Molecular mechanisms of resveratrol and EGCG in the inhibition of Aß42 aggregation and disruption of Aß42 protofibril: similarities and differences.

The aggregation of amyloid-ß protein (Aß) into fibrillary deposits is implicated in Alzheimer's disease (AD), and inhibiting Aß aggregation and clearing Aß fibrils are considered as promising strategies to treat AD. It has been reported that resveratrol (RSV) and epigallocatechin-3-gallate (EGCG), two of the most extensively studied natural polyphenols, are able to inhibit Aß fibrillization and remodel the preformed fibrillary aggregates into amorphous, non-toxic species. However, the mechanisms by which RSV inhibits Aß42 aggregation and disrupts Aß42 protofibril, as well as the inhibitory/disruptive mechanistic similarities and differences between RSV and EGCG, remain mostly elusive. Herein, we performed extensive all-atom molecular dynamics (MD) simulations on Aß42 dimers (the early aggregation state of Aß42) and protofibrils (the intermediate of Aß42 fibril formation and elongation) in the absence/presence of RSV or EGCG molecules. Our simulations show that both RSV and EGCG can bind with Aß42 monomers and inhibit the dimerization of Aß42. The binding of RSV with Aß42 peptide is mostly viaπ-π stacking interactions, while the binding of EGCG with Aß42 is mainly through hydrophobic, π-π stacking, and hydrogen-bonding interactions. Moreover, both RSV and EGCG disrupt the ß-sheet structure and K28-A42 salt bridges, leading to a disruption of Aß42 protofibril structure. RSV mainly binds with residues whose side-chains point inwards from the surface of the protofibril, while EGCG mostly binds with residues whose side-chains point outwards from the surface of the protofibril. Furthermore, RSV interacts with Aß42 protofibrils mostly viaπ-π stacking interactions, while EGCG interacts with Aß42 protofibrils mainly via hydrogen-bonding and hydrophobic interactions. For comparison, we also explore the effects of RSV/EGCG molecules on the aggregation inhibition and protofibril disruption of the Iowa mutant (D23N) Aß. Our findings may pave the way for the design of more effective drug candidates as well as the utilization of cocktail therapy using RSV and EGCG for the treatment of AD.

Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.

Conjugation of the small ubiquitin-like modifier (SUMO) to protein substrates is an important disease-associated posttranslational modification, although few inhibitors of this process are known. Herein, we report the discovery of an allosteric small-molecule binding site on Ubc9, the sole SUMO E2 enzyme. An X-ray crystallographic screen was used to identify two distinct small-molecule fragments that bind to Ubc9 at a site distal to its catalytic cysteine. These fragments and related compounds inhibit SUMO conjugation in biochemical assays with potencies of 1.9-5.8 mm. Mechanistic and biophysical analyses, coupled with molecular dynamics simulations, point toward ligand-induced rigidification of Ubc9 as a mechanism of inhibition.

Five similar anthocyanidin molecules display distinct disruptive effects and mechanisms of action on Aß1-42 protofibril: A molecular dynamic simulation study.

Alzheimer's disease (AD) is associated with the deposition of amyloid-ß (Aß) fibrillary aggregates. Disaggregation of Aß fibrils is considered as one of the promising AD treatments. Recent experimental studies showed that anthocyanidins, one type of flavonoids abundant in fruits/vegetables, can disaggregate Aß fibrillary aggregates. However, their relative disruptive capacities and underlying mechanisms are largely unknown. Herein, we investigated the detailed interactions between five most common anthocyanidins (cyanidin, aurantinidin, peonidin, delphinidin, and pelargonidin) and Aß protofibril (an intermediate of Aß fibrillization) by performing microsecond molecular dynamic simulations. We found that all five anthocyanidins can destroy F4-L34-V36 hydrophobic core and K28-A42 salt bridge, leading to Aß protofibril destabilization. Aurantinidin exhibits the strongest damage to Aß protofibril (with the most severe disruption on K28-A42 salt bridges), followed by cyanidin (with the most destructive effect on F4-L34-V36 core). Detailed analyses reveal that the protofibril-destruction capacities of anthocyanidins are subtly modulated by the interplay of anthocyanidin-protofibril hydrogen bonding, hydrophobic, aromatic stacking interactions, which are dictated by the number or location of hydroxyl/methyl groups of anthocyanidins. These findings provide important mechanistic insights into Aß protofibril disaggregation by anthocyanidins, and suggest that aurantinidin/cyanidin may serve as promising starting-points for the development of new drug candidates against AD.

Dissecting the Inhibitory Mechanism of the αB-Crystallin Domain against Aß42 Aggregation and Its Effect on Aß42 Protofibrils: A Molecular Dynamics Simulation Study.

Alzheimer's disease (AD) is related to the misfolding and aggregation of amyloid-ß (Aß) protein, and its major pathological hallmark is fibrillary ß-amyloid plaques. Impeding the formation of Aß ß-structure-rich aggregates and dissociating Aß 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 Aß 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 Aß42 aggregation. Our simulations show that αBC greatly impedes the formation of ß-structure contents. We find that the binding of αBC to the Aß42 monomer is driven by polar, hydrophobic, and H-bonding interactions. To explore whether αBC could destabilize Aß42 protofibrils, we also carried out MD simulations of Aß42 protofibrils with and without αBC. The results show that αBC interacts with three binding sites of the Aß42 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 ß-structure content, kink angle, and K28-A42 salt bridges. Overall, this study not only discloses the molecular mechanism of αBC against Aß42 aggregation but also demonstrates the disruption effects of αBC on Aß42 protofibrils, which yields an avenue for designing anti-AD drug candidates.

Green tea extract EGCG plays a dual role in Aß42 protofibril disruption and membrane protection: A molecular dynamic study.

Amyloid plaques accumulated by the amyloid-ß (Aß) fibrillar aggregates are the major pathological hallmark of the Alzheimer's disease (AD). Inhibiting aggregation and disassembling preformed fibrils of Aß by natural small molecules have developed into a promising therapeutic strategy for AD. Previous experiments reported that the green tea extract epigallocatechin-3-gallate (EGCG) can disrupt Aß fibril and reduce Aß cytotoxicity. The inhibitory ability of EGCG can also be affected by cellular membranes. Thus, it is essential to consider the membrane influences in the investigation of protofibril-disruptive capability of EGCG. Here, we performed multiple all-atom molecular dynamic simulations to investigate the effect of EGCG on the Aß42 protofibril in the presence of a mixed POPC/POPG (7:3) lipid bilayer and the underlying molecular mechanisms of action. Our simulations show that in the presence of membrane bilayers, EGCG has a preference to bind to the membrane, and this binding alters the binding modes between Aß42 protofibril and the lipid bilayer, leading to a reduced membrane thinning, indicative of a protective effect of EGCG on the membrane. And EGCG still displays a disruptive effect on Aß42 protofibril, albeit with a lesser extent of disruption than that in the membrane-free environment. EGCG destabilizes the two hydrophobic core regions (L17-F19-I31 and F4-L34-V36), and disrupts the intrachain K28-A42 salt bridges. Our results reveal that in the presence of lipid bilayers, EGCG plays a dual role in Aß42 protofibril disruption and membrane protection, suggesting that EGCG could be a potential effective drug candidate for the treatment of AD.

Natural stereoisomeric flavonoids exhibit different disruptive effects and the mechanism of action on Aß42 protofibril.

Our simulations reveal that two enantiomeric catechins display a better disruptive effect on Aß42 protofibril than their stereoisomer epicatechin. Unexpectedly, we find that catechins adopt both collapsed and extended states, while epicatechin populates only an extended state. Their different protofibril-disruptive effects are mostly attributed to the steric effect caused by the conformational differences.

Serotonin and Melatonin Show Different Modes of Action on Aß42 Protofibril Destabilization.

Alzheimer's disease (AD) is associated with the aberrant self-assembly of amyloid-ß (Aß) protein into fibrillar deposits. The disaggregation of Aß fibril is believed as one of the major therapeutic strategies for treating AD. Previous experimental studies reported that serotonin (Ser), one of the indoleamine neurotransmitters, and its derivative melatonin (Mel) are able to disassemble preformed Aß fibrils. However, the fibril-disruption mechanisms are unclear. As the first step to understand the underlying mechanism, we investigated the interactions of Ser and Mel molecules with the LS-shaped Aß42 protofibril by performing a total of nine individual 500 ns all-atom molecular dynamics (MD) simulations. The simulations demonstrate that both Ser and Mel molecules disrupt the local ß-sheet structure, destroy the salt bridges between K28 side chain and A42 COO-, and consequently destabilize the global structure of Aß42 protofibril. The Mel molecule exhibits a greater binding capacity than the Ser molecule. Intriguingly, we find that Ser and Mel molecules destabilize Aß42 protofibril through different modes of action. Ser preferentially binds with the aromatic residues in the N-terminal region through π-π stacking interactions, while Mel binds not only with the N-terminal aromatic residues but also with the C-terminal hydrophobic residues via π-π and hydrophobic interactions. This work reveals the disruptive mechanisms of Aß42 protofibril by Ser and Mel molecules and provides useful information for designing drug candidates against AD.

A Comprehensive Insight into the Mechanisms of Dopamine in Disrupting Aß Protofibrils and Inhibiting Aß Aggregation.

Fibrillary aggregates of amyloid-ß (Aß) are the pathological hallmark of Alzheimer's disease (AD). Clearing Aß deposition or inhibiting Aß aggregation is a promising approach to treat AD. Experimental studies reported that dopamine (DA), an important neurotransmitter, can inhibit Aß aggregation and disrupt Aß fibrils in a dose-dependent manner. However, the underlying molecular mechanisms still remain mostly elusive. Herein, we investigated the effect of DA on Aß42 protofibrils at three different DA-to-Aß molar ratios (1:1, 2:1, and 10:1) using all-atom molecular dynamics simulations. Our simulations demonstrate that protonated DA at a DA-to-Aß ratio of 2:1 exhibits stronger Aß protofibril disruptive capacity than that at a molar-ratio of 1:1 by mostly disrupting the F4-L34-V36 hydrophobic core. When the ratio of DA-to-Aß increases to 10:1, DA has a high probability to bind to the outer surface of protofibril and has negligible effect on the protofibril structure. Interestingly, at the same DA-to-Aß ratio (10:1), a mixture of protonated (DA+) and deprotonated (DA0) DA molecules significantly disrupts Aß protofibrils by the binding of DA0 to the F4-L34-V36 hydrophobic core. Replica-exchange molecular dynamics simulations of Aß42 dimer show that DA+ inhibits the formation of ß-sheets, K28-A42/K28-D23 salt-bridges, and interpeptide hydrophobic interactions and results in disordered coil-rich Aß dimers, which would inhibit the subsequent fibrillization of Aß. Further analyses reveal that DA disrupts Aß protofibril and prevents Aß dimerization mostly through π-π stacking interactions with residues F4, H6, and H13, hydrogen bonding interactions with negatively charged residues D7, E11, E22 and D23, and cation-π interactions with residues R5. This study provides a complete picture of the molecular mechanisms of DA in disrupting Aß protofibril and inhibiting Aß aggregation, which could be helpful for the design of potent drug candidates for the treatment/intervention of AD.

Green Tea Extracts EGCG and EGC Display Distinct Mechanisms in Disrupting Aß42 Protofibril.

The amyloid beta (Aß) fibrillar aggregate is the hallmark of Alzheimer's disease (AD). Disassembling preformed fibril or inhibiting Aß aggregation is considered as a therapeutic strategy for AD. Increasing evidence shows that green tea extracts, epigallocatechin-3-gallate (EGCG, containing an extra gallic acid ester group compared to EGC) and epigallocatechin (EGC), can disassociate Aß fibrils and attenuate Aß toxicity. However, the underlying molecular mechanism is poorly understood. Herein, we performed microsecond all-atom molecular dynamics (MD) simulations to investigate the influences of EGCG/EGC on the newly cryo-EM resolved LS-shaped Aß42 protofibrils and their detailed interactions. MD simulations demonstrate that both EGCG and EGC can disrupt Aß42 protofibril and EGCG displays a higher disruptive capacity than EGC. EGCG alters the L-shape of Aß42 protofibril by breaking the hydrogen bond between H6 and E11 through π-π interactions with residues H14/Y10 and hydrogen-bonding interactions with E11, while EGC remodels the L-shape by inserting into the hydrophobic core formed by A2, F4, L34, and V36 and via aromatics interaction with H6/Y10. EGCG disrupts the salt bridges between the K28 side chain and A42 COO- through hydrogen-bonding interaction with A42 and cation-π interaction between its gallic acid ester group and K28, while EGC damages the salt bridges through hydrophobic interactions with V39 and I41 as well as with I32, M35, and V40 located in the C-terminal hydrophobic core. This study demonstrates the pivotal role of the gallic acid ester group of EGCG in disrupting Aß42 protofibril and provides atomic-level insights into the distinct mechanism by which EGCG and EGC disrupt Aß protofibril, which could be useful for designing amyloid inhibitors.

Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System.

Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a ß-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.

Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization.

MyD88 is an essential adaptor protein, which mediates the signaling of the toll-like and interleukin-1 receptors' superfamily. The MyD88 L252P (L265P) mutation has been identified in diffuse large B-cell lymphoma. The identification of this mutation has been a major advance in the diagnosis of patients with aldenstrom macroglobulinemia and related lymphoid neoplasms. Here we used computational methods to characterize the conformational effects of the mutation. Our molecular dynamics simulations revealed that the mutation allosterically quenched the global conformational dynamics of the toll/IL-1R (TIR) domain, and readjusted its salt bridges and dynamic community network. Specifically, the mutation changed the orientation and reduced the fluctuation of α-helix 3, possibly through eliminating/weakening ~8 salt bridges and enhancing the salt bridge D225-K258. Using the energy landscape of the TIR domains of MyD88, we identified two dynamic conformational basins, which correspond to the binding sites used in homo- and hetero-oligomerization, respectively. Our results indicate that the mutation stabilizes the core of the homo-dimer interface of the MyD88-TIR domain, and increases the population of homo-dimer-compatible conformational states in MyD88 family proteins. However, the dampened motion restricts its ability to heterodimerize with other TIR domains, thereby curtailing physiological signaling. In conclusion, the L252P both shifts the landscape toward homo-dimerization and restrains the dynamics of the MyD88-TIR domain, which disfavors its hetero-dimerization with other TIR domains. We further put these observations within the framework of MyD88-mediated cell signaling.