Distinct Binding Dynamics, Sites and Interactions of Fullerene and Fullerenols with Amyloid-β Peptides Revealed by Molecular Dynamics Simulations

Dose-dependent binding behavior of anthraquinone derivative purpurin interacting with tau-derived peptide protofibril

Alzheimer's disease is hallmarked by microtubule-associated protein tau tangles and amyloid-β plaques. The β-structure propensity of tau inclusions is closely related to the hexapeptide motif VQIVYK (termed PHF6), and disruption of this motif prevents tau aggregation. Small-molecule inhibitors are considered a promising therapeutic strategy, but the molecular mechanisms underlying the correlation between dose and inhibitory effects are still unclear. In this work, we investigated the dose-induced influence of purpurin, an anthraquinone derivative, on the structural stability of the PHF6 fibrillar nucleus by performing microsecond all-atom molecular dynamics simulations in explicit water. The stability of PHF6 protofibrils of different sizes was first examined, and it was found that the structural stability of fibrillar oligomers increases with oligomer size, and that the octamer is the minimal stable nucleus for fibril formation. When purpurin molecules were added to the protofibril octamer at a low purpurin/peptide ratio, they bound to the octamer with different coupling states, and the different states may transition to each of the other states through an uncoupling state or directly through a short-time transition. With increasing purpurin/peptide ratio, purpurins tend to self-aggregate rather than bind to the protein surface. Interestingly, the contacts between individual purpurins and the octamer as a function of the purpurin number show a power-law behavior, which may serve as a useful indicator to reflect the binding efficiency of ligands to proteins in drug screening. The interaction analysis reveals that purpurin prefers to bind to the hydrophilic and aromatic Tyr and has the lowest probability with the hydrophobic Val located in the middle of PHF6. Aromatic stacking plays a key role in the octamer-purpurin interaction, in which the three aromatic rings of purpurin have different contributions. In addition, purpurin shows a remarkable disruptive effect on the protofibril octamer when the molar ratio of purpurin to peptide is 1 : 2; above this ratio, the binding mode and disruption effect of purpurin do not change significantly. Our work provides a detailed picture of the dynamics and interactions of purpurin binding to the PHF6 protofibril and expands the understanding of the dose-induced inhibitory mechanism.

Computational Investigations into Two-Photon Fibril Imaging Using the DANIR-2c Probe

The design of novel fibril imaging molecules for medical diagnosis requires the simultaneous optimization of fibril-specific optical properties and binding specificity toward amyloid fibrils. Because of the possibility to monitor internal organs and deep tissues, the two-photon probes that can absorb in the infrared (IR) and near-IR (NIR) region with a significant two-photon absorption cross section are of immense interest. To contribute to this exploration of chemical compounds suitable for two-photon fibril imaging, we have computationally studied the one- and two-photon properties of a donor-acceptor-substituted DANIR-2c probe, which was used for in vivo detection of β-amyloid deposits using fluorescence spectroscopy. In particular, a multiscale computational approach was employed involving molecular docking, molecular dynamics, hybrid QM/MM molecular dynamics, and coupled-cluster/MM to study the binding of the studied probe to amyloid fibril and its one- and two-photon absorption properties in the fibrillar environment. Multiple binding sites are available for this probe in amyloid fibril, and the one corresponding to the largest binding affinity exhibits also the largest and experimentally meaningful two-photon absorption cross section, thus demonstrating the potential of the studied probe in two-photon microscopy.

Enhancing the Amyloid-β Anti-Aggregation Properties of Curcumin via Arene-Ruthenium(II) Derivatization

Alzheimer’s disease (AD) is a fatal neurodegenerative disorder associated with severe dementia, progressive cognitive decline, and irreversible memory loss. Although its etiopathogenesis is still unclear, the aggregation of amyloid-β (Aβ) peptides into supramolecular structures and their accumulation in the central nervous system play a critical role in the onset and progression of the disease. On such a premise, the inhibition of the early stages of Aβ aggregation is a potential prevention strategy for the treatment of AD. Since several natural occurring compounds, as well as metal-based molecules, showed promising inhibitory activities toward Aβ aggregation, we herein characterized the interaction of an organoruthenium derivative of curcumin with Aβ(1–40) and Aβ(1–42) peptides, and we evaluated its ability to inhibit the oligomerization/fibrillogenesis processes by combining in silico and in vitro methods. In general, besides being less toxic to neuronal cells, the derivative preserved the amyloid binding ability of the parent compound in terms of equilibrium dissociation constants but (most notably) was more effective both in retarding the formation and limiting the size of amyloid aggregates by virtue of a higher hindering effect on the amyloid–amyloid elongation surface. Additionally, the complex protected neuronal cells from amyloid toxicity.

Multiadducts of C60 Modulate Amyloid-β Fibrillation with Dual Acetylcholinesterase Inhibition and Antioxidant Properties: In Vitro and In Silico Studies

Background: Amyloid-β (Aβ) fibrils induce cognitive impairment and neuronal loss, leading to onset of Alzheimer’s disease (AD). The inhibition of Aβ aggregation has been proposed as a therapeutic strategy for AD. Pristine C60 has shown the capacity to interact with the Aβ peptide and interfere with fibril formation but induces significant toxic effects in vitro and in vivo. Objective: To evaluate the potential of a series of C60 multiadducts to inhibit the Aβ fibrillization. Methods: A series of C60 multiadducts with four to six diethyl malonyl and their corresponding disodium-malonyl substituents were synthesized as individual isomers. Their potential on Aβ fibrillization inhibition was evaluated in vitro, in cellulo, and silico. Antioxidant activity, acetylcholinesterase inhibition capacity, and toxicity were assessed in vitro. Results: The multiadducts modulate Aβ fibrils formation without inducing cell toxicity, and that the number and polarity of the substituents play a significant role in the adducts efficacy to modulate Aβ aggregation. The molecular mechanism of fullerene-Aβ interaction and modulation was identified. Furthermore, the fullerene derivatives exhibited antioxidant capacity and reduction of acetylcholinesterase activity. Conclusion: Multiadducts of C60 are novel multi-target-directed ligand molecules that could hold considerable promise as the starting point for the development of AD therapies.

Structure and mechanism behind the inhibitory effect of water soluble metalloporphyrins on Aβ1-42 aggregation

Although the exact molecular mechanism of the pathogenesis of Alzheimer’s disease (AD) is still unclear, compounds that can inhibit the aggregation of amyloid-β peptide (Aβ1-42) or scavenge the highly toxic...

Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60

Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C₆₀. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol⁻¹, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol⁻¹ for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C₆₀ was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C₆₀ binding.

Self-Assembling Peptides and Carbon Nanomaterials Join Forces for Innovative Biomedical Applications

Self-assembling peptides and carbon nanomaterials have attracted great interest for their respective potential to bring innovation in the biomedical field. Combination of these two types of building blocks is not trivial in light of their very different physico-chemical properties, yet great progress has been made over the years at the interface between these two research areas. This concise review will analyze the latest developments at the forefront of research that combines self-assembling peptides with carbon nanostructures for biological use. Applications span from tissue regeneration, to biosensing and imaging, and bioelectronics.

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.

Serotonin and Melatonin Show Different Modes of Action on Aβ42 Protofibril Destabilization

Alzheimer's disease (AD) is associated with the aberrant self-assembly of amyloid-β (Aβ) protein into fibrillar deposits. The disaggregation of Aβ fibril is believed as one of the major therapeutic strategies for treating AD. Previous experimental studies reported that serotonin (Ser), one of the indoleamine neurotransmitters, and its derivative melatonin (Mel) are able to disassemble preformed Aβ fibrils. However, the fibril-disruption mechanisms are unclear. As the first step to understand the underlying mechanism, we investigated the interactions of Ser and Mel molecules with the LS-shaped Aβ₄₂ protofibril by performing a total of nine individual 500 ns all-atom molecular dynamics (MD) simulations. The simulations demonstrate that both Ser and Mel molecules disrupt the local β-sheet structure, destroy the salt bridges between K28 side chain and A42 COO^-, and consequently destabilize the global structure of Aβ₄₂ protofibril. The Mel molecule exhibits a greater binding capacity than the Ser molecule. Intriguingly, we find that Ser and Mel molecules destabilize Aβ₄₂ protofibril through different modes of action. Ser preferentially binds with the aromatic residues in the N-terminal region through π-π stacking interactions, while Mel binds not only with the N-terminal aromatic residues but also with the C-terminal hydrophobic residues via π-π and hydrophobic interactions. This work reveals the disruptive mechanisms of Aβ₄₂ protofibril by Ser and Mel molecules and provides useful information for designing drug candidates against AD.

Investigating the Size-Dependent Binding of Pristine nC60 to Bovine Serum Albumin by Multi-Spectroscopic Techniques

The morphology of nanomaterials may affect their interaction with biomacromolecules such as proteins. Previous work has studied the size-dependent binding of pristine nC₆₀ to bovine/human serum albumin using the fluorometric method and found that the fluorescence inner filter effect might affect this interaction. However, if it is necessary to accurately calculate and obtain binding information, the fluorescence inner filter effect should not be ignored. This work aimed to further investigate the effect of the fluorescence inner filter on the interaction between pristine nC₆₀ with different particle sizes (140–160, 120–140, 90–110, 50–70, and 30–50 nm) and bovine serum albumin for a more accurate comprehension of the binding of pristine nC₆₀ to bovine serum albumin. The nC₆₀ nanoparticles with different size distributions used in the experiments were obtained by the solvent displacement and centrifugation method. UV-Vis spectroscopy and fluorescence spectroscopy were used to study the binding of nC₆₀ with different size distributions to bovine serum albumin (BSA) before and after eliminating the fluorescence inner filter effect. The results showed that the fluorescence inner filter effect had an influence on the interaction between nC₆₀ and proteins to some extent, and still did not change the rule of the size-dependent binding of nC₆₀ nanoparticles to BSA. Further studies on the binding parameters (binding constants and the number of binding sites) between them were performed, and the effect of the binding on BSA structures and conformation were also speculated.

Fullerenes as an Effective Amyloid Fibrils Disaggregating Nanomaterial

Nowadays, determining the disassembly mechanism of amyloids under nanomaterials action is a crucial issue for their successful future use in therapy of neurodegenerative and overall amyloid-related diseases. In this study, the antiamyloid disassembly activity of fullerenes C₆₀ and C₇₀ dispersed in 1-methyl-2-pyrrolidinone (NMP) toward amyloid fibrils preformed from lysozyme and insulin was investigated using a combination of different experimental techniques. Thioflavin T fluorescence assay and atomic force microscopy were applied for monitoring of disaggregation activity of fullerenes. It was demonstrated that both types of fullerene-based complexes are very effective in disassembling preformed fibrils, and characterized by the low apparent half-maximal disaggregation concentration (DC₅₀) in the range of ∼22-30 μg mL^-1. Small-angle neutron scattering was employed to monitor the different stages of the disassembly process with respect to the size and morphology of the aggregates. Based on the obtained results, a possible disassembly mechanism for amyloid fibrils interacting with fullerene/NMP complexes was proposed. The study is a principal step in understanding of the fullerenes destruction mechanism of the protein amyloids, as well as providing valuable information on how macromolecules can be engineered to disassemble unwanted amyloid aggregates by different mechanisms.

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.

Critical nucleus of Greek-key-like core of α-synuclein protofibril and its disruption by dopamine and norepinephrine

Protofibrillar trimer is the critical nucleus for the αS fibril formation, and the tetramer is the minimal stable nucleus. The interactions of DA/NE with αS trimer/tetramer disrupt the backbone H-bonds and destabilize the αS protofibrils.

Bleomycin modulates amyloid aggregation in β-amyloid and hIAPP

Aberrant misfolding and amyloid aggregation, which result in amyloid fibrils, are frequent and critical pathological incidents in various neurodegenerative disorders. Multiple drugs or inhibitors have been investigated to avert amyloid aggregation in individual peptides, exhibiting sequence-dependent inhibition mechanisms. Establishing or inventing inhibitors capable of preventing amyloid aggregation in a wide variety of amyloid peptides is quite a daunting task. Bleomycin (BLM), a complex glycopeptide, has been widely used as an antibiotic and antitumor drug due to its ability to inhibit DNA metabolism, and as an antineoplastic, especially for solid tumors. In this study, we investigated the dual inhibitory effects of BLM on Aβ aggregation, associated with Alzheimer's disease and hIAPP, which is linked to type 2 diabetes, using both computational and experimental techniques. Combined results from drug repurposing and replica exchange molecular dynamics simulations demonstrate that BLM binds to the β-sheet region considered a hotspot for amyloid fibrils of Aβ and hIAPP. BLM was also found to be involved in β-sheet destabilization and, ultimately, in its reduction. Further, experimental validation through in vitro amyloid aggregation assays was obtained wherein the fibrillar load was decreased for the BLM-treated Aβ and hIAPP peptides in comparison to controls. For the first time, this study shows that BLM is a dual inhibitor of Aβ and hIAPP amyloid aggregation. In the future, the conformational optimization and processing of BLM may help develop various efficient sequence-dependent inhibitors against amyloid aggregation in various amyloid peptides.

Bleomycin acts as a dual inhibitor against both amyloid β and human islet amyloid polypeptide by binding to the β-sheet grooves considered as the amyloids hotspot.

Structural Influence and Interactive Binding Behavior of Dopamine and Norepinephrine on the Greek-Key-Like Core of α-Synuclein Protofibril Revealed by Molecular Dynamics Simulations

The pathogenesis of Parkinson’s disease (PD) is closely associated with the aggregation of α-synuclein (αS) protein. Finding the effective inhibitors of αS aggregation has been considered as the primary therapeutic strategy for PD. Recent studies reported that two neurotransmitters, dopamine (DA) and norepinephrine (NE), can effectively inhibit αS aggregation and disrupt the preformed αS fibrils. However, the atomistic details of αS-DA/NE interaction remain unclear. Here, using molecular dynamics simulations, we investigated the binding behavior of DA/NE molecules and their structural influence on αS44–96 (Greek-key-like core of full length αS) protofibrillar tetramer. Our results showed that DA/NE molecules destabilize αS protofibrillar tetramer by disrupting the β-sheet structure and destroying the intra- and inter-peptide E46–K80 salt bridges, and they can also destroy the inter-chain backbone hydrogen bonds. Three binding sites were identified for both DA and NE molecules interacting with αS tetramer: T54–T72, Q79–A85, and F94–K96, and NE molecules had a stronger binding capacity to these sites than DA. The binding of DA/NE molecules to αS tetramer is dominantly driven by electrostatic and hydrogen bonding interactions. Through aromatic π-stacking, DA and NE molecules can bind to αS protofibril interactively. Our work reveals the detailed disruptive mechanism of protofibrillar αS oligomer by DA/NE molecules, which is helpful for the development of drug candidates against PD. Given that exercise as a stressor can stimulate DA/NE secretion and elevated levels of DA/NE could delay the progress of PD, this work also enhances our understanding of the biological mechanism by which exercise prevents and alleviates PD.