Inhibitor Discovery Targeting the Intermediate Structure of β-Amyloid Peptide on the Conformational Transition Pathway: Implications in the Aggregation Mechanism of β-Amyloid Peptide

Danshensu inhibits Aβ aggregation and neurotoxicity as one of the main prominent features of Alzheimer's disease

It has been found that the main cause of neurodegenerative proteinopathies, especially Alzheimer's disease (AD) is the formation of Aβ amyloid plaques, which can be regulated by application of potential small molecules. In the present study, we aimed to investigate the inhibitory effect of danshensu on Aβ(1-42) aggregation and relevant apoptotic pathway in neurons. A broad range of spectroscopic, theoretical, and cellular assays were done to investigate the anti-amyloidogenic characteristics of danshensu. It was found that danshensu triggers its inhibitory effect against Aβ(1-42) aggregation through modulation of hydrophobic patches as well as structural and morphological changes through a stacking interaction. Furthermore, it was observed that incubation of Aβ(1-42) samples with danshensu during aggregation process recovered the cell viability and mitigated the expression of caspase-3 mRNA and protein as well caspase-3 activity deregulated by Aβ(1-42) amyloid fibrils alone. In general, obtained data showed that danshensu potentially inhibits Aβ(1-42) aggregation and associated proteinopathies through regulation of apoptotic pathway in a concentration-dependent manner. Therefore, danshensu may be used as a promising biomolecule against the Aβ aggregation and associated proteinopathies, which can be further analyzed in the future studies for the treatment of AD.

Bioinformatics analysis of adhesin-binding potential and ADME/Tox profile of anti-Helicobacter pylori peptides derived from wheat germ proteins

Anti-adhesive activity of wheat germ-derived peptides, which is considered as one of the promising strategies for preventing Helicobacter pylori infection, was investigated. The underlying mechanism of anti-adhesive action was due to peptides acting as receptor analogues and binding to H. pylori adhesin proteins. However, there is lack of information on the nature and strength of this molecular interaction as well as the participating species and drug-likeness of the food-derived bioactive peptides. In this study, the biostability and ADME/Tox (absorption, distribution, metabolism, excretion and toxicity) profile of the anti-adhesive peptides were analyzed using bioinformatic tools, and their binding potential to H. pylori's adhesins estimated by molecular docking. Binding is facilitated by mostly hydrogen bonding and hydrophobic interaction occurring in the active site of the adhesin proteins with affinities ranging from -6.0 to -7.4 and -6.0 to -7.8 kcal/mol for BabA and SabA, respectively. The results indicate highly possible binding capabilities of the peptides to adhesin proteins. Out of 16 peptides studied, 14 bound in the vicinity of the active site of BabA and SabA whereas two different peptides demonstrated allosteric binding. The most hydrophobic peptide, P210 showed strong binding affinity for both BabA and SabA and, therefore, predicted to be the most promising peptide for further development in the prevention, management and treatment of H. pylori infection. The selected peptides were shown to be non-toxic, and to have high potential of localized effect of interfering with bacterial adherence. This work provides insights into the anti-adhesive mechanism of peptides and new evidence demonstrating bioactive peptides as promising nutraceutical candidates for preventing H. pylori infection.

Synthesis, Characterization, and Cytotoxicity of Morpholine-Containing Ruthenium(II) p-Cymene Complexes

Morpholine motif is an important pharmacophore and, depending on the molecular design, may localize in cellular acidic vesicles. To understand the importance of the presence of pendant morpholine in a metal complex, six bidentate N,O-donor ligands with or without a pendant morpholine unit and their corresponding ruthenium(II) p-cymene complexes (1-6) are synthesized, purified, and structurally characterized by various analytical methods including X-ray diffraction. Complexes 2-4 crystallized in the P2₁/c space group, whereas 5 and 6 crystallized in the P1̅ space group. The solution stability studies using ¹H NMR support instantaneous hydrolysis of the native complexes to form monoaquated species in a solution of 3:7 (v/v) dimethyl sulfoxide-d₆ and 20 mM phosphate buffer (pH* 7.4, containing 4 mM NaCl). The monoaquated complexes are stable for at least up to 24 h. The complexes display excellent in vitro antiproliferative activity (IC₅₀ ca. 1-14 μM) in various cancer cell lines, viz., MDA-MB-231, MiaPaCa2, and Hep-G2. The presence of the pendant morpholine does not improve the dose efficacy, but rather, with 2-[[(2,6-dimethylphenyl)imino]methyl]phenol (HL1) and its pendant morpholine analogue (HL3) giving complexes 1 and 3, respectively, the antiproliferative activity was poorer with 3. MDA-MB-231 cells treated with the complexes show that the acidic vesicles remain acidic, but the population of acidic vesicles increases or decreases with time of exposure, as observed from the dispersed red puncta, depending on the complex used. The presence of the 2,6-disubstituted aniline and the naphthyl group seems to improve the antiproliferative dose. The complex treated MDA-MB-231 cells show that cathepsin D, which is otherwise present in the cytosolic lysosomes, translocates to the nucleus as a result of exposure to the complexes. Irrespective of the presence of a morpholine motif, the complexes do not activate caspase-3 to induce apoptosis and seem to favor the necrotic pathway of cell killing.

Mamma Mia, P-glycoprotein binds again

The levels of amyloid peptides in the brain are regulated by a clearance pathway from neurons to the blood-brain barrier. The first step is thought to involve diffusion from the plasma membrane to the interstitium. However, amyloid peptides are hydrophobic and avidly intercalate within membranes. The ABC transporter P-glycoprotein is implicated in the clearance of amyloid peptides across the blood-brain, but its role at neurons is undetermined. We here propose that P-glycoprotein mediates 'exit' of amyloid peptides from neurons. Indeed, amyloid peptides have physicochemical similarities to substrates of P-glycoprotein, but their larger size represents a conundrum. This review probes the plausibility of a mechanism for amyloid peptide transport by P-glycoprotein exploiting evolving biochemical and structural models.

Biological evaluation of naturally occurring bulbocodin D as a potential multi-target agent for Alzheimer's disease

In recent years, with the in-depth understanding of the pathogenesis of Alzheimer's disease (AD) and the development of advanced pharmacological technology, "multi-target" strategy has recently attracted the wide interest of scientists. The purpose of this study was to investigate the protective effect and mechanism of bulbocodin D for AD in vitro. In this study, we established the oxidative stress model of SH-SY5Y cells mediated by H₂O₂ and the inflammatory model of BV2 cells stimulated by LPS. Western blot was used to analysis the expression of mitochondrial apoptosis and inflammation related proteins. Moreover, predicted binding modes of bulbocodin D with AChE and GSK3β were performed by molecular docking analysis. We found that bulbocodin D could reduce cell apoptosis, reduce ROS production in SH-SY5Y cell, and inhibit the secretion of inflammatory cytokines in BV2 cell. Furthermore, western blot results showed that bulbocodin D could regulate mitochondrial apoptotic pathway and MAPKs pathway. In addition, bulbocodin D can reduce the aggregation of Aβ. We also found that bulbocodin D had a good inhibitory effect on AChE and GSK3β. In summary, bulbocodin D might be a potential multi-target agent for Alzheimer's disease.

Morpholine As a Scaffold in Medicinal Chemistry: An Update on Synthetic Strategies

Morpholine is a frequently used heterocycle in medicinal chemistry and a privileged structural component of bioactive molecules. This is mainly due to its contribution to a plethora of biological activities as well as to an improved pharmacokinetic profile of such bioactive molecules. The synthesis of morpholines is a subject of much study due to their biological and pharmacological importance, with the last such review being published in 2013. Here, an overview of the main approaches toward morpholine synthesis or functionalization is presented, emphasizing on novel work which has not been reviewed so far. This review is an update on synthetic strategies leading to easily accessible libraries of bioactives which are of interest for drug discovery projects.

Morpholine as a privileged structure: A review on the medicinal chemistry and pharmacological activity of morpholine containing bioactive molecules

Morpholine is a heterocycle featured in numerous approved and experimental drugs as well as bioactive molecules. It is often employed in the field of medicinal chemistry for its advantageous physicochemical, biological, and metabolic properties, as well as its facile synthetic routes. The morpholine ring is a versatile and readily accessible synthetic building block, it is easily introduced as an amine reagent or can be built according to a variety of available synthetic methodologies. This versatile scaffold, appropriately substituted, possesses a wide range of biological activities. There are many examples of molecular targets of morpholine bioactive in which the significant contribution of the morpholine moiety has been demonstrated; it is an integral component of the pharmacophore for certain enzyme active-site inhibitors whereas it bestows selective affinity for a wide range of receptors. A large body of in vivo studies has demonstrated morpholine's potential to not only increase potency but also provide compounds with desirable drug-like properties and improved pharamacokinetics. In this review we describe the medicinal chemistry/pharmacological activity of morpholine derivatives on various therapeutically related molecular targets, attempting to highlight the importance of the morpholine ring in drug design and development as well as to justify its classification as a privileged structure.

Hydrophobic Modification of Carboxyl-Terminated Polyamidoamine Dendrimer Surface Creates a Potent Inhibitor of Amyloid-β Fibrillation

Amyloid β-peptide (Aβ) fibrillogenesis is a major hallmark of Alzheimer's disease (AD); inhibition of Aβ fibrillation is thus considered as a promising strategy for AD prevention and treatment. Our group has previously proposed the hydrophobic binding-electrostatic repulsion (HyBER) hypothesis, which provides guidance for the design of new amyloid inhibitors. Inspired by the HyBER hypothesis, we have herein proposed to synthesize hydrophobic-modified generation 5 carboxyl-terminated polyamidoamine dendrimer, denoted as PAMP, to create a potent inhibitor with a negatively charged hydrophobic surface. Results indicate that the PAMP with a proper degree of phenyl substitution (30-42%) alters the conformation of Aβ₄₂ through both hydrophobic binding and electrostatic repulsive forces on its surface. With these well-balanced interactions, the inhibitor can even completely inhibit the formation of β-sheet structure of the peptide, accompanied by changes at the level of the fibrillary architecture. Moreover, the results also indicate that changes of Aβ₄₂ aggregation pathway influenced by the PAMP occur at the very early stage, so the PAMP can significantly avoid the formation of toxic intermediates of Aβ₄₂ aggregation.

Isotope-edited FTIR reveals distinct aggregation and structural behaviors of unmodified and pyroglutamylated amyloid β peptides

Amyloid β peptide (Aβ) is causatively associated with Alzheimer's disease (AD), and N-terminally truncated and pyroglutamylated Aβ peptides (AβpE) exert hypertoxic effect by an unknown mechanism. Recent evidence has identified the prefibrillar oligomers of Aβ, not the fibrils, as the prevalent cytotoxic species. Structural characterization of Aβ and AβpE oligomers is therefore important for better understanding of their toxic effect. Here we have used isotope-edited Fourier transform infrared (FTIR) spectroscopy to identify the conformational changes in Aβ(1-42) and AβpE(3-42) upon aggregation, individually and in 1 : 1 molar combination. During the first two hours of exposure to aqueous buffer, the peptides undergo transition from mostly α-helical to mostly β-sheet structure. Data on peptides (13)C,(15)N-labeled at K(16)L(17)V(18) or V(36)G(37)G(38)V(39) allowed construction of structural models for the monomer and early oligomers. The peptide monomer comprises a β-hairpin that involves residues upstream of the K(16)L(17)V(18) sequence and an N-terminal α-helix. The oligomers form by non-H-bonding interactions between the β-strands of neighboring β-hairpins, in lateral or staggered manner, with the strands running parallel or antiparallel. Relative α-helical and β-sheet propensities of Aβ(1-42) and AβpE(3-42) depend on the ionic strength of the buffer, emphasizing the importance of ionic interactions in Aβ peptide structure and aggregation. It is inferred that N-terminal modification of AβpE(3-42) affects the helix stability and thereby modulates β-sheet oligomer formation. The data thus provide new insight into the molecular mechanism of Aβ oligomerization by emphasizing the role of the N-terminal transient α-helical structure and by identifying structural constraints for molecular organization of the oligomers.

Applying high-performance computing in drug discovery and molecular simulation

In recent decades, high-performance computing (HPC) technologies and supercomputers in China have significantly advanced, resulting in remarkable achievements. Computational drug discovery and design, which is based on HPC and combines pharmaceutical chemistry and computational biology, has become a critical approach in drug research and development and is financially supported by the Chinese government. This approach has yielded a series of new algorithms in drug design, as well as new software and databases. This review mainly focuses on the application of HPC to the fields of drug discovery and molecular simulation at the Chinese Academy of Sciences, including virtual drug screening, molecular dynamics simulation, and protein folding. In addition, the potential future application of HPC in precision medicine is briefly discussed.

3,5-Diarylpyrazole Derivatives Obtained by Ammonolysis of the Total Flavonoids from Chrysanthemum indicum Extract Show Potential for the Treatment of Alzheimer's Disease

Four new 3,5-diarylpyrazole analogues (1-4) were isolated from an extract of the flowers of Chrysanthemun indicum using a combination of ammonolysis of the total flavonoid extract and an Aβ aggregation inhibitory activity guided purification procedure. All four compounds (1-4) showed moderate to potent activity against Aβ aggregation with EC50 values of 4.3, 15.8, 1.3, and 2.9 μM, respectively. Moreover, compound 3 showed low cytotoxicity and significant neuroprotective activity against Aβ-induced cytotoxicity in the SH-SY5Y cell line. This report is the first to show that 3,5-diarylpyrazole analogues can inhibit Aβ aggregation and exhibit neuroprotective activity with potential for the treatment of Alzheimer's disease. Taken together, the method presented here offers an alternative approach to yield bioactive compounds.

Role of membrane biophysics in Alzheimer's-related cell pathways

Cellular membrane alterations are commonly observed in many diseases, including Alzheimer's disease (AD). Membrane biophysical properties, such as membrane molecular order, membrane fluidity, organization of lipid rafts, and adhesion between membrane and cytoskeleton, play an important role in various cellular activities and functions. While membrane biophysics impacts a broad range of cellular pathways, this review addresses the role of membrane biophysics in amyloid-β peptide aggregation, Aβ-induced oxidative pathways, amyloid precursor protein processing, and cerebral endothelial functions in AD. Understanding the mechanism(s) underlying the effects of cell membrane properties on cellular processes should shed light on the development of new preventive and therapeutic strategies for this devastating disease.

Rational design of an orthosteric regulator of hIAPP aggregation

Compounds that can block hIAPP toxic oligomer but not fibril formation have been rationally designed based on the helix aggregation mechanism.

The mechanisms of flavonoids inhibiting conformational transition of amyloid-β42monomer: a comparative molecular dynamics simulation study

Flavonoids can bind Aβ₄₂to inhibit the aggregation of Aβ₄₂monomer.

Silymarin effect on amyloid-β plaque accumulation and gene expression of APP in an Alzheimer's disease rat model

Background

The deposition of amyloid peptides is associated with Alzheimer’s disease (AD). These amyloid peptides are derived from the amyloid protein precursor (APP). Silymarin, a standardized extract of milk thistle, which is currently used in liver diseases, may be effective in the inhibition of amyloid formation. However, its effect has not been assessed on APP expression.

Results

In this study, first, the effect of silymarin was examined on the passive avoidance learning in a rat model of AD. This model was induced by the intracerebroventricular injection of Aβ peptide (Aβ_1–42) in Wistar rats. Rats were treated with 70 and 140 mg/kgof the extract, once a day, for 4 weeks. Memory function that was evaluated in a shuttle-cage test, showed improvement upon administration of this extract. Brain amyloid plaques had also decreased upon administration of the extract. Furthermore, APP gene expression was compared in treated and untreated groups. The result showed that silymarin was able to suppress APP expression.

Conclusion

Our results are in accordance with the in vitro tests concerning the positive antiamyloidogenic property of the main component of silymarin, namely silibinin. We suggest that the beneficial effect of sylimarin in the AD model is related to its capacity to disaggregate amyloid plaques and to suppress APP expression. Considering the limited side effects of silymarin, this compound could be of use in AD therapy.

Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) were found to be widely associated with human diseases and may serve as potential drug design targets. However, drug design targeting IDPs is still in the very early stages. Progress in drug design is usually achieved using experimental screening; however, the structural disorder of IDPs makes it difficult to characterize their interaction with ligands using experiments alone. To better understand the structure of IDPs and their interactions with small molecule ligands, we performed extensive simulations on the c-Myc₃₇₀₋₄₀₉ peptide and its binding to a reported small molecule inhibitor, ligand 10074-A4. We found that the conformational space of the apo c-Myc₃₇₀₋₄₀₉ peptide was rather dispersed and that the conformations of the peptide were stabilized mainly by charge interactions and hydrogen bonds. Under the binding of the ligand, c-Myc₃₇₀₋₄₀₉ remained disordered. The ligand was found to bind to c-Myc₃₇₀₋₄₀₉ at different sites along the chain and behaved like a 'ligand cloud'. In contrast to ligand binding to more rigid target proteins that usually results in a dominant bound structure, ligand binding to IDPs may better be described as ligand clouds around protein clouds. Nevertheless, the binding of the ligand and a non-ligand to the c-Myc₃₇₀₋₄₀₉ target could be clearly distinguished. The present study provides insights that will help improve rational drug design that targets IDPs.

Microsecond molecular dynamics simulation of Aβ42 and identification of a novel dual inhibitor of Aβ42 aggregation and BACE1 activity

AIM

To study the conformational changes of Aβ42 and discover novel inhibitors of both Aβ42 aggregation and β-secretase (BACE1).

METHODS

A molecular dynamics (MD) simulation at a microsecond level was performed to explore stable conformations of Aβ42 monomer in aqueous solution. Subsequently, structure-based virtual screening was used to search for inhibitors of both Aβ42 aggregation and BACE1. Protein purification and in vitro activity assays were performed to validate the inhibition of the compounds identified via virtual screening.

RESULTS

The initial α-helical conformation of Aβ42, which was unstable in aqueous solution, turned into a β-sheet mixed with a coil structure through a transient and fully random coil. The conformation of Aβ42 mainly comprising β-sheets and coils structure was used for further virtual screening. Five compounds were identified as inhibitors for Aβ42 aggregation, and one of them, AE-848, was discovered to be a dual inhibitor of both Aβ42 aggregation and BACE1, with IC50 values of 36.95 μmol/L and 22.70 μmol/L, respectively.

CONCLUSION

A helical to β-sheet conformational change in Aβ42 occurred in a 1.8 microsecond MD simulation. The resulting β-sheet structure of the peptide is an appropriate conformation for the virtual screening of inhibitors against Aβ42 aggregation. Five compounds were identified as inhibitors of Aβ42 aggregation by in vitro activity assays. It was particularly interesting to discover a dual inhibitor that targets both Aβ42 aggregation and BACE1, the two crucial players in the pathogenesis of Alzheimer's disease.

Molecular dynamics simulations to investigate the aggregation behaviors of the Abeta(17-42) oligomers

The amyloid beta-peptides (Abetas) are the main protein components of amyloid deposits in Alzheimer's disease (AD). Detailed knowledge of the structure and assembly dynamics of Abeta is important for the development of properly targeted AD therapeutics. So far, the process of the monomeric Abeta assembling into oligomeric fibrils and the mechanism underlying the aggregation process remain unclear. In this study, several molecular dynamics simulations were conducted to investigate the aggregation behaviors of the Abeta(17-42) oligomers associated with various numbers of monomers (dimer, trimer, tetramer, and pentamer). Our results showed that the structural stability of the Abeta(17-42) oligomers increases with increasing the number of monomer. We further demonstrated that the native hydrophobic contacts are positive correlated with the beta-sheet contents, indicating that hydrophobic interaction plays an important role in maintaining the structural stability of the Abeta(17-42) oligomers, particularly for those associated with more monomers. Our results also showed that the stability of the C-terminal hydrophobic segment 2 (residues 30-42) is higher than that of the N-terminal hydrophobic segment 1 (residues 17-21), suggesting that hydrophobic segment 2 may act as the nucleation site for aggregation. We further identified that Met35 residue initiates the hydrophobic interactions and that the intermolecular contact pairs, Gly33-Gly33 and Gly37-Gly37, form a stable "molecular notch", which may mediate the packing of the beta-sheet involving many other hydrophobic residues during the early stage of amyloid-like fibril formation.

Isobavachalcone and bavachinin from Psoraleae Fructus modulate Aβ42 aggregation process through different mechanisms in vitro

Spontaneous aggregation of Aβ is a key factor in the development of Alzheimer's disease. In searching for Aβ aggregation inhibitors from traditional Chinese herbal medicines, we identified two active compounds from Psoraleae Fructus, namely isobavachalcone and bavachinin. We further demonstrated that the two compounds modulate Aβ42 aggregation process through different mechanisms. Isobavachalcone significantly inhibits both oligomerization and fibrillization of Aβ42, whereas bavachinin inhibits fibrillization and leads to off-pathway aggregation. Both of the compounds attenuated Aβ42-induced toxicity in a SH-SY5Y cell model. These findings may provide valuable information for new drug development and Alzheimer's therapy in the future.

Anti-aggregating effect of the naturally occurring dipeptide carnosine on aβ1-42 fibril formation

Carnosine is an endogenous dipeptide abundant in the central nervous system, where by acting as intracellular pH buffering molecule, Zn/Cu ion chelator, antioxidant and anti-crosslinking agent, it exerts a well-recognized multi-protective homeostatic function for neuronal and non-neuronal cells. Carnosine seems to counteract proteotoxicity and protein accumulation in neurodegenerative conditions, such as Alzheimer's Disease (AD). However, its direct impact on the dynamics of AD-related fibril formation remains uninvestigated. We considered the effects of carnosine on the formation of fibrils/aggregates of the amyloidogenic peptide fragment Aβ1-42, a major hallmark of AD injury. Atomic force microscopy and thioflavin T assays showed inhibition of Aβ1-42 fibrillogenesis in vitro and differences in the aggregation state of Aβ1-42 small pre-fibrillar structures (monomers and small oligomers) in the presence of carnosine. in silico molecular docking supported the experimental data, calculating possible conformational carnosine/Aβ1-42 interactions. Overall, our results suggest an effective role of carnosine against Aβ1-42 aggregation.

The role of molecular simulations in the development of inhibitors of amyloid β-peptide aggregation for the treatment of Alzheimer's disease

The pathogenic aggregation of the amyloid β-peptide (Aβ) is considered a hallmark of the progression of Alzheimer's disease, the leading cause of senile dementia in the elderly and one of the principal causes of death in the United States. In the absence of effective therapeutics, the incidence and economic burden associated with the disease are expected to rise dramatically in the coming decades. Targeting Aβ aggregation is an attractive therapeutic approach, though structural insights into the nature of Aβ aggregates from traditional experiments are elusive, making drug design difficult. Theoretical methods have been used for several years to augment experimental work and drive progress forward in Alzheimer's drug design. In this Review, we will describe how two common techniques, molecular docking and molecular dynamics simulations, are being applied in developing small molecules as effective therapeutics against monomeric, oligomeric, and fibrillated forms of Aβ. Recent successes and important limitations will be discussed, and we conclude by providing a perspective on the future of this field by citing recent examples of sophisticated approaches used to better characterize interactions of small molecules with Aβ and other amyloidogenic proteins.

Modulation of amyloid-β 1-42 structure and toxicity by proline-rich whey peptides

A proline-rich peptide product prepared from bovine whey protein that was enriched in several hydrophobic amino acids including proline (whey proline-rich peptide, wPRP) was shown to modulate the folding pathway of human amyloid beta peptide 1-42 (Aβ42) into oligomers. Concentration-dependent changes in ThT-binding to Ab42 by wPRP indicated suppression of oligomerisation, that was supported by Transmission Electron Microscopy. Suppression of β-sheet and specifically, anti-parallel β-sheet structures by wPRP was demonstrated by ATR-FTIR spectroscopy, where evidence for capacity of wPRP to dissociate pre-existing β-sheet structures in Aβ42 was also apparent. Suppression of anti-parallel β-sheets of oligomeric Aβ42 was associated with rescue of yeast and SH-SY5Y neuronal cells providing important evidence for the association between anti-parallel β-sheet structure and oligomer toxicity. It was proposed that the interaction of wPRP with Aβ42 interfered with the anti-parallel folding pathway of oligomeric Aβ42 and ultimately produced 'off-pathway' structures of lowered total β-sheet content, with attenuated cellular toxicity.

Treatment strategies targeting amyloid β-protein

With the advent of the key discovery in the mid-1980s that the amyloid β-protein (Aβ) is the core constituent of the amyloid plaque pathology found in Alzheimer disease (AD), an intensive effort has been underway to attempt to mitigate its role in the hope of treating the disease. This effort fully matured when it was clarified that the Aβ is a normal product of cleavage of the amyloid precursor protein, and well-defined proteases for this process were identified. Further therapeutic options have been developed around the concept of anti-Aβ aggregation inhibitors and the surprising finding that immunization with Aβ itself leads to reduction of pathology in animal models of the disease. Here we review the progress in this field toward the goal of targeting Aβ for treatment and prevention of AD and identify some of the major challenges for the future of this area of medicine.

Ordered self-assembly mechanism of a spherical oncoprotein oligomer triggered by zinc removal and stabilized by an intrinsically disordered domain

Background

Self-assembly is a common theme in proteins of unrelated sequences or functions. The human papillomavirus E7 oncoprotein is an extended dimer with an intrinsically disordered domain, that can form large spherical oligomers. These are the major species in the cytosol of HPV transformed and cancerous cells. E7 binds to a large number of targets, some of which lead to cell transformation. Thus, the assembly process not only is of biological relevance, but represents a model system to investigate a widely distributed mechanism.

Methodology/Principal Findings

Using various techniques, we monitored changes in secondary, tertiary and quaternary structure in a time course manner. By applying a robust kinetic model developed by Zlotnik, we determined the slow formation of a monomeric “Z-nucleus” after zinc removal, followed by an elongation phase consisting of sequential second-order events whereby one monomer is added at a time. This elongation process takes place at a strikingly slow overall average rate of one monomer added every 28 seconds at 20 µM protein concentration, strongly suggesting either a rearrangement of the growing complex after binding of each monomer or the existence of a “conformation editing” mechanism through which the monomer binds and releases until the appropriate conformation is adopted. The oligomerization determinant lies within its small 5 kDa C-terminal globular domain and, remarkably, the E7 N-terminal intrinsically disordered domain stabilizes the oligomer, preventing an insoluble amyloid route.

Conclusion

We described a controlled ordered mechanism with features in common with soluble amyloid precursors, chaperones, and other spherical oligomers, thus sharing determining factors for symmetry, size and shape. In addition, such a controlled and discrete polymerization reaction provides a valuable tool for nanotechnological applications. Finally, its increased immunogenicity related to its supramolecular structure is the basis for the development of a promising therapeutic vaccine candidate for treating HPV cancerous lesions.

Observation of molecular inhibition and binding structures of amyloid peptides

Unveiling interactions between labeling molecules and amyloid fibrils is essential to develop new detection methods for studying amyloid structures under various conditions. This review endeavours to reflect the progress in studying interactions between molecular inhibitors and amyloid peptides using a series of experimental approaches, such as X-ray diffraction, nuclear magnetic resonance, scanning probe microscopy, and electron microscopy. The revealed binding mechanisms of anti-amyloid drugs and target proteins could benefit the rational design of drugs for prevention or treatment of amyloidal diseases.

The synaptic protein neuroligin-1 interacts with the amyloid β-peptide. Is there a role in Alzheimer's disease?

Amyloid β-peptide (Aβ) is the main component of the amyloid plaques associated with Alzheimer's disease (AD). In the early steps of the disease soluble Aβ oligomers are produced. According to the current "amyloid hypothesis" these oligomers can accumulate over time, leading progressively to the loss of synaptic function and the cognitive failure characteristic of AD. To understand the role of oligomeric Aβ species in AD pathology, it is important to understand the mechanism by which Aβ oligomers are targeted to synaptic junction. We report here the interaction between Aβ with neuroligin-1 (NL-1), a postsynaptic cell-adhesion protein specific for excitatory synapses, which shares a high degree of similarity with acetylcholinesterase, the first synaptic protein described to interact with Aβ. Using intrinsic fluorescence and surface plasmon resonance, we found that Aβ binds to the extracellular domain of NL-1 with a K(d) in the nanomolar range. In the case of NL-2, a postsynaptic cell-adhesion protein specific for inhibitory synapses, just a very weak interaction with Aβ was observed. Aβ polymerization analysis-studied by thioflavin-T assay and electron microscopy-indicated that NL-1 stabilized Aβ aggregates in vitro. Moreover, NL-1 acts as a nucleating factor during the Aβ aggregation process, stimulating the formation of Aβ oligomers. Besides, immunoprecipitation assays confirm that Aβ oligomers interact with NL-1 but not with NL-2. In conclusion, our results show that NL-1 interacts with Aβ increasing the formation of Aβ oligomers, suggesting that this interaction could triggers the targeting of Aβ oligomer to the postsynaptic regions of excitatory synapses.

Impacts of membrane biophysics in Alzheimer's disease: from amyloid precursor protein processing to aβ Peptide-induced membrane changes

An increasing amount of evidence supports the notion that cytotoxic effects of amyloid-β peptide (Aβ), the main constituent of senile plaques in Alzheimer's disease (AD), are strongly associated with its ability to interact with membranes of neurons and other cerebral cells. Aβ is derived from amyloidogenic cleavage of amyloid precursor protein (AβPP) by β- and γ-secretase. In the nonamyloidogenic pathway, AβPP is cleaved by α-secretases. These two pathways compete with each other, and enhancing the non-amyloidogenic pathway has been suggested as a potential pharmacological approach for the treatment of AD. Since AβPP, α-, β-, and γ-secretases are membrane-associated proteins, AβPP processing and Aβ production can be affected by the membrane composition and properties. There is evidence that membrane composition and properties, in turn, play a critical role in Aβ cytotoxicity associated with its conformational changes and aggregation into oligomers and fibrils. Understanding the mechanisms leading to changes in a membrane's biophysical properties and how they affect AβPP processing and Aβ toxicity should prove to provide new therapeutic strategies for prevention and treatment of AD.

A nonhuman primate model of Alzheimer's disease generated by intracranial injection of amyloid-β42 and thiorphan

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive impairment and neuropathological changes, including the deposition of amyloid-beta (Aβ) peptide. Aged monkeys have proven to be invaluable in the study of AD, as their brains naturally develop amyloid plaques similar to those in AD brains. However, spontaneous development of AD-like pathologies in aged monkeys is time-consuming, often taking several years. Here, we created an experimentally induced AD model in middle-aged (16-17 years) rhesus monkeys by intracranial injection of Aβ42 and thiorphan, an inhibitor of neprilysin that is responsible for Aβ clearance. The working memory capacity of the monkeys in a delayed-response task was little affected following the delivery of Aβ42 and thiorphan. However, the administration of Aβ42 and thiorphan resulted in a significant intracellular accumulation of Aβ in the neurons of the basal ganglia, the cortex, and the hippocampus, accompanied by neuronal atrophy and loss. Moreover, immunohistochemistry revealed a degeneration of choline acetyltransferase-positive cholinergic neurons and an increase of glial fibrillary acidic protein-positive astrocytes. In conclusion, our data demonstrate a primate model of AD generated by combined infusion of Aβ42 and thiorphan, which duplicates a subset of neuropathological changes in AD brains, thereby having implications in the elucidation of this disease.

Destabilizing Alzheimer's Abeta(42) protofibrils with morin: mechanistic insights from molecular dynamics simulations

Alzheimer's disease is a progressive, neurodegenerative disorder that is the leading cause of senile dementia, afflicting millions of individuals worldwide. Since the identification of the amyloid beta-peptide (Abeta) as the principal toxic entity in the progression of Alzheimer's disease, numerous attempts have been made to reduce endogenous Abeta production and deposition, including designing inhibitors of the proteases that generate the peptide, generating antibodies against Abeta aggregates, utilizing metal chelators, and identifying small molecules that target the peptide during the aggregation pathway. The last approach is particularly attractive, as Abeta is normally present in vivo, but aggregation is a purely pathological event. Studies conducted in vitro and in vivo have suggested that administration of flavonoids, compounds naturally present in many foods, including wine and tea, can prevent and reverse Abeta aggregation, but mechanistic details are lacking. In this work, we employ atomistic, explicit-solvent molecular dynamics (MD) simulations to identify the mechanism of Abeta fibril destabilization by morin, one of the most effective anti-aggregation flavonoids, using a model of the mature Abeta fibril. Through the course of 24 simulations totaling 4.3 mus, we find that morin can bind to the ends of the fibrils to block the attachment of an incoming peptide and can penetrate into the hydrophobic core to disrupt the Asp23-Lys28 salt bridges and interfere with backbone hydrogen bonding. The combination of hydrophobicity, aromaticity, and hydrogen bonding capacity of morin imparts the observed behavior.

An enzyme-linked immunosorbent assay to compare the affinity of chemical compounds for β-amyloid peptide as a monomer

Aβ(1-42) is the proteolytic cleavage product of cleavage of the amyloid precursor protein by β- and γ-secretases. The aggregation of Aβ(1-42) plays a causative role in the development of Alzheimer's disease. To lock Aβ(1-42) in a homogenous state, we embedded the Aβ(1-42) sequence in an unstructured region of Bcl-x(L). Both the N-terminus and the C-terminus of Aβ(1-42) were constrained in the disordered region, whereas the conjunction did not introduce any folding to Aβ(1-42) but maintained the sequence as a monomer in solution. With Bcl-x(L)-Aβ(42), we developed an enzyme-linked immunosorbent assay to compare the affinity of compounds for monomeric Aβ(1-42). Bcl-x(L)-Aβ(42) was coated on a microplate and this was followed by incubation with different concentrations of compounds. Compounds binding to Leu17-Val24 of Aβ(1-42) inhibited the interaction between Bcl-x(L)-Aβ(42) and antibody 4G8. The method can not only reproduce the activities of the reported Aβ(1-42) inhibitors such as dopamine, tannin, and morin but can also differentiate decoy compounds that do not bind to Aβ(1-42). Remarkably, using this method, we discovered a new inhibitor that binds to monomeric Aβ(1-42) and inhibits Aβ(1-42) fibril formation. As the structure of Bcl-x(L)-Aβ(42) monomer is stable in solution, the assay could be adapted for high-throughput screening with a series of antibodies that bind the different epitopes of Aβ(1-42). In addition, the monomeric form of the Aβ(1-42) sequence in Bcl-x(L)-Aβ(42) would also facilitate the identification of Aβ(1-42) binding partners by coimmunoprecipitation, cocrystallization, surface plasmon resonance technology, or the assay as described here.

Pyrroloquinoline quinone inhibits the fibrillation of amyloid proteins

Several neurodegenerative diseases involve the selective damage of neuron cells resulting from the accumulation of amyloid fibril formation. Considering that the formation of amyloid fibrils as well as their precursor oligomers is cytotoxic, the agents that prevent the formation of oligomers and/or fibrils might allow the development of a novel therapeutic approach to neurodegenerative diseases. Here, we show pyrroloquinoline quinone (PQQ) inhibits the amyloid fibril formation of the amyloid proteins, amyloid beta (1-42) and mouse prion protein. The fibril formation of mouse prion protein in the presence of PQQ was dramatically prevented. Similarly, the fibril formation of amyloid beta (1-42) also decreased. With further advanced pharmacological approaches, PQQ may become a leading anti-neurodegenerative compound in the treatment of neurodegenerative diseases.

Targeting the early steps of Abeta16-22 protofibril disassembly by N-methylated inhibitors: a numerical study

Aggregation of the Abeta1-40/Abeta1-42 peptides is a key factor in Alzheimer's disease. Though the inhibitory effect of N-methylated Abeta16-22 (mAbeta16-22) peptides is well characterized in vitro, there is little information on how they disassemble full-length Abeta fibrils or block fibril formation. Here, we report coarse-grained implicit solvent molecular dynamics (MD) and replica exchange molecular dynamics (REMD) simulations on Abeta16-22 and mAbeta16-22 monomers, and then a preformed six-chain Abeta16-22 bilayer with either four copies of Abeta16-22 or four copies of mAbeta16-22. Our simulations show that the effect of N-methylation on mAbeta16-22 monomer is to reduce the density of compact forms. While 100 ns MD trajectories do not reveal any significant differences between the two ten-chain systems, the REMD simulations totaling 1 micros help understand the first steps of Abeta16-22 protofibril disassembly by N-methylated inhibitors. Notably, we find that mAbeta16-22 preferentially interacts with Abeta16-22 by blocking both beta-sheet extension and lateral association of layers, but also by intercalation of the inhibitors allowing sequestration of Abeta16-22 peptides. This third binding mode is particularly appealing for blocking Abeta fibrillogenesis.

Insight into the kinetic of amyloid beta (1-42) peptide self-aggregation: elucidation of inhibitors' mechanism of action

The initial transition of amyloid beta (1-42) (Abeta42) soluble monomers/small oligomers from unordered/alpha-helix to a beta-sheet-rich conformation represents a suitable target to design new potent inhibitors and to obtain effective therapeutics for Alzheimer's disease. Under optimized conditions, this reliable and reproducible CD kinetic study showed a three-step sigmoid profile that was characterized by a lag phase (prevailing unordered/alpha-helix conformation), an exponential growth phase (increasing beta-sheet secondary structure) and a plateau phase (prevailing beta-sheet secondary structure). This kinetic analysis brought insight into the inhibitors' mechanism of action. In fact, an increase in the duration of the lag phase can be related to the formation of an inhibitor-Abeta complex, in which the non-amyloidogenic conformation is stabilized. When the exponential rate is affected exclusively, such as in the case of Congo red and tetracycline, then the inhibitor affinity might be higher for the pleated beta-sheet structure. Finally, by adding the inhibitor at the end of the exponential phase, the soluble protofibrils can be disrupted and the Abeta amyloidogenic structure can revert into monomers/small oligomers. Congo red and tetracycline preferentially bind to amyloid in the beta-sheet conformation because both decreased the slope of the exponential growth, even if to a different extent, whereas no effect was observed for tacrine and galantamine. Some very preliminary indications can be derived about the structural requirements for binding to nonamyloidogenic or beta-sheet amyloid secondary structure for the development of potent antiaggregating agents. On these premises, memoquin, a multifunctional molecule that was designed to become a drug candidate for the treatment of Alzheimer's disease, was investigated under the reported circular dichroism assay and its anti-amyloidogenic mechanism of action was elucidated.

Chemical chaperone and inhibitor discovery: potential treatments for protein conformational diseases

Protein misfolding and aggregation cause a large number of neurodegenerative diseases in humans due to (i) gain of function as observed in Alzheimer’s disease, Huntington’s disease, Parkinson’s disease, and Prion’s disease or (ii) loss of function as observed in cystic fibrosis and α1-antitrypsin deficiency. These misfolded proteins could either lead to the formation of harmful amyloids that become toxic for the cells or to be recognized and prematurely degraded by the protein quality control system. An increasing number of studies has indicated that some low-molecular-weight compounds named as chemical chaperones can reverse the mislocalization and/or aggregation of proteins associated with human conformational diseases. These small molecules are thought to non-selectively stabilize proteins and facilitate their folding. In this review, we summarize the probable mechanisms of protein conformational diseases in humans and the use of chemical chaperones and inhibitors as potential therapeutic agents against these diseases. Furthermore, recent advanced experimental and theoretical approaches underlying the detailed mechanisms of protein conformational changes and current structure-based drug designs towards protein conformational diseases are also discussed. It is believed that a better understanding of the mechanisms of conformational changes as well as the biological functions of these proteins will lead to the development and design of potential interfering compounds against amyloid formation associated with protein conformational diseases.

Kinetics of amyloid formation and membrane interaction with amyloidogenic proteins

Interest in amyloidogenesis has exploded in recent years, as scientists recognize the role of amyloid protein aggregates in degenerative diseases such as Alzheimer's and Parkinson's disease. Assembly of proteins or peptides into mature amyloid fibrils is a multistep process initiated by conformational changes, during which intermediate aggregation states such as oligomers, protofibrils, and filaments are sampled. Although once it was assumed that the mature fibril was the biologically toxic species, more recently it has been widely speculated that soluble intermediates are the most damaging. Because of its relevance to mechanism of disease, the paths traversed during fibrillogenesis, and the kinetics of the process, are of considerable interest. In this review we discuss various kinetic models used to describe amyloidogenesis. Although significant advances have been made, construction of rigorous, detailed, and experimentally validated quantitative models remains a work in progress. We briefly review recent literature that illustrates the interplay between kinetics and amyloid-membrane interactions: how do different intermediates interact with lipid bilayers, and how does the lipid bilayer affect kinetics of amyloidogenesis?

Computational simulations of the early steps of protein aggregation

There is strong evidence that the oligomers of key proteins, formed during the early steps of aggregation, could be the primary toxic species associated with human neuro-degenerative diseases, such as Alzheimer's and prion diseases. Here, we review recent progress in the development of computational approaches in order to understand the structures, dynamics and free energy surfaces of oligomers. We also discuss possible research directions for the coming years.

Integration of virtual and physical screening

High-throughput screening (HTS) represents the dominant technique for the identification of new lead compounds in current drug discovery. It consists of physical screening (PS) of large libraries of chemicals against one or more specific biological targets. Virtual screening (VS) is a strategy for in silico evaluation of chemical libraries for a given target, and can be integrated to focus the PS process. The present work addresses the integration of both PS and VS, respectively.