Inhibition of Amyloid-β Aggregation by Cobalt(III) Schiff Base Complexes: A Computational and Experimental Approach

Acid-Resistant and Viscosity-Sensitive Proteome Aggregation Sensor To Visualize Cellular Aggrephagy in Live Cells and Clinical Samples

Aggrephagy in cells is defined as the degradation of intracellular aggregated proteins via the macroautophagy process. This process sequesters protein aggregates into autolysosomes, which bear characteristic viscous and acidic microenvironments. Limited protein aggregation sensors are environmentally compatible with the cellular aggrephagy process. Here, we report an acid-resistant and viscosity-sensitive proteome aggregation sensor to detect cellular aggrephagy in stressed cells and clinical samples. This sensor fluoresces upon selectively and ubiquitously binding to different aggregated proteins. Importantly, unlike other reported protein aggregation sensors, our probe offers unique acid-resistant fluorescence inside aggregated proteins, enabling its application in the acidic autolysosome microenvironment. In live cells under various stressed conditions, the optimal probe (A6) successfully detects aggregated proteome in autolysosomes, as validated by colocalization with a lysosomal tracker. Additionally, we demonstrate that the sensor can detect proteome aggregation in heat-stressed clinical tissue samples biopsied from cancer patients undergoing thermal perfusion treatment. Together, the reported acid-resistant and viscosity-sensitive protein aggregation sensor facilitates the detection of cellular aggrephagy by chemically matching its microenvironmental characteristics.

Heterobimetallic ferrocenyl-chromone compounds as selective inhibitors of amyloid aggregation

Amyloid aggregation is a key process in neurodegeneration, producing toxic species that contribute to disease progression. This underscores the urgent need to identify novel agents capable of reducing toxicity by modulating this aggregation process. Two heterobimetallic complexes incorporating a ferrocenyl-chromone (Fc-Chr) core were investigated: one featuring an additional gold(I) triphenylphosphine moiety, Fc-Chr-AuP(Ph)₃, and the other containing a dicobalt hexacarbonyl-alkyne unit, Fc-Chr-Co₂(CO)₆. Their effects were evaluated toward on the aggregation of two amyloid models: the peptide spanning residues 264-277 of nucleophosmin 1 (NPM1264-277) and the C-terminal fragment of the amyloid-β peptide (Aβ21-40) each with unique primary sequences, self-aggregation mechanisms and kinetics. Thioflavin T- assays allowed to assess the impact of the metal complexes on the aggregation of two amyloids. Results indicate that the two complexes inhibit the early stages of the aggregation of peptides in a dose-dependent manner and a greater effect on NPM1264-277 when compared to Aβ21-40 was observed. Native electrospray ionization mass spectrometry revealed the formation of peculiar metal/peptide adducts in dependence on different metal-units in the complexes. Scanning electron microscopy (SEM) and density function theory (DFT) were also employed to further characterize the interaction between the metal compounds and the investigated peptides, while preliminary cell viability assays in SH-SY5Y cells supported inhibitory effects on the aggregation and showed reduction of amyloid cytotoxicity. Fc-Chr-Co₂(CO)₆ demonstrated the highest efficacy in modulating peptide aggregation, exerting a more significant impact on NMP1264-277 relative to Aβ₂₁₋₄₀. These results support the use of ferrocenyl-chromone containing metal complexes as modulators of amyloid peptide aggregation.

Schiff Base-platinum and ruthenium complexes and anti-Alzheimer properties

This study investigates the effects of Pt and Ru complexes containing a Schiff base with a diimine structure on Alzheimer's disease. The Schiff base (N1E,N2E)-N1,N2-bis(isoquinolin-4-ylmethylene)benzene-1,2-diamine (I) and the novel Pt(II) and Ru(II) complexes (Ia and Ib) were synthesized and characterized using FTIR, NMR (1H, 13C), mass spectrometry, and elemental analyses. Their ability to inhibit amyloid beta (Aβ1-42) aggregation was determined in vitro using the SH-SY5Y cell line. Fluorescence spectroscopy investigated the early aggregation kinetics and dose-dependent characteristics of Aβ1-42 with the complexes. Transmission electron microscopy confirmed the results. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 1H NMR spectroscopy examined the interaction with Aβ1-16. Electrochemical analysis using square wave voltammetry monitored the interaction with Aβ1-42. The synthesized complexes were active in inhibiting amyloid aggregation at a low molar ratio.

From experimental studies to computational approaches: recent trends in designing novel therapeutics for amyloidogenesis

Amyloidosis is a condition marked by misfolded proteins that build up in tissues and eventually destroy organs. It has been connected to a number of fatal illnesses, including non-neuropathic and neurodegenerative conditions, which in turn have a significant influence on the worldwide health sector. The inability to identify the underlying etiology of amyloidosis has hampered efforts to find a treatment for the condition. Despite the identification of a multitude of putative pathogenic variables that may operate independently or in combination, the molecular mechanisms responsible for the development and progression of the disease remain unclear. A thorough investigation into protein aggregation and the impacts of toxic aggregated species will help to clarify the cytotoxicity of aggregation-mediated cellular apoptosis and lay the groundwork for future studies aimed at creating effective treatments and medications. This review article provides a thorough summary of the combination of various experimental and computational approaches to modulate amyloid aggregation. Further, an overview of the latest developments of novel therapeutic agents is given, along with a discussion of the possible obstacles and viewpoints on this developing field. We believe that the information provided by this review will help scientists create innovative treatment strategies that affect the way proteins aggregate.

Synthesis of novel pyrimidine-based Schiff base complexes: Targeting Amyloid-β aggregation in Alzheimer's disease

A novel Schiff base with imine/amine donors, 5-((3,3-diphenylalilidene)amino)pyrimidine-4-amine (L), and its new Platinum(II) and Ruthenium(II) complexes (I and II) were synthesized and characterized using FT-IR, 1H NMR, 13C NMR, mass spectrometry and elemental analyses. The ability of these complexes to inhibit amyloid beta (Aβ1-42) aggregation was evaluated using the human neuroblastoma cell line (SH-SY5Y). The complexes effectively inhibited Aβ1-42 aggregation at a 1:1 M ratio. Both complexes increased cell viability up to 80 % at concentrations of 10 μM. At this concentration, the cell viability value found by Aβ1-42 aggregation is around 65 %. Aggregation kinetics were fluorometrically monitored using Thioflavin T. These findings were further supported by scanning electron microscopy and transmission electron microscopy. In addition, the interaction of the complexes with Aβ1-16 was investigated using MALDI-TOF/MS and 1H NMR spectroscopy. All findings showed that Aβ1-42 in both complexes is active in the inhibition of amyloid aggregation.

Small molecule inhibits BACE1 activity by a dual mechanism confirmed by simulations-based study

Alzheimer's disease (AD) is a progressive and largely incurable neurodegenerative disorder that affects millions of people worldwide. It is characterised by the accumulation of amyloid-beta plaques and neurofibrillary tangles in the brain. It is commenced by cleavage of amyloid precursor protein (APP) by β-secretase, β-site amyloid precursor protein cleaving enzyme (BACE1; also called Asp2, memapsin 2). Therefore, BACE1 is a prime target for developing therapeutics against AD. In this study, we have identified a small molecule that potentially inhibits the activity of BACE1 by interacting with the active site residues. Also, the flap region seems to be involved in enhancing the stability of the small molecule at the active site. We have used Umibecestat (CNP-520) as a positive control. Our in silico results show that the identified molecule has a much better orientation at the active site of BACE1 than Umibecestat and inhibits by blocking the active site and modulating flap dynamics. We have utilised virtual high-throughput screening assay, ADME profiling, and blood-brain-barrier crossing ability to narrow down potential leads. The two shortlisted molecules were then subjected to atomistic molecular dynamics simulations study. Overall, our study proposes a much better inhibitor and a rational molecule for lead development against AD.

Transition Metal Complexes as Therapeutics: A New Frontier in Combatting Neurodegenerative Disorders through Protein Aggregation Modulation

Neurodegenerative disorders (NDDs) are a class of debilitating diseases that progressively impair the protein structure and result in neurological dysfunction in the nervous system. Among these disorders, Alzheimer's disease (AD), prion diseases such as Creutzfeldt-Jakob disease (CJD), and Parkinson's disease (PD) are caused by protein misfolding and aggregation at the cellular level. In recent years, transition metal complexes have gained significant attention for their potential applications in diagnosing, imaging, and curing these NDDs. These complexes have intriguing possibilities as therapeutics due to their diverse ligand systems and chemical properties and can interact with biological systems with minimal detrimental effects. This review focuses on the recent progress in transition metal therapeutics as a new era of hope in the battle against AD, CJD, and PD by modulating protein aggregation in vitro and in vivo. It may shed revolutionary insights into unlocking new opportunities for researchers to develop metal-based drugs to combat NDDs.

Natural compound plumbagin based inhibition of hIAPP revealed by Markov state models based on MD data along with experimental validations

Human islet amyloid polypeptide (amylin or hIAPP) is a 37 residue hormone co-secreted with insulin from β cells of the pancreas. In patients suffering from type-2 diabetes, amylin self-assembles into amyloid fibrils, ultimately leading to the death of the pancreatic cells. However, a research gap exists in preventing and treating such amyloidosis. Plumbagin, a natural compound, has previously been demonstrated to have inhibitory potential against insulin amyloidosis. Our investigation unveils collapsible regions within hIAPP that, upon collapse, facilitates hydrophobic and pi-pi interactions, ultimately leading to aggregation. Intriguingly plumbagin exhibits the ability to bind these specific collapsible regions, thereby impeding the aforementioned interactions that would otherwise drive hIAPP aggregation. We have used atomistic molecular dynamics approach to determine secondary structural changes. MSM shows metastable states forming native like hIAPP structure in presence of PGN. Our in silico results concur with in vitro results. The ThT assay revealed a striking 50% decrease in fluorescence intensity at a 1:1 ratio of hIAPP to Plumbagin. This finding suggests a significant inhibition of amyloid fibril formation by plumbagin, as ThT fluorescence directly correlates with the presence of these fibrils. Further TEM images revealed disappearance of hIAPP fibrils in plumbagin pre-treated hIAPP samples. Also, we have shown that plumbagin disrupts the intermolecular hydrogen bonding in hIAPP fibrils leading to an increase in the average beta strand spacing, thereby causing disaggregation of pre-formed fibrils demonstrating overall disruption of the aggregation machinery of hIAPP. Our work is the first to report a detailed atomistic simulation of 22 μs for hIAPP. Overall, our studies put plumbagin as a potential candidate for both preventive and therapeutic candidate for hIAPP amyloidosis.

Effects of anthocyanidins on the conformational transition of Aβ(1-42) peptide: Insights from molecular docking and molecular dynamics simulations

Recent evidence from in vitro and in vivo studies has shown that anthocyanins and anthocyanidins can reduce and inhibit the amyloid beta (Aβ) species, one of the hallmarks of Alzheimer's disease (AD). However, their inhibition mechanisms on Aβ species at molecular details remain elusive. Therefore, in the present study, molecular modelling methods were employed to investigate their inhibitory mechanisms on Aβ(1-42) peptide. The results highlighted that anthocyanidins effectively inhibited the conformational transitions of helices into beta-sheet (β-sheet) conformation within Aβ(1-42) peptide by two different mechanisms: 1) the obstruction of two terminals from coming into contact due to the binding of anthocyanidins with residues of N- and second hydrophobic core (SHC)-C-terminals, and 2) the prevention of the folding process due to the binding of anthocyanidin with the central polar (Asp23 and Lys28) and native helix (Asp23, Lys28, and Leu34) residues. These new findings on the inhibition of β-sheet formation by targeting both N- and SHC-C-terminals, and the long-established target, D23-K28 salt bridge residues, not with the conventional central hydrophobic core (CHC) as reported in the literature, might aid in designing more potent inhibitors for AD treatment.

Targeting misfolding and aggregation of the amyloid-β peptide and mutant p53 protein using multifunctional molecules

Biomolecule misfolding and aggregation play a major role in human disease, spanning from neurodegeneration to cancer. Inhibition of these processes is of considerable interest, and due to the multifactorial nature of these diseases, the development of drugs that act on multiple pathways simultaneously is a promising approach. This Feature Article focuses on the development of multifunctional molecules designed to inhibit the misfolding and aggregation of the amyloid-β (Aβ) peptide in Alzheimer's disease (AD), and the mutant p53 protein in cancer. While for the former, the goal is to accelerate the removal of the Aβ peptide and associated aggregates, for the latter, the goal is reactivation via stabilization of the active folded form of mutant p53 protein and/or aggregation inhibition. Due to the similar aggregation pathway of the Aβ peptide and mutant p53 protein, a common therapeutic approach may be applicable.

Synthesis, Spectroscopic and Nonlinear Optical Properties, and Antimicrobial Activity of Cu(II), Co(II), and Ni(II) Complexes: Experimental and Theoretical Studies

Currently, we report the preparation of transition metal complexes Co(II), Ni(II), and Cu(II) of hydrazone Schiff base ligands, which are obtained by the condensation reaction of substituted salicylaldehyde and hydrazines. The synthesized hydrazone ligands and their metal complexes were characterized by spectroscopic methods such as Fourier transform infrared (FT-IR), UV-vis, nuclear magnetic resonance (1H NMR and C13 NMR), and mass spectrometry analyses. All of the quantum chemistry calculations were performed using DFT executed in the Gaussian 09 software package. The geometry was optimized by using the density functional theory (DFT) approximation at the B3LYP level with a basis set of 6-31G (d, p). There was excellent agreement between the FT-IR values obtained experimentally and those obtained theoretically for the test compounds. It is worth noting that none of the optimized geometries for any of the Schiff base and metal complexes had any eigenvalues that were negative, indicating that these geometries represent the true minimum feasible energy surfaces. We also analyzed the electrostatic potential of the molecule and NBO calculation at the same level of theory. Gauss View 6 was utilized for the file organization of the input data. Gauss View 6.0, Avogadro, and Chemcraft were used to determine the data. Additionally, synthesized compounds were screened for antimicrobial activity against Gram-negative bacteria (Salmonella typhi, Escherichia coli) and Gram-positive bacteria (Bacillus halodurans, Micrococcus luteus) and two fungal strains (Aspergillus flavus, Aspergillus niger). These research findings have established the potential of ligands and their metal complexes as antimicrobial agents. Additionally, the compounds demonstrated promising nonlinear optical (NLO) properties, with potential applications across a wide range of contemporary technologies.

Tailoring the Amphiphilicity of Fluorescent Protein Chromophores to Detect Intracellular Proteome Aggregation in Diverse Biological Samples

The formation of amorphous misfolded and aggregated proteins is a hallmark of proteome stress in diseased cells. Given its lack of defined targeting sites, the rational design of intracellular proteome aggregation sensors has been challenging. Herein, we modulate the amphiphilicity of fluorescent protein chromophores to enable selective detection of aggregated proteins in different biological samples, including recombinant proteins, stressed live cells, intoxicated mouse liver tissue, and human hepatocellular carcinoma tissue. By tuning the number of hydroxyl groups, we optimize the selectivity of fluorescent protein chromophores toward aggregated proteins in these biological samples. In recombinant protein applications, the most hydrophobic P0 (cLogP = 5.28) offers the highest fold change (FC = 31.6), sensitivity (LLOD = 0.1 μM), and brightness (Φ = 0.20) upon binding to aggregated proteins. In contrast, P4 of balanced amphiphilicity (cLogP = 2.32) is required for selective detection of proteome stresses in live cells. In mouse and human liver histology tissues, hydrophobic P1 exhibits the best performance in staining the aggregated proteome. Overall, the amphiphilicity of fluorescent chromophores governs the sensor's performance by matching the diverse nature of different biological samples. Together with common extracellular amyloid sensors (e.g., Thioflavin T), these sensors developed herein for intracellular amorphous aggregation complement the toolbox to study protein aggregation.

Design and synthesis of ruthenium complexes and their studies on the inhibition of amyloid β (1-42) peptide aggregation

Misfolding and protein aggregation have been linked to numerous human neurodegenerative disorders such as Alzheimer's, prions, and Parkinson's. Due to their interesting photophysical properties, ruthenium (Ru) complexes have received considerable attention in studying protein aggregation. In this study, we synthesized the novel Ru complexes ([Ru(p-cymene)Cl(L-1)][PF₆](Ru-1), and [Ru(p-cymene)Cl(L-2)][PF₆](Ru-2)) and investigated their inhibitory activity against the bovine serum albumin (BSA) aggregation and the Aβ_1-42 peptides amyloid formation. Several spectroscopic methods were used to characterize the complexes, and the molecular structure was determined by X-ray crystallography. Amyloid aggregation and inhibition activity were examined using the Thioflavin-T (ThT) assay, and secondary structures were analyzed by circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). The cell viability assay was carried out on the neuroblastoma cell line, revealing that the Ru-2 complex showed better protective effects against Aβ_1-42 peptide toxicity on neuro-2a cells than the Ru-1 complex. Molecular docking studies elucidate binding sites and interactions between the Ru-complexes and the Aβ_1-42 fibrils. The experimental studies revealed that these complexes significantly inhibited BSA aggregation and Aβ_1-42 amyloid fibril formation at 1:3 and 1:1 equimolar concentrations, respectively. Antioxidant assays demonstrated that these complexes act as antioxidants, protecting from amyloid-induced oxidative stress. Molecular docking studies with the monomeric Aβ_1-42 (PDB: 1IYT) show hydrophobic interaction, and both complexes bind preferably in the central region of the peptide and coordinate with two binding sites of the peptide. Hence, we suggest that the Ru-based complexes could be applied as a potential agent in metallopharmaceutical research against Alzheimer's disease.

Mechanistic Insights of TiO2 Nanoparticles with Different Surface Charges on Aβ42 Peptide Early Aggregation: An In Vitro and In Silico Study

Humans may intendedly or unintendedly be exposed to nanomaterials through food, water, and air. Upon exposure, nanomaterials can pierce the bloodstream and translocate to secondary organs, including the brain, which warrants increased concern for the potential health impacts of nanomaterials. Due to their large surface area and interaction energy, nanomaterials can adsorb surrounding proteins. The misfolding and self-aggregation of amyloid-β (Aβ) have been considered significant factors in the pathogenesis of Alzheimer's disease. We thus hypothesize that brain-targeted nanomaterials may modulate Aβ aggregation and cause related neurotoxicity. Here, we showed that TiO₂ nanoparticles (NPs) and their aminated analogue (TiO₂-NH₂ NPs) adsorb the Aβ₄₂ peptide and accelerate its early oligomerization. Molecular dynamics simulation indicated that the adsorption onto TiO₂ NPs and TiO₂-NH₂ NPs surfaces can stabilize the β-sheet-rich conformations formed by the Aβ₄₂ peptide. The binding sites between TiO₂-NH₂ NPs and the Aβ₄₂ oligomer surface were mainly concentrated in the hydrophobic core region, and the β-sheet conformation spontaneously formed by Aβ₄₂ oligomers can be better stabilized through a hydrogen bond, electrostatic attraction, and hydrophobic interaction. This study will further help in the understanding of nanomaterial-related neurotoxicities and the regulation of their applications.

Rational design of photoactivatable metal complexes to target and modulate amyloid-β peptides

The accumulation of amyloid-β (Aβ) aggregates is found in the brains of Alzheimer's disease patients. Thus, numerous efforts have been made to develop chemical reagents capable of targeting Aβ peptides and controlling their aggregation. In particular, tunable coordination and photophysical properties of transition metal complexes, with variable oxidation and spin states on the metal centers, can be utilized to probe Aβ aggregates and alter their aggregation profiles. In this review, we illustrate some rational strategies for designing photoactivatable metal complexes as chemical sensors for Aβ peptides or modulators against their aggregation pathways, with some examples.

Metal-organic frameworks: A promising option for the diagnosis and treatment of Alzheimer's disease

Beta-amyloid (Aβ) peptide is one of the main characteristic biomarkers of Alzheimer's disease (AD). Previous clinical investigations have proposed that unusual concentrations of this biomarker in cerebrospinal fluid, blood, and brain tissue are closely associated with the AD progression. Therefore, the critical point of early diagnosis, prevention, and treatment of AD is to monitor the levels of Aβ. In view of the potential of metal-organic frameworks (MOFs) for diagnosing and treating the AD, much attention has been focused in recent years. This review discusses the latest advances in the applications of MOFs for the early diagnosis of AD via fluorescence and electrochemiluminescence (ECL) detection of AD biomarkers, fluorescence detection of the main metal ions in the brain (Zn2+, Cu2+, Mn2+, Fe3+, and Al3+) in addition to magnetic resonance imaging (MRI) of the Aβ plaques. The current challenges and future strategies for translating the in vitro applications of MOFs into in vivo diagnosis of the AD are discussed.

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.

Covalent Solvatochromic Proteome Stress Sensor Based on the Schiff Base Reaction

Covalent-type probes or sensors have been seldom reported for aggregated proteins. Herein, we reported a series of covalent solvatochromic probes to selectively modify and detect aggregated proteomes through the Schiff base reaction. Such covalent modification was discovered by serendipity using the P1 probe with an aldehyde functional group, exhibiting enhanced fluorescence intensity and unusually large blue shift upon protein aggregation. Supported by the biochemical and mass spectrometry results, we identified that this probe can modify the lysine residue of aggregated proteins selectively over folded ones via the Schiff base reaction. The generality of designing such a covalent-type probe was demonstrated in multiple probe scaffolds using different model proteins. Finally, we exploited the distinct solvatochromism of P1 after Schiff base linkage with aggregated proteins to visualize the distinct morphology of aggregated proteomes, as well as to quantify the polarity heterogeneity inside it. This work may intrigue the exploration of other chemical reaction types to covalently functionalize aggregated proteins that were difficult to analyze.

Based on molecular structures: Amyloid-β generation, clearance, toxicity and therapeutic strategies

Amyloid-β (Aβ) has long been considered as one of the most important pathogenic factors in Alzheimer’s disease (AD), but the specific pathogenic mechanism of Aβ is still not completely understood. In recent years, the development of structural biology technology has led to new understandings about Aβ molecular structures, Aβ generation and clearance from the brain and peripheral tissues, and its pathological toxicity. The purpose of the review is to discuss Aβ metabolism and toxicity, and the therapeutic strategy of AD based on the latest progress in molecular structures of Aβ. The Aβ structure at the atomic level has been analyzed, which provides a new and refined perspective to comprehend the role of Aβ in AD and to formulate therapeutic strategies of AD.

Functional Disruption of Gli1-DNA Recognition via a Cobalt(III) Complex

The aberrant activation of the Gli family of zinc finger transcription factors (ZFTFs) is associated with several types of human cancer, including medulloblastoma and basal cell carcinoma. We have reported the use of cobalt(III) Schiff-base complexes (Co(III)-sb) as potent inhibitors of ZFTFs in vivo. These complexes inhibit transcription by displacing the zinc finger domain's structural Zn(II) ion, destabilizing the alpha helix necessary for DNA recognition. Here, we describe the use of Co(III)-sb complexes for the selective inhibition of Gli1. Spectroscopic and computational studies of the Gli1 DNA binding domain found that Co(III)-sb displaced Zn(II) through direct coordination with the His residues of the Cys2 His2 Zn(II) binding site. As a result, there is a dose-dependent degradation of the alpha-helix content in the DNA binding domain of Gli1 and corresponding inhibition of consensus sequence recognition. We conclude that this strategy is well suited for the development of new and potent inhibitors of Gli1.

Design of Gallic Acid-Glutamine Conjugate and Chemical Implications for Its Potency Against Alzheimer's Amyloid-β Fibrillogenesis

Epigallocatechin-3-gallate (EGCG) has been widely recognized as a potent inhibitor of Alzheimer's amyloid-β (Aβ) fibrillogenesis. We found that gallic acid (GA) has superior inhibitory effects over EGCG at the same mass concentrations and assumed the pivotal role of the carboxyl group in GA. Therefore, we designed five GA-derivatives to investigate the significance of carboxyl groups in modulating Aβ fibrillogenesis, including carboxyl-amidated GA (GA-NH₂), GA-glutamic acid conjugate (GA-E), and GA-E derivatives with amidated either of the two carboxyl groups (GA-Q and GA-E-NH₂) or with two amidated-carboxyl groups (GA-Q-NH₂). Intriguingly, only GA-Q shows significantly stronger potency than GA and extends the life span of the AD transgenic nematode by over 30%. Thermodynamic studies reveal that GA-Q has a strong binding affinity for Aβ₄₂ with two binding sites, one stronger (site 1, K_a1 = 3.1 × 10⁶ M^-1) and the other weaker (site 2, K_a2 = 0.8 × 10⁶ M^-1). In site 1, hydrogen bonding, electrostatic interactions, and hydrophobic interactions all have contributions, while in site 2, only hydrogen bonding and electrostatic interactions work. The two sites are confirmed by molecular simulations, and the computations specified the key residues. GA-Q has strong binding to Asp23, Gly33, Gly38, Ala30, Ile31, and Leu34 via hydrogen bonding and electrostatic interactions, while it interacts with Phe19, Ala21 Gly25, and Asn27 via hydrophobic interactions. Consequently, GA-Q destroys Asp23-Lys28 salt bridges and restricts β-sheet/bridge structures. The thermodynamic and molecular insight into the GA-Q functions on inhibiting Aβ fibrillogenesis would pave a new way to the design of potent molecules against Alzheimer's amyloid.

Multifunctional fluorescent probe for effective visualization, inhibition, and detoxification of β-amyloid aggregation via covalent binding

A multifunctional reactive fluorescent probe DTB was constructed for biosensing, aggregation inhibition, and toxicity alleviation of β-amyloid. The synergistic effect of hydrophobic interaction and covalent interaction makes DTB have more stable binding and better selectivity to Aβ. The detoxification effect of DTB on Aβ aggregates was also verified in live nerve cells and microglia cells. Furthermore, DTB exhibits an excellent staining of Aβ plaques.

Ruthenium(II)–arene complexes with chelating quinoline ligands as anti-amyloid agents

Recent recognition of the soluble form of the amyloid-beta (Aβ) peptide as a neurotoxic agent in Alzheimer’s disease (AD) has spurred the development of agents to target this species. Because Aβ is known to chelate metal ions in solution, metal-based therapeutics are uniquely suited to exploit this affinity, where coordination to Aβ has been shown to impact the neurotoxicity of the peptide. Ruthenium(II)–arene complexes are unique candidates for evaluation, as one face of the molecule is blocked by the hydrophobic arene ring, while coordination to the Aβ peptide can occur on the other side of the molecule. We have prepared and evaluated two Ru(II)–arene complexes with chelating quinoline-based ligands, Ru1 and Ru2, for their respective anti-amyloid abilities. Although both complexes decreased the aggregation of soluble Aβ, Ru1 displayed promise in disrupting formed aggregates of the peptide. These findings represent an exciting new avenue for therapeutic development in AD, where both sides of the aggregation equilibrium are affected.

Regulation of Fluorescence Solvatochromism To Resolve Cellular Polarity upon Protein Aggregation

Common solvatochromic fluorophores exhibit a bathochromic fluorescence emission wavelength shift accompanied by intensity attenuation due to the presence of nonradiative decay pathways at the excited state. Such intrinsic but inevitable fluorescence quenching of solvatochromism impedes its applications to faithfully quantify local polarity, especially in a polar environment. Herein, we report a new donor-π-acceptor (D-π-A) type solvatochromic fluorophore scaffold containing a perfluorophenyl group that exhibits both a solvatochromic emission wavelength shift and a controllable emission intensity upon polarity fluctuation. The regulation of fluorescence solvatochromism and colors was achieved by tuning the aryl donors. We exploited such desired solvatochromism of these probes to monitor protein misfolding and aggregation via wavelength shift. Finally, the polarity of pathogenic aggregated proteins was quantified by HaloTag bioorthogonal labeling technology in live cells. While much effort has been devoted to resolving the morphology of pathogenic aggregated proteins, this work provides quantitative hints regarding the chemical information at this disease-related protein interphase.

Enzyme-Induced Transformable Peptide Nanocarriers with Enhanced Drug Permeability and Retention to Improve Tumor Nanotherapy Efficacy

Temporal persistence is as important for nanocarriers as spatial accuracy. However, because of the insufficient aggreagtion and short retention time of chemotherapy drugs in tumors, their clinical application is greatly limited. A drug delivery approach dependent on the sensitivity to an enzyme present in the microenvironment of the tumor is designed to exhibit different sizes in different sites, achieving enhanced drug permeability and retention to improve tumor nanotherapy efficacy. In this work, we report a small-molecule peptide drug delivery system containing both tumor-targeting groups and enzyme response sites. This system enables the targeted delivery of peptide nanocarriers to tumor cells and a unique response to alkaline phosphatase (ALP) in the tumor microenvironment to activate morphological transformation and drug release. The amphiphilic peptide AYR self-aggregated into a spherical nanoparticle structure after encapsulating the lipid-soluble model drug doxorubicin (DOX) and rapidly converted to nanofibers via the induction of ALP. This morphological transformation toward a high aspect ratio allowed rapid, as well as effective drug release to tumor location while enhancing specific toxicity to tumor cells. Interestingly, this "transformer"-like drug delivery strategy can enhance local drug accumulation and effectively inhibit drug efflux. In vitro along with in vivo experiments further proved that the permeability and retention of antitumor drugs in tumor cells and tissues were significantly enhanced to reduce toxic side effects, and the therapeutic effect was remarkably improved compared with that of nondeformable drug-loaded peptide nanocarriers. The developed AYR nanoparticles with the ability to undergo morphological transformation in situ can improve local drug aggregation and retention time at the tumor site. Our findings provide a new and simple method for nanocarrier morphology transformation in novel cancer treatments.

Destabilization of the Alzheimer's amyloid-β peptide by a proline-rich β-sheet breaker peptide: a molecular dynamics simulation study

The amyloid-β peptide exists in the form of fibrils in the plaques found in the brains of patients with Alzheimer's disease. One of the therapeutic strategies is the design of molecules which can destabilize these fibrils. We present a designed peptide KLVFFP₅ with two segments: the self-recognition sequence KLVFF and a β-sheet breaker proline pentamer. Molecular dynamics simulations and docking results showed that this peptide could bind to the protofibrils and destabilize them by establishing hydrophobic contacts and hydrogen bonds with a higher affinity than the KLVFF peptide. In the presence of the KLVFFP₅ peptide, the β-sheet content of the protofibrils was reduced significantly; the hydrogen bonding network and the salt bridges were disrupted to a greater extent than the KLVFF peptide. Our results indicate that the KLVFFP₅ peptide is an effective β-sheet disruptor which can be considered in the therapy of Alzheimer's disease.

Enzyme-induced morphological transformation of drug carriers: Implications for cytotoxicity and the retention time of antitumor agents

Nanocarriers have been widely employed to deliver chemotherapeutic drugs for cancer treatment. However, the insufficient accumulation of nanoparticles in tumors is an important reason for the poor efficacy of nanodrugs. In this study, a novel drug delivery system with a self-assembled amphiphilic peptide was designed to respond specifically to alkaline phosphatase (ALP), a protease overexpressed in cancer cells. The amphiphilic peptide self-assembled into spherical and fibrous nanostructures, and it easily assembled into spherical drug-loaded peptide nanoparticles after loading of a hydrophobic chemotherapeutic drug. The cytotoxicity of the drug carriers was enhanced against tumor cells over time. These spherical nanoparticles transformed into nanofibers under the induction of ALP, leading to efficient release of the encapsulated drug. This drug delivery strategy relying on responsiveness to an enzyme present in the tumor microenvironment can enhance local drug accumulation at the tumor site. The results of live animal imaging showed that the residence time of the morphologically transformable drug-loaded peptide nanoparticles at the tumor site was prolonged in vivo, confirming their potential use in antitumor therapy. These findings can contribute to a better understanding of the influence of drug carrier morphology on intracellular retention.

A Solvatochromic Fluorescent Probe Reveals Polarity Heterogeneity upon Protein Aggregation in Cells

We report a crystallization-induced emission fluorophore to quantitatively interrogate the polarity of aggregated proteins. This solvatochromic probe, namely "AggRetina" probe, inherently binds to aggregated proteins and exhibits both a polarity-dependent fluorescence emission wavelength shift and a viscosity-dependent fluorescence intensity increase. Regulation of its polarity sensitivity was achieved by extending the conjugation length. Different proteins bear diverse polarity upon aggregation, leading to different resistance to proteolysis. Polarity primarily decreases during protein misfolding but viscosity mainly increases upon the formation of insoluble aggregates. We quantified the polarity of aggregated protein-of-interest in live cells via HaloTag bioorthogonal labeling, revealing polarity heterogeneity within cellular aggregates. The enriched micro-environment details inside misfolded and aggregated proteins may correlate to their bio-chemical properties and pathogenicity.

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.

Inhibition of Aβ peptide aggregation by ruthenium(II) polypyridyl complexes through copper chelation

Alzheimer's disease (AD) is known as a complex multifactorial syndrome and both metal chelators and amyloid β peptide (Aβ) inhibitors show promise against AD. Herein, four small hybrid compounds have been designed and synthesized utilizing 8-hydroxyquinoline, pyridine or imidazole as chelators and benzimidazole as the recognition moiety for AD treatment. These conjugates can capture Cu²⁺ from Aβ and become dimers upon Cu²⁺ coordination and show high efficiency for both Cu²⁺ elimination and Aβ assembly inhibition. Besides, these designed complexes can inhibit the production of Aβ-induced reactive oxygen species (ROS), protect mitochondria from damage, and improve the survival rate of neuron cells. Our work provides a new strategy to combine hydrophobic interaction and metal ion chelation to design amyloid inhibitors.

Modulation of amyloid-β aggregation by metal complexes with a dual binding mode and their delivery across the blood-brain barrier using focused ultrasound

One of the key hallmarks of Alzheimer's disease is the aggregation of the amyloid-β peptide to form fibrils. Consequently, there has been great interest in studying molecules that can disrupt amyloid-β aggregation. While a handful of molecules have been shown to inhibit amyloid-β aggregation in vitro, there remains a lack of in vivo data reported due to their inability to cross the blood-brain barrier. Here, we investigate a series of new metal complexes for their ability to inhibit amyloid-β aggregation in vitro. We demonstrate that octahedral cobalt complexes with polyaromatic ligands have high inhibitory activity thanks to their dual binding mode involving π-π stacking and metal coordination to amyloid-β (confirmed via a range of spectroscopic and biophysical techniques). In addition to their high activity, these complexes are not cytotoxic to human neuroblastoma cells. Finally, we report for the first time that these metal complexes can be safely delivered across the blood-brain barrier to specific locations in the brains of mice using focused ultrasound.

Rational Design of Crystallization-Induced-Emission Probes To Detect Amorphous Protein Aggregation in Live Cells

Unlike amyloid aggregates, amorphous protein aggregates with no defined structures have been challenging to target and detect in a complex cellular milieu. In this study, we rationally designed sensors of amorphous protein aggregation from aggregation-induced-emission probes (AIEgens). Utilizing dicyanoisophorone as a model AIEgen scaffold, we first sensitized the fluorescence of AIEgens to a nonpolar and viscous environment mimicking the interior of amorphous aggregated proteins. We identified a generally applicable moiety (dimethylaminophenylene) for selective binding and fluorescence enhancement. Regulation of the electron-withdrawing groups tuned the emission wavelength while retaining selective detection. Finally, we utilized the optimized probe to systematically image aggregated proteome upon proteostasis network regulation. Overall, we present a rational approach to develop amorphous protein aggregation sensors from AIEgens with controllable sensitivity, spectral coverage, and cellular performance.

Importance of Hydrogen Bonding: Structure-Activity Relationships of Ruthenium(III) Complexes with Pyridine-Based Ligands for Alzheimer's Disease Therapy

Alzheimer's disease (AD) is the most common form of dementia, where one of the pathological hallmarks of AD is extracellular protein deposits, the primary component of which is the peptide amyloid-β (Aβ). Recently, the soluble form of Aβ has been recognized as the primary neurotoxic species, making it an important target for therapeutic development. Metal-based drugs are promising candidates to target Aβ, as the interactions with the peptide can be tuned by ligand design. In the current study, 11 ruthenium complexes containing pyridine-based ligands were prepared, where the functional groups at the para position on the coordinated pyridine ligand were varied to determine structure-activity relationships. Overall, the complexes with terminal primary amines had the greatest impact on modulating the aggregation of Aβ and diminishing its cytotoxicity. These results identify the importance of specific intermolecular interactions and are critical in the advancement of metal-based drugs for AD therapy.

One-Pot Synthesis of Schiff Bases by Defect-Induced TiO2-x-Catalyzed Tandem Transformation from Alcohols and Nitro Compounds

Schiff bases that are generally formed from condensation reactions of aldehydes (or ketones) and amino groups could also be produced by a photodriven one-pot tandem reaction between alcohols and nitro compounds, in our case. Herein, TiO_2-x porous cages derived from NH₂-MIL-125 by a self-sacrificing template route are used to study the organic transformation and exhibit 100% conversion efficiency of nitrobenzene and 100% selectivity for Schiff bases in the system of benzyl alcohol (5 mL) and nitrobenzene (41 μL) upon light irradiation, but hydrogen by dehydrogenation of benzyl alcohol cannot be detected. Successful occurrence of the organic transformation is mainly attributed to Ti(III)-oxygen vacancy associates. Surface oxygen vacancy-related Ti(III) sites are responsible for binding with nitro groups, and low-coordinated Ti_5c sites selectively adsorb hydroxyl groups of benzyl alcohol. The Ti(III) and oxygen vacancy associates capture photogenerated electrons for achievement of multielectron reduction of nitrobenzene and the subsequent Schiff base condensation reaction with the as-formed benzaldehyde.

Computational Methods and Tools in Antimicrobial Peptide Research

The evolution of antibiotic-resistant bacteria is an ongoing and troubling development that has increased the number of diseases and infections that risk going untreated. There is an urgent need to develop alternative strategies and treatments to address this issue. One class of molecules that is attracting significant interest is that of antimicrobial peptides (AMPs). Their design and development has been aided considerably by the applications of molecular models, and we review these here. These methods include the use of tools to explore the relationships between their structures, dynamics, and functions and the increasing application of machine learning and molecular dynamics simulations. This review compiles resources such as AMP databases, AMP-related web servers, and commonly used techniques, together aimed at aiding researchers in the area toward complementing experimental studies with computational approaches.

Quantitative interrogation of protein co-aggregation using multi-color fluorogenic protein aggregation sensors

Co-aggregation of multiple pathogenic proteins is common in neurodegenerative diseases but deconvolution of such biochemical process is challenging. Herein, we developed a dual-color fluorogenic thermal shift assay to simultaneously report on the aggregation of two different proteins and quantitatively study their thermodynamic stability during co-aggregation. Expansion of spectral coverage was first achieved by developing multi-color fluorogenic protein aggregation sensors. Orthogonal detection was enabled by conjugating sensors of minimal fluorescence crosstalk to two different proteins via sortase-tag technology. Using this assay, we quantified shifts in melting temperatures in a heterozygous model protein system, revealing that the thermodynamic stability of wild-type proteins was significantly compromised by the mutant ones but not vice versa. We also examined how small molecule ligands selectively and differentially interfere with such interplay. Finally, we demonstrated these sensors are suited to visualize how different proteins exert influence on each other upon their co-aggregation in live cells.

Membrane Anchored Polymers Modulate Amyloid Fibrillation

The nucleating role of cellular membrane components, such as lipid moieties on amyloid beta (Aβ_1-40 ) fibrillation, has been reported in recent years. The influence of conjugates fabricated from lipid anchors (cholesterol, diacylglycerol) and hydrophilic polymers on Aβ_1-40 fibrillation is reported here, aiming to understand the impact of polymers cloud point temperature (T_cp ) and its hydrophobic tails on the amyloid fibrillation. Novel lipid-polymer conjugates, consisting of poly(oligo(ethylene glycol)_m acrylates) and hydrophobic groups (diacylglyceryl-, cholesteryl-, octyl-, decyl-, hexadecyl-) as anchors are synthesized using reversible addition-fragmentation chain transfer (RAFT) polymerization, allowing to tune the hydrophilic-hydrophobic profile of the conjugates by varying both, the degree of polymerization (n) and number of ethylene glycol units (m) in their side chain. The impact of these conjugates on Aβ_1-40 fibrillation is investigated via in vitro kinetic studies and transmission electron microscopy (TEM). Hydrophobic lipid-anchors are significantly delaying fibrillation (both lag- and half times), observing similar fibrillar structures via TEM when compared to native Aβ_1-40 . Other hydrophobic end groups are also delaying fibrillation of Aβ_1-40 , irrespective of their "n" and "m," whereas more hydrophilic polymers (both with longer ethylene glycol-sidechains, m = 3 for octyl, decyl and m = 5 for cholesterol) are only marginally inhibited fibrillation.

Evaluation of antioxidant and inhibitory properties of Citrus aurantium L. on the acetylcholinesterase activity and the production of amyloid nano-bio fibrils

The blossoms of Citrus aurantium are considered for the treatment of Alzheimer's disease because of their fragrant essential oils. The aim of this study was to investigate the antioxidant and inhibitory effects of Citrus aurantium extract on the acetylcholinesterase and production of amyloid nanobiofibrils from bovine serum albumin (BSA). The Citrus aurantium petals were harvested from Rasht city in northern IRAN. Chemical composition was investigated by GC-MS. The anti-Alzheimer's effects were evaluated by determining the antioxidant percentage by DPPH method and determining acetylcholinesterase activity. Congored spectroscopy was used for investigation of the inhibitory properties of the extract on the production of amyloid nanobiofibrils, and amyloid fibers was confirmed by electron microscopy. The most abundant ingredients were D-Glucuronic acid (9.53%), D-Limonene (5.54%), Linalool (2.06%), Daphnetin (3.73%), Phthalic acid (0.72%), Octadecenoic acid (3.98%), Hexadecanoic acid (2.13%), Pyrrolidinone (1.17%) and the highest antioxidant capacity was at 8 mg/ml (EC₅₀: 2.36 mg/ml). The extract reduced the Acetylcholinesterase activity less than 47.04% (IC₅₀: 42.8 mg/ml) and amyloid production less than 22% (EC₅₀: 3.135). Citrus aurantium petals with inhibitory properties for the production of amyloid nanobiofibrils, can be used as a beneficial drugs for reducing side effects of Alzheimer's disease.

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

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

Colorimetric determination of amyloid-β peptide using MOF-derived nanozyme based on porous ZnO-Co3O4 nanocages

A sensitive and rapid colorimetric biosensor has been developed for determination of amyloid-β peptide (Aβ) and study of amyloidogenesis based on the high peroxidase-like activity of porous bimetallic ZnO-Co₃O₄ nanocages (NCs). Due to the high binding ability of Aβ monomer to ZnO-Co₃O₄ NCs, the catalytic activity of ZnO-Co₃O₄ NCs can be significantly suppressed by Aβ monomer. This finding forms the basis for a colorimetric assay for Aβ monomer detection. The detection limit for Aβ monomer is 3.5 nM with a linear range of 5 to 150 nM (R² = 0.997). The system was successfully applied to the determination of Aβ monomer in rat cerebrospinal fluid. Critically, the different inhibition effects of monomeric and aggregated Aβ species on the catalytic activity of ZnO-Co₃O₄ NCs enabled the sensor to be used for tracking the dynamic progress of Aβ aggregation and screening Aβ inhibitors. Compared with the commonly used thioflavin T fluorescence assay, this method provided higher sensitivity to the formation of Aβ oligomer at the very early assembly stage. Our assay shows potential application in early diagnosis and therapy of Alzheimer's disease (AD).

Peptide-Peptide Co-Assembly: A Design Strategy for Functional Detection of C-peptide, A Biomarker of Diabetic Neuropathy

Diabetes-related neuropathy is a debilitating condition that may be averted if it can be detected early. One possible way this can be achieved at low cost is to utilise peptides to detect C-peptide, a biomarker of diabetic neuropathy. This depends on peptide-peptide co-assembly, which is currently in a nascent stage of intense study. Instead, we propose a bead-based triple-overlay combinatorial strategy that can preserve inter-residue information during the screening process for a suitable complementary peptide to co-assemble with C-peptide. The screening process commenced with a pentapeptide general library, which revealed histidine to be an essential residue. Further screening with seven tetrapeptide focused libraries led to a table of self-consistent peptide sequences that included tryptophan and lysine at high frequencies. Three complementary nonapeptides (9mer com-peptides), wpkkhfwgq (Trp-D), kwkkhfwgq (Lys-D), and KWKKHFWGQ (Lys-L) (as a negative control) were picked from this table for co-assembly studies with C-peptide. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) and circular dichroism (CD) spectroscopies were utilized to study inter-peptide interactions and changes in secondary structures respectively. ATR-FTIR studies showed that there is indeed inter-peptide interaction between C-peptide and the tryptophan residues of the 9mer com-peptides. CD studies of unaggregated and colloidal C-peptide with the 9mer com-peptides suggest that the extent of co-assembly of C-peptide with Trp-D is greatest, followed by Lys-D and Lys-L. These results are promising and indicate that the presented strategy is viable for designing and evaluating longer complementary peptides, as well as complementary peptides for co-assembly with other polypeptides of interest and importance. We discuss the possibility of designing complementary peptides to inhibit toxic amyloidosis with this approach.

Cobalt(III) Schiff base complexes stabilize non-fibrillar amyloid-β aggregates with reduced toxicity

The aggregation of amyloid-β (Aβ) is believed to be foundational to the pathogenesis of Alzheimer's disease (AD). In vitro aggregation kinetics have been shown to correlate with rates of disease progression in both AD patients and animal models, thus proving to be a useful metric for testing Aβ-targeted therapeutics. Here we present evidence of cobalt(III) Schiff base complex ([Co(acetylacetonate)(NH₃)₂]Cl; Co(III)-sb) modulation of Aβ aggregation kinetics by a variety of complementary techniques. These include Thioflavin T (ThT) fluorescence, circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM). Our data was fitted to kinetic rate laws using a mathematical model developed by Knowles et al. in order to extract mechanistic information about the effect of Co(III)-sb on aggregation kinetics. Our analysis revealed that Co(III)-sb alters Aβ aggregation by decreasing the polymerization rate and increasing the nucleation rate, suggesting that Co(III)-sb causes Aβ to rapidly stabilize oligomeric species with reduced elongation into mature fibrils. This result was corroborated by TEM and AFM of Aβ aggregates in vitro. We also demonstrate that Aβ aggregate mixtures produced in the presence of Co(III)-sb exhibit decreased cytotoxicity compared to untreated samples.