Molecular dynamics simulations reveal the destabilization mechanism of Alzheimer's disease-related tau R3-R4 Protofilament by norepinephrine

A Focus on the Link Between Metal Dyshomeostasis, Norepinephrine, and Protein Aggregation

Neurodegenerative disorders are one of the main public health problems worldwide and, for this reason, they have attracted the attention of several researchers who aim to better understand the molecular processes linked to the etiology of these disorders, including Alzheimer's and Parkinson's diseases. In this review, we describe both the beneficial and toxic effect of norepinephrine (NE) and its connected ROS/metal-mediated pathways, which end in neuromelanin (NM) formation and protein aggregation. In particular, we emphasize the importance of stabilizing the delicate homeostatic balance that regulates (i) the metal/ROS-promoted oxidation of catecholamines, as NE, and (ii) the generation of oxidative by-products capable of covalently and non-covalently modifying neuroproteins, thus altering their stability and their oligomerization; these processes may end in (iii) the incorporation of protein conjugates into vesicles, which then evolve into neuromelanin (NM) organelles. In general, we aim to provide an up-to-date overview of the challenges and controversies emerging from the current literature to delineate a direction for future research.

Spatiotemporal patterns of locus coeruleus integrity predict cortical tau and cognition

Autopsy studies indicated that the locus coeruleus (LC) accumulates hyperphosphorylated tau before allocortical regions in Alzheimer's disease. By combining in vivo longitudinal magnetic resonance imaging measures of LC integrity, tau positron emission tomography imaging and cognition with autopsy data and transcriptomic information, we examined whether LC changes precede allocortical tau deposition and whether specific genetic features underlie LC's selective vulnerability to tau. We found that LC integrity changes preceded medial temporal lobe tau accumulation, and together these processes were associated with lower cognitive performance. Common gene expression profiles between LC-medial temporal lobe-limbic regions map to biological functions in protein transport regulation. These findings advance our understanding of the spatiotemporal patterns of initial tau spreading from the LC and LC's selective vulnerability to Alzheimer's disease pathology. LC integrity measures can be a promising indicator for identifying the time window when individuals are at risk of disease progression and underscore the importance of interventions mitigating initial tau spread.

Destabilization mechanism of R3-R4 tau protofilament by purpurin: a molecular dynamics study

The accumulation of tau protein aggregates is a common feature observed in many neurodegenerative diseases. However, the structural characteristics of tau aggregates can vary among different tauopathies. It has been established that the structure of the tau protofilament in Chronic traumatic encephalopathy (CTE) is similar to that of Alzheimer's disease (AD). In addition, a previous study found that purpurin, an anthraquinone, could inhibit and disassemble the pre-formed ³⁰⁶VQIVYK³¹¹ isoform of AD-tau protofilament. Herein, we used all-atom molecular dynamic (MD) simulation to investigate the distinctive features between CTE-tau and AD-tau protofilament and the influence of purpurin on CTE-tau protofilament. Our findings revealed notable differences at the atomic level between CTE-tau and AD-tau protofilaments, particularly in the β6-β7 angle and the solvent-accessible surface area (SASA) of the β4-β6 region. These structural disparities contributed to the distinct characteristics observed in the two types of tau protofilaments. Our simulations substantiated that purpurin could destabilize the CTE-tau protofilament and decrease β-sheet content. Purpurin molecules could insert the β4-β6 region and weaken the hydrophobic packing between β1 and β8 through π-π stacking. Interestingly, each of the three rings in purpurin exhibited unique binding preferences with the CTE-tau protofilament. Overall, our study sheds light on the structural distinctions between CTE-tau and AD-tau protofilaments, as well as the destabilizing mechanism of purpurin on CTE-tau protofilament, which may be helpful to the development of drugs to prevent CTE.

Illustrating the Effect of Small Molecules Derived from Natural Resources on Amyloid Peptides

The onset of amyloidogenic diseases is associated with the misfolding and aggregation of proteins. Despite extensive research, no effective therapeutics are yet available to treat these chronic degenerative diseases. Targeting the aggregation of disease-specific proteins is regarded as a promising new approach to treat these diseases. In the past few years, rapid progress in this field has been made in vitro, in vivo, and in silico to generate potential drug candidates, ranging from small molecules to polymers to nanoparticles. Small molecular probes, mostly those derived from natural sources, have been of particular interest among amyloid inhibitors. Here, we summarize some of the most important natural small molecular probes which can inhibit the aggregation of Aβ, hIAPP, and α-syn peptides and discuss how their binding efficacy and preference for the peptides vary with their structure and conformation. This provides a comprehensive idea of the crucial factors which should be incorporated into the future design of novel drug candidates useful for the treatment of amyloid diseases.

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.

On the Tracks of the Aggregation Mechanism of the PHF6 Peptide from Tau Protein: Molecular Dynamics, Energy, and Interaction Network Investigations

The formation of neurofibrillary tangles (NFTs), composed of tau protein aggregates, is a hallmark of some neurodegenerative diseases called tauopathies. NFTs are composed of paired helical filaments (PHFs) of tau protein with a dominant β-sheet secondary structuration. The NFT formation mechanism is not known yet. This study focuses on PHF6, a crucial hexapeptide responsible for tau aggregation. A 2 μs molecular dynamics simulation was launched to determine the keys of the PHF6 aggregation mechanism. Hydrogen bonding, van der Waals, and other non-covalent interactions as π-stacking were investigated. Parallel aggregation was slightly preferred due to its adaptability, but antiparallel aggregation remained widely present during the PHF6 aggregation. The analysis highlighted the leading role of hydrogen bonds identified at the atomic level for each aggregation process. The aggregation study emphasized the importance of Tyr310 during the β-sheets' complexation through π-stacking.

Mechanistic insight into the disruption of Tau R3-R4 protofibrils by curcumin and epinephrine: an all-atom molecular dynamics study

The accumulation of Tau protein aggregates is a pathological hallmark of tauopathy, including chronic traumatic encephalopathy (CTE). Inhibiting Tau aggregation or disrupting preformed Tau fibrils is considered one of the rational therapeutic strategies to combat tauopathy. Previous studies reported that curcumin (Cur, a molecule of a labile natural product) and epinephrine (EP, an important neurotransmitter) could effectively inhibit the formation of Tau fibrillar aggregates and disassociate preformed fibrils. However, the underlying molecular mechanisms remain elusive. In this study, we performed multiple molecular dynamics simulations for 17.5 μs in total to investigate the influence of Cur and EP on the C-shaped Tau protofibril associated with CTE. Our simulations show that the protofibrillar pentamer is the smallest stable Tau R3-R4 protofibril. Taking the pentamer as a protofibril model, we found that both Cur and EP molecules could affect the shape of the Tau pentamer by changing the β2-β3 and β7-β8 angles, leading to a more extended structure. Cur and EP display a disruptive effect on the local β-sheets and the formation of hydrogen bonds, and thus destabilize the global protofibril structure. The contact number analysis shows that Cur has a higher binding affinity with the Tau pentamer than EP, especially in the nucleating segment PHF6. Hydrophobic, π-π and cation-π interactions together facilitate the binding of Cur and EP with the Tau pentamer. Cur exhibits stronger hydrophobic and π-π interactions with Tau than EP, and EP displays a stronger cation-π interaction. Our findings provide molecular insights into the disruptive mechanisms of the Tau R3-R4 protofibrils by curcumin and epinephrine, which may be useful for the design of effective drug candidates for the treatment of CTE.

Deciphering the Role of ATP on PHF6 Aggregation

The aggregation of Tau protein, which are involved in Alzheimer's disease, are associated with the self-assembly of the hexapeptide sequence, paired helical filament 6 (PHF6) from repeat 3 of Tau. In order to treat Alzheimer's disease and other such tauopathies, one of the therapeutic strategies is to inhibit aggregation of Tau and its nucleating segments. Therefore, we have studied the effect of adenosine triphosphate (ATP) on the aggregation of PHF6. ATP has, interestingly, demonstrated its ability to inhibit and dissolve protein aggregates. Using classical molecular dynamics simulations, we observed that the hydrophobic core of PHF6 segment displays extended β-sheet conformation, which stabilizes PHF6 aggregates. However, the distribution of ATP around the vicinity of the peptides enables PHF6 to remain discrete and attain random coil conformers. The interpeptide interactions are substituted by PHF6-ATP interactions through hydrogen bonding and hydrophobic interactions (including π-π stacking). Furthermore, the adenosine moiety of ATP contributes more than the triphosphate chain toward PHF6-ATP interaction. Ultimately, this work establishes the inhibitory activity of ATP against Tau aggregation; hence, the therapeutic effect of ATP should be explored further in regard to the effective treatment of Alzheimer's disease.

Destructive Mechanism of Aβ1-42 Protofibril by Norepinephrine revealed via Molecular Dynamics Simulations

Amyloid-β (Aβ) fibrillary plaques represent the main hallmarks of Alzheimer’s disease (AD), in addition to tau neurofibrillary tangles. Disrupting early-formed Aβ protofibril is considered as one of the primary therapeutic...

A phase II study repurposing atomoxetine for neuroprotection in mild cognitive impairment

The locus coeruleus (LC) is the initial site of Alzheimer's disease neuropathology, with hyperphosphorylated Tau appearing in early adulthood followed by neurodegeneration in dementia. LC dysfunction contributes to Alzheimer's pathobiology in experimental models, which can be rescued by increasing norepinephrine (NE) transmission. To test NE augmentation as a potential disease-modifying therapy, we performed a biomarker-driven phase II trial of atomoxetine, a clinically-approved NE transporter inhibitor, in subjects with mild cognitive impairment due to Alzheimer's disease. The design was a single-center, 12-month double-blind crossover trial. Thirty-nine participants with mild cognitive impairment (MCI) and biomarker evidence of Alzheimer's disease were randomized to atomoxetine or placebo treatment. Assessments were collected at baseline, 6- (crossover) and 12-months (completer). Target engagement was assessed by CSF and plasma measures of NE and metabolites. Prespecified primary outcomes were CSF levels of IL1α and Thymus-Expressed Chemokine. Secondary/exploratory outcomes included clinical measures, CSF analyses of Aβ42, Tau, and pTau181, mass spectrometry proteomics, and immune-based targeted inflammation-related cytokines, as well as brain imaging with MRI and FDG-PET. Baseline demographic and clinical measures were similar across trial arms. Dropout rates were 5.1% for atomoxetine and 2.7% for placebo, with no significant differences in adverse events. Atomoxetine robustly increased plasma and CSF NE levels. IL-1α and Thymus-Expressed Chemokine were not measurable in most samples. There were no significant treatment effects on cognition and clinical outcomes, as expected given the short trial duration. Atomoxetine was associated with a significant reduction in CSF Tau and pTau181 compared to placebo, but not associated with change in Aβ42. Atomoxetine treatment also significantly altered CSF abundances of protein panels linked to brain pathophysiologies, including synaptic, metabolism, and glial immunity, as well as inflammation-related CDCP1, CD244, TWEAK, and OPG proteins. Treatment was also associated with significantly increased BDNF and reduced triglycerides in plasma. Resting state fMRI showed significantly increased inter-network connectivity due to atomoxetine between the insula and the hippocampus. FDG-PET showed atomoxetine-associated increased uptake in hippocampus, parahippocampal gyrus, middle temporal pole, inferior temporal gyrus, and fusiform gyrus, with carry-over effects six months after treatment. In summary, atomoxetine treatment was safe, well tolerated, and achieved target engagement in prodromal Alzheimer's disease. Atomoxetine significantly reduced CSF Tau and pTau, normalized CSF protein biomarker panels linked to synaptic function, brain metabolism, and glial immunity, and increased brain activity and metabolism in key temporal lobe circuits. Further study of atomoxetine is warranted for repurposing the drug to slow Alzheimer's disease progression.

Alzheimer's Disease: Current Perspectives and Advances in Physiological Modeling

Though Alzheimer's disease (AD) is the most common cause of dementia, complete disease-modifying treatments are yet to be fully attained. Until recently, transgenic mice constituted most in vitro model systems of AD used for preclinical drug screening; however, these models have so far failed to adequately replicate the disease's pathophysiology. However, the generation of humanized APOE4 mouse models has led to key discoveries. Recent advances in stem cell differentiation techniques and the development of induced pluripotent stem cells (iPSCs) have facilitated the development of novel in vitro devices. These "microphysiological" systems-in vitro human cell culture systems designed to replicate in vivo physiology-employ varying levels of biomimicry and engineering control. Spheroid-based organoids, 3D cell culture systems, and microfluidic devices or a combination of these have the potential to replicate AD pathophysiology and pathogenesis in vitro and thus serve as both tools for testing therapeutics and models for experimental manipulation.

Mechanisms of melatonin binding and destabilizing the protofilament and filament of tau R3-R4 domains revealed by molecular dynamics simulation

The accumulation of β-amyloid (Aβ) and tau protein is considered to be an important pathological characteristic of Alzheimer's disease (AD). Failure of medicine targeting Aβ has drawn more attention to the influence of tau protein and its fibrillization on neurodegeneration. Increasing evidence shows that melatonin (Mel) can effectively inhibit the formation of tau fibrils and disassemble preformed tau fibrils. However, the underlying mechanism is poorly understood. In this work, we investigated the kinetics of melatonin binding and destabilizing the tetrameric protofilament and octameric filament of tau R3-R4 domains by performing microsecond all-atom molecular dynamics simulations. Our results show that Mel is able to disrupt the C-shaped structure of the tau protofilament and filament, and destabilizes the association between N- and C-termini. Mel predominantly binds to β1 and β6-β8 regions and favors contact with the elongation surface, which is dominantly driven by hydrogen bonding interactions and facilitated by other interactions. The strong π-π stacking interaction of Mel with Y310 impedes the intramolecular CH-π interaction between I308 and Y310, and the cation-π interaction of Mel with R379 interferes with the formation of the D348-R379 salt bridge. Moreover, Mel occupies the protofilament surface in the tetrameric protofilament and prevents the formation of intermolecular hydrogen bonds between residues K331 and Q336 in the octameric filament. Our work provides molecular insights into Mel hindering tau fibrillization or destabilizing the protofilament and filament, and the revealed inhibitory mechanisms provide useful clues for the design of efficient anti-amyloid agents.

Enhancing the binding of the β-sheet breaker peptide LPFFD to the amyloid-β fibrils by aromatic modifications: A molecular dynamics simulation study

Alzheimer's is a fatal neurodegenerative disease for which there is no cure at present. The disease is characterized by the presence of plaques in the brains of a patient, which are composed mainly of aggregates of the amyloid-β peptide in the form of β-sheet fibrils. Here, we investigated the possibility of exploiting the superior binding ability of aromatic amino acids to a particular model of the amyloid-β fibrils. which is a difficult target for drug design. The β-sheet breaker peptide LPFFD was modified with aromatic amino acids and its binding to these fibrils was studied. We found that the orientation and the electrostatic complementarity of the modified peptide with respect to the fibrils played a crucial role in determining whether its binding was improved by the aromatic amino acids. The modified LPFFD peptides were able to bind to those fibril residues. which are important in the aggregation of amyloid-β peptides and thus can potentially inhibit the further aggregation of the amyloid-beta peptides by blocking their interactions. We found that the tryptophan modified LPFFD peptides had the best binding affinities. In most cases, the aromatic amino acids in the N-terminus of the modified peptides made more contacts with the fibrils than those in the C-terminus. We also found that increasing the aromatic content did not significantly improve the binding of the LPFFD peptide to the fibrils. Our study can serve as a basis for the design of novel peptide-based drugs for Alzheimer's disease in which aromatic interactions play an important role.