The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective

Unraveling binding interactions between methasterone and bovine serum albumin (BSA): A spectroscopic and computational study

In this study, binding interactions between methasterone and bovine serum albumin (BSA) were analyzed using spectroscopic techniques and molecular docking. UV absorption spectroscopy showed the formation of a ground-state complex between methasterone and bovine serum albumin (BSA). Thermodynamic parameters from fluorometric analysis indicated that the hydrogen bonding and van der Waal forces were the main interacting forces between the complex and the reaction was found to be spontaneous. Molecular docking further validated it. Nano differential scanning fluorimetry showed the protein was found to be more thermally stable in the presence of methasterone. Circular dichroism spectroscopy revealed slight reduction in the helicity after binding with methasterone suggesting conformational changes to promote binding. As no prior information exists on the binding interactions between methasterone and BSA, this study provides insights into methasterone-BSA interactions, which can serve as a foundation for future investigations into its pharmacological properties.

Insights into the Binding of Metadoxine with Bovine Serum Albumin: A Multi-Spectroscopic Investigation Combined with Molecular Docking

BACKGROUND

Metadoxine, also known as pyruvate dehydrogenase activator, is a small molecule drug that has been used in the treatment of various medical conditions. Bovine serum albumin is a commonly studied protein that serves as a plasmatic for understanding protein-drug interactions due to its abundance.

OBJECTIVE

This research suggests that metadoxine can bind to bovine serum albumin with moderate affinity, leading to an alteration in the secondary structure of the protein, which may also influence the protein's stability and function, which could provide a comprehensive understanding of the interaction at a molecular level. In this study, a variety of methodologies wereused to determine various thermodynamic parameters.

METHODS

The study uses UV-visible, Fluorescence, Fourier-transform infrared, Circular dichroism spectroscopy, and Molecular docking to analyze the interaction between bovine serum albumin and metadoxine, providing thermodynamic parameters for understanding the protein structure and its binding.

RESULT

The binding of metadoxine with bovine serum albumin, causes a hyperchromic shift. In fluorescence spectroscopy, the value of the Stern Volmer increases constantly with an increase in temperature, suggesting a stronger interaction between the Metadoxine and the Bovine serum albumin, leading to dynamic quenching. Additionally, Fourier-transform infrared and circular dichroism indicated a reduction in the secondary structure of Bovine serum albumin.

CONCLUSION

The interactions between metadoxine and bovine serum albumin, cause hyperchromic shift revealed by UV-visible spectroscopy, whereas in Fluorescence spectroscopy, the value of the Stern Volmer constant increases with an increase in temperature, suggesting a stronger interaction between the MD and the BSA, leading to dynamic quenching. Additionally, Fourier-transform infrared and circular dichroism spectroscopy indicated a reduction in the secondary structure of the protein, as evidenced by the shifting of the amide II band and leading to a slight decrease in the α- helix content. The molecular docking shows that metadoxine was docked in the subdomain IIA binding pocket of BSA.

Insights into the interaction between the kusaginin and bovine serum albumin: Multi-spectroscopic techniques and computational approaches

Kusaginin, as a phenylethanoid glycoside, which has exhibited wide antioxidant and antimicrobial properties. The molecular mechanism underlying the broad biological activities of kusaginin has not yet been well documented. In this paper, the interaction of kusaginin with bovine serum albumin (BSA) has been explored by fluorescence spectra, UV-vis absorption spectra, and circular dichroism (CD) spectra along with computational approaches. The fluorescence experiments showed that kusaginin could strongly quench the intrinsic fluorescence of BSA through both dynamic and static quenching mechanisms. The thermodynamic analysis suggested that hydrophobic force was the main force in stabilizing the BSA-kusaginin complex. In addition, conformation changes of BSA were observed from three-dimensional and synchronous fluorescence spectra, UV spectra, and CD spectra under experimental conditions. All these experimental results have been complemented and validated by the molecular docking and dynamic simulation studies, which revealed that kusaginin was bound on the hydrophobic cavity in subdomain IIA of BSA and formed a stable BSA-kusaginin complex. Finally, density functional theory (DFT) calculation further implied that hydrogen bonds also support stabilizing the BSA-kusaginin complex. This research may aid in understanding the pharmacological characteristics of kusaginin and provide a vital reference modeling for the design of analogues drugs.

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.

Impact of Au144 metal clusters on the structural and inhibitory mechanism of Aβ42 peptide: A theoretical approach

One of the main causes for Alzheimer disease is the abnormal self-assembly of the amyloid-beta (Aβ) peptide, which in turn forms a toxic β-rich aggregation. A recent study suggests that gold nanoparticles (AuNPs) can inhibit the Aβ aggregation. Nevertheless, the effects of AuNPs on Aβ peptide system are still ambiguous and needs exploration that is more detailed. Molecular dynamics simulations have been carried out to investigate the aggregation mechanism of Aβ₄₂ peptide for 500 ns. During simulation, C-terminus regions of Met 35-Ala42 residues exhibits β-sheet conformations. Meanwhile, the Au₁₄₄MC coordination induces substantial α-helical character, both α-helix and 3₁₀-helix structure at 0-500ns, in the region of Asp1-Arg5 and Val36-Ile41 residues. The Au₁₄₄MC strongly coordinates with Asp1, Ala2, Glu3, Phe4, Asp7, Tyr10 and Gln15 residues that plays the significant effects to loss the β-sheet geometry in the N-terminal region and it converted into random α-helix, turn and bend conformation. On comparing the RMSF of the Aβ₄₂ peptide and Aβ₄₂-Au₁₄₄MC complex shows that the coordination of Au₁₄₄MC results in greater rigidity of the Aβ₄₂ peptide backbone regions with exemptions for the Asp1, Ala2, Glu3, Leu34, Ile41 and Ala42 residues due to the strong binding between the metal cluster and the CHC (Leu17-Ala21) region. The structural stability of the Aβ₄₂ peptide and Aβ₄₂-Au₁₄₄MC complex is enhanced by the several intermolecular and intramolecular interactions and it was visibly revealed in the H-bond. From the above results, it is very evident that the Au₁₄₄MC can be used as inhibitor agent for the oligomerization of Aβ₄₂.

Inhibition of BACE1 and amyloid β aggregation by polyketide from Streptomyces sp

Alzheimer's disease (AD) causes cognitive impairment in the elderly and is a severe problem worldwide. One of the major reasons for the pathogenesis of AD is thought to be due to the accumulation of amyloid beta (Aβ) peptides that result in neuronal cell death in the brain. In this study, bioassay-guided fractionation was performed to develop seed compounds for anti-AD drugs that can act as dual inhibitors of BACE1 and Aβ aggregation from secondary metabolites produced by Streptomyces sp. To improve the solubility, the crude extracts were methylated with trimethylsilyl (TMS) diazomethane and then purified to yield polyketides 1-5, including the new compound 1. We synthesized the compounds 6 and 7 (original compounds 2 and 3, respectively), and their activities were evaluated. KS-619-1, the demethylated form of 4 and 5, was isolated and evaluated for its inhibitory activity. The IC₅₀ values for BACE1 and Aβ aggregation were found to be 0.48 and 1.1 μM, respectively, indicating that KS-619-1 could be a lead compound for the development of therapeutic agents for AD.

An update in toxicology of ageing

The field of ageing research has been rapidly advancing in recent decades and it had provided insight into the complexity of ageing phenomenon. However, as the organism-environment interaction appears to significantly affect the organismal pace of ageing, the systematic approach for gerontogenic risk assessment of environmental factors has yet to be established. This puts demand on development of effective biomarker of ageing, as a relevant tool to quantify effects of gerontogenic exposures, contingent on multidisciplinary research approach. Here we review the current knowledge regarding the main endogenous gerontogenic pathways involved in acceleration of ageing through environmental exposures. These include inflammatory and oxidative stress-triggered processes, dysregulation of maintenance of cellular anabolism and catabolism and loss of protein homeostasis. The most effective biomarkers showing specificity and relevancy to ageing phenotypes are summarized, as well. The crucial part of this review was dedicated to the comprehensive overview of environmental gerontogens including various types of radiation, certain types of pesticides, heavy metals, drugs and addictive substances, unhealthy dietary patterns, and sedentary life as well as psychosocial stress. The reported effects in vitro and in vivo of both recognized and potential gerontogens are described with respect to the up-to-date knowledge in geroscience. Finally, hormetic and ageing decelerating effects of environmental factors are briefly discussed, as well.

Expression of N-Terminal Cysteine Aβ42 and Conjugation to Generate Fluorescent and Biotinylated Aβ42

Fluorescent derivatives of the β-amyloid peptides (Aβ) are valuable tools for studying the interactions of Aβ with cells. Facile access to labeled expressed Aβ offers the promise of Aβ with greater sequence and stereochemical integrity, without impurities from amino acid deletion and epimerization. Here, we report methods for the expression of Aβ42 with an N-terminal cysteine residue, Aβ(C1-42), and its conjugation to generate Aβ42 bearing fluorophores or biotin. The methods rely on the hitherto unrecognized observation that expression of the Aβ(MC1-42) gene yields the Aβ(C1-42) peptide, because the N-terminal methionine is endogenously excised by Escherichia coli. Conjugation of Aβ(C1-42) with maleimide-functionalized fluorophores or biotin affords the N-terminally labeled Aβ42. The expression affords ∼14 mg of N-terminal cysteine Aβ from 1 L of bacterial culture. Subsequent conjugation affords ∼3 mg of labeled Aβ from 1 L of bacterial culture with minimal cost for labeling reagents. High-performance liquid chromatography analysis indicates the N-terminal cysteine Aβ to be >97% pure and labeled Aβ peptides to be 94-97% pure. Biophysical studies show that the labeled Aβ peptides behave like unlabeled Aβ and suggest that labeling of the N-terminus does not substantially alter the properties of the Aβ. We further demonstrate applications of the fluorophore-labeled Aβ peptides by using fluorescence microscopy to visualize their interactions with mammalian cells and bacteria. We anticipate that these methods will provide researchers convenient access to useful N-terminally labeled Aβ, as well as Aβ with an N-terminal cysteine that enables further functionalization.

The nickel-chelator dimethylglyoxime inhibits human amyloid beta peptide in vitro aggregation

One of the hallmarks of the most common neurodegenerative disease, Alzheimer's disease (AD), is the extracellular deposition and aggregation of Amyloid Beta (Aβ)-peptides in the brain. Previous studies have shown that select metal ions, most specifically copper (Cu) and zinc (Zn) ions, have a synergistic effect on the aggregation of Aβ-peptides. In the present study, inductively coupled plasma mass spectrometry (ICP-MS) was used to determine the metal content of a commercial recombinant human Aβ40 peptide. Cu and Zn were among the metals detected; unexpectedly, nickel (Ni) was one of the most abundant elements. Using a fluorescence-based assay, we found that Aβ40 peptide in vitro aggregation was enhanced by addition of Zn2+ and Ni2+, and Ni2+-induced aggregation was facilitated by acidic conditions. Nickel binding to Aβ40 peptide was confirmed by isothermal titration calorimetry. Addition of the Ni-specific chelator dimethylglyoxime (DMG) inhibited Aβ40 aggregation in absence of added metal, as well as in presence of Cu2+ and Ni2+, but not in presence of Zn2+. Finally, mass spectrometry analysis revealed that DMG can coordinate Cu or Ni, but not Fe, Se or Zn. Taken together, our results indicate that Ni2+ ions enhance, whereas nickel chelation inhibits, Aβ peptide in vitro aggregation. Hence, DMG-mediated Ni-chelation constitutes a promising approach towards inhibiting or slowing down Aβ40 aggregation.

Exploring interactions between lipids and amyloid-forming proteins: A review on applying fluorescence and NMR techniques

A hallmark of Alzheimer's, Parkinson's, and other amyloid diseases is the assembly of amyloid proteins into amyloid aggregates or fibrils. In many cases, the formation and cytotoxicity of amyloid assemblies are associated with their interaction with cell membranes. Despite studied for many years, the characterization of the interaction is challenged for reasons on the multiple aggregation states of amyloid-forming proteins, transient and weak interactions in the complex system. Although several strategies such as computation biology, spectroscopy, and imaging methods have been performed, there is an urgent need to detail the molecular mechanism in different time scales and high resolutions. This review highlighted the recent applications of fluorescence, solution and solid-state NMR in exploring the interactions between amyloid protein and membranes attributing to their advantages of high sensitivity and atomic resolution.

Real-Time Analysis of Specific Binding between Apolipoprotein E Isoforms and Amyloid β-Peptide by Dual Polarization Interferometry

One of the pathogenesis hypotheses of Alzheimer's disease (AD) is amyloid depositions and neurofibrillary tangles. Apolipoprotein E (Apo E) acts a vital part in the development of AD by affecting the aggregation and clearance of amyloid-β (Aβ). In this paper, a dual polarization interferometry (DPI) technique was employed for a real-time investigation toward the binding events of Apo E isoforms, for instance, Apo E2, Apo E3, and Apo E4, with Aβ_1-40. By evaluation of detailed binding information provided by DPI, the affinities between Apo E isoforms and Aβ_1-40 follow the order of E4 > E3 > E2, and the dissociation constants (K_D) of Aβ_1-40 with Apo E2, Apo E3, and Apo E4 were determined to be 251 ± 37, 40 ± 0.65, and 24.6 ± 2.42 nM, respectively. Our findings reveal the isoform-specific binding behaviors from a kinetics perspective, which can help us understand that Apo E4 has a higher risk of causing AD because of its promoting effect on Aβ aggregation and fibrillation and inefficient clearance of Aβ. Remarkably, this work provides a promising method for exploring the dynamics of interactions between biomolecules and expectantly contributes to the development of AD drugs and therapies targeting Apo E and Aβ.

The Impact of Halogenated Phenylalanine Derivatives on NFGAIL Amyloid Formation

The hexapeptide hIAPP22-27 (NFGAIL) is known as a crucial amyloid core sequence of the human islet amyloid polypeptide (hIAPP) whose aggregates can be used to better understand the wild-type hIAPP's toxicity to β-cell death. In amyloid research, the role of hydrophobic and aromatic-aromatic interactions as potential driving forces during the aggregation process is controversially discussed not only in case of NFGAIL, but also for amyloidogenic peptides in general. We have used halogenation of the aromatic residue as a strategy to modulate hydrophobic and aromatic-aromatic interactions and prepared a library of NFGAIL variants containing fluorinated and iodinated phenylalanine analogues. We used thioflavin T staining, transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) to study the impact of side-chain halogenation on NFGAIL amyloid formation kinetics. Our data revealed a synergy between aggregation behavior and hydrophobicity of the phenylalanine residue. This study introduces systematic fluorination as a toolbox to further investigate the nature of the amyloid self-assembly process.