Identification of a Novel Multifunctional Ligand for Simultaneous Inhibition of Amyloid-Beta (Aβ42) and Chelation of Zinc Metal Ion

A Molecular Integrative Study on the Inhibitory Effects of WRR and ERW on Amyloid β Peptide (1-42) Polymerization and Cell Toxicity

Alzheimer's disease (AD) is a neurodegenerative disease and the main pathological characteristic of AD is the deposition of Aβ42 in the brain. Inhibition of Aβ42 polymerization is one of the important research directions. Due to the pathological complexity of Alzheimer's disease, studies on Aβ42 polymerization inhibitors have not made significant progress worldwide. Using an independently constructed structure database of oligopeptides, in this study, molecular docking, umbrella sampling analysis of free energy, ThT fluorescence detection of Aβ42 polymerization, transmission electron microscopy, and flow cytometry detection of reactive oxygen species (ROS) and apoptosis were performed to screen tripeptides and pentapeptides that inhibit polymerization. It was found that two tripeptides, i.e., WRR and ERW, bind stably to the core of Aβ42 polymerization in the molecular dynamics analysis, and they significantly inhibited the aggregation of Aβ42 and reduced their cell toxicity in vitro.

Peptide-Based Materials That Exploit Metal Coordination

Metal-ion coordination has been widely exploited to control the supramolecular behavior of a variety of building blocks into functional materials. In particular, peptides offer great chemical diversity for metal-binding modes, combined with inherent biocompatibility and biodegradability that make them attractive especially for medicine, sensing, and environmental remediation. The focus of this review is the last 5 years' progress in this exciting field to conclude with an overview of the future directions that this research area is currently undertaking.

Design and Study of In Silico Binding Dynamics of Certain Isoxazole Bearing Leads Against Aβ-42 and BACE-1 Loop in Protein Fibrillation

Aims:

Design isoxazole bearing leads as dual inhibitors against Amyloid β and BACE-1 loop in protein fibrillation.

Background:

Protein fibrillation is one of the key reasons for several diseases, namely Alzheimer’s, Parkinson’s, and many others. One of the key strategies of preventing protein fibrillation is destabilizing the protein fibrils themselves or inhibiting the amyloid fibril-forming pathway in the initial stage.

Introduction:

Attempts have been taken to design newer leads to inhibit protein fibrillation by targeting the β-amyloidogenesis pathway in the brain. To exploit interfenestration between Amyloid β -42 protein and BACE-1 (β-site amyloid precursor protein cleaving enzyme) for amyloidogenesis, studies are undertaken to design dual inhibitors against the same.

Method:

In vitro binding interactions were found using docking, de novo ligand design, and MD simulation study.

Results:

Three compounds bearing an isoxazole heterocyclic nucleus were designed which could successfully bind to the hydrophobic raft and salt bridge residues Asp 23-Lys-26 of Amyloid β, destabilizing the growing fibril. Additionally, one of our candidate compounds exhibited force of interaction with Thr232 at the S3 pocket of BACE-1, interacted with key residue Asp228, Tyr71, and Thr72 of the β-hairpin flap and hydrogen bonding with Gly11 at loop 10s.

Conclusion:

Protein flexibility dynamics of the Aβ-42 protein revealed that there is a considerable conformational change of the same with or without ligand binding. The lower RMSF of the bound region and reprogramming residual contacts within the Aβ-42 protein suggested successful binding of the ligand with the protein, lowering the access for further β-β dimerization.

Semax, a Synthetic Regulatory Peptide, Affects Copper-Induced Abeta Aggregation and Amyloid Formation in Artificial Membrane Models

Alzheimer’s disease, the most common form of dementia, is characterized by the aggregation of amyloid beta protein (Aβ). The aggregation and toxicity of Aβ are strongly modulated by metal ions and phospholipidic membranes. In particular, Cu²⁺ ions play a pivotal role in modulating Aβ aggregation. Although in the last decades several natural or synthetic compounds were evaluated as candidate drugs, to date, no treatments are available for the pathology. Multifunctional compounds able to both inhibit fibrillogenesis, and in particular the formation of oligomeric species, and prevent the formation of the Aβ:Cu²⁺ complex are of particular interest. Here we tested the anti-aggregating properties of a heptapeptide, Semax, an ACTH-like peptide, which is known to form a stable complex with Cu²⁺ ions and has been proven to have neuroprotective and nootropic effects. We demonstrated through a combination of spectrofluorometric, calorimetric, and MTT assays that Semax not only is able to prevent the formation of Aβ:Cu²⁺ complexes but also has anti-aggregating and protective properties especially in the presence of Cu²⁺. The results suggest that Semax inhibits fiber formation by interfering with the fibrillogenesis of Aβ:Cu²⁺ complexes.

Novel strategies for the fight of Alzheimer's disease targeting amyloid-β protein

Alzheimer's disease (AD), which is recognised as a devastating neurodegenerative disease throughout the world and lack of effective treatments, is a growing concern in modern society with a growing population of elderly patients. A growing number of studies reveal that abnormal accumulation and deposition of Aβ is responsible for AD. Inspired by this, strategies for the treatment of AD targeting-Aβ clearance have been discussed for a long period, exploring new drugs which is capable of destroying soluble Aβ oligomers and unsolvable Aβ aggregates. In this paper, results of recent clinical trials on several anti-amyloid-β drugs are presented and several emerging anti-amyloid AD therapies based on recent studies are reviewed. Furthermore, some of the current challenges and novel strategies to prevent AD are addressed. Herein, this review focuses on current pharmacotherapy of AD targeting-Aβ and intends to design a promising therapeutic agent for AD treatment.

Tau/Aβ chimera peptides: A Thioflavin-T and MALDI-TOF study of Aβ amyloidosis in the presence of Cu(II) or Zn(II) ions and total lipid brain extract (TLBE) vesicles

Currently, Alzheimer's Disease (AD) is a complex neurodegenerative condition, with limited therapeutic options. Several factors, like Amyloid β (Aβ) aggregation, tau protein hyperphosphorylation, bio-metals dyshomeostasis and oxidative stress contribute to AD pathogenesis. These pathogenic processes might occur in the aqueous phase but also on neuronal membranes. Thus, investigating the connection between Aβ and biomembranes, becomes important for unveiling the molecular mechanism underlying Aβ amyloidosis as a critical event in AD pathology. In this work, the interaction of two peptides, made up with hybrid sequences from Tau protein 9-16 (EVMEDHAG) or 26-33 (QGGYTMHQ) N-terminal domain and Aβ_16-20 (KLVFF) hydrophobic region, with full length Aβ40 or Aβ42 peptides is reported. The studied "chimera" peptides Ac-EVMEDHAGKLVFF-NH₂ (τ_9-16-KL) and Ac-QGGYTMHQKLVFF-NH₂ (τ_26-33-KL) are endowed with Aβ recognition and metal ion interaction capabilities provided by the tau or Aβ sequences, respectively. These peptides were characterized in previous study along with their metal dependent interaction and amyloidogenesis, either in the presence or absence of metal ion and artificial membranes made up with Total Lipid Brain Extract (TLBE) components, (Sciacca et al., 2020). In the present paper, the ability of the two peptides to inhibit Aβ aggregation is studied using composite experimental conditions including aqueous solution, the presence of metal ions (Cu or Zn), the presence of lipid vesicles mimicking neuronal membranes as well as the co-presence of metals and TLBE artificial membranes. We used Thioflavine-T (ThT) fluorescence or MALDI-TOF spectrometry analysis of Aβ limited proteolysis to respectively monitor the Aβ aggregation kinetic or validation of the Aβ interacting regions. We demonstrate that τ_9-16-KL and τ_26-33-KL peptides differently affect Aβ aggregation kinetics, with the tau sequence playing a crucial role. The results are discussed in terms of chimera's peptides hydrophobicity and electrostatic driven interactions at the aqueous/membrane interface.

Evaluating the Multifunctionality of a New Modulator of Zinc-Induced Aβ Aggregation Using a Novel Computational Approach

The high concentration of zinc metal ions in Aβ aggregations is one of the most cited hallmarks of Alzheimer's disease (AD), and several substantial pieces of evidence emphasize the key role of zinc metal ions in the pathogenesis of AD. In this study, while designing a multifunctional peptide for simultaneous targeting Aβ aggregation and chelating the zinc metal ion, a novel and comprehensive approach is introduced for evaluating the multifunctionality of a multifunctional drugs based on computational methods. The multifunctional peptide consists of inhibitor and chelator domains, which are included in the C-terminal hydrophobic region of Aβ, and the first four amino acids of human albumin. The ability of the multifunctional peptide in zinc ion chelation has been investigated using molecular dynamics (MD) simulations of the peptide-zinc interaction for 300 ns, and Bennett's acceptance ratio (BAR) method has been used to accurately calculate the chelation free energy. Data analysis demonstrates that the peptide chelating domain can be stably linked to the zinc ion. Besides, the introduced method used for evaluating chelation and calculating the free energy of peptide binding to zinc ions was successfully validated by comparison with previous experimental and theoretical published data. The results indicate that the multifunctional peptide, coordinating with the zinc metal ion, can be effective in Aβ inhibition by preserving the native helical structure of the Aβ₄₂ monomer as well as disrupting the β-sheet structure of Aβ₄₂ aggregates. Detailed assessments of the Aβ₄₂-peptide interactions elucidate that the inhibition of Aβ is achieved by considerable hydrophobic interactions and hydrogen bonding between the multifunctional peptide and the hydrophobic Aβ regions, along with interfering in stable bridges formed inside the Aβ aggregate.

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

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

Impact of Mutations on the Conformational Transition from α-Helix to β-Sheet Structures in Arctic-Type Aβ40: Insights from Molecular Dynamics Simulations

The amyloid-β (Aβ) protein aggregation into toxic oligomers and fibrils has been recognized as a key player in the pathogenesis of Alzheimer's disease. Recent experiments reported that a double alanine mutation (L17A/F19A) in the central hydrophobic core (CHC) region of [G22]Aβ₄₀ (familial Arctic mutation) diminished the self-assembly propensity of [G22]Aβ₄₀. However, the molecular mechanism behind the decreased aggregation tendency of [A17/A19/G22]Aβ₄₀ is not well understood. Herein, we carried out molecular dynamics simulations to elucidate the structure and dynamics of [G22]Aβ₄₀ and [A17/A19/G22]Aβ₄₀. The results for the secondary structure analysis reveal a significantly increased amount of the helical content in the CHC and C-terminal region of [A17/A19/G22]Aβ₄₀ as compared to [G22]Aβ₄₀. The bending free-energy analysis of D23-K28 salt bridge suggests that the double alanine mutation in the CHC region of [G22]Aβ₄₀ has the potential to reduce the fibril formation rate by 0.57 times of [G22]Aβ₄₀. Unlike [G22]Aβ₄₀, [A17/A19/G22]Aβ₄₀ largely sampled helical conformation, as determined by the minimum energy conformations extracted from the free-energy landscape. The present study provided atomic level details into the experimentally observed diminished aggregation tendency of [A17/A19/G22]Aβ₄₀ as compared to [G22]Aβ₄₀.

PASylation Enhances the Stability, Potency, and Plasma Half-Life of Interferon α-2a: A Molecular Dynamics Simulation

In this study, the effectiveness of PASylation in enhancing the potency and plasma half-life of pharmaceutical proteins has been accredited as an alternative technique to the conventional methods such as PEGylation. Proline, alanine, and serine (PAS) chain has shown some advantages including biodegradability improvement and plasma half-life enhancement while lacking immunogenicity or toxicity. Although some experimental studies have been performed to find the mechanism behind PASylation, the detailed mechanism of PAS effects on the pharmaceutical proteins has remained obscure, especially at the molecular level. In this study, the interaction of interferon α-2a (IFN) and PAS chain is investigated using molecular dynamics simulation method. Several important parameters including secondary structure, root-mean-square distance, and solvent accessible surface area to investigate the stability, bioavailability, and bioactivity of the PASylated protein are studied. The results demonstrate that IFN conformation is not affected critically through PASylation while it results in improvement of the protein stability and bioactivity. Therefore, PASylation can be considered as a proper biological alternative technique to increase the plasma half-life of the biopharmaceutical proteins through enlarging apparent volume. The proposed simulation represents a computational approach that would provide a basis for the study of PASylated pharmaceutical proteins for different future applications.

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

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