Five similar anthocyanidin molecules display distinct disruptive effects and mechanisms of action on Aβ1-42 protofibril: A molecular dynamic simulation study

Alzheimer's disease (AD) is associated with the deposition of amyloid-β (Aβ) fibrillary aggregates. Disaggregation of Aβ fibrils is considered as one of the promising AD treatments. Recent experimental studies showed that anthocyanidins, one type of flavonoids abundant in fruits/vegetables, can disaggregate Aβ fibrillary aggregates. However, their relative disruptive capacities and underlying mechanisms are largely unknown. Herein, we investigated the detailed interactions between five most common anthocyanidins (cyanidin, aurantinidin, peonidin, delphinidin, and pelargonidin) and Aβ protofibril (an intermediate of Aβ fibrillization) by performing microsecond molecular dynamic simulations. We found that all five anthocyanidins can destroy F4-L34-V36 hydrophobic core and K28-A42 salt bridge, leading to Aβ protofibril destabilization. Aurantinidin exhibits the strongest damage to Aβ protofibril (with the most severe disruption on K28-A42 salt bridges), followed by cyanidin (with the most destructive effect on F4-L34-V36 core). Detailed analyses reveal that the protofibril-destruction capacities of anthocyanidins are subtly modulated by the interplay of anthocyanidin-protofibril hydrogen bonding, hydrophobic, aromatic stacking interactions, which are dictated by the number or location of hydroxyl/methyl groups of anthocyanidins. These findings provide important mechanistic insights into Aβ protofibril disaggregation by anthocyanidins, and suggest that aurantinidin/cyanidin may serve as promising starting-points for the development of new drug candidates against AD.

Lycopene destabilizes preformed Aβ fibrils: Mechanistic insights from all-atom molecular dynamics simulation

The therapeutic strategy employing destabilization of the preformed Aβ fibril by various natural compounds, as studied by experimental and computational methods, has been reported significant in curing Alzheimer's disease (AD). However, lycopene (a carotenoid), from terpenes family, needs investigation for its destabilization potential of Aβ fibril. The highest antioxidant potential and ability to cross blood brain barrier makes lycopene a preferred choice as drug lead for treating AD. The current study focuses on investigating the destabilization potential and underpinning mechanism of lycopene on different polymorphic forms of Aβ fibril via Molecular Dynamics (MD) simulation. The key findings highlight binding of lycopene to the outer surface of the chain F of the fibril (2NAO). Herein G9, K16 and V18 residues were found to be involved in van der Waals with the methyl groups of the lycopene. Additionally, Y10 and F20 residues were observed to interact via π-π interactions with CC bonds of the lycopene. The surface mediated binding of lycopene to the fibril is attributed to the large size and structural rigidity of lycopene along with the bulky size of 2NAO and narrow space of fibrillar cavity. The destabilization of the fibril is evident by breakage of inherent H-bonds and hydrophobic interactions in the presence of one lycopene molecule. The lesser β-sheet content explains disorganization of the fibril and bars the higher order aggregation curbing neurotoxicity of the fibril. The higher concentration of the lycopene is not found to be linearly correlated with the extent of destabilization of the fibril. Lycopene is also observed to destabilize the other polymorphic form of Aβ fibril (2BEG), by accessing the fibrillar cavity and lowering the β-sheet content. The destabilization observed by lycopene on two major polymorphs of Aβ fibril explains its potency towards developing an effective therapeutic approach in treating AD.

Dissecting the Inhibitory Mechanism of the αB-Crystallin Domain against Aβ42 Aggregation and Its Effect on Aβ42 Protofibrils: A Molecular Dynamics Simulation Study

Alzheimer's disease (AD) is related to the misfolding and aggregation of amyloid-β (Aβ) protein, and its major pathological hallmark is fibrillary β-amyloid plaques. Impeding the formation of Aβ β-structure-rich aggregates and dissociating Aβ fibrils are considered potent strategies to suppress the onset and progression of AD. As a molecular chaperone, human αB-crystallin has received extensive attention in the inhibition of protein aggregation. Previous experiments reported that the structured core region of αB-crystallin (αBC) exhibits a better preventive effect on Aβ aggregation and toxicity than the full-length protein. However, the molecular mechanism behind the effect of inhibition remains mostly unknown. Herein, we carried out six 500 ns molecular dynamics (MD) simulations to investigate the inhibitory mechanism of αBC on Aβ₄₂ aggregation. Our simulations show that αBC greatly impedes the formation of β-structure contents. We find that the binding of αBC to the Aβ₄₂ monomer is driven by polar, hydrophobic, and H-bonding interactions. To explore whether αBC could destabilize Aβ₄₂ protofibrils, we also carried out MD simulations of Aβ₄₂ protofibrils with and without αBC. The results show that αBC interacts with three binding sites of the Aβ₄₂ protofibril, and the binding is mainly driven by polar and H-bonding interactions. The binding of αBC at these three sites has a preferred dissociation effect on the β-structure content, kink angle, and K28-A42 salt bridges. Overall, this study not only discloses the molecular mechanism of αBC against Aβ₄₂ aggregation but also demonstrates the disruption effects of αBC on Aβ₄₂ protofibrils, which yields an avenue for designing anti-AD drug candidates.

Biflavones inhibit the fibrillation and cytotoxicity of human islet amyloid polypeptide

Biflavones are a kind of natural compounds with a variety of biological activities, which have the effects of reversing diabetes and neurodegenerative diseases. Human islet amyloid polypeptide (hIAPP) is closely...

A buried glutamate in the cross-β core renders β-endorphin fibrils reversible

Functional amyloids are abundant in living organisms from prokaryotes to eukaryotes playing diverse biological roles. In contrast to the irreversible aggregation of most known pathological amyloids, we postulate that naturally-occurring functional amyloids are reversible under evolutionary pressure to be able to modulate the fibrillization process, reuse the composite peptides, or perform their biological functions. β-Endorphin, an endogenous opioid peptide hormone, forms such kinds of reversible amyloid fibrils in secretory granules for efficient storage and returns to the functional state of monomers upon release into the blood. The environmental change between low pH in secretory granules and neutral pH in extracellular spaces is believed to drive the reversible fibrillization of β-endorphin. Here, we investigate the critical role of a buried glutamate, Glu8, in the pH-responsive disassembly of β-endorphin fibrils using all-atom molecular dynamics simulations along with structure-based pKa prediction. The fibril was stable at pH 5.5 or lower with all the buried Glu8 residues protonated and neutrally charged. After switching to neutral pH, the Glu8 residues of peptides at the outer layers of the ordered fibrils became deprotonated due to partial solvent exposure, causing sheet-to-coil conformational changes and subsequent exposure of adjacent Glu8 residues in the inner chains. Via iterative deprotonation of Glu8 and induced structural disruption, all Glu8 residues would be progressively deprotonated. Electrostatic repulsion between deprotonated Glu8 residues along with their high solvation tendency disrupted the hydrogen bonding between the β1 strands and increased the solvent exposure of those otherwise buried residues in the cross-β core. Overall, our computational study reveals that the strategic positioning of ionizable residues into the cross-β core is a potential approach for designing reversible amyloid fibrils as pH-responsive smart bio-nanomaterials.

A Comprehensive Insight into the Mechanisms of Dopamine in Disrupting Aβ Protofibrils and Inhibiting Aβ Aggregation

Fibrillary aggregates of amyloid-β (Aβ) are the pathological hallmark of Alzheimer's disease (AD). Clearing Aβ deposition or inhibiting Aβ aggregation is a promising approach to treat AD. Experimental studies reported that dopamine (DA), an important neurotransmitter, can inhibit Aβ aggregation and disrupt Aβ fibrils in a dose-dependent manner. However, the underlying molecular mechanisms still remain mostly elusive. Herein, we investigated the effect of DA on Aβ₄₂ protofibrils at three different DA-to-Aβ molar ratios (1:1, 2:1, and 10:1) using all-atom molecular dynamics simulations. Our simulations demonstrate that protonated DA at a DA-to-Aβ ratio of 2:1 exhibits stronger Aβ protofibril disruptive capacity than that at a molar-ratio of 1:1 by mostly disrupting the F4-L34-V36 hydrophobic core. When the ratio of DA-to-Aβ increases to 10:1, DA has a high probability to bind to the outer surface of protofibril and has negligible effect on the protofibril structure. Interestingly, at the same DA-to-Aβ ratio (10:1), a mixture of protonated (DA⁺) and deprotonated (DA⁰) DA molecules significantly disrupts Aβ protofibrils by the binding of DA⁰ to the F4-L34-V36 hydrophobic core. Replica-exchange molecular dynamics simulations of Aβ₄₂ dimer show that DA⁺ inhibits the formation of β-sheets, K28-A42/K28-D23 salt-bridges, and interpeptide hydrophobic interactions and results in disordered coil-rich Aβ dimers, which would inhibit the subsequent fibrillization of Aβ. Further analyses reveal that DA disrupts Aβ protofibril and prevents Aβ dimerization mostly through π-π stacking interactions with residues F4, H6, and H13, hydrogen bonding interactions with negatively charged residues D7, E11, E22 and D23, and cation-π interactions with residues R5. This study provides a complete picture of the molecular mechanisms of DA in disrupting Aβ protofibril and inhibiting Aβ aggregation, which could be helpful for the design of potent drug candidates for the treatment/intervention of AD.

Interactive Mechanism of Potential Inhibitors with Glycosyl for SARS-CoV-2 by Molecular Dynamics Simulation

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a type of Ribonucleic Acid (RNA) coronavirus and it has infected and killed many people around the world. It is reported that the receptor binding domain of the spike protein (S_RBD) of the SARS-CoV-2 virus is responsible for attachment to human angiotensin converting enzyme II (ACE2). Many researchers are attempting to search potential inhibitors for fighting SARS-CoV-2 infection using theoretical or experimental methods. In terms of experimental and theoretical research, Cefuroxime, Erythromycin, Lincomycin and Ofloxacin are the potential inhibitors of SARS-CoV-2. However, the interactive mechanism of the protein SARS-CoV-2 and the inhibitors are still elusive. Here, we investigated the interactions between S_RBD and the inhibitors using molecular dynamics (MD) simulations. Interestingly, we found that there are two binding sites of S_RBD for the four small molecules. In addition, our analysis also illustrated that hydrophobic and π-π stacking interactions play crucial roles in the interactions between S_RBD and the small molecules. In our work, we also found that small molecules with glycosyl group have more effect on the conformation of S_RBD than other inhibitors, and they are also potential inhibitors for the genetic variants of SARS-CoV-2. This study provides in silico-derived mechanistic insights into the interactions of S_RBD and inhibitors, which may provide new clues for fighting SARS-CoV-2 infection.

Molecular mechanisms of resveratrol and EGCG in the inhibition of Aβ42 aggregation and disruption of Aβ42 protofibril: similarities and differences

The aggregation of amyloid-β protein (Aβ) into fibrillary deposits is implicated in Alzheimer's disease (AD), and inhibiting Aβ aggregation and clearing Aβ fibrils are considered as promising strategies to treat AD. It has been reported that resveratrol (RSV) and epigallocatechin-3-gallate (EGCG), two of the most extensively studied natural polyphenols, are able to inhibit Aβ fibrillization and remodel the preformed fibrillary aggregates into amorphous, non-toxic species. However, the mechanisms by which RSV inhibits Aβ₄₂ aggregation and disrupts Aβ₄₂ protofibril, as well as the inhibitory/disruptive mechanistic similarities and differences between RSV and EGCG, remain mostly elusive. Herein, we performed extensive all-atom molecular dynamics (MD) simulations on Aβ₄₂ dimers (the early aggregation state of Aβ₄₂) and protofibrils (the intermediate of Aβ₄₂ fibril formation and elongation) in the absence/presence of RSV or EGCG molecules. Our simulations show that both RSV and EGCG can bind with Aβ₄₂ monomers and inhibit the dimerization of Aβ₄₂. The binding of RSV with Aβ₄₂ peptide is mostly viaπ-π stacking interactions, while the binding of EGCG with Aβ₄₂ is mainly through hydrophobic, π-π stacking, and hydrogen-bonding interactions. Moreover, both RSV and EGCG disrupt the β-sheet structure and K28-A42 salt bridges, leading to a disruption of Aβ₄₂ protofibril structure. RSV mainly binds with residues whose side-chains point inwards from the surface of the protofibril, while EGCG mostly binds with residues whose side-chains point outwards from the surface of the protofibril. Furthermore, RSV interacts with Aβ₄₂ protofibrils mostly viaπ-π stacking interactions, while EGCG interacts with Aβ₄₂ protofibrils mainly via hydrogen-bonding and hydrophobic interactions. For comparison, we also explore the effects of RSV/EGCG molecules on the aggregation inhibition and protofibril disruption of the Iowa mutant (D23N) Aβ. Our findings may pave the way for the design of more effective drug candidates as well as the utilization of cocktail therapy using RSV and EGCG for the treatment of AD.

The Pathogenesis Mechanism, Structure Properties, Potential Drugs and Therapeutic Nanoparticles against the Small Oligomers of Amyloid-β

Alzheimer's Disease (AD) is a devastating neurodegenerative disease that affects millions of people in the world. The abnormal aggregation of amyloid β protein (Aβ) is regarded as the key event in AD onset. Meanwhile, the Aβ oligomers are believed to be the most toxic species of Aβ. Recent studies show that the Aβ dimers, which are the smallest form of Aβ oligomers, also have the neurotoxicity in the absence of other oligomers in physiological conditions. In this review, we focus on the pathogenesis, structure and potential therapeutic molecules against small Aβ oligomers, as well as the nanoparticles (NPs) in the treatment of AD. In this review, we firstly focus on the pathogenic mechanism of Aβ oligomers, especially the Aβ dimers. The toxicity of Aβ dimer or oligomers, which attributes to the interactions with various receptors and the disruption of membrane or intracellular environments, were introduced. Then the structure properties of Aβ dimers and oligomers are summarized. Although some structural information such as the secondary structure content is characterized by experimental technologies, detailed structures are still absent. Following that, the small molecules targeting Aβ dimers or oligomers are collected; nevertheless, all of these ligands have failed to come into the market due to the rising controversy of the Aβ-related "amyloid cascade hypothesis". At last, the recent progress about the nanoparticles as the potential drugs or the drug delivery for the Aβ oligomers are present.

Molecular Dynamics Simulations Reveal the Modulated Mechanism of STING Conformation

Stimulator of interferon genes (STING), which is an integral ER-membrane protein, could induce an antiviral state and boost antitumor immunity. Recent experiments reported that different small molecules could modulate the conformation of the STING. However, the mechanism of small molecules modulating the conformation of STING is still unknown. To illustrate the conformational modulated mechanism of STING by small molecules at atomic level, we investigated the interactions between STING and the small molecules: cGAMP and diABZI with molecular dynamics (MD) simulations method. Interestingly, we found that the residues of STING in the binding pocket are more flexible in the monomers of STING than that in the dimer of STING. We also demonstrated that cGAMP and diABZI have a similar binding mode to STING monomers/dimer, and π-π stacking interactions play important roles for the agonists and STING. Our study proposed mechanistic insights into the STING conformation modulated by small molecules and we suggested that the special molecule (e. g. diABZI) could induce the conformational transition of STING from the "open" monomers to the "closed" dimer state. Our research may provide a clue for the development of cancer immunotherapy.

Improving the inhibition of β-amyloid aggregation by withanolide and withanoside derivatives

Here, we have studied the ameliorative effects of Withania somnifera derivatives (Withanolide A, Withanolide B, Withanoside IV, and Withanoside V) on the fibril formation of amyloid-β ₄₂ for Alzheimer's disease. We analyzed reduction in the aggregation of β amyloid protein with these Ashwagandha derivatives by Thioflavin T assay in the oligomeric and fibrillar state. We have tested the cytotoxic activity of these compounds against human SK-N-SH cell line for 48 h, and the IC ₅₀ value found to be 28.61 ± 2.91, 14.84 ± 1.45, 18.76 ± 0.76 and 30.14 ± 2.59 μM, respectively. After the treatment of the cells with half the concentration of IC ₅₀ value, there was a remarkable decrease in the number of apoptotic cells stained by TUNEL assay indicating the DNA damage and also observed significant decrease of reactive oxygen species. Also, the binding and molecular stability of these derivatives with amyloid β was also studied using bioinformatics tools where these molecules were interacted at LVFFA region which is inhibition site of amyloid-β1 ₄₂. These studies revealed that the Withanolides and Withanosides interact with the hydrophobic core of amyloid-β _1-42 in the oligomeric stage, preventing further interaction with the monomers and diminishing aggregation.

An α-helix mimetic oligopyridylamide, ADH-31, modulates Aβ42 monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations

Alzheimer's disease (AD), an epidemic growing worldwide due to no effective medical aid available in the market, is a neurological disorder. AD is known to be directly associated with the toxicity of amyloid-β (Aβ) aggregates. In search of potent inhibitors of Aβ aggregation, Hamilton and co-workers reported an α-helix mimetic, ADH-31, which acts as a powerful antagonist of Aβ42 aggregation. To identify the key interactions between protein-ligand complexes and to gain insights into the inhibitory mechanism of ADH-31 against Aβ42 aggregation, molecular dynamics (MD) simulations were performed in the present study. The MD simulations highlighted that ADH-31 showed distinct binding capabilities with residues spanning from the N-terminal to the central hydrophobic core (CHC) region of Aβ42 and restricted the conformational transition of the helix-rich structure of Aβ42 into another form of secondary structures (coil/turn/β-sheet). Hydrophobic contacts, hydrogen bonding and π-π interaction contribute to the strong binding between ADH-31 and Aβ42 monomer. The Dictionary of Secondary Structure of Proteins (DSSP) analysis highlighted that the probability of helical content increases from 38.5% to 50.2% and the turn content reduces from 14.7% to 6.2% with almost complete loss of the β-sheet structure (4.5% to 0%) in the Aβ42 monomer + ADH-31 complex. The per-residue binding free energy analysis demonstrated that Arg5, Tyr10, His14, Gln15, Lys16, Val18, Phe19 and Lys28 residues of Aβ42 are responsible for the favourable binding free energy in Aβ42 monomer + ADH-31 complex, which is consistent with the 2D HSQC NMR of the Aβ42 monomer that depicted a change in the chemical shift of residues spanning from Glu11 to Phe20 in the presence of ADH-31. The MD simulations highlighted the prevention of sampling of amyloidogenic β-strand conformations in Aβ42 trimer in the presence of ADH-31 as well as the ability of ADH-31 to destabilize Aβ42 trimer and protofibril structures. The lower binding affinity between Aβ42 trimer chains in the presence of ADH-31 highlights the destabilization of the Aβ42 trimer structure. Overall, MD results highlighted that ADH-31 inhibited Aβ42 aggregation by constraining Aβ peptides into helical conformation and destabilized Aβ42 trimer as well as protofibril structures. The present study provides a theoretical insight into the atomic level details of the inhibitory mechanism of ADH-31 against Aβ42 aggregation as well as protofibril destabilization and could be implemented in the structure-based drug design of potent therapeutic agents for AD.

Epigallocatechin Gallate Destabilizes α-Synuclein Fibril by Disrupting the E46-K80 Salt-Bridge and Inter-protofibril Interface

The accumulation and deposition of fibrillar aggregates of α-synuclein (α-syn) into Lewy bodies are the major hallmarks of Parkinson's disease (PD) for which there is no cure yet. Disrupting preformed α-syn fibrils is considered one of the rational therapeutic strategies to combat PD. Experimental studies reported that epigallocatechin gallate (EGCG), a polyphenol extracted from green tea, can disrupt α-syn fibrils into benign amorphous aggregates. However, the molecular mechanism of action is poorly understood. Herein, we performed molecular dynamics simulations on a newly released Greek-key-like α-syn fibril with or without EGCG to investigate the influence of EGCG on α-syn fibril. Our simulations show that EGCG disrupts the local β-sheet structure, E46-K80 salt-bridge crucial for the stabilization of the Greek-key-like structure, and hydrophobic interactions stabilizing the inter-protofibril interface and destabilizes the global structure of the α-syn fibril. Interaction analyses reveal that hydrophobic and hydrogen-bonding interactions between EGCG and α-syn fibrils play important roles in the destabilization of the fibril. We find that the disruption of the E46-K80 salt-bridge closely correlates with the formation of hydrogen-bonds (H-bonds) between EGCG and E46/K80. Our results provide mechanistic insights into the disruption modes of α-syn fibril by EGCG, which may pave the way for designing drug candidates targeting α-syn fibrillization to treat PD.

Latent Models of Molecular Dynamics Data: Automatic Order Parameter Generation for Peptide Fibrillization

Variational autoencoders are artificial neural networks with the capability to reduce highly dimensional sets of data to smaller dimensional, latent representations. In this work, these models are applied to molecular dynamics simulations of the self-assembly of coarse-grained peptides to obtain a singled-valued order parameter for amyloid aggregation. This automatically learned order parameter is constructed by time-averaging the latent parametrizations of internal coordinate representations and compared to the nematic order parameter which is commonly used to study ordering of similar systems in literature. It is found that the latent space value provides more tailored insight into the aggregation mechanism's details, correctly identifying fibril formation in instances where the nematic order parameter fails to do so. A means is provided by which the latent space value can be analyzed so that the major contributing internal coordinates are identified, allowing for a direct interpretation of the latent space order parameter in terms of the behavior of the system. The latent model is found to be an effective and convenient way of representing the data from the dynamic ensemble and provides a means of reducing the dimensionality of a system whose scale exceeds molecular systems so-far considered with similar tools. This bypasses a need for researcher speculation on what elements of a system best contribute to summarizing major transitions and suggests latent models are effective and insightful when applied to large systems with a diversity of complex behaviors.

Molecular basis for the inhibitory effects of 5-hydroxycyclopenicillone on the conformational transition of Aβ40 monomer

Previous studies have indicated that 5-hydroxycyclopenicillone (HCP), an active compound derived from marine sponge, could inhibit oligomerization of amyloid β-protein (Aβ). However, the molecular basis for the interaction between HCP and Aβ remains unclear. Herein, all-atom molecular dynamics (MD) simulations were used to explore the conformational conversion of an Aβ₄₀ monomer at different concentrations (0-40 mM) of HCP at the atomic level. It is confirmed that the conformational transition of the Aβ₄₀ monomer is prevented by HCP in a concentration-dependent manner in silico. In 40 mM HCP solution, the initial α-helix-rich conformation of Aβ₄₀ monomer is kept under the action of HCP. The intra-peptide hydrophobic collapse and D23-K28 salt bridge are prevented by HCP. Moreover, it is indicated that the non-polar binding energy dominates the binding between HCP and Aβ₄₀ monomer as evaluated by molecular mechanics Poisson-Boltzmann surface area method. And, the residues of F4, Y10, V12, L17 and L34 in Aβ₄₀ might contribute to the binding energy in HCP-Aβ₄₀ complex. All these results elucidate the molecular mechanism underlying the inhibitory effects of HCP against the conformational transformation of Aβ₄₀, providing a support that HCP may be developed as a potential anti-Aβ compound for the treatment of Aβ-related diseases.Communicated by Ramaswamy H. Sarma.

How Does the Mono-Triazole Derivative Modulate Aβ42 Aggregation and Disrupt a Protofibril Structure: Insights from Molecular Dynamics Simulations

Clinical studies have identified that abnormal self-assembly of amyloid-β (Aβ) peptide into toxic fibrillar aggregates is associated with the pathology of Alzheimer's disease (AD). The most acceptable therapeutic approach to stop the progression of AD is to inhibit the formation of β-sheet-rich structures. Recently, we designed and evaluated a series of novel mono-triazole derivatives 4(a-x), where compound 4v was identified as the most potent inhibitor of Aβ₄₂ aggregation and disaggregates preformed Aβ₄₂ fibrils significantly. Moreover, 4v strongly averts the Cu²⁺-induced Aβ₄₂ aggregation and disaggregates the preformed Cu²⁺-induced Aβ₄₂ fibrils, halts the generation of reactive oxygen species, and shows neuroprotective effects in SH-SY5Y cells. However, the underlying molecular mechanism of inhibition of Aβ₄₂ aggregation by 4v and disaggregation of preformed Aβ₄₂ fibrils remains obscure. In this work, molecular dynamics (MD) simulations have been performed to explore the conformational ensemble of the Aβ₄₂ monomer and a pentameric protofibril structure of Aβ₄₂ in the presence of 4v. The MD simulations highlighted that 4v binds preferentially at the central hydrophobic core region of the Aβ₄₂ monomer and chains D and E of the Aβ₄₂ protofibril. The dictionary of secondary structure of proteins analysis indicated that 4v retards the conformational conversion of the helix-rich structure of the Aβ₄₂ monomer into the aggregation-prone β-sheet conformation. The binding free energy calculated by the molecular mechanics Poisson-Boltzmann surface area method revealed an energetically favorable process with ΔG _binding = -44.9 ± 3.3 kcal/mol for the Aβ₄₂ monomer-4v complex. The free energy landscape analysis highlighted that the Aβ₄₂ monomer-4v complex sampled conformations with significantly higher helical contents (35 and 49%) as compared to the Aβ₄₂ monomer alone (17%). Compound 4v displayed hydrogen bonding with Gly37 (chain E) and π-π interactions with Phe19 (chain D) of the Aβ₄₂ protofibril. Further, the per-residue binding free energy analysis also highlighted that Phe19 (chain D) and Gly37 (chain E) of the Aβ₄₂ protofibril showed the maximum contribution in the binding free energy. The decreased binding affinity and residue-residue contacts between chains D and E of the Aβ₄₂ protofibril in the presence of 4v indicate destabilization of the Aβ₄₂ protofibril structure. Overall, the structural information obtained through MD simulations indicated that 4v stabilizes the native helical conformation of the Aβ₄₂ monomer and persuades a destabilization in the protofibril structure of Aβ₄₂. The results of the study will be useful in the rational design of potent inhibitors against amyloid aggregation.

Coassembly-Induced Transformation of Dipeptide Amyloid-Like Structures into Stimuli-Responsive Supramolecular Materials

Conformational transition of proteins and peptides into highly stable, β-sheet-rich structures is observed in many amyloid-associated neurodegenerative disorders, yet the precise mechanism of amyloid formation at the molecular level remains poorly understood due to the complex molecular structures. Short peptides provide simplified models for studying the molecular basis of the assembly mechanism that governs β-sheet fibrillation processes underlying the formation and inhibition of amyloid-like structures. Herein, we report a supramolecular coassembly strategy for the inhibition and transformation of stable β-sheet-rich amyloid-derived dipeptide self-assemblies into adaptable secondary structural fibrillar assemblies by mixing with bipyridine derivatives. The interplay between the type and mixing ratio of bipyridine derivatives allowed the variable coassembly process with stimuli-responsive functional properties, studied by various experimental characterizations and computational methods. Furthermore, the resulting coassemblies showed functional redox- and photoresponsive properties, making them promising candidates for controllable drug release and fluorescent imprint. This work presents a coassembly strategy not only to explore the mechanism of amyloid-like structure formation and inhibition at the molecular level but also to manipulate amyloid-like structures into responsive supramolecular coassemblies for material science and biotechnology applications.

Green Tea Extracts EGCG and EGC Display Distinct Mechanisms in Disrupting Aβ42 Protofibril

The amyloid beta (Aβ) fibrillar aggregate is the hallmark of Alzheimer's disease (AD). Disassembling preformed fibril or inhibiting Aβ aggregation is considered as a therapeutic strategy for AD. Increasing evidence shows that green tea extracts, epigallocatechin-3-gallate (EGCG, containing an extra gallic acid ester group compared to EGC) and epigallocatechin (EGC), can disassociate Aβ fibrils and attenuate Aβ toxicity. However, the underlying molecular mechanism is poorly understood. Herein, we performed microsecond all-atom molecular dynamics (MD) simulations to investigate the influences of EGCG/EGC on the newly cryo-EM resolved LS-shaped Aβ₄₂ protofibrils and their detailed interactions. MD simulations demonstrate that both EGCG and EGC can disrupt Aβ₄₂ protofibril and EGCG displays a higher disruptive capacity than EGC. EGCG alters the L-shape of Aβ₄₂ protofibril by breaking the hydrogen bond between H6 and E11 through π-π interactions with residues H14/Y10 and hydrogen-bonding interactions with E11, while EGC remodels the L-shape by inserting into the hydrophobic core formed by A2, F4, L34, and V36 and via aromatics interaction with H6/Y10. EGCG disrupts the salt bridges between the K28 side chain and A42 COO^- through hydrogen-bonding interaction with A42 and cation-π interaction between its gallic acid ester group and K28, while EGC damages the salt bridges through hydrophobic interactions with V39 and I41 as well as with I32, M35, and V40 located in the C-terminal hydrophobic core. This study demonstrates the pivotal role of the gallic acid ester group of EGCG in disrupting Aβ₄₂ protofibril and provides atomic-level insights into the distinct mechanism by which EGCG and EGC disrupt Aβ protofibril, which could be useful for designing amyloid inhibitors.

Structural Insight into the Interactions between Structurally Similar Inhibitors and SIRT6

Sirtuin 6 (SIRT6) is an NAD+-dependent deacetylase with a significant role in 20% of all cancers, such as colon cancers and rectal adenocarcinoma. However, there is currently no effective drug for cancers related to SIRT6. To explore potential inhibitors of SIRT6, it is essential to reveal details of the interaction mechanisms between inhibitors and SIRT6 at the atomic level. The nature of small molecules from herbs have many advantages as inhibitors. Based on the conformational characteristics of the inhibitor Compound 9 (Asinex ID: BAS13555470), we explored the natural molecule Scutellarin, one compound of Huang Qin, which is an effective herb for curing cancer that has been described in the Traditional Chinese Medicine (TCMS) library. We investigated the interactions between SIRT6 and the inhibitors using molecular dynamics (MD) simulations. We illustrated that the structurally similar inhibitors have a similar binding mode to SIRT6 with residues—Leu9, Phe64, Val115, His133 and Trp188. Hydrophobic and π-stacking interactions play important roles in the interactions between SIRT6 and inhibitors. In summary, our results reveal the interactive mechanism of SIRT6 and the inhibitors and we also provide Scutellarin as a new potential inhibitor of SIRT6. Our study provides a new potential way to explore potential inhibitors from TCMS.

Protofibrils of Amyloid-β are Important Targets of a Disease-Modifying Approach for Alzheimer's Disease

Worldwide, Alzheimer’s disease (AD) is the most common age-related neurodegenerative disease and is characterized by unique pathological hallmarks in the brain, including plaques composed of amyloid β-protein (Aβ) and neurofibrillary tangles of tau protein. Genetic studies, biochemical data, and animal models have suggested that Aβ is responsible for the pathogenesis of AD (i.e., the amyloid hypothesis). Indeed, Aβ molecules tend to aggregate, forming oligomers, protofibrils, and mature fibrils. However, while these Aβ species form amyloid plaques of the type implicated in AD neurodegeneration, recent clinical trials designed to reduce the production of Aβ and/or the plaque burden have not demonstrated clinical efficacy. In addition, recent studies using synthetic Aβ peptides, cell culture models, Arctic transgenic mice, and human samples of AD brain tissues have suggested that the pre-fibrillar forms of Aβ, particularly Aβ protofibrils, may be the most critical species, compared with extracellular fibrillar forms. We recently reported that protofibrils of Aβ_1-42 disturbed membrane integrity by inducing reactive oxygen species generation and lipid peroxidation, resulting in decreased membrane fluidity, intracellular calcium dysregulation, depolarization, and synaptic toxicity. Therefore, the therapeutic reduction of protofibrils may prevent the progression of AD by ameliorating neuronal damage and cognitive dysfunction through multiple mechanisms.

Identifying the key residues instrumental in imparting stability to amyloid beta protofibrils - a comparative study using MD simulations of 17-42 residues

Extracellular plaques, the hallmark of Alzheimer's disease brains, consist of insoluble amyloid fibrils that result from the aggregation of amyloid beta peptides. None of the few therapeutic options currently adopted, address the cause of the disease. Instead, they reduce symptom of the disease. Inhibition of aggregation or destabilization of aggregates therefore, emerges as a preferable therapeutic approach. Designing inhibitors or destabilizers demands comprehensive knowledge of the residues of amyloid beta responsible for the phenomenal structural stability of the aggregate. For the purpose, we have compared the effect on structural destabilization of 13 in silico mutations (single and double) with the wild type counterpart of beta-strand-turn-beta-strand motif of the amyloid beta protofibrils by molecular dynamics simulation. Besides the already known salt bridge interaction between K28 and D23, our analyses expose more significant role of K28 as the only positive charge present in the vicinity. Amongst the two consecutive aromatic residues, F19 is involved in stacking interaction; although effect of F20 mutation is more pronounced. Face to face arrangement of A21 and V36 acts as a pillar maintaining the necessary optimum distance between consecutive chains to promote stabilizing interactions. In addition to providing stability to the first beta-strand, large sized negatively charged E22 facilitates salt bridge formation by ensuring fixed relative position of D23 and in turn K28. Likewise, the hydrophobic residues I32 and L34 pack the protofibril core, once again fostering salt bridge interaction. Prospectively, these findings may be compiled for efficient identification or design of scaffolds accountable for protofibril destabilization.Communicated by Ramaswamy H. Sarma.

Interactions of a multifunctional di-triazole derivative with Alzheimer's Aβ42monomer and Aβ42protofibril: a systematic molecular dynamics study

The molecular dynamics simulations results highlighted that the multi-target-directed ligand6nstabilizes the native α-helix conformation of the Aβ₄₂monomer and induces a sizable destabilization in the Aβ₄₂protofibril structure.

Destabilization potential of phenolics on Aβ fibrils: mechanistic insights from molecular dynamics simulation

Ellagic acid from pomegranate and walnuts is found to destabilize Aβ fibrils. It can be a potential drug to treat AD.

Dihydrochalcones: Methods of Acquisition and Pharmacological Properties-A First Systematic Review

Dihydrochalcones are a class of secondary metabolites, for which demand in biological and pharmacological applications is still growing. They posses several health-endorsing properties and, therefore, are promising candidates for further research and development. However, low content of dihydrochalcones in plants along with their low solubility and bioavailability restrict the development of these compounds as clinical therapeutics. Therefore, chemomicrobial and enzymatic modifications are required to expand their application. This review aims at analyzing and summarizing the methods of obtaining dihydrochalcones and of presenting their pharmacological actions that have been described in the literature to support potential future development of this group of compounds as novel therapeutic drugs. We have also performed an evaluation of the available literature on beneficial effects of dihydrochalcones with potent antioxidant activity and multifactorial pharmacological effects, including antidiabetic, antitumor, lipometabolism regulating, antioxidant, anti-inflammatory, antibacterial, antiviral, and immunomodulatory ones. In addition, we provide useful information on their properties, sources, and usefulness in medicinal chemistry.

Caffeine destabilizes preformed Aβ protofilaments: insights from all atom molecular dynamics simulations

The aggregation and deposition of neurotoxic Aβ fibrils are key in the etiology of Alzheimer's disease (AD). It has been clinically recognized as a major form of dementia across the globe. Finding and testing various natural compounds to target Aβ fibrils to disrupt their stable structures seems to be a promising and attractive therapeutic strategy. The destabilization effects of caffeine on Aβ fibrils are investigated via in silico studies, where a series of molecular dynamics (MD) simulations, each of 100 ns, was conducted. The simulation outcomes obtained henceforth clearly indicated the drift of the terminal chains from the protofibrils, leading to disorganization of the characteristically organized cross-β structures of Aβ fibrils. The structural instability of Aβ17-42 protofibrils is explained through enhanced fluctuations in the RMSD, radius of gyration and RMSF values in the presence of caffeine. The key interactions providing stability, comprising D23-K28 salt bridges, intra- and inter-chain hydrogen bonding and hydrophobic interactions involving interchain A21-V36 and F19-G38 and intrachain L34-V36, were found to be disrupted due to increases in the distances between the participating components. The loss of β-sheet structure with the introduction of turns and α-helices in terminal chains may further inhibit the formation of higher order aggregates, which is necessary to stop the progression of the disease. The atomistic details obtained via MD studies relating to the mechanism behind the underlying destabilization of Aβ17-42 protofibrils by caffeine encourage further investigations exploring the potency of natural compounds to treat AD via disrupting preformed neurotoxic Aβ protofibrils.

Recent Advances by In Silico and In Vitro Studies of Amyloid-β 1-42 Fibril Depicted a S-Shape Conformation

The amyloid-β 1-42 (Aβ1-42) peptide is produced by proteolytic cleavage of the amyloid precursor protein (APP) by sequential reactions that are catalyzed by γ and β secretases. Aβ1-42, together with the Tau protein are two principal hallmarks of Alzheimer's disease (AD) that are related to disease genesis and progression. Aβ1-42 possesses a higher aggregation propensity, and it is able to form fibrils via nucleated fibril formation. To date, there are compounds available that prevent Aβ1-42 aggregation, but none have been successful in clinical trials, possibly because the Aβ1-42 structure and aggregation mechanisms are not thoroughly understood. New molecules have been designed, employing knowledge of the Aβ1-42 structure and are based on preventing or breaking the ionic interactions that have been proposed for formation of the Aβ1-42 fibril U-shaped structure. Recently, a new Aβ1-42 fibril S-shaped structure was reported that, together with its aggregation and catalytic properties, could be helpful in the design of new inhibitor molecules. Therefore, in silico and in vitro methods have been employed to analyze the Aβ1-42 fibril S-shaped structure and its aggregation to obtain more accurate Aβ1-42 oligomerization data for the design and evaluation of new molecules that can prevent the fibrillation process.