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

The 3-(3-oxoisoindolin-1-yl)pentane-2,4-dione (ISOAC1) as a new molecule able to inhibit Amyloid β aggregation and neurotoxicity

Amyloid β 1-42 (Aβ1-42) protein aggregation is considered one of the main triggers of Alzheimer's disease (AD). In this study, we examined the in vitro anti-amyloidogenic activity of the isoindolinone derivative 3-(3-oxoisoindolin-1-yl)pentane-2,4-dione (ISOAC1) and its neuroprotective potential against the Aβ1-42 toxicity. By performing the Thioflavin T fluorescence assay, Western blotting analyses, and Circular Dichroism experiments, we found that ISOAC1 was able to reduce the Aβ1-42 aggregation and conformational transition towards β-sheet structures. Interestingly, in silico studies revealed that ISOAC1 was able to bind to both the monomer and a pentameric protofibril of Aβ1-42, establishing a hydrophobic interaction with the PHE19 residue of the Aβ1-42 KLVFF motif. In vitro analyses on primary cortical neurons showed that ISOAC1 counteracted the increase of intracellular Ca2+ levels and decreased the Aβ1-42-induced toxicity, in terms of mitochondrial activity reduction and increase of reactive oxygen species production. In addition, confocal microscopy analyses showed that ISOAC1 was able to reduce the Aβ1-42 intraneuronal accumulation. Collectively, our results clearly show that ISOAC1 exerts a neuroprotective effect by reducing the Aβ1-42 aggregation and toxicity, hence emerging as a promising compound for the development of new Aβ-targeting therapeutic strategies for AD treatment.

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

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

Enhanced stability of a disaggregated Aβ fibril on removal of ligand inhibits refibrillation: An all atom Molecular Dynamics simulation study

The extraneuronally deposited senile plaques, composed of neurotoxic aggregates of Aβ fibril, define Alzheimer's disease (AD). Natural compounds have been tested for their destabilization potential on Aβ fibril, thereby curing AD. However, the resultant destabilized Aβ fibril, needs to be checked for its irreversibility to the native organized state after removal of the ligand. Herein, we assessed the stability of a destabilized fibril after the ligand (ellagic acid represented as REF) is removed from the complex. The study has been conducted via Molecular Dynamics (MD) simulation of 1 μs for both Aβ-Water (control) and Aβ-REF″ (test or REF removed) system. The increased value of RMSD, R_g, SASA, lower β-sheet content and reduced number of H-bonds explains enhanced destabilization observed in Aβ-REF″ system. The increased inter-chain distance demonstrates breaking of the residual contacts, testifying the drift of terminal chains from the pentamer. The increased SASA along with the ∆G_ps(polar solvation energy) accounts for the reduced interaction amongst residues, and more with solvent molecules, governing irreversibility to native state. The higher Gibb's free energy of the misaligned structure of Aβ-REF″ ensures irreversibility to the organized structure due to its inability to cross such high energy barrier. The observed stability of the disaggregated structure, despite ligand elimination, establishes the effectiveness of the destabilization technique as a promising therapeutic approach towards treating AD.

Consecutive Aromatic Residues Are Required for Improved Efficacy of β-Sheet Breakers

Alzheimer’s disease is a fatal neurodegenerative malady which up to very recently did not have approved therapy modifying its course. After controversial approval of aducanumab (monoclonal antibody clearing β-amyloid plaques) by FDA for use in very early stages of disease, possibly new avenue opened for the treatment of patients. In line with this approach is search for compounds blocking aggregation into amyloid oligomers subsequently forming fibrils or compounds helping in getting rid of plaques formed by β-amyloid fibrils. Here we present in silico work on 627 sixtapeptide β-sheet breakers (BSBs) containing consecutive three aromatic residues. Three of these BSBs caused dissociation of one or two β-amyloid chains from U-shaped β-amyloid protofibril model 2BEG after docking and subsequent molecular dynamics simulations. Thorough analysis of our results let us postulate that the first steps of binding these successful BSBs involve π–π interactions with stacked chains of F19 and later also with F20 (F3 and F4 in 2BEG model of protofibril). The consecutive location of aromatic residues in BSBs makes them more attractive for chains of stacked F3 and F4 within the 2BEG model. Spotted by us, BSBs may be prospective lead compounds for an anti-Alzheimer’s therapy.

Molecular mechanisms of amyloid disaggregation

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Importance of disaggregation mechanism and innate disaggregation in living systems.

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Different types and mechanism of disaggregation reported in literature.

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Structural details of the interactions and the disaggregation mechanisms.

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Amyloid disaggregation in protein aggregation disorders as a potential treatment.

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Proposed amyloid disaggregation mechanism of an ATP-independent chaperone (L-PGDS).

Introduction

Protein aggregation and deposition of uniformly arranged amyloid fibrils in the form of plaques or amorphous aggregates is characteristic of amyloid diseases. The accumulation and deposition of proteins result in toxicity and cause deleterious effects on affected individuals known as amyloidosis. There are about fifty different proteins and peptides involved in amyloidosis including neurodegenerative diseases and diseases affecting vital organs. Despite the strenuous effort to find a suitable treatment option for these amyloid disorders, very few compounds had made it to unsuccessful clinical trials. It has become a compelling challenge to understand and manage amyloidosis with the increased life expectancy and ageing population.

Objective

While most of the currently available literature and knowledge base focus on the amyloid inhibitory mechanism as a treatment option, it is equally important to organize and understand amyloid disaggregation strategies. Disaggregation strategies are important and crucial as they are present innately functional in many living systems and dissolution of preformed amyloids may provide a direct benefit in many pathological conditions. In this review, we have compiled the known amyloid disaggregation mechanism, interactions, and possibilities of using disaggregases as a treatment option for amyloidosis.

Methods

We have provided the structural details using protein-ligand docking models to visualize the interaction between these disaggregases with amyloid fibrils and their respective proposed amyloid disaggregation mechanisms.

Results

After reviewing and comparing the different amyloid disaggregase systems and their proposed mechanisms, we presented two different hypotheses for ATP independent disaggregases using L-PGDS as a model.

Conclusion

Finally, we have highlighted the importance of understanding the underlying disaggregation mechanisms used by these chaperones and organic compounds before the implementation of these disaggregases as a potential treatment option for amyloidosis.

Destabilization potential of beta sheet breaker peptides on Abeta fibril structure: an insight from molecular dynamics simulation study

Alzheimer's disease is characterized by amyloid-β aggregation. Currently, all the approved medications are to treat the symptoms but there is no clinically approved treatment for the cure or to prevent the progression of Alzheimer's disease (AD). Earlier reports suggest the use of small molecules and peptides to target and destabilize the amyloid fibril. The use of Beta Sheet Breaker (BSB) peptides seems to be a promising and attractive therapeutic approach as it can strongly bind and destabilize the preformed amyloid fibril. There are experimental studies describing the destabilization role of various BSB peptides, but the exact mechanism remains elusive. In the current work, an attempt is made to study the destabilization mechanism of different BSB peptides on preformed amyloid protofibril using molecular docking and simulations. Molecular docking of eight different BSB peptides of varying length (5-mer to 10-mer) on the Abeta protofibril was done. Docking was followed by multiple sets of molecular simulations for the Abeta protofibril–BSB peptide complex for each of the top ranked poses of the eight BSB peptides. As a control, multiple sets of simulations for the Abeta protofibril (APO) were also carried out. An increase in the RMSD, decrease in the number of interchain hydrogen bonds, destabilization of important salt bridge interactions (D23–K28), and destabilization of interchain hydrophobic interactions suggested the destabilization of Abeta protofibril by BSB peptides. The MM-GBSA free energy of binding for each of the BSB peptides was calculated to measure the binding affinity of BSB peptides to Abeta protofibril. Further residue wise contribution of free energy of binding was also calculated. The study showed that 7-mer peptides tend to bind strongly to Abeta protofibril as compared to other BSB peptides. The KKLVFFA peptide showed better destabilization potential as compared to the other BSB peptides. The details about the destabilization mechanism of BSB peptides will help in the design of other peptides for the therapeutic intervention for AD.

Destabilzation of Abeta protofibril by Beta Sheet Breaker (BSB) peptides.

Fucosterol from Sargassum horridum as an amyloid-beta (Aβ1-42) aggregation inhibitor: in vitro and in silico studies

The number of patients diagnosed with Alzheimer's disease (AD) increases each year, and there are currently few treatment strategies to decrease the symptoms of AD; furthermore, these strategies are not sufficient to reduce memory loss in AD patients. In this work, in vitro and in silico studies were performed to evaluate the effects of fucosterol, which was extracted from an algal source and characterized by liquid chromatography-mass spectra (LC-MS), as an inhibitor of Aβ1-42 aggregation. Experimental studies, including protein gel electrophoresis, atomic force microscopy and fluorescence studies with thioflavin T (ThT), highlighted that fucosterol can decrease oligomer formation more than galantamine, which was used as a positive control. Docking and molecular dynamics simulations coupled with an MMGBSA approach showed that fucosterol is capable of recognizing the hydrophobic regions of monomeric Aβ1-42, suggesting that fucosterol could affect amyloid-beta (Aβ1-42) aggregation by preventing the formation of oligomers, preventing the development of AD.Communicated by Ramaswamy H. Sarma.

Probing the fibrillation of lysozyme by nanoscale-infrared spectroscopy

Amyloid fibrillation is the root cause of several neuro as well as non-neurological disorders. Understanding the molecular basis of amyloid aggregate formation is crucial for deciphering various neurodegenerative diseases. In our study, we have examined the lysozyme fibrillation process using nano-infrared spectroscopy (nanoIR). NanoIR enabled us to investigate both structural and chemical characteristics of lysozyme fibrillar species concurrently. The spectroscopic results indicate that lysozyme transformed into a fibrillar structure having mainly parallel β-sheets, with almost no antiparallel β-sheets. Features such as protein stiffness have a good correlation with obtained secondary structural information showing the state of the protein within the fibrillation state. The structural and chemical details were compared with transmission electron microscopy (TEM) and circular dichroism (CD). We have utilized nanoIR and measured infrared spectra to characterize lysozyme amyloid fibril structures in terms of morphology, molecular structure, secondary structure content, stability, and size of the cross-β core. We have shown that the use of nanoIR can complement other biophysical studies to analyze the aggregation process and is particularly useful for studying proteins involved in aggregation to help in designing molecules against amyloid aggregation. Specifically, the nanoIR spectra afford higher resolution information and a characteristic fingerprint for determining states of aggregation.Communicated by Ramaswamy H. Sarma.

Atomic-scale modeling of the effect of lipid peroxidation on the permeability of reactive species

Biomembranes and lipid systems are rich in unsaturated lipid components and are subject to photo-induced lipid peroxidation. The peroxidized lipid products in cellular systems are known to affect the structural organization and function of the biomembrane. We employed molecular dynamics simulations to study the effects of phospholipid peroxidation on membrane properties and the permeability of different reactive species. The results suggest that when the lipids are peroxidized, the peroxide group moves toward the membrane surface, which causes the membrane system to expand laterally and increase in area. The permeability profile revealed that nitrogen species can easily permeate through the native and peroxidized system in comparison to oxygen species, suggesting its importance in plasma-based treatment. Thus, by breaching the energy barrier with lower energy, they can traverse the cell membrane and induce oxidative stress, which leads to apoptosis.Communicated by Ramaswamy H. Sarma.