Surface plasmon resonance, fluorescence, and circular dichroism studies for the characterization of the binding of BACE-1 inhibitors

Efficient characterization of multiple binding sites of small molecule imaging ligands on amyloid-beta, tau and alpha-synuclein

PURPOSE

There is an unmet need for compounds to detect fibrillar forms of alpha-synuclein (αSyn) and 4-repeat tau, which are critical in many neurodegenerative diseases. Here, we aim to develop an efficient surface plasmon resonance (SPR)-based assay to facilitate the characterization of small molecules that can bind these fibrils.

METHODS

SPR measurements were conducted to characterize the binding properties of fluorescent ligands/compounds toward recombinant amyloid-beta (Aβ)42, K18-tau, full-length 2N4R-tau and αSyn fibrils. In silico modeling was performed to examine the binding pockets of ligands on αSyn fibrils. Immunofluorescence staining of postmortem brain tissue slices from Parkinson's disease patients and mouse models was performed with fluorescence ligands and specific antibodies.

RESULTS

We optimized the protocol for the immobilization of Aβ42, K18-tau, full-length 2N4R-tau and αSyn fibrils in a controlled aggregation state on SPR-sensor chips and for assessing their binding to ligands. The SPR results from the analysis of binding kinetics suggested the presence of at least two binding sites for all fibrils, including luminescent conjugated oligothiophenes, benzothiazole derivatives, nonfluorescent methylene blue and lansoprazole. In silico modeling studies for αSyn (6H6B) revealed four binding sites with a preference for one site on the surface. Immunofluorescence staining validated the detection of pS129-αSyn positivity in the brains of Parkinson's disease patients and αSyn preformed-fibril injected mice, 6E10-positive Aβ in arcAβ mice, and AT-8/AT-100-positivity in pR5 mice.

CONCLUSION

SPR measurements of small molecules binding to Aβ42, K18/full-length 2N4R-tau and αSyn fibrils suggested the existence of multiple binding sites. This approach may provide efficient characterization of compounds for neurodegenerative disease-relevant proteinopathies.

Inhibitory mechanism of O-methylated quercetins, highly potent β-secretase inhibitors isolated from Caragana balchaschensis (Kom.) Pojark

ETHNOPHARMACOLOGICAL RELEVANCE

Caragana has a standing history of implementation in Traditional Chinese Medicine (TCM). Most species of this genus have been explored for multi-functional purposes, such as promoting blood circulation and curing neuralgia, fatigue, migraine, arthritis, and vascular hypertension (Meng et al., 2009). Among them, the well-known species C. sinica showed the most promising potential to increase the expression of ADAM10 among 313 tested medicinal plants, which is one of the promising approach for the treatment of Alzheimer's disease (AD). (Schuck et al., 2015).

AIM OF THIS STUDY

The aim of this work is to explore β-secretase inhibitory activity of compounds isolated from the aerial part of endemic Caragana balchaschensis (Kom.) Pojark. We provided a full characterization of their inhibitory mechanisms, binding affinities, and binding modes.

MATERIALS AND METHODS

The isolation of quercetin derivatives was accomplished by various chromatographical approaches and their structures were annotated by spectroscopic analysis. The detailed kinetic behavior of β-secretase inhibitors was determined by estimation of kinetic parameters (K_m, V_max, K_I, and K_IS). Binding affinities (K_SV) and binding modes of inhibitors were elucidated by fluorescence quenching and molecular docking studies, respectively.

RESULTS

O-methylated quercetins (2-7) were significantly effective in β-secretase inhibition with IC₅₀ ranging from 1.2 to 6.5 μM. The most active one (6) was 20-fold effective than the mother skeleton, quercetin. The O-methyl motif was a critical factor in β-secretase inhibition: tri-O-methylated (1.2 μM) > di-O-methylated (3.5 μM) > mono-O-methylated (6.5 μM) > quercetin (25.2 μM). In the kinetic study, all quercetins (1-7) showed a noncompetitive inhibition, but glucoside ones (8 and 9) were mixed type I inhibitors. The binding affinities (K_SV) were agreed with inhibitory potencies. The O-methylated quercetins were annotated as the most natural abundant metabolites in the aerial part by LC-ESI-TOF/MS. Binding modes of inhibitors to enzyme were elucidated by molecular docking experiments.

CONCLUSION

This study disclosed that most of the major phenolic metabolites of the aerial part of C. balchaschensis are O-methylated quercetins, which have a significant inhibitory effect on β-secretase, which is a critical factor for AD.

Glycosaminoglycans from Litopenaeus vannamei Inhibit the Alzheimer's Disease β Secretase, BACE1

Only palliative therapeutic options exist for the treatment of Alzheimer's Disease; no new successful drug candidates have been developed in over 15 years. The widely used clinical anticoagulant heparin has been reported to exert beneficial effects through multiple pathophysiological pathways involved in the aetiology of Alzheimer's Disease, for example, amyloid peptide production and clearance, tau phosphorylation, inflammation and oxidative stress. Despite the therapeutic potential of heparin as a multi-target drug for Alzheimer's disease, the repurposing of pharmaceutical heparin is proscribed owing to the potent anticoagulant activity of this drug. Here, a heterogenous non-anticoagulant glycosaminoglycan extract, obtained from the shrimp Litopenaeus vannamei, was found to inhibit the key neuronal β-secretase, BACE1, displaying a more favorable therapeutic ratio compared to pharmaceutical heparin when anticoagulant activity is considered.

The dark side of Alzheimer's disease: unstructured biology of proteins from the amyloid cascade signaling pathway

Alzheimer's disease (AD) is a leading cause of age-related dementia worldwide. Despite more than a century of intensive research, we are not anywhere near the discovery of a cure for this disease or a way to prevent its progression. Among the various molecular mechanisms proposed for the description of the pathogenesis and progression of AD, the amyloid cascade hypothesis, according to which accumulation of a product of amyloid precursor protein (APP) cleavage, amyloid β (Aβ) peptide, induces pathological changes in the brain observed in AD, occupies a unique niche. Although multiple proteins have been implicated in this amyloid cascade signaling pathway, their structure-function relationships are mostly unexplored. However, it is known that two major proteins related to AD pathology, Aβ peptide, and microtubule-associated protein tau belong to the category of intrinsically disordered proteins (IDPs), which are the functionally important proteins characterized by a lack of fixed, ordered three-dimensional structure. IDPs and intrinsically disordered protein regions (IDPRs) play numerous vital roles in various cellular processes, such as signaling, cell cycle regulation, macromolecular recognition, and promiscuous binding. However, the deregulation and misfolding of IDPs may lead to disturbed signaling, interactions, and disease pathogenesis. Often, molecular recognition-related IDPs/IDPRs undergo disorder-to-order transition upon binding to their biological partners and contain specific disorder-based binding motifs, known as molecular recognition features (MoRFs). Knowing the intrinsic disorder status and disorder-based functionality of proteins associated with amyloid cascade signaling pathway may help to untangle the mechanisms of AD pathogenesis and help identify therapeutic targets. In this paper, we have used multiple computational tools to evaluate the presence of intrinsic disorder and MoRFs in 27 proteins potentially relevant to the amyloid cascade signaling pathway. Among these, BIN1, APP, APOE, PICALM, PSEN1 and CD33 were found to be highly disordered. Furthermore, their disorder-based binding regions and associated short linear motifs have also been identified. These findings represent important foundation for the future research, and experimental characterization of disordered regions in these proteins is required to better understand their roles in AD pathogenesis.

Glutathione peroxidase 6 from Arabidopsis thaliana as potential biomarker for plants exposure assessment to di-(2-ethylhexyl) phthalate

As a most abundant plasticizer, Di-(2-ethylhexyl) phthalate (DEHP) has been widely used in agriculture with an associated potential toxicity to many species including plants via the production of the excessive reactive oxygen species (ROS). However, the potential toxic mechanisms of the plasticizer DEHP-induced oxidative damage to plants remain unknown. The antioxidant enzyme glutathione peroxidase has been suggested as biomarkers to reflect over excessive oxidative stress. In this study, the effect of DEHP on AtGPX6 was evaluated by multi-spectroscopic techniques and molecular docking method. The fluorescence intensity of AtGPX6 was reduced by the static quenching mechanism upon the addition of DEHP. The predominant forces in complex formation was mainly impelled by hydrogen bonding and Van der Waals forces based on the negative ΔH and ΔS, which was in accordance with the molecular docking results. In addition, the secondary structural changes resulted from the complex formation were investigated in presence of different amounts of DEHP by the combination of fluorescence, UV-vis absorption and Circular dichroism spectra, which revealed the loosening and unfolding of the framework of AtGPX6 accompanied with the enhancement of the hydrophilicity around the tryptophan residues. The exploration of the interaction mechanism of DEHP with AtGPX6 at molecular level would help to evaluate the toxicity of the plasticizers and forecast the related adverse effects on plants.

Probing the molecular toxic mechanism of lead (II) ions with glutathione peroxidase 6 from Arabidopsis thaliana

Along with non-biodegradability and accumulation in agricultural soil, lead (II) ions exert considerable harmful effects on plants even at trace amount, especially for the oxidative damages elicited by the lead ions-induced excessive reactive oxygen species (ROS). The glutathione peroxidases were reported to be correspondent with the oxidative stress induced by heavy metals. However, limited data are available about the potential hazardous mechanisms of the lead ions-induced oxidative damage to plants at molecular level. In this study, the harmful impacts of lead ions on Arabidopsis thaliana glutathione peroxidase 6 (AtGPX6) were assessed based on multi-spectroscopic measurements and molecular docking study. The characteristic fluorescence of AtGPX6 was quenched by lead ions with static mechanism at different temperatures. AtGPX6 exhibits a single binding site with lead ions, and then the complex formation was mainly driven by hydrogen bonding interaction and van der Waals forces on account of the negative ΔH and ΔS. The secondary structural changes were observed from the synchronous fluorescence, UV-visible absorption and Circular dichroism spectra, which led to loosen and unfold of the protein framework accompanied by the incremental hydrophobicity around the vicinity of the tryptophan residues. Therefore, this work illustrates the detailed binding mode between lead (II) ions and glutathione peroxidase 6 from Arabidopsis thaliana and the toxic effects on antioxidative defense system induced by lead ions at molecular level.

Molecular mechanism study on the interactions of cadmium (II) ions with Arabidopsis thaliana glutathione transferase Phi8

Accumulation of cadmium ions may result in adverse effects on plant due to the oxidative stress via destructions of antioxidants and antioxidant enzymes. As the core component of the glutathione antioxidant system, glutathione S-transferases (GSTs) have been reported as biomarkers for evaluating the metal-induced oxidative damage to plants, but the potential toxicity and underlying toxic molecular mechanisms remain unknown. This article investigated the molecular interactions of cadmium ions with Arabidopsis thaliana glutathione S-transferase phi8 (AtGSTF8) by multi-spectroscopic techniques and enzyme activity measurements. The intrinsic fluorescence of AtGSTF8 was quenched statically upon the addition of cadmium ions accompanied with the complex formation and structural and conformational alterations from multiple spectroscopic measurements, resulting in deconstructed protein skeleton and microenvironmental alterations around the Tyr and Trp residues. A single binding site was predicted for AtGSTF8 towards cadmium ions and the van der Walls interactions and hydrogen bonds are the major driving forces of the interaction. In addition, the transferase activity changes of AtGSTF8 upon the addition of cadmium ions have been observed. The implementation of this work helps to clarify the mechanism of oxidative damage and antioxidant enzymes response induced by heavy metal accumulation in plant at molecular level.

A Glycosaminoglycan Extract from Portunus pelagicus Inhibits BACE1, the β Secretase Implicated in Alzheimer's Disease

Therapeutic options for Alzheimer's disease, the most common form of dementia, are currently restricted to palliative treatments. The glycosaminoglycan heparin, widely used as a clinical anticoagulant, has previously been shown to inhibit the Alzheimer's disease-relevant β-secretase 1 (BACE1). Despite this, the deployment of pharmaceutical heparin for the treatment of Alzheimer's disease is largely precluded by its potent anticoagulant activity. Furthermore, ongoing concerns regarding the use of mammalian-sourced heparins, primarily due to prion diseases and religious beliefs hinder the deployment of alternative heparin-based therapeutics. A marine-derived, heparan sulphate-containing glycosaminoglycan extract, isolated from the crab Portunus pelagicus, was identified to inhibit human BACE1 with comparable bioactivity to that of mammalian heparin (IC50 = 1.85 μg mL-1 (R2 = 0.94) and 2.43 μg mL-1 (R2 = 0.93), respectively), while possessing highly attenuated anticoagulant activities. The results from several structural techniques suggest that the interactions between BACE1 and the extract from P. pelagicus are complex and distinct from those of heparin.

Molecular mechanism investigation on the interactions of copper (II) ions with glutathione peroxidase 6 from Arabidopsis thaliana

Accumulation of copper (II) ions in plant leads to the excessive reactive oxygen species (ROS) which attributes to the depletion of the antioxidants in the cell and destruction to antioxidant enzymes. The antioxidant enzyme glutathione peroxidase has been used as biomarkers to reflect metal-induced oxidative stress. However, the underlying toxic mechanisms of the copper ions(II)-induced oxidative damage to plants remain unknown. In the work, a detailed molecular interaction of copper (II) ions with Arabidopsis thaliana glutathione peroxidase 6 (AtGPX6) in relation with poisonous effects of exposure to heavy metal was investigated by multiple spectroscopic techniques. The intrinsic fluorescence of AtGPX6 was quenched upon the addition of copper (II) ions by the combination of static and dynamic quenching mechanisms accompanied by complex formation and conformational changes. A single binding site was revealed for AtGPX6 towards copper ions. The binding process was hydrophobic effect accompanied by positive entropy change and enthalpy change. The secondary structure of AtGPX6 was changed by the addition of copper ions investigated by synchronous fluorescence spectroscopy, ultraviolet-visible absorption spectroscopy and circular dichroism spectroscopy, resulting in loosened and deconstructed protein skeleton and increased hydrophobicity around the Trp residues. This study helps to illuminate the detailed interactions between copper ions and plant glutathione peroxidase and elucidate the destructive mechanism to antioxidative defense system caused by heavy metal exposure at molecular level.

Surface plasmon resonance prism coupler for enhanced circular dichroism sensing

A novel method for enhanced circular dichroism (CD) detection is proposed based on a surface plasmon resonance (SPR) prism coupler and a polarization scanning ellipsometry technique. An analytical model is derived to extract the CD and degree of polarization (DOP) properties of optical samples with and without scattering effects, respectively. The validity of the analytical model is confirmed by means of numerical simulations. The simulation results show that the proposed detection method has a sensitivity of 10^-5~10^-6 RIU (refractive index unit) for refractive indices in the range of 1.32~1.36 and 1.3100~1.3118. The practical feasibility of the proposed method is demonstrated by the experimental results for the sensitivity of the CD with the chlorophyllin samples with/without scattering effect. It is shown that for both types of sample, the extracted CD value increases linearly with the chlorophyll concentration over the considered range. In general, the results obtained in this study show that the measured CD response is highly sensitive to the polarization scanning angle. Consequently, the potential of polarization scanning ellipsometry for high-resolution CD detection is confirmed.

Novel Tacrine-Benzofuran Hybrids as Potent Multitarget-Directed Ligands for the Treatment of Alzheimer's Disease: Design, Synthesis, Biological Evaluation, and X-ray Crystallography

Twenty-six new tacrine-benzofuran hybrids were designed, synthesized, and evaluated in vitro on key molecular targets for Alzheimer's disease. Most hybrids exhibited good inhibitory activities on cholinesterases and β-amyloid self-aggregation. Selected compounds displayed significant inhibition of human β-secretase-1 (hBACE-1). Among the 26 hybrids, 2e showed the most interesting profile as a subnanomolar selective inhibitor of human acetylcholinesterase (hAChE) (IC50 = 0.86 nM) and a good inhibitor of both β-amyloid aggregation (hAChE- and self-induced, 61.3% and 58.4%, respectively) and hBACE-1 activity (IC50 = 1.35 μM). Kinetic studies showed that 2e acted as a slow, tight-binding, mixed-type inhibitor, while X-ray crystallographic studies highlighted the ability of 2e to induce large-scale structural changes in the active-site gorge of Torpedo californica AChE (TcAChE), with significant implications for structure-based drug design. In vivo studies confirmed that 2e significantly ameliorates performances of scopolamine-treated ICR mice. Finally, 2e administration did not exhibit significant hepatotoxicity.