloid β, TNF-α and IL-6 levels and the decrease of dopamine and serotonin. Pretreatment with EGCG also significantly ameliorated the irradiation-induced increase in the 4-HNE and protein carbonyl levels and the decreased antioxidants including glutathione level, and the activities of glutathione peroxidase and glutathione reductase in the hippocampus. EGCG treatment prior to radiation exposure protected against DNA damage and apoptosis in the hippocampus. The increase in the levels of p53, Cytochrome-c, Bax and caspases 3 and 9 in the hippocampus were significantly ameliorated with a significant increase in Bcl-2. These changes were supported by marked protection of the dentate gyrus that exhibited a similar histological structure of the control animals.

CONCLUSIONS

EGCG can attenuate the severity of radiation-induced damage and cell death in hippocampus recommending polyphenols as successful option for protecting against radiation-induced hippocampal damage.

The influences of E22Q mutant on solvated 3Aβ11-40 peptide: A REMD study

The residue E22 plays a critical role in the aggregation process of Amyloid beta (Aβ) peptides. The effect of E22Q mutant on the shapes of the solvated Aβ_11-40 trimer is clarified using a replica exchange molecular dynamics (REMD) simulation employing ∼20.6 μs of MD simulations with 48 disparate replicas. The increase of intramolecular polar contacts and salt bridge between the residue D23 to residues (24-29) was observed. The residual secondary structure of the mutated trimer is shifted in a similar way to the picture observed in previous investigations of F19W mutant. The free energy surface (FES) of the mutated E22Q system has a fewer number of minima in comparison with the wild-type trimer. The optimized shapes of the mutated E22Q form a significant increase in beta structure (47%) and serious decrease in coil content (46%) compared with the wild-type (of 36 and 56%, respectively). The binding affinity of constituting chains to the rest is of -43.7 ± 6.5 kcal/mol, implying that the representative structure of E22Q is more stable than the wild-type one. Furthermore, the E22Q mutant increases the size of stable structures due to larger collision cross section (CCS) and solvent accessible area (SASA). The observed results may enhance the Aβ inhibition throughout the contribution to the knowledge of the Aβ oligomerization/aggregation.

In silico studies of solvated F19W amyloid β (11–40) trimer

REMD studies shows that F19W mutation does not change in the overall structure of Aβ_11–40 trimer significantly but increases it flexibility, consistent with the observed formation of the same fibril structures at slower rates.