Association Constants of Pyridine and Piperidine Alkaloids to Amyloid ß Peptide Determined by Electrochemical Impedance Spectroscopy

Bitter yet beneficial: The dual role of dietary alkaloids in managing diabetes and enhancing cognitive function

With the rising prevalence of diabetes and its association with cognitive impairment, interest in the use of dietary alkaloids and other natural products has grown significantly. Understanding how these compounds manage diabetic cognitive dysfunction (DCD) is crucial. This comprehensive review explores the etiology of DCD and the effects of alkaloids in foods and dietary supplements that have been investigated as DCD therapies. Data on how dietary alkaloids like berberine, trigonelline, caffeine, capsaicin, 1-deoxynojirimycin, nuciferine, neferine, aegeline, tetramethylpyrazine, piperine, and others regulate cognition in diabetic disorders were collected from PubMed, Research Gate, Web of Science, Science Direct, and other relevant databases. Dietary alkaloids could improve memory in behavioral models and modulate the mechanisms underlying the cognitive benefits of these compounds, including their effects on glucose metabolism, gut microbiota, vasculopathy, neuroinflammation, and oxidative stress. Evidence suggests that dietary alkaloids hold promise for improving cognition in diabetic patients and could open exciting avenues for future research in diabetes management.

Caspase-1 and Cathepsin B Inhibitors from Marine Invertebrates, Aiming at a Reduction in Neuroinflammation

Neuroinflammation is a condition associated with several types of dementia, such as Alzheimer’s disease (AD), mainly caused by an inflammatory response to amyloid peptides that induce microglial activation, with subsequent cytokine release. Neuronal caspase-1 from inflammasome and cathepsin B are key enzymes mediating neuroinflammation in AD, therefore, revealing new molecules to modulate these enzymes may be an interesting approach to treat neurodegenerative diseases. In this study, we searched for new caspase-1 and cathepsin B inhibitors from five species of Brazilian marine invertebrates (four cnidarians and one echinoderm). The results show that the extract of the box jellyfish Chiropsalmus quadrumanus inhibits caspase-1. This extract was fractionated, and the products monitored for their inhibitory activity, until the obtention of a pure molecule, which was identified as trigonelline by mass spectrometry. Moreover, four extracts inhibit cathepsin B, and Exaiptasia diaphana was selected for subsequent fractionation and characterization, resulting in the identification of betaine as being responsible for the inhibitory action. Both molecules are already found in marine organisms, however, this is the first study showing a potent inhibitory effect on caspase-1 and cathepsin B activities. Therefore, these new prototypes can be considered for the enzyme inhibition and subsequent control of the neuroinflammation.

Electrochemical flow injection analysis of the interaction between pyrroloquinoline quinone (PQQ) and α-synuclein peptides related to Parkinson's disease

α-Synuclein (α-syn) is a hallmark protein of Parkinson's disease (PD). The aggregation process of α-syn has been heavily associated with the pathogenesis of PD. With the exponentially growing number of potential therapeutic compounds that can inhibit the aggregation of α-syn, there is now a significant demand for a high-throughput analysis system. Herein, a novel flow injection analysis system with an electrochemical biosensor as the detector was developed to study the interaction of a well-described antioxidant and amyloid inhibitor, pyrroloquinoline quinone (PQQ) with α-synuclein peptides. Screen-printed gold electrodes (SPEs) were modified using heptapeptides from α-syn wild-type (WT) and mutants such as lysine knock-out (ETEE) and E46K. Affinity binding events between these peptides and PQQ were analyzed by electrochemical impedance spectroscopy (EIS) and further confirmed by high-performance liquid chromatography (HPLC), liquid chromatography/mass spectrometry (LC/MS), and nuclear magnetic resonance (NMR) spectroscopy. HPLC and LC/MS results revealed that PQQ formed a stable complex with α-syn. NMR results confirmed that the α-syn-PQQ complex was formed via a Schiff base formation-like process. In addition, results showed that lysine residues influenced the binding event, in which the presence of an extra lysine stabilized the α-syn-PQQ complex, and the absence of a lysine significantly decreased the interaction of α-syn with PQQ. Therefore, we concluded that EIS is a promising technique for the evaluation of the interaction between PQQ-based amyloid inhibitors and α-syn. The electrochemical flow injection analysis assembly provided a rapid and low-cost drug discovery platform for the evaluation of small molecule-protein interactions.

Interactions of Aβ1-42 Peptide and Its Three Fragments (Aβ8-12, Aβ8-13, and Aβ5-16) with Selected Nonsteroidal Drugs and Compounds of Natural Origin

In the following paper, we present the results of our studies on the interactions of the Aβ1-42 peptide and its three short fragments, namely Aβ5-16 (RHDSGYEVHHQK; HZ1), Aβ8-13 (SGYEVH; HZ2), and Aβ8-12 (SGYEV; HZ3) with selected painkillers (ibuprofen and aspirin) and compounds of natural origin (anabasine and epinephrine). Steady-state fluorescence spectroscopy was used to study the binding properties of the selected systems. Additionally, based on molecular dynamics (MD) calculations supported by NMR-derived restrains, we have proposed the most likely area of the interactions of Aβ1-42 and Aβ5-16 peptides with the investigated compounds. The influence of symmetrically oriented side chains of amino acid residues present in the first part of the Aβ1-42 sequence on the stability of the resulting complexes has been discussed. Finally, the changes in the peptide structures on account of complex formation were analyzed.

Computational analysis and optimization of carcinoembryonic antigen aptamers and experimental evaluation

Carcinoembryonic antigen (CEA), a highly glycosylated protein, overexpresses in many cancers. In this study, computational methods were used to optimize CEA aptamers. Experimental evaluvation of selected aptamers were conducted through electrochemical impedance spectroscopy. After two and three-dimensional structure modeling, the complexes of twelve reported aptamers against CEA were simulated using the ZDOCK server. Based on docking scores, two aptamer sequences (CSR59 and CSR57.1) were selected and used to create a new library. This ssDNA aptamer library consisting of 91 sequences was created using diverse in silico mutational methods. We obtained seventeen sequences having higher binding scores than reported sequences. Based on ZDOCK scores, the interaction domain of CEA, and steric hindrance due to glycosylation, two aptamer sequences (G3S1.5 and G2S2.2) were selected. An impedimetric aptasensor was designed, and selected aptamers were used as biorecognition elements. Resistance to charge transfer (Rct) quantities confirmed the bioinformatic approach and molecular docking scores. The result showed that the interaction ability of selected aptamers was about 13.5 fold higher than the control. It can be concluded that the selected aptamers have good potential for detection of carcinoembryonic antigen biomarker.

Probing the binding of Cu(2+) ions to a fragment of the Aβ(1-42) polypeptide using fluorescence spectroscopy, isothermal titration calorimetry and molecular dynamics simulations

Steady-state and time-resolved fluorescence quenching measurements supported by isothermal titration calorimetry (ITC) and molecular dynamics simulations (MD), with the NMR-derived restraints, were used to investigate the interactions of Cu(2+) ions with a fragment of the Aβ(1-42) polypeptide, Aβ(5-16) with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, denoted as HZ1. The studies presented in this paper, when compared with our previous results (Makowska et al., Spectrochim. Acta A 153: 451-456), show that the affinity of the peptide to metal ions is conformation-dependent. All the measurements were carried out in 20mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution, pH6.0. The Stern-Volmer equations, along with spectroscopic observations, were used to determine the quenching and binding parameters. The obtained results unequivocally suggest that Cu(2+) ions quench the fluorescence of HZ1 only through a static quenching mechanism, in contrast to the fragment from the N-terminal part of the FPB28 protein, with sequence Ac-Tyr-Lys-Thr-Ala-Asp-Gly-Lys-Thr-Tyr- NH2 (D9) and its derivative with a single point mutation: Ac-Tyr-Lys-Thr-Ala-Asn-Gly-Lys-Thr-Tyr- NH2 (D9_M), where dynamic quenching occurred. The thermodynamic parameters (ΔITCH, ΔITCS) for the interactions between Cu(2+) ions and the HZ1 peptide were determined from the calorimetric data. The conditional thermodynamic parameters suggest that, under the experimental conditions, the formation of the Cu(2+)-HZ1 complex is both an enthalpy and entropy driven process.

An immunosensor based on antibody binding fragments attached to gold nanoparticles for the detection of peptides derived from avian influenza hemagglutinin H5

This paper concerns the development of an immunosensor for detection of peptides derived from avian influenza hemagglutinin H5. Its preparation consists of successive gold electrode modification steps: (i) modification with 1,6-hexanedithiol and gold colloidal nanoparticles; (ii) immobilization of antibody-binding fragments (Fab') of anti-hemagglutinin H5 monoclonal antibodies Mab 6-9-1 via S-Au covalent bonds; and (iii) covering the remaining free space on the electrode surfaces with bovine serum albumin. The interactions between Fab' fragments and hemagglutinin (HA) variants have been explored with electrochemical impedance spectroscopy (EIS) in the presence of [Fe(CN)6](3-/4-) as an electroactive marker. The immunosensor was able to recognize three different His-tagged variants of recombinant hemagglutinin from H5N1 viruses: H1 subunit (17-340 residues) of A/swan/Poland/305-135V08/2006, the long HA (17-530 residues) A/Bar-headed Goose/Qinghai/12/2005 and H1 subunit (1-345 residues) of A/Vietnam/1194/2004. The strongest response has been observed for the long variant with detection limit of 2.2 pg/mL and dynamic range from 4.0 to 20.0 pg/mL.

Size does matter! Label-free detection of small molecule-protein interaction

This review is focused on methods for detecting small molecules and, in particular, the characterisation of their interaction with natural proteins (e.g. receptors, ion channels). Because there are intrinsic advantages to using label-free methods over labelled methods (e.g. fluorescence, radioactivity), this review only covers label-free techniques. We briefly discuss available techniques and their advantages and disadvantages, especially as related to investigating the interaction between small molecules and proteins. The reviewed techniques include well-known and widely used standard analytical methods (e.g. HPLC-MS, NMR, calorimetry, and X-ray diffraction), newer and more specialised analytical methods (e.g. biosensors), biological systems (e.g. cell lines and animal models), and in-silico approaches.

Electrochemical detection of β-amyloid peptides on electrode covered with N-terminus-specific antibody based on electrocatalytic O2 reduction by Aβ(1-16)-heme-modified gold nanoparticles

β-Amyloid (Aβ) peptides are believed to be important for the diagnosis and prognosis of Alzheimer's disease (AD) serving as reliable molecular biomarkers. In this work, we reported a simple and sensitive electrochemical strategy for the detection of total Aβ peptides using gold nanoparticles modified with Aβ(1-16)-heme (denoted as Aβ(1-16)-heme-AuNPs). Monoclonal antibody (mAb) specific to the common N-terminus of Aβ was immobilized onto gold electrode for the capture of Aβ(1-16)-heme-AuNPs. The anchored Aβ(1-16)-heme-AuNPs showed strong electrocatalytic O2 reduction. Pre-incubation of the mAb-covered electrode with native Aβ decreased the amount of Aβ(1-16)-heme-AuNPs immobilized onto the electrode, resulting in the decrease of the reduction current of O2 to H2O2. The competitive assay is sensitive and selective to Aβ peptides. The voltammetric responses were found to be proportional to the concentrations of Aβ ranging from 0.02 to 1.50nM, and a detection limit of 10 pM was achieved. To demonstrate the viability of the method for the analysis of Aβ in real sample, artificial cerebrospinal fluid (aCSF) containing Aβ(1-40), Aβ(1-42) and Aβ(1-16) was tested. We believe that the method would offer a useful means for quantifying Aβ in a biological matrix, and be valuable in the design of new types of electrochemical biosensors for the detection of peptides and proteins.

Surface plasmon resonance based biosensors for exploring the influence of alkaloids on aggregation of amyloid-β peptide

The main objective of the presented study was the development of a simple analytical tool for exploring the influence of naturally occurring compounds on the aggregation of amyloid-β peptide (Aβ₄₀) in order to find potential anti-neurodegenerative drugs. The gold discs used for surface plasmon resonance (SPR) measurements were modified with thioaliphatic acid. The surface functionalized with carboxylic groups was used for covalent attaching of Aβ₄₀ probe by creation of amide bonds in the presence of EDC/NHS. The modified SPR gold discs were used for exploring the Aβ₄₀ aggregation process in the presence of selected alkaloids: arecoline hydrobromide, pseudopelletierine hydrochloride, trigonelline hydrochloride and α-lobeline hydrochloride. The obtained results were discussed with other parameters which govern the phenomenon studied such as lipophilicity/hydrophilicy and Aβ₄₀-alkaloid association constants.

Immunosensor incorporating anti-His (C-term) IgG F(ab') fragments attached to gold nanorods for detection of His-tagged proteins in culture medium

Immunosensors based on gold electrodes (electrochemical) or gold discs (optical) modified with 1,6-hexanedithiol, gold nanorods and Anti-His (C-term) monoclonal antibody F(ab’) fragment are described. The antigen detected by the sensing platform is a recombinant histidine-tagged silk proteinase inhibitor (rSPI2-His₆). Electrochemical impedance spectroscopy (EIS) and surface plasmon resonance (SPR) techniques were used as methods for detection of the antigen. This approach allows to detect the antigen protein in concentration of 10 pg per mL (0.13 pM) of culture medium. The immunosensor shows good reproducibility due to covalent immobilization of F(ab’) fragments to gold nanorods layer.