Metabolomic approach to Alzheimer’s disease diagnosis based on mass spectrometry

Alzheimer??s disease is the most common neurodegenerative disease, but there is still no cure and early diagnosis remains very difficult. For this reason, the discovery of new biomarkers is of great importance. The application of metabolomics is emerging in this field, based on the use of mass spectrometry as a technique of analysis. In this work, blood serum samples (from Alzheimer??s disease patients and healthy controls) were analysed by mass spectrometry in order to search for potential metabolomic biomarkers. The application of multivariate statistical tools (PLS-DA) enabled us to discriminate between groups. In addition, some phosphatidylcholine compounds were identified as markers of the disease.     

Application of multilayered strategy for variable selection in QSAR modeling of PET and SPECT imaging agents as diagnostic agents for Alzheimer’s disease

Structural Chemistry - Non-invasive imaging of amyloid beta (Aβ) and tau fibrils in the brain may support an early and precise diagnosis of Alzheimer’s disease. Molecular imaging...     

Utilisation of the OliveNet™ Library to investigate phenolic compounds using molecular modelling studies in the context of Alzheimer’s disease

Alzheimer’s disease (AD) is a debilitating neurodegenerative disease that affects over 47 million people worldwide, and is the most common form of dementia. There is a vast body of literature demonstrating that the disease is caused by an accumulation of toxic extracellular amyloid-β (Aβ) peptides and intracellular neurofibrillary tangles that consist of hyperphosphorylated tau. Adherence to the Mediterranean diet has been shown to reduce the incidence of AD and the phenolic compounds in extra virgin olive oil, including oleocanthal, have gained a significant amount of attention. A large number of these ligands have been described in the pre-existing literature and 222 of these compounds have been characterised in the OliveNet™ database. In this study, molecular docking was used to screen the 222 phenolic compounds from the OliveNet™ database and assess their ability to bind to various forms of the Aβ and tau proteins. The phenolic ligands were found to be binding strongly to the hairpin-turn of the Aβ₁₋₄₀ and Aβ₁₋₄₂ monomers, and binding sites were also identified in the tau fibril protein structures. Luteolin-4′-O-rutinoside, oleuricine A, isorhoifolin, luteolin-7-O-rutinoside, cyanidin-3-O-rutinoside and luteolin-7,4-O-diglucoside were predicted to be novel lead compounds. Molecular dynamics (MD) simulations performed using well-known olive ligands bound to Aβ₁₋₄₂ oligomers highlighted that future work may examine potential anti-aggregating properties of novel compounds in the OliveNet™ database. This may lead to the development and evaluation of new compounds that may have efficacy against Alzheimer’s disease.     

Metal-amyloid-β peptide interactions: a preliminary investigation of molecular mechanisms for Alzheimer’s disease

Although humans have spent exactly 100 years combating Alzheimer’s disease (AD), the molecular mechanisms of AD remain unclear. Owing to the rapid growth of the oldest age groups of the popula-tion and the continuous increase of the incidence of AD, it has become one of the crucial problems to modern sciences. It would be impossible to prevent or reverse AD at the root without elucidating its molecular mechanisms. From the point of view of metal-amyloid-β peptide (Aβ) interactions, we review the molecular mechanisms of AD, mainly including Cu2 and Zn2 inducing the aggregation of Aβ, cata-lysing the production of active oxygen species from Aβ, as well as interacting with the ion-channel-like structures of Aβ. Moreover, the development of therapeutic drugs on the basis of metal-Aβ interactions is also briefly introduced. With the increasingly rapid progress of the molecular mechanisms of AD, we are now entering a new dawn that promises the delivery of revolutionary developments for the control of dementias.     

Using direct infusion mass spectrometry for serum metabolomics in Alzheimer’s disease

Currently, there is no cure for Alzheimer’s disease and early diagnosis is very difficult, since no biomarkers have been established with the necessary reliability and specificity. For the discovery of new biomarkers, the application of omics is emerging, especially metabolomics based on the use of mass spectrometry. In this work, an analytical approach based on direct infusion electrospray mass spectrometry was applied for the first time to blood serum samples in order to elucidate discriminant metabolites. Complementary methodologies of extraction and mass spectrometry analysis were employed for comprehensive metabolic fingerprinting. Finally, the application of multivariate statistical tools allowed us to discriminate Alzheimer patients and healthy controls, and identify some compounds as potential markers of disease. This approach provided a global vision of disease, given that some important metabolic pathways could be studied, such as membrane destabilization processes, oxidative stress, hypometabolism, or neurotransmission alterations. Most remarkable results are the high levels of phospholipids containing saturated fatty acids, respectively, polyunsaturated ones and the high concentration of whole free fatty acids in Alzheimer’s serum samples. Thus, these results represent an interesting approximation to understand the pathogenesis of disease and the identification of potential biomarkers. Graphical Abstract

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Chemometric modeling of PET imaging agents for diagnosis of Parkinson’s disease: a QSAR approach

Structural Chemistry - Recently, adenosine A2A receptor antagonists have been identified as an interesting drug target for the treatment of Parkinson’s disease (PD). Radiolabelled molecular...     

Computational systematic selectivity of the Fasalog inhibitors between ROCK-I and ROCK-II kinase isoforms in Alzheimer’s disease

Human Rho-associated coiled-coil forming kinase (ROCK) is a class of essential neurokinases that consists of two structurally conserved isoforms ROCK-I and ROCK-II; they have been revealed to play distinct roles in the pathogenesis of Alzheimer’s disease (AD) and other neurological disorders. Selective targeting of the two kinase isoforms with small-molecule inhibitors is a great challenge due to the surprisingly high homology in kinase domain (92 %) and the full identity in kinase active site (100 %). Here, we describe a computational protocol to systematically profile the selectivity of Fasudil and its 25 analogs (termed as Fasalogs) between the two kinase isoforms. It is suggested that the substitution of Fasudil’s 1,4-diazepane moiety with rigid ring such as Ripasudil and Dimehtylfasudil would render the resulting inhibitors of ROCK-II over ROCK-I (II-o-I) selectivity, while the substitution with long, flexible group such as H-89 and BDBM92607 tends to have I-o-II selectivity. Structural analysis reveals that the inhibitor affinity is not only determined by the identical active site, but also contributed from the non-identical first and second shells of the site as well as other non-conserved kinase regions, which can indirectly influence the active site and inhibitor binding through allosteric effect. A further kinase assay basically confirms the computational findings, which also exhibits a good consistence with theoretical selectivity over 10 tested samples (R_p = 0.89). In particular, the Fasalog compounds Dimehtylfasudil and H-89 are identified as II-o-I and I-o-II selective inhibitors. They can be considered as promising lead molecular entities to develop new specific ROCK isoform-selective Fasalog inhibitors.     

New approach to Tian’s equation applied to heat conduction and liquid injection calorimeters

In the calorimeters used for the determination of thermodynamical properties of liquid environments, the mixture takes place when injecting liquid in the mixture zone, this injection incorporates an additional calorific power that is a function of the volumetric heat capacity of the injected liquid and the injection flow. In this article, it is rewritten Tian??s equation including this additional power to relate correctly the experimental output to the mixture enthalpy. It is applied Tian??s equation, once it has been corrected, to two types of calorimeters: flow-microcalorimeters and isothermal titration calorimeters. In this second case, it has been taken into account the classical operating mode (titration) and the continuous liquid injection mode. Tian??s equation, completed with all the energetic terms additional to the mixture process, is of great interest for the scientific and academic community because it allows to explain, in a simple and effective way, the operation of these instruments.     

Infrared spectroscopic analysis of mononuclear leukocytes in peripheral blood from Alzheimer’s disease patients

Peripheral mononuclear leukocytes from Alzheimer’s disease (AD) patients were analyzed by infrared spectroscopy and their spectroscopic properties were compared with those from age-matched healthy controls. Two-dimensional correlation analysis of mean spectra measured at various disease stages shows that the protein secondary structure from AD patients involves β-sheet enrichment and carbonyl intensity increase relative to healthy controls. The area percentages of β-sheets, which were obtained by using a peak ratio second-derivative spectral treatment, were used for receiver operating characteristic (ROC) analysis to distinguish between patients with AD and age-matched healthy controls. The critical concentration and area under the curve (AUC) were determined by this curve analysis which showed a good performance for this quantitative assay. The results were 90% sensitivity and 90.5% specificity for determinations involving mild and moderate AD patients, and 82.1% sensitivity and 90.5% specificity for determinations involving patients at the three AD stages (mild, moderate, and severe). The AUC was greater than 0.85 in both scenarios. Taken together these results show that healthy controls are distinguished from mild and moderate AD patients better than from patients with severe disease and suggest that this infrared analysis is a promising strategy for AD diagnostics.     

Pharmacophore modeling coupled with molecular dynamic simulation approach to identify new leads for meprin-β metalloprotease

Human meprin beta metalloprotease, a small subgroup of the astacin family, is a potent drug target for the treatment of several disorders such as fibrosis, neurodegenerative disease in particular Alzheimer and inflammatory bowel diseases. In this study, a ligand-based pharmacophore approach has been used for the selection of potentially active compounds to understand the inhibitory activities of meprin-β by using the sulfonamide scaffold based inhibitors. Using this dataset, a pharmacophore model (Hypo1) was selected on the basis of a highest correlation coefficient (0.959), lowest total cost (105.89) and lowest root mean square deviation (1.31 Å) values. All the pharmacophore hypotheses generated from the candidate inhibitors comprised four features: two hydrogen-bond acceptor, one hydrogen-bond donor and one zinc binder feature. The best validated pharmacophore model (Hypo1) was used for virtual screening of compounds from several databases. The selective hit compounds were filtered by drug likeness property, acceptable ADMET profile, molecular docking and DFT study. Molecular dynamic simulations with the final 10 hit compounds revealed that a large number of non-covalent interactions were formed with the active site and specificity sub-pockets of the meprin beta metalloprotease. This study assists in the development of the new lead molecules as well as gives a better understanding of their interaction with meprin-β.     

Electrophoretic Determination of Formaldehyde in Human Urine: Application to Alzheimer’s Disease

The primary clinical diagnosis of Alzheimer’s disease is mainly based on medical history and neuropsychiatric inventory. It is urgent to seek biological indicators with better sensitivity and higher specificity to clinically diagnose and evaluate Alzheimer’s disease. In this work, an electrophoretic method based on 2-thiobarbituric acid derivatization and amperometric detection was developed to determine formaldehyde as a urinary biomarker of Alzheimer’s disease. Under the optimum conditions, the formaldehyde derivative was well separated from the coexisting interferences in urine sample. The limit of detection for formaldehyde was 80.0?nM (2.4?ng/?mL) based on an electrophoretic stacking technology. The average recovery values were in the range of 91.7–110%, and the relative standard deviation values were less than 4.1%. This method has been applied to analyze human urine samples from healthy volunteers and patients with different degrees of Alzheimer’s disease. The assay results showed that the content of urinary formaldehyde in patients suffering Alzheimer’s disease was significantly higher than that in healthy subjects (P?相似文献   

Iron, cysteine and Parkinson’s disease

Abstract  

A short review of the role of cysteine and iron in the progression of Parkinson’s disease is presented. The complex chemistry of cysteine and iron and its interactions are discussed and put into the context of oxidative stress during neurodegeneration.     

Strategies for examination of Alzheimer’s disease amyloid precursor protein isoforms

We describe a proteomics procedure using bioinformatics, immunoprecipitation, two-dimensional gel electrophoresis, Western blotting, in-gel digestion, LC–MS, MALDI–MS, and MS–MS for isolation and identification of amyloid precursor protein (APP) isoforms APP₆₉₅, APP₇₅₁, and APP₇₇₀. Retinoic acid-induced Ntera 2 cell line, derived from a human teratocarcinoma cells, was the in-vitro source of APP. Initial isolation of whole APP was performed by immunoprecipitation, using AB10, a monoclonal antibody raised to amino acids 1–17 of the β-amyloid peptide sequence, which is present in all three alpha secretase-cleaved isoforms of interest. The next stage was separation of whole APP into its isoform components by two-dimensional gel electrophoresis. Because of low APP concentrations, detection by the usual staining methods, for example Sypro Ruby, able to detect low picomole concentrations, did not enable visualisation of the isoforms. Western analysis, however, enabled primary detection of APP, because of the inherent sensitivity of antibodies raised to specific isoform regions. This initial visualization acted as a template for excision of isoforms from 2D gels, which were then subjected to peptide mass mapping. Initial theoretical digestion of each isoform revealed the presence of specific peptides, which were then used as “tags” for isoform detection.     

Hippocampal metabolomics using ultrahigh-resolution mass spectrometry reveals neuroinflammation from Alzheimer’s disease in CRND8 mice

In the wake of genomics, metabolomics characterizes the small molecular metabolites revealing the phenotypes induced by gene mutants. To address the metabolic signatures in the hippocampus of the amyloid-beta (Aβ) peptides produced in transgenic (Tg) CRND8 mice, high-field ion cyclotron resonance–Fourier transform mass spectrometry supported by LC-LTQ-Orbitrap was introduced to profile the extracted metabolites. More than 10,000 ions were detected in the mass profile for each sample. Subsequently, peak alignment and the 80 % rule followed by feature selection based on T score computation were performed. The putative identification was also conducted using the highly accurate masses with isotopic distribution by interfacing the MassTRIX database as well as MS/MS fragmentation generated in the LTQ-Orbitrap after chromatographic separation. Consequently, 58 differentiating masses were tentatively identified while up to 44 differentiating elemental compositions could not be biologically annotated in the databases. Nonetheless, of the putatively annotated masses, eicosanoids in arachidonic acid metabolism, fatty acid beta-oxidation disorders as well as disturbed glucose metabolism were highlighted as metabolic traits of Aβ toxicity in Tg CRND8 mice. Furthermore, a web-based bioinformatic tool was used for simulation of the metabolic pathways. As a result of the obtained metabolic signatures, the arachidonic acid metabolism dominates the metabolic perturbation in hippocampal tissues of Tg CRND8 mice compared to non-Tg littermates, indicating that Aβ toxicity functions neuroinflammation in hippocampal tissue and new theranostic opportunities might be offered by characterization of altered arachidonic acid metabolism for Alzheimer’s disease.      

In silico modeling for dual inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes in Alzheimer’s disease

In this research, we have implemented two-dimensional quantitative structure-activity relationship (2D-QSAR) modeling using two different datasets, namely, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzyme inhibitors. A third dataset has been derived based on their selectivity and used for the development of partial least squares (PLS) based regression models. The developed models were extensively validated using various internal and external validation parameters. The features appearing in the model against AChE enzyme suggest that a small ring size, higher number of −CH2- groups, higher number of secondary aromatic amines and higher number of aromatic ketone groups may contribute to the inhibitory activity. The features obtained from the model against BuChE enzyme suggest that the sum of topological distances between two nitrogen atoms, higher number of fragments X-C(=X)-X, higher number of secondary aromatic amides, fragment R--CR-X may be more favorable for inhibition. The features obtained from selectivity based model suggest that the number of aromatic ethers, unsaturation content relative to the molecular size and molecular shape may be more specific for the inhibition of the AChE enzyme in comparison to the BuChE enzyme. Moreover, we have implemented the molecular docking studies using the most and least active molecules from the datasets in order to identify the binding pattern between ligand and target enzyme. The obtained information is then correlated with the essential structural features associated with the 2D-QSAR models.     

Determination of Meserine,a new candidate for Alzheimer’s disease in mice brain by liquid chromatography-tandem mass spectrometry and its application to a pharmacokinetic and tissue distribution study

A rapid and sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for determination of Meserine ((?)-meptazinol phenylcarbamate), a novel potent inhibitor of acetylcholinesterase (AChE), was developed, validated, and applied to a pharmacokinetic study in mice brain. The lower limit of quantification (LLOQ) was 1 ng mL^?1 and the linear range was 1–1,000 ng mL^?1. The analyte was eluted on a Zorbax SB-Aq column (2.1?×?100 mm, 3.5 μm) with the mobile phase composed of methanol and water (70:30, v/v, aqueous phase contained 10 mM ammonium formate and 0.3 % formic acid) using isocratic elution, and monitored by positive electrospray ionization in multiple reaction monitoring (MRM) mode. The flow rate was 0.25 mL min^?1. The injection volume was 5 μL and total run time was 4 min. The relative standard deviation (RSD) of intraday and interday variation was 2.49–7.81 and 3.01–7.67 %, respectively. All analytes were stable after 4 h at room temperature and 6 h in autosampler. The extraction recoveries of Meserine in brain homogenate were over 90 %. The main brain pharmacokinetic parameters obtained after intranasal administration were T _max?=?0.05 h, C _max?=?462.0?±?39.7 ng g^?1, T _1/2?=?0.4 h, and AUC_(0-∞)?=?283.1?±?9.1 ng h g^?1. Moreover, Meserine was distributed rapidly and widely into brain, heart, liver, spleen, lung, and kidney tissue. The method is validated and could be applied to the pharmacokinetic and tissue distribution study of Meserine in mice.