Structures of Aβ17-42 trimers in isolation and with five small-molecule drugs using a hierarchical computational procedure

Unlocking novel therapies: cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning

Existing therapies for neurodegenerative diseases like Parkinson's and Alzheimer's address only their symptoms and do not prevent disease onset. Common therapeutic agents, such as small molecules and antibodies struggle with insufficient selectivity, stability and bioavailability, leading to poor performance in clinical trials. Peptide-based therapeutics are emerging as promising candidates, with successful applications for cardiovascular diseases and cancers due to their high bioavailability, good efficacy and specificity. In particular, cyclic peptides have a long in vivo stability, while maintaining a robust antibody-like binding affinity. However, the de novo design of cyclic peptides is challenging due to the lack of long-lived druggable pockets of the target polypeptide, absence of exhaustive conformational distributions of the target and/or the binder, unknown binding site, methodological limitations, associated constraints (failed trials, time, money) and the vast combinatorial sequence space. Hence, efficient alignment and cooperation between disciplines, and synergies between experiments and simulations complemented by popular techniques like machine-learning can significantly speed up the therapeutic cyclic-peptide development for neurodegenerative diseases. We review the latest advancements in cyclic peptide design against amyloidogenic targets from a computational perspective in light of recent advancements and potential of machine learning to optimize the design process. We discuss the difficulties encountered when designing novel peptide-based inhibitors and we propose new strategies incorporating experiments, simulations and machine learning to design cyclic peptides to inhibit the toxic propagation of amyloidogenic polypeptides. Importantly, these strategies extend beyond the mere design of cyclic peptides and serve as template for the de novo generation of (bio)materials with programmable properties.

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.

Identifying the Template for Oligomer to Fibril Conversion for Amyloid-β (1-42) Oligomers using Hamiltonian Replica Exchange Molecular Dynamics

The toxicity of amyloid-β (Aβ) oligomers has been known to be higher compared to mature fibrils. Yet the presence of plaques in Alzheimer's disease patients indicates the significance of oligomer to fibril conversion for Aβ aggregates. In this study, we investigate Aβ_13-42 oligomers having two to five peptide chains using extensive all-atom molecular dynamics simulations to identify the on- or off-pathway intermediates in fibril formation pathway. Hamiltonian replica exchange method through solute tempering (REST2) has been employed to explore the different structures attained by these aggregates. Using intra-chain and inter-chain contacts as reaction coordinates, we obtain the free energy surface for the Aβ_13-42 oligomers. Consequently, their stable conformations and structural features have been identified. The found conformations belonging to most probable structures possess both parallel and anti-parallel β-sheets, characteristic of on- and off-pathway intermediates, respectively. Further, we have measured the tendency to form fibril like interactions among the β-sheet forming residues. Our analysis finds that residues 30-36 possess higher tendency to form fibril like contacts among all the residues. While we find stronger interaction among residues 30-36, these amino acids are also found to be more shielded from water compared to others. With previous experimental studies finding these residues to be more crucial for the stability of Aβ42 oligomers, we propose that interactions within this patch could trigger seed formation that leads to conversion of on-pathway oligomers into disease relevant fibrils.

Insights into Molecular Mechanisms of EGCG and Apigenin on Disrupting Amyloid-Beta Protofibrils Based on Molecular Dynamics Simulations

The fibrillization and deposition of amyloid-beta (Aβ) protofibrils are one of the important factors leading to Alzheimer's disease. Molecular dynamics simulations can offer information on intermolecular interaction mechanisms between Aβ protofibrils and Aβ fibrillization inhibitors. Here, in this work, we explore the early molecular mechanisms of (-)-epigallocatechin-3-gallate (EGCG) and apigenin on disrupting Aβ42 protofibrils based on molecular simulations. The binding modes of EGCG and apigenin with the Aβ42 protofibril are obtained. Furthermore, we compare the behavioral mechanisms of EGCG and apigenin on disturbing the Aβ42 protofibril. Both EGCG and apigenin are able to decrease the proportion of the β-sheet and bend structures of the Aβ42 protofibril while inducing random coil structures. The results of hydrogen bonds and D23-K28 salt bridges illustrate that EGCG and apigenin have the ability of destabilizing the Aβ42 protofibril. Meanwhile, the van der Waals interactions between the EGCG and Aβ42 protofibril are shown to be larger than that of apigenin with the Aβ42 protofibril, but the electrostatic interactions between apigenin and the Aβ42 protofibril are dominant in the binding affinity. Our findings may help in designing effective drug candidates for disordering the Aβ protofibril and impeding Aβ fibrillization.

Interactions of Curcumin's Degradation Products with the Aβ42 Dimer: A Computational Study

Amyloid-β (Aβ) dimers are the smallest toxic species along the amyloid-aggregation pathway and among the most populated oligomeric accumulations present in the brain affected by Alzheimer's disease (AD). A proposed therapeutic strategy to avoid the aggregation of Aβ into higher-order structures is to develop molecules that inhibit the early stages of aggregation, i.e., dimerization. Under physiological conditions, the Aβ dimer is highly dynamic and does not attain a single well-defined structure but is rather characterized by an ensemble of conformations. In a recent study, a highly heterogeneous library of conformers of the Aβ dimer was generated by an efficient sampling method with constraints based on ion mobility mass spectrometry data. Here, we make use of the Aβ dimer library to study the interaction with two curcumin degradation products, ferulic aldehyde and vanillin, by molecular dynamics (MD) simulations. Ensemble docking and MD simulations are used to provide atomistic detail of the interactions between the curcumin degradation products and the Aβ dimer. The simulations show that the aromatic residues of Aβ, and in particular ¹⁹FF²⁰, interact with ferulic aldehyde and vanillin through π-π stacking. The binding of these small molecules induces significant changes on the ¹⁶KLVFF²⁰ region.

Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation

Protein aggregation can lead to well-defined structures that are functional, but is also the cause of the death of neuron cells in many neurodegenerative diseases. The complexity of the molecular events involved in the aggregation kinetics of amyloid proteins and the transient and heterogeneous characters of all oligomers prevent high-resolution structural experiments. As a result, computer simulations have been used to determine the atomic structures of amyloid proteins at different association stages as well as to understand fibril dissociation. In this chapter, we first review the current computer simulation methods used for aggregation with some atomistic and coarse-grained results aimed at better characterizing the early formed oligomers and amyloid fibril formation. Then we present the applications of non-equilibrium molecular dynamics simulations to comprehend the dissociation of protein assemblies.

Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations

Amyloid fibril formation is an intrinsic property of short peptides, non-disease proteins, and proteins associated with neurodegenerative diseases. Aggregates of the Aβ and tau proteins, the α-synuclein protein, and the prion protein are observed in the brain of Alzheimer's, Parkinson's, and prion disease patients, respectively. Due to the transient short-range and long-range interactions of all species and their high aggregation propensities, the conformational ensemble of these devastating proteins, the exception being for the monomeric prion protein, remains elusive by standard structural biology methods in bulk solution and in lipid membranes. To overcome these limitations, an increasing number of simulations using different sampling methods and protein models have been performed. In this chapter, we first review our main contributions to the field of amyloid protein simulations aimed at understanding the early aggregation steps of short linear amyloid peptides, the conformational ensemble of the Aβ40/42 dimers in bulk solution, and the stability of Aβ aggregates in lipid membrane models. Then we focus on our studies on the interactions of amyloid peptides/inhibitors to prevent aggregation, and long amyloid sequences, including new results on a monomeric tau construct.

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.

Cholesterol Molecules Alter the Energy Landscape of Small Aβ1-42 Oligomers

Small amyloid-β (Aβ) oligomers are believed to be key pathogenic species in Alzheimer's disease (AD). One suggested toxicity mechanism is the detergent model where oligomers remove lipid molecules from the bilayer. Senile plaques of AD patients also accumulate a 1:1 ratio of cholesterol/Aβ. What are the dominant structures of small Aβ42 oligomers with cholesterol molecules in aqueous solution? Here, we answer this question by performing atomistic replica exchange molecular dynamics simulations of Aβ42 dimers and trimers. Our simulations demonstrate that the interactions with cholesterol molecules change completely the energy landscape of small Aβ42 oligomers. This result shows that simulations in the bulk solution cannot recapitulate aggregation in the brain extracellular space.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study

Amyloid-β (Aβ) peptides form assemblies that are pathological hallmarks of Alzheimer's disease. Aβ oligomers are soluble, mobile, and toxic forms of the peptide that act in the extracellular space before assembling into protofibrils and fibrils. Therefore, oligomers play an important role in the mechanism of Alzheimer's disease. Since it is difficult to determine by experiment the atomic structures of oligomers, which accumulate fast and are polymorphic, computer simulation is a useful tool to investigate elusive oligomers' structures. In this work, we report extended all-atom molecular dynamics simulations, both canonical and replica exchange, of Aβ(1-42) trimer starting from two different initial conformations: (i) the pose produced by the best docking of a monomer aside of a dimer (simulation 1), representing oligomers freshly formed by assembling monomers, and (ii) a configuration extracted from an experimental mature fibril structure (simulation 2), representing settled oligomers in equilibrium with extended fibrils. We showed that in simulation 1, regions with small β-barrels are populated, indicating the chance of spontaneous formation of domains resembling channel-like structures. These structural domains are alternative to those more representative of mature fibrils (simulation 2), the latter showing a stable bundle of C-termini that is not sampled in simulation 1. Moreover, trimer of Aβ(1-42) can form internal pores that are large enough to be accessed by water molecules and Ca2+ ions.

Interaction of amyloid beta with humanin and acetylcholinesterase is modulated by ATP

Humanin (HN) is known to bind amyloid beta (Aβ)‐inducing cytoprotective effects, while binding of acetylcholinesterase (AChE) to Aβ increases its aggregation and cytotoxicity. Previously, we showed that binding of HN to Aβ blocks aggregation induced by AChE and that HN decreases but does not abolish Aβ‐AChE interactions in A549 cell media. Here, we set out to shed light on factors that modulate the interactions of Aβ with HN and AChE. We found that binding of either HN or AChE to Aβ is not affected by heparan sulfate, while ATP, thought to reduce misfolding of Aβ, weakened interactions between AChE and Aβ but strengthened those between Aβ and HN. Using media from either A549 or H1299 lung cancer cells, we observed that more HN was bound to Aβ upon addition of ATP, while levels of AChE in a complex with Aβ were decreased by ATP addition to A549 cell media. Exogenous addition of ATP to either A549 or H1299 cell media increased interactions of endogenous HN with Aβ to a comparable extent despite differences in AChE expression in the two cell lines, and this was correlated with decreased binding of exogenously added HN to Aβ. Treatment with exogenous ATP had no effect on cell viability under all conditions examined. Exogenously added ATP did not affect viability of cells treated with AChE‐immunodepleted media, and there was no apparent protection against the cytotoxicity resulting from immunodepletion of HN. Moreover, exogenously added ATP had no effect on the relative abundance of oligomer versus total Aβ in either cell line.

Structures of the intrinsically disordered Aβ, tau and α-synuclein proteins in aqueous solution from computer simulations

Intrinsically disordered proteins (IDPs) play many biological roles in the human proteome ranging from vesicular transport, signal transduction to neurodegenerative diseases. The Aβ and tau proteins, and the α-synuclein protein, key players in Alzheimer's and Parkinson's diseases, respectively are fully disordered at the monomer level. The structural heterogeneity of the monomeric and oligomeric states and the high self-assembly propensity of these three IDPs have precluded experimental structural determination. Simulations have been used to determine the atomic structures of these IDPs. In this article, we review recent computer models to capture the equilibrium ensemble of Aβ, tau and α-synuclein proteins at different association steps in aqueous solution and present new results of the PEP-FOLD framework on α-synuclein monomer.

Humanin Blocks the Aggregation of Amyloid-β Induced by Acetylcholinesterase, an Effect Abolished in the Presence of IGFBP-3

It is known that the humanin (HN) peptide binding to amyloid-β (Aβ) protects against its cytotoxic effects, while acetylcholinesterase (AChE) binding to Aβ increases its aggregation and cytotoxicity. HN is also known to bind the insulin-like growth factor binding protein-3 (IGFBP-3). Here, we examined the regulation of Aβ conformations by HN, AChE, and IGFBP-3 both in vitro and in the conditioned media from A549 and H1299 lung cancer cells. Our in vitro results showed the following: IGFBP-3 binds HN and blocks it from binding Aβ in the absence or presence of AChE; HN and AChE can simultaneously bind Aβ but not when in the presence of IGFBP-3; HN is unable to reduce the aggregation of Aβ in the presence of IGFBP-3; and HN abolishes the aggregation of Aβ induced by the addition of AChE in the absence of IGFBP-3. In the media, AChE and HN can simultaneously bind Aβ. While both AChE and HN are detected when using 6E10 Aβ antibodies, only AChE is detected when using the Aβ 17-24 antibody 4G8, the anti-oligomer A11, and the anti-amyloid fibril LOC antibodies. No signal was observed for IGFBP-3 with any of the anti-amyloid antibodies used. Exogenously added IGFBP-3 reduced the amount of HN found in a complex when using 6E10 antibodies and correlated with a concomitant increase in the amyloid oligomers. Immunodepletion of HN from the media of the A549 and H1299 cells increased the relative abundance of the oligomer vs the total amount of Aβ, the A11-positive prefibrillar oligomers, and to a lesser extent the LOC-positive fibrillar oligomers, and was also correlated with diminished cell viability and increased apoptosis.

Cyanidin-3-O-glucoside inhibits Aβ40 fibrillogenesis, disintegrates preformed fibrils, and reduces amyloid cytotoxicity

Alzheimer's disease (AD) is mainly caused by the fibrillogenesis of amyloid-β protein (Aβ). Therefore, the development of effective inhibitors against Aβ fibrillogenesis offers great hope for the treatment of AD. Cyanidin-3-O-glucoside (Cy-3G) is a commonly found anthocyanin that is mainly present in fruits, with established neuroprotective effects in situ. However, it remains unknown if Cy-3G can prevent Aβ fibrillogenesis and alleviate the corresponding cytotoxicity. In this study, extensive biochemical, biophysical, biological and computational experiments were combined to address this issue. It was found that Cy-3G significantly inhibits Aβ40 fibrillogenesis and disintegrates mature Aβ fibrils, and its inhibitory capacity is dependent on the Cy-3G concentration. The circular dichroism results showed that Cy-3G and Aβ40 at a molar ratio of 3 : 1 slightly prevents the structural transformation of Aβ40 from its initial random coil to the β-sheet-rich structure. Co-incubation of Aβ40 with Cy-3G significantly reduced the production of intracellular reactive oxygen species induced by Aβ40 fibrillogenesis and thus reduced Aβ40-induced cytotoxicity. Molecular dynamics simulations revealed that Cy-3G disrupted the β-sheet structure of the Aβ40 trimer. Cy-3G was found to mainly interact with the N-terminal region, the central hydrophobic cluster and the β-sheet region II via hydrophobic and electrostatic interactions. The ten hot spot residues D7, Y10, E11, F19, F20, E22, I31, I32, M35 and V40 were also identified. These findings not only enable a comprehensive understanding of the inhibitory effect of Cy-3G on Aβ40 fibrillogenesis, but also allow the identification of a valuable dietary ingredient that possesses great potential to be developed into functional foods to alleviate AD.

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.

Stability of Aβ11-40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation

The aggregation of the amyloid (Aβ) peptide of 39-43 amino acids into plaques is observed in the brain of Alzheimer's disease (AD) patients, but the mechanisms underlying the neurotoxicity of Aβ oligomers are still elusive. One suggested initial mechanism is related to the implications of amyloid membrane interactions, but characterization of these assemblies is challenging by experimental means. In this study, we have explored the stability of a trimer of Aβ11-40 in parallel and antiparallel β-sheet structures for the wild-type sequence and its F20W mutant in a dipalmitoylphosphatidylcholine membrane using atomistic replica exchange molecular dynamic simulations. We show that both the U-shape organization and the assembly of β-hairpins are maintained in the membrane and are resistant to the mutation F20W. In contrast the models are destabilized by the F19P mutation. Overall, our results indicate that these two assemblies represent minimal seeds or nuclei for the formation of either amyloid fibrils, a variety of β-barrel pores, or various aggregates for many Aβ sequences in a membrane-mimicking environment.

Naphthoquinone Tryptophan Hybrids: A Promising Small Molecule Scaffold for Mitigating Aggregation of Amyloidogenic Proteins and Peptides

A current challenge faced by researchers is the lack of disease-modifying therapeutics for amyloid formation that is associated with several human diseases. Although the monomeric proteins or peptides involved in various amyloidogenic diseases do not have amino acid sequence homology, there appears to be a structural correlation among the amyloid assemblies, which are responsible for distinct pathological conditions. Here, we review our work on Naphthoquinone Tryptophan (NQTrp) hybrids, a small molecule scaffold that can generically modulate neuronal and non-neuronal amyloid aggregation both in vitro and in vivo. NQTrp reduces the net amyloid load by inhibiting the process of amyloid formation and disassembling the pre-formed fibrils, both in a dose-dependent manner. As a plausible mechanism of action, NQTrp effectively forms hydrogen bonding and hydrophobic interactions, such as π-π stacking, with the vital residues responsible for the initial nucleation of protein/peptide aggregation. This review highlights the effectiveness of the NQTrp hybrid scaffold for developing novel small molecule modulators of amyloid aggregation.

Hexahydropyrrolo[2,3-b]indole Compounds as Potential Therapeutics for Alzheimer's Disease

Alzheimer's disease (AD) is the most common form of dementia among the elderly and has become a leading public health concern worldwide. It represents a huge economic and psychological burden to caregivers and families. The presence of extracellular amyloid beta (Aβ) plaques is one of the hallmarks of this neurodegenerative disorder. Amyloid plaques are comprised of aggregates of Aβ peptides, mainly Aβ₄₂, originated by the cleavage of the amyloid precursor protein (APP). Aβ is a crucial target for the treatment of AD, but to date, no effective treatment for the clearance of Aβ has been found. We have identified four new hexahydropyrroloindoles (HPI) synthetic compounds that are able to inhibit the aggregation of Aβ₄₂ and/or disaggregate the fibril. Docking experiments suggest that the nonpolar component of the interaction of compounds with Aβ₄₂ contributes favorably to the binding free energy of each complex. Molecular dynamics simulations suggested fibril disaggregating activity of compounds 1 via interaction with hydrophobic moieties of the fibril. Consistently, compounds 1 and 2 were able to mitigate Aβ₄₂ fibrils induced death in rat pheochromocytoma cells (PC 12). One of the compounds reduces the formation of Aβ aggregates in vivo and the paralysis associated with Aβ toxicity in Caenorhabditis elegans. Our study thus augments efforts for the identification and characterization of new agents that may help stop or delay the progression of AD.

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.

Binding Modes of a Glycopeptidomimetic Molecule on Aβ Protofibrils: Implication for Its Inhibition Mechanism

We recently reported that a glycopeptidomimetic molecule significantly delays the fibrillization process of Aβ₄₂ peptide involved in Alzheimer's disease. However, the binding mode of this compound, named 3β, was not determined at the atomic scale, hindering our understanding of its mechanism of action and impeding structure-based design of new inhibitors. In the present study, we performed molecular docking calculations and molecular dynamics simulations to investigate the most probable structures of 3β complexed with Aβ protofibrils. Our results show that 3β preferentially binds to an area of the protofibril surface that coincides with the protofibril dimerization interface observed in the solid-state NMR structure 5KK3 from the PDB. Based on these observations, we propose a model of the inhibition mechanism of Aβ fibrillization by compound 3β.

Targeting intrinsically disordered proteins at the edge of chaos

Intrinsically disordered proteins or intrinsically disordered regions (IDPs or IDRs) are those that do not fold into defined tertiary structures under physiological conditions. Given their prevalence in various diseases, IDPs are attractive therapeutic targets. However, because of the dynamic nature of the IDP structure, conventional structure-based drug design methods cannot be directly applied. Thanks to recent progress in understanding the mechanisms underlying IDP and ligand interactions, computational strategies for IDP-targeted rational drug discovery are emerging. Here, we summarize recent developments in computational IDP drug design strategies and their successful applications, analyze the typical properties of reported IDP-binding compounds (iIDPs), and discuss the major challenges ahead as well as possible solutions.

Targeting Amyloid Aggregation: An Overview of Strategies and Mechanisms

Amyloids result from the aggregation of a set of diverse proteins, due to either specific mutations or promoting intra- or extra-cellular conditions. Structurally, they are rich in intermolecular β-sheets and are the causative agents of several diseases, both neurodegenerative and systemic. It is believed that the most toxic species are small aggregates, referred to as oligomers, rather than the final fibrillar assemblies. Their mechanisms of toxicity are mostly mediated by aberrant interactions with the cell membranes, with resulting derangement of membrane-related functions. Much effort is being exerted in the search for natural antiamyloid agents, and/or in the development of synthetic molecules. Actually, it is well documented that the prevention of amyloid aggregation results in several cytoprotective effects. Here, we portray the state of the art in the field. Several natural compounds are effective antiamyloid agents, notably tetracyclines and polyphenols. They are generally non-specific, as documented by their partially overlapping mechanisms and the capability to interfere with the aggregation of several unrelated proteins. Among rationally designed molecules, we mention the prominent examples of β-breakers peptides, whole antibodies and fragments thereof, and the special case of drugs with contrasting transthyretin aggregation. In this framework, we stress the pivotal role of the computational approaches. When combined with biophysical methods, in several cases they have helped clarify in detail the protein/drug modes of interaction, which makes it plausible that more effective drugs will be developed in the future.

Understanding the Twisted Structure of Amyloid Fibrils via Molecular Simulations

Accumulation and aggregation of amyloid are associated with the pathogenesis of many human diseases, such as Alzheimer's disease and Type 2 diabetes mellitus. Therefore, a quantitative understanding of the molecular mechanisms causing different aggregated structures and biomechanical properties of amyloid fibrils could shed some light into the progression of these diseases. In this work, we develop coarse-grained molecular dynamics (CGMD) models to simulate the dynamic self-assembly of two types of amyloids (amylin and amyloid β (Aβ)). We investigate the structural and mechanical properties of different types of aggregated amyloid fibrils. Our simulations demonstrate that amyloid fibrils could result from longitudinal growth of protofilament bundles, confirming one of the hypotheses on the fibril formation. In addition, we find that the persistence length of amylin fibrils increases concurrently with their pitch length, suggesting that the bending stiffness of amylin fibrils becomes larger when the amylin fibrils are less twisted. Similar results are observed for Aβ fibrils. These findings quantify the connection between the structural and the biomechanical properties of the fibrils. The CGMD models developed in this work can be potentially used to examine efficacy of anti-aggregation drugs, which could help in developing new treatments.

Computational Molecular Docking and X-ray Crystallographic Studies of Catechins in New Drug Design Strategies

Epidemiological and laboratory studies have shown that green tea and green tea catechins exert beneficial effects on a variety of diseases, including cancer, metabolic syndrome, infectious diseases, and neurodegenerative diseases. In most cases, (-)-epigallocatechin gallate (EGCG) has been shown to play a central role in these effects by green tea. Catechins from other plant sources have also shown health benefits. Many studies have revealed that the binding of EGCG and other catechins to proteins is involved in its action mechanism. Computational docking analysis (CMDA) and X-ray crystallographic analysis (XCA) have provided detailed information on catechin-protein interactions. Several of these studies have revealed that the galloyl moiety anchors it to the cleft of proteins through interactions with its hydroxyl groups, explaining the higher activity of galloylated catechins such as EGCG and epicatechin gallate than non-galloylated catechins. In this paper, we review the results of CMDA and XCA of EGCG and other plant catechins to understand catechin-protein interactions with the expectation of developing new drugs with health-promoting properties.

Curcumin derivatives and Aβ-fibrillar aggregates: An interactions' study for diagnostic/therapeutic purposes in neurodegenerative diseases

Several neurodegenerative diseases, like Alzheimer's (AD), are characterized by amyloid fibrillar deposition of misfolded proteins, and this feature can be exploited for both diagnosis and therapy design. In this paper, structural modifications of curcumin scaffold were examined in order to improve its bioavailability and stability in physiological conditions, as well as its ability to interfere with β-amyloid fibrils and aggregates. The acid-base behaviour of curcumin derivatives, their pharmacokinetic stability in physiological conditions, and in vitro ability to interfere with Aβ fibrils at different incubation time were investigated. The mechanisms governing these phenomena have been studied at atomic level by means of molecular docking and dynamic simulations. Finally, biological activity of selected curcuminoids has been investigated in vitro to evaluate their safety and efficiency in oxidative stress protection on hippocampal HT-22 mouse cells. Two aromatic rings, π-conjugated structure and H-donor/acceptor substituents on the aromatic rings showed to be the sine qua non structural features to provide interaction and disaggregation activity even at very low incubation time (2h). Computational simulations proved that upon binding the ligands modify the conformational dynamics and/or interact with the amyloidogenic region of the protofibril facilitating disaggregation. Significantly, in vitro results on hippocampal cells pointed out protection against glutamate toxicity and safety when administered at low concentrations (1 μM). On the overall, in view of its higher stability in physiological conditions with respect to curcumin, of his rapid binding to fibrillar aggregates and strong depolymerizing activity, phtalimmide derivative K2F21 appeared a good candidate for both AD diagnostic and therapeutic purposes.

Computational Insight into the Effect of Natural Compounds on the Destabilization of Preformed Amyloid-β(1⁻40) Fibrils

One of the principal hallmarks of Alzheimer’s disease (AD) is related to the aggregation of amyloid-β fibrils in an insoluble form in the brain, also known as amyloidosis. Therefore, a prominent therapeutic strategy against AD consists of either blocking the amyloid aggregation and/or destroying the already formed aggregates. Natural products have shown significant therapeutic potential as amyloid inhibitors from in vitro studies as well as in vivo animal tests. In this study, the interaction of five natural biophenols (curcumin, dopamine, (-)-epigallocatechin-3-gallate, quercetin, and rosmarinic acid) with amyloid-β(1–40) fibrils has been studied through computational simulations. The results allowed the identification and characterization of the different binding modalities of each compounds and their consequences on fibril dynamics and aggregation. It emerges that the lateral aggregation of the fibrils is strongly influenced by the intercalation of the ligands, which modulates the double-layered structure stability.

Beneficial Effects of Green Tea Catechins on Neurodegenerative Diseases

Tea is one of the most consumed beverages in the world. Green tea, black tea, and oolong tea are made from the same plant Camellia sinensis (L.) O. Kuntze. Among them, green tea has been the most extensively studied for beneficial effects on diseases including cancer, obesity, diabetes, and inflammatory and neurodegenerative diseases. Several human observational and intervention studies have found beneficial effects of tea consumption on neurodegenerative impairment, such as cognitive dysfunction and memory loss. These studies supported the basis of tea's preventive effects of Parkinson's disease, but few studies have revealed such effects on Alzheimer's disease. In contrast, several human studies have not reported these favorable effects with regard to tea. This discrepancy may be due to incomplete adjustment of confounding factors, including the method of quantifying consumption, beverage temperature, cigarette smoking, alcohol consumption, and differences in genetic and environmental factors, such as race, sex, age, and lifestyle. Thus, more rigorous human studies are required to understand the neuroprotective effect of tea. A number of laboratory experiments demonstrated the benefits of green tea and green tea catechins (GTCs), such as epigallocatechin gallate (EGCG), and proposed action mechanisms. The targets of GTCs include the abnormal accumulation of fibrous proteins, such as Aβ and α-synuclein, inflammation, elevated expression of pro-apoptotic proteins, and oxidative stress, which are associated with neuronal cell dysfunction and death in the cerebral cortex. Computational molecular docking analysis revealed how EGCG can prevent the accumulation of fibrous proteins. These findings suggest that GTCs have the potential to be used in the prevention and treatment of neurodegenerative diseases and could be useful for the development of new drugs.

In Vitro and In Silico Studies of the Molecular Interactions of Epigallocatechin-3-O-gallate (EGCG) with Proteins That Explain the Health Benefits of Green Tea

Green tea has been shown to have beneficial effects on many diseases such as cancer, obesity, inflammatory diseases, and neurodegenerative disorders. The major green tea component, epigallocatechin-3-O-gallate (EGCG), has been demonstrated to contribute to these effects through its anti-oxidative and pro-oxidative properties. Furthermore, several lines of evidence have indicated that the binding affinity of EGCG to specific proteins may explain its mechanism of action. This review article aims to reveal how EGCG-protein interactions can explain the mechanism by which green tea/EGCG can exhibit health beneficial effects. We conducted a literature search, using mainly the PubMed database. The results showed that several methods such as dot assays, affinity gel chromatography, surface plasmon resonance, computational docking analyses, and X-ray crystallography have been used for this purpose. These studies have provided evidence to show how EGCG can fit or occupy the position in or near functional sites and induce a conformational change, including a quaternary conformational change in some cases. Active site blocking, steric hindrance by binding of EGCG near an active site or induced conformational change appeared to cause inhibition of enzymatic activity and other biological activities of proteins, which are related to EGCG’s biological oligomer and formation of their toxic aggregates, leading to the prevention of neurodegenerative diseases and amyloidosis. In conclusion, these studies have provided useful information on the action of green tea/catechins and would lead to future studies that will provide further evidence for rational EGCG therapy and use EGCG as a lead compound for drug design.

HP-β-cyclodextrin as an inhibitor of amyloid-β aggregation and toxicity

Amyloid deposits of misfolded amyloid-β protein (Aβ) on neuronal cells are a pathological hallmark of Alzheimer's disease (AD). Prevention of the abnormal Aβ aggregation has been considered as a promising therapeutic strategy for AD treatment. To prevent reinventing the wheel, we proposed to search the existing drug database for other diseases to identify potential Aβ inhibitors. Herein, we reported the inhibitory activity of HP-β-cyclodextrin (HP-β-CD), a well-known sugar used in drug delivery, genetic vector, environmental protection and treatment of Niemann-Pick disease type C1 (NPC1), against Aβ1-42 aggregation and Aβ-induced toxicity, with the aim of adding a new function as a sugar-based Aβ inhibitor. Experimental data showed that HP-β-CD molecules were not only nontoxic to cells, but also greatly inhibited Aβ fibrillization and reduced Aβ-induced toxicity in a concentration-dependent manner. At an optimal molar ratio of Aβ : HP-β-CD = 1 : 2, HP-β-CD enabled the reduction of 60% of Aβ fibrils and increased the cell viability to 92%. Such concentration-dependent inhibitor capacity of HP-β-CD was likely attributed to several combined effects, including the enhancement of Aβ-HP-β-CD interactions, prevention of structural transition of Aβ peptides towards β-sheet structures, and reduction of self-aggregation of HP-β-CD. In parallel, molecular simulations further revealed the atomic details of HP-β-CD interacting with the Aβ oligomer, showing that HP-β-CD had a high tendency to interact with hydrophobic residues of Aβ in two β-strands and the N-terminal tail. More importantly, we identified that the inner hydrophobic cavity of HP-β-CD was a key active site for Aβ inhibition. Once the inner cavity of HP-β-CD was blocked by a small hydrophobic molecule of ferulic acid, HP-β-CD completely lost its inhibition capacity against Aβ. Given the already established pharmaceutical functions of HP-β-CD in drug delivery, our findings suggest that HP-β-CD has great potential to be designed as a sugar-based Aβ inhibitor.

Major Reaction Coordinates Linking Transient Amyloid-β Oligomers to Fibrils Measured at Atomic Level

The structural underpinnings for the higher toxicity of the oligomeric intermediates of amyloidogenic peptides, compared to the mature fibrils, remain unknown at present. The transient nature and heterogeneity of the oligomers make it difficult to follow their structure. Here, using vibrational and solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, we show that freely aggregating Aβ₄₀ oligomers in physiological solutions have an intramolecular antiparallel configuration that is distinct from the intermolecular parallel β-sheet structure observed in mature fibrils. The intramolecular hydrogen-bonding network flips nearly 90°, and the two β-strands of each monomeric unit move apart, to give rise to the well-known intermolecular in-register parallel β-sheet structure in the mature fibrils. Solid-state nuclear magnetic resonance distance measurements capture the interstrand separation within monomer units during the transition from the oligomer to the fibril form. We further find that the D23-K28 salt-bridge, a major feature of the Aβ₄₀ fibrils and a focal point of mutations linked to early onset Alzheimer's disease, is not detectable in the small oligomers. Molecular dynamics simulations capture the correlation between changes in the D23-K28 distance and the flipping of the monomer secondary structure between antiparallel and parallel β-sheet architectures. Overall, we propose interstrand separation and salt-bridge formation as key reaction coordinates describing the structural transition of the small Aβ₄₀ oligomers to fibrils.

Identification of Key Interactions in the Initial Self-Assembly of Amylin in a Membrane Environment

Islet amyloid polypeptide, also known as amylin, forms aggregates that reduce the amount of insulin-producing cells in patients with type II diabetes mellitus. Much remains unknown about the process of aggregation and cytotoxicity, but it is known that certain cell membrane components can alter the rate of aggregation. Using atomistic molecular dynamics simulations combined with the highly mobile membrane mimetic model incorporating enhanced sampling of lipid diffusion, we investigate interaction of amylin peptides with the membrane components as well as the self-assembly of amylin. Consistent with experimental evidence, we find that an initial membrane-bound α-helical state folds into stable β-sheet structures upon self-assembly. Our results suggest the following mechanism for the initial phase of amylin self-assembly. The peptides move around on the membrane with the positively charged N-terminus interacting with the negatively charged lipid headgroups. When the peptides start to interact, they partly unfold and break some of the contacts with the membrane. The initial interactions between the peptides are dominated by aromatic and hydrophobic interactions. Oligomers are formed showing both intra- and interpeptide β-sheets, initially with interactions mainly in the C-terminal domain of the peptides. Decreasing the pH to 5.5 is known to inhibit amyloid formation. At low pH, His18 is protonated, adding a fourth positive charge at the peptide. With His18 protonated, no oligomerization is observed in the simulations. The additional charge gives a strong midpoint anchoring of the peptides to negatively charged membrane components, and the peptides experience additional interpeptide repulsion, thereby preventing interactions.

N-Terminus Binding Preference for Either Tanshinone or Analogue in Both Inhibition of Amyloid Aggregation and Disaggregation of Preformed Amyloid Fibrils-Toward Introducing a Kind of Novel Anti-Alzheimer Compounds

Amyloid-β (Aβ₄₀/Aβ₄₂) peptide with a length of 40 or 42 residues is naturally secreted as cleavage product of the amyloid precursor protein, and formation of Aβ aggregates in a patient's brain is a hallmark of Alzheimer's disease (AD). Therefore, disaggregation and disruption provide potential therapeutic approaches to reduce, inhibit, and even reverse Aβ aggregation. The disaggregation/inhibition effect of the inhibitors applies generally to both Aβ₄₀ and Aβ₄₂ aggregations. Here we capture the atomic-level details of the interaction between Aβ₄₀/Aβ₄₂ and either natural tanshinone compound TS1 or its derivative TS0, and observe novel results by using molecular dynamics simulations. We observe that the natural TS1 indeed inhibits the monomolecular Aβ₄₂ (mAβ₄₂) aggregation and disaggregates Aβ₄₂ amyloid fibrils, being in good agreement with the experimental results. TS1 is favorable to stabilize mAβ₄₀ and even Aβ₄₀ fibril, playing an opposite role to that in the Aβ₄₂ counterpart, however. TS0 can inhibit the misfolding of either mAβ₄₀ or mAβ₄₂ and disaggregate Aβ₄₂ fibril but stabilize the Aβ₄₀ fibril. Using a combination of secondary structural analysis, MM-PBSA binding energy calculations, and radial distribution functions computations, we find that both TS0 and TS1, especially the former, prefer to bind at the charged residues within disordered N-terminus with a scarce positive binding energy and disappear the characteristic C-terminal bend region of Aβ₄₂ fibril, as well as twist the Aβ₄₂ fibril seriously. It turns out to destabilize the Aβ₄₂ fibril and enable the conversion of U-shaped Aβ₄₂ fibril from the onefold to the twofold morphologies. The N-terminal binding preference helps us to identify N-terminal region as the specific epitope for specific inhibitors/drugs (such as TS0 and analogues), heralding unusual inhibition/disaggregation or stabilization mechanisms, and offering an alternative direction in engineering new inhibitors to treat AD.

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

An extensive replica exchange molecular dynamics (REMD) simulation was performed to investigate the progress patterns of the inhibition of (-)-epigallocatechin-3-gallate (EGCG) on the Aβ_16-22 hexamer. Structural variations of the oligomers without and with EGCG were monitored and analyzed in detail. It has been found that EGCG prevents the formation of Aβ oligomer through two different ways by either accelerating the Aβ oligomerization or reducing the β-content of the hexamer. It also decreases the potential "highly toxic" conformations of Aβ oligomer, which is related to the conformations having high order β-sheet sizes. Both electrostatic and van der Waals interaction energies are found to be involved to the binding process. Computed results using quantum chemical methods show that the π-π stacking is a critical factor of the interaction between EGCG and the peptides. As a result, the binding free energy of the EGCG to the Aβ peptides is slightly larger than that of the curcumin.

High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields

The dimer of the amyloid-β peptide Aβ of 42 residues is the smallest toxic species in Alzheimer's disease, but its equilibrium structures are unknown. Here we determined the equilibrium ensembles generated by the four atomistic OPLS-AA, CHARMM22*, AMBER99sb-ildn, and AMBERsb14 force fields with the TIP3P water model. On the basis of 144 μs replica exchange molecular dynamics simulations (with 750 ns per replica), we find that the four force fields lead to random coil ensembles with calculated cross-collision sections, hydrodynamics properties, and small-angle X-ray scattering profiles independent of the force field. There are, however, marked differences in secondary structure, with the AMBERsb14 and CHARMM22* ensembles overestimating the CD-derived helix content, and the OPLS-AA and AMBER99sb-ildn secondary structure contents in agreement with CD data. Also the intramolecular beta-hairpin content spanning residues 17-21 and 30-36 varies between 1.5% and 13%. Overall, there are significant differences in tertiary and quaternary conformations among all force fields, and the key finding, irrespective of the force field, is that the dimer is stabilized by nonspecific interactions, explaining therefore its possible transient binding to multiple cellular partners and, in part, its toxicity.

Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides

Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

Two decades of new drug discovery and development for Alzheimer's disease

Alzheimer's disease is a progressive and irreversible neurodegenerative disease, associated with a decreased cognitive function and severe behavioral abnormalities.

Replica exchange molecular dynamics study of the truncated amyloid beta (11–40) trimer in solution

The structure of the 3Aβ_11–40 oligomer is determined for the first time using T-REMD simulations.

Polymorphism of fibrillar structures depending on the size of assembled Aβ17-42 peptides

The size of assembled Aβ_17-42 peptides can determine polymorphism during oligomerization and fibrillization, but the mechanism of this effect is unknown. Starting from separate random monomers, various fibrillar oligomers with distinct structural characteristics were identified using discontinuous molecular dynamics simulations based on a coarse-grained protein model. From the structures observed in the simulations, two characteristic oligomer sizes emerged, trimer and paranuclei, which generated distinct structural patterns during fibrillization. A majority of the simulations for trimers and tetramers formed non-fibrillar oligomers, which primarily progress to off-pathway oligomers. Pentamers and hexamers were significantly converted into U-shape fibrillar structures, meaning that these oligomers, called paranuclei, might be potent on-pathway intermediates in fibril formation. Fibrillar oligomers larger than hexamers generated substantial polymorphism in which hybrid structures were readily formed and homogeneous fibrillar structures appeared infrequently.

Assembly of Triblock Amphiphilic Peptides into One-Dimensional Aggregates and Network Formation

Peptide assembly plays a key role in both neurological diseases and development of novel biomaterials with well-defined nanostructures. Synthetic model peptides provide a unique platform to explore the role of intermolecular interactions in the assembly process. A triblock peptide architecture designed by the Hartgerink group is a versatile system which relies on Coulomb interactions, hydrogen bonding, and hydrophobicity to guide these peptides' assembly at three different length scales: β-sheets, double-wall ribbon-like aggregates, and finally a highly porous network structure which can support gels with ≤1% by weight peptide concentration. In this study, by using molecular dynamics simulations of a structure based implicit solvent coarse grained model, we analyzed this hierarchical assembly process. Parametrization of our CG model is based on multiple-state points from atomistic simulations, which enables this model to represent the conformational adaptability of the triblock peptide molecule based on the surrounding medium. Our results indicate that emergence of the double-wall β-sheet packing mechanism, proposed in light of the experimental evidence, strongly depends on the subtle balance of the intermolecular forces. We demonstrate that, even though backbone hydrogen bonding dominates the early nucleation stages, depending on the strength of the hydrophobic and Coulomb forces, alternative structures such as zero-dimensional aggregates with two β-sheets oriented orthogonally (which we refer to as a cross-packed structure) and β-sheets with misoriented hydrophobic side chains are also feasible. We discuss the implications of these competing structures for the three different length scales of assembly by systematically investigating the influence of density, counterion valency, and hydrophobicity.

Anti-arrhythmic Medication Propafenone a Potential Drug for Alzheimer's Disease Inhibiting Aggregation of Aβ: In Silico and in Vitro Studies

Alzheimer's disease (AD) is the most common form of dementia caused by the formation of Aβ aggregates. So far, no effective medicine for the treatment of AD is available. Many efforts have been made to find effective medicine to cope with AD. Curcumin is a drug candidate for AD, being a potent anti-amyloidogenic compound, but the results of clinical trials for it were either negative or inclusive. In the present study, we took advantages from accumulated knowledge about curcumin and have screened out four compounds that have chemical and structural similarity with curcumin more than 80% from all FDA-approved oral drugs. Using all-atom molecular dynamics simulation and the free energy perturbation method we showed that among predicted compounds anti-arrhythmic medication propafenone shows the best anti-amyloidogenic activity. The in vitro experiment further revealed that it can inhibit Aβ aggregation and protect cells against Aβ induced cytotoxicity to almost the same extent as curcumin. Our results suggest that propafenone may be a potent drug for the treatment of Alzheimer's disease.