Advanced analytical methodologies in Alzheimer’s disease drug discovery

Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta

Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.

Electroacupuncture Enhances the Functional Connectivity of Limbic System to Neocortex in the 5xFAD Mouse Model of Alzheimer's Disease

Our previous study revealed that acupuncture may exhibit therapeutic effects on Alzheimer's disease (AD) through the activation of metabolism in memory-related brain regions. However, the underlying functional mechanism remains poorly understood and warrants further investigation. In this study, we used resting-state functional magnetic resonance imaging (rsfMRI) to explore the potential effect of electroacupuncture (EA) on the 5xFAD mouse model of AD. We found that the EA group exhibited significant improvements in the number of platforms crossed and the time spent in the target quadrant when compared with the Model group (p < 0.05). The functional connectivity (FC) of left hippocampus (Hip) was enhanced significantly among 12 regions of interest (ROIs) in the EA group (p < 0.05). Based on the left Hip as the seed point, the rsfMRI analysis of the entire brain revealed increased FC between the limbic system and the neocortex in the 5xFAD mice after EA treatment. Additionally, the expression of amyloid-β(Aβ) protein and deposition in the Hip showed a downward trend in the EA group compared to the Model group (p < 0.05). In conclusion, our findings indicate that EA treatment can improve the learning and memory abilities and inhibit the expression of Aβ protein and deposition of 5xFAD mice. This improvement may be attributed to the enhancement of the resting-state functional activity and connectivity within the limbic-neocortical neural circuit, which are crucial for cognition, motor function, as well as spatial learning and memory abilities in AD mice.

Novel perspective for protein-drug interaction analysis: atomic force microscope

Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.

Study on Phenolic and Organic Acid Compositions and Antioxidant and Enzyme Inhibition Activities of Agaricomycetes Mushroom Species from Turkey

Mushrooms stand out as one of nature's best gifts among the natural product sources with their diversity, therapeutic values and increasing popularity. In this study, antioxidant (ABTS·+ scavenging, β-carotene-bleaching, cupric-reducing antioxidant capacity (CUPRAC), DPPH· scavenging, and metal chelating assays), and enzyme (buty-rylcholinesterase (BChE) and acetylcholinesterase (AChE), α-amylase and α-glucosidase) inhibition activities of the extracts obtained from Coprinus comatus (O.F. Müll.) Pers., Cerrena unicolor (Bull.) Murrill, Inocutis rheades (Pers.) Fiasson & Niemela and Leptoporus mollis (Pers.) Quél. mushroom species were investigated. The presence of phenolic and organic acid compounds associated with the bioactive properties of the mushroom species was determined by HPLC-DAD. Fumaric acid was found to be prominent compound in C. comatus (43.90 µg/g dw) and C. unicolor (659.9 µg/g dw), vanillin in L. mollis (19.48 µg/g dw), and p-coumaric acid in I. rheades (21.32 µg/g dw). L. mollis methanol extract, as well as higher antioxidant activity than the standards in CUPRAC and β-carotene-bleaching assays, was noted as superior antioxidant active in all assays (except metal chelating). C. comatus possessed the highest inhibition activity on α-amylase (IC50: 0.23 mg/mL for methanol extract), AChE (IC50: 125.50 µg/mL for hexane extract), and BChE (IC50: 61.03 µg/mL for methanol extract). Also, C. comatus methanol (IC50: 0.09 mg/mL) and L. mollis hexane (IC50 : 0.11 mg/ mL) extracts were better α-glucosidase inhibition active than the acarbose (IC50: 0.37 mg/mL). Our study ascertained that the studied mushroom species are particularly sources of biochemically active compounds with therapeutic potential.

The Immune System as a Therapeutic Target for Alzheimer’s Disease

Alzheimer’s disease (AD) is a heterogeneous neurodegenerative disorder and is the most common cause of dementia. Furthermore, aging is considered the most critical risk factor for AD. However, despite the vast amount of research and resources allocated to the understanding and development of AD treatments, setbacks have been more prominent than successes. Recent studies have shown that there is an intricate connection between the immune and central nervous systems, which can be imbalanced and thereby mediate neuroinflammation and AD. Thus, this review examines this connection and how it can be altered with AD. Recent developments in active and passive immunotherapy for AD are also discussed as well as suggestions for improving these therapies moving forward.

Effects of Electroacupuncture on the Correlation between Serum and Central Immunity in AD Model Animals

Objective

The goal was to investigate the connection between neuroinflammation in the brain and serum inflammatory markers as Alzheimer's disease progressed. We also sought to determine whether electroacupuncture had an effect on inflammatory markers found in blood and other brain regions.

Methods

As an animal model for AD, we used senescence-accelerated mouse prone 8 (SAMP8) mice. To examine the effects and probable mechanism of electroacupuncture, we used HE staining, immunofluorescence staining, western blotting, and enzyme-linked immunosorbent assay.

Results

Electroacupuncture therapy protected neurons, significantly downregulated the Iba-1 level in the hippocampus (p value was 0.003), frontal lobe cortex (p value was 0.042), and temporal lobe cortex (p value was 0.013) of the AD animal model, all of which had significantly lower levels of IL-6 (p value was 0.001), IL-1β (p value was 0.001), and TNF-α (p value was 0.001) in their serum.

Conclusion

The amounts of IL-6, IL-1β, and TNF-α detected in the serum were strongly linked to the levels discovered in the hippocampus and the frontal lobes of the brain, respectively. A better understanding of the electroacupuncture process as well as the course of Alzheimer's disease and the therapeutic benefits of electroacupuncture may be gained by using biomarkers such as serum inflammatory marker biomarkers.

Synthesis of New 3-Arylcoumarins Bearing N-Benzyl Triazole Moiety: Dual Lipoxygenase and Butyrylcholinesterase Inhibitors With Anti-Amyloid Aggregation and Neuroprotective Properties Against Alzheimer’s Disease

A novel series of coumarin derivatives linked to the N-benzyl triazole group were synthesized and evaluated against 15-lipoxygenase (15-LOX), and acetyl- and butyrylcholinesterase (AChE and BuChE) to find the most potent derivative against Alzheimer’s disease (AD). Most of the compounds showed weak to moderate activity against ChEs. Among the most active BuChE and 15-LOX inhibitors, 8l and 8n exhibited an excellent neuroprotective effect, higher than the standard drug (quercetin) on the PC12 cell model injured by H2O2 and significantly reduced aggregation of amyloid Aβ1-42, with potencies of 1.44 and 1.79 times higher than donepezil, respectively. Compound 8l also showed more activity than butylated hydroxytoluene (BHT) as the reference antioxidant agent in reducing the levels of H2O2 activated by amyloid β in BV2 microglial cells. Kinetic and ligand–enzyme docking studies were also performed for better understanding of the mode of interaction between the best BuChE inhibitor and the enzyme. Considering the acceptable BuChE and 15-LOX inhibition activities as well as significant neuroprotection, and anti-amyloid aggregation activities, 8l and 8n could be considered as potential MTDLs for further modification and studies against AD.

Alzheimer's Disease and β-Secretase Inhibition: An Update With a Focus on Computer-Aided Inhibitor Design

INTRODUCTION

Alzheimer's disease (AD) is an intensifying neurodegenerative illness due to its irreversible nature. Identification of β-site amyloid precursor protein (APP) cleaving enzyme1 (BACE1) has been a significant medicinal focus towards AD treatment, and this has opened ground for several investigations. Despite the numerous works in this direction, no BACE1 inhibitor has made it to the final approval stage as an anti-AD drug.

METHOD

We provide an introductory background of the subject with a general overview of the pathogenesis of AD. The review features BACE1 inhibitor design and development with a focus on some clinical trials and discontinued drugs. Using the topical keywords BACE1, inhibitor design, and computational/theoretical study in the Web of Science and Scopus database, we retrieved over 49 relevant articles. The search years are from 2010 and 2020, with analysis conducted from May 2020 to March 2021.

RESULTS AND DISCUSSION

Researchers have employed computational methodologies to unravel potential BACE1 inhibitors with a significant outcome. The most used computer-aided approach in BACE1 inhibitor design and binding/interaction studies are pharmacophore development, quantitative structure-activity relationship (QSAR), virtual screening, docking, and molecular dynamics (MD) simulations. These methods, plus more advanced ones including quantum mechanics/molecular mechanics (QM/MM) and QM, have proven substantial in the computational framework for BACE1 inhibitor design. Computational chemists have embraced the incorporation of in vitro assay to provide insight into the inhibition performance of identified molecules with potential inhibition towards BACE1. Significant IC₅₀ values up to 50 nM, better than clinical trial compounds, are available in the literature.

CONCLUSION

The continuous failure of potent BACE1 inhibitors at clinical trials is attracting many queries prompting researchers to investigate newer concepts necessary for effective inhibitor design. The considered properties for efficient BACE1 inhibitor design seem enormous and require thorough scrutiny. Lately, researchers noticed that besides appreciable binding affinity and blood-brain barrier (BBB) permeation, BACE1 inhibitor must show low or no affinity for permeability-glycoprotein. Computational modeling methods have profound applications in drug discovery strategy. With the volume of recent in silico studies on BACE1 inhibition, the prospect of identifying potent molecules that would reach the approved level is feasible. Investigators should try pushing many of the identified BACE1 compounds with significant anti-AD properties to preclinical and clinical trial stages. We also advise computational research on allosteric inhibitor design, exosite modeling, and multisite inhibition of BACE1. These alternatives might be a solution to BACE1 drug discovery in AD therapy.

The functional potential of nine Allium species related to their untargeted phytochemical characterization, antioxidant capacity and enzyme inhibitory ability

In this study, the aerial parts and bulbs of nine Allium species were investigated for their functional phytochemical profile, in vitro antioxidant activities, acetylcholinesterase (AChE), butyrylcholinesterase (BChE), α-amylase, α-glucosidase, and tyrosinase inhibitory properties. Phenolics, alkaloids, glucosinolates and other sulfur-containing compounds were distinctively profiled in the different species. Maceration in methanol allowed recovering the highest cumulative phenolic content in A. scabrifolium (42.31 mg/g), followed by A. goekyigiti (33.15 mg/g) and A. atroviolaceum (28.35 mg/g). The aerial parts of all Allium species showed high in vitro antioxidant activity whereas methanolic extract of A. cappadocicum bulb showed the highest inhibition against AChE (2.44 mg galantamine equivalent/g) and the water extracts of A. isauricum aerial part were the best BChE inhibitors (4.31 mg galantamine equivalent/g). Bulbs were the richer source of oligosaccharides, and in vitro digestion determined an increase of oligosaccharides bioaccessibility. A promising nutraceutical potential could be highlighted in our understudied Allium species.

Development and Application of Activity-based Fluorescent Probes for High-Throughput Screening

High-throughput screening facilitates the rapid identification of novel hit compounds; however, it remains challenging to design effective high-throughput assays, partially due to the difficulty of achieving sensitivity in the assay techniques. Among the various analytical methods that are used, fluorescence-based assays dominate owing to their high sensitivity and ease of operation. Recent advances in activity-based sensing/imaging have further expanded the availability of fluorescent probes as monitors for high-throughput screening of result outputs. In this study, we have reviewed various activity-based fluorescent probes used in high-throughput screening assays, emphasizing their structure-related working mechanisms. Moreover, we have explored the possibility of the development of additional and better probes to boost hit identification and drug development against various targets.

Alzheimer Disease Clinical Trials Targeting Amyloid: Lessons Learned From Success in Mice and Failure in Humans

BACKGROUND

The goal of slowing or halting the development of Alzheimer disease (AD) has resulted in the huge allocation of resources by academic institutions and pharmaceutical companies to the development of new treatments. The etiology of AD is elusive, but the aggregation of amyloid-β and tau peptide and oxidative processes are considered critical pathologic mechanisms. The failure of drugs with multiple mechanisms to meet efficacy outcomes has caused several companies to decide not to pursue further AD studies and has left the field essentially where it has been for the past 15 years. Efforts are underway to develop biomarkers for detection and monitoring of AD using genetic, imaging, and biochemical technology, but this is of minimal use if no intervention can be offered.

REVIEW SUMMARY

In this review, we consider the natural progression of AD and how it continues despite present attempts to modify the amyloid-related machinery to alter the disease trajectory. We describe the mechanisms and approaches to AD treatment targeting amyloid, including both passive and active immunotherapy as well as inhibitors of enzymes in the amyloidogenic pathway.

CONCLUSION

Lessons learned from clinical trials of amyloid reduction strategies may prove crucial for the leap forward toward novel therapeutic targets to treat AD.

Study on Three Sarcocapnos Species as Potential Sources of Bioactive Compounds: Relation between Phenolic Content and Bioactivity by Multivariate Analysis

In this work, we report the phenolic composition and bioactivity of the aerial parts of three species of Sarcocapnos (S. enneaphylla, S. pulcherrima, and S. saetabensis) to study their potential as sources of bioactive compounds to revalorize them and contribute to the conservation of these plant species. Samples were collected in different locations in the province of Jaén (southeast of Spain), and qualitative and quantitative analyses of phenolic compounds were performed by high-performance liquid chromatography with diode array and mass spectrometry detection. S. enneaphylla presented the highest concentration of phenolic compounds (58 mg/g DE). The most abundant compound in S. enneaphylla and S. saetabensis was rutin (35 mg/g DE and 11.7 mg/g DE, respectively), whereas isorhamnetin-O-rutinoside was dominant in S. pulcherrima (11.5 mg/g DE). Several assays were performed to evaluate the potential bioactivity of the three species of Sarcocapnos. These assays included antioxidant and radical scavenging (ABTS and DPPH), reducing power (CUPRAC and FRAP), phosphomolybdenum and metal chelating, and enzyme inhibitory activity (acetylcholinesterase, amylase, butyrylcholinesterase, glucosidase, and tyrosinase). In general, all methanolic extracts presented the highest phenolic and flavonoid contents, as well as the highest radical scavenging, antioxidant, and enzyme inhibitory properties. This relationship between phenolics and bioactivity was confirmed by multivariate analysis.