Structural Dynamics of Amyloid β Peptide Binding to Acetylcholine Receptor and Virtual Screening for Effective Inhibitors

The interaction between Amyloid β (Aβ) peptide and acetylcholine receptor is the key for our understanding of how Aβ fragments block the ion channels within the synapses and thus induce Alzheimer's disease. Here, molecular docking and molecular dynamics (MD) simulations were performed for the structural dynamics of the docking complex consisting of Aβ and α7-nAChR (α7 nicotinic acetylcholine receptor), and the inter-molecular interactions between ligand and receptor were revealed. The results show that A\begin{document}$ \beta_{25-35} $\end{document} is bound to α7-nAChR through hydrogen bonds and complementary shape, and the A\begin{document}$ \beta_{25-35} $\end{document} fragments would easily assemble in the ion channel of \begin{document}$ \alpha $\end{document}7-nAChR, then block the ion transfer process and induce neuronal apoptosis. The simulated amide-I band of A\begin{document}$ \beta_{25-35} $\end{document} in the complex is located at 1650.5 cm\begin{document}$ ^{-1} $\end{document}, indicating the backbone of A\begin{document}$ \beta_{25-35} $\end{document} tends to present random coil conformation, which is consistent with the result obtained from cluster analysis. Currently existing drugs were used as templates for virtual screening, eight new drugs were designed and semi-flexible docking was performed for their performance. The results show that, the interactions between new drugs and \begin{document}$ \alpha $\end{document}7-nAChR are strong enough to inhibit the aggregation of A\begin{document}$ \beta_{25-35} $\end{document} fragments in the ion channel, and also be of great potential in the treatment of Alzheimer's disease.     

Probing the Binding of Syzygium-Derived α-Glucosidase Inhibitors with N- and C-Terminal Human Maltase Glucoamylase by Docking and Molecular Dynamics Simulation

Human maltase glucoamylase (MGAM) is a potent molecular target for controlling post prandial glucose surplus in type 2 diabetes. Binding of small molecules from Syzygium sp. with α-glucosidase inhibitory potential in MGAM has been investigated in silico. Our results suggest that myricetin was the most potent inhibitor with high binding affinity for both N- and C-terminals of MGAM. Molecular dynamics revealed that myricetin interacts in its stretched conformation through water-mediated interactions with C-terminal of MGAM and by normal hydrogen bonding with the N-terminal. W1369 of the extended 21 amino acid residue helical loop of C-terminal plays a major role in myricetin binding. Owing to its additional sugar sites, overall binding of small molecules favours C-terminal MGAM.     

Identification of Novel β3-Adrenoceptor Agonists Using Energetic Analysis, Structure Based Pharmacophores and Virtual Screening

β3 Adrenergic receptor (β3-AR), is a potential therapeutic target for the treatment of type II diabetes and obesity. We report the identification of novel compounds as β3-AR agonists by integrating different approaches of energetic analysis, structure based pharmacophore designing and virtual screening. In a step wise filtering protocol, structure based virtual screening of 2,33,450 compounds was done. These molecules were docked into the active site of the receptor utilizing three levels of accuracy; ligands passing the HTVS (high throughput virtual screening) step were subsequently analyzed in Glide SP (Standard Precision) and finally in Glide XP (Extra Precision) to estimate the receptor ligand binding affinities. In the second step a total of 300 pharmacophore hypotheses were generated from a set of known and diverse β3-AR agonists. The best hypothesis showed six features: three hydrogen bond acceptors, one positively charged group, and two aromatic rings. To cross validate, pharmacophore filtering was done on the set of shortlisted compounds from structure based VS (virtual screening). The different screening techniques employed were validated using enrichment factor calculations. The energetic based Pharmacophore performed fairly well at distinguishing active from the inactive compounds and yielded a greater diversity of active molecules whereas the number of actives retrieved in the case of structure based screening was the highest.     

Insights into Molecular Assembly of ACCase Heteromeric Complex in Chlorella variabilis—A Homology Modelling, Docking and Molecular Dynamic Simulation Study

Acetyl-CoA carboxylase (ACCase), a biotin-dependent enzyme that catalyses the first committed step of fatty acid biosynthesis, is considered as a potential target for improving lipid accumulation in oleaginous feedstocks, including microalgae. ACCase is composed of three distinct conserved domains, and understanding the structural details of each catalytic domain assumes great significance to gain insights into the molecular basis of the complex formation and mechanism of biotin transport. In the absence of a crystal structure for any single heteromeric ACCase till date, here we report the first heteromeric association model of ACCase from an oleaginous green microalga, Chlorella variabilis, using a combination of homology modelling, docking and molecular dynamic simulations. The binding site of the docked biotin carboxylase (BC) and carboxyltransferase (CT) were predicted to be contiguous but distinct in biotin carboxyl carrier protein (BCCP) molecule. Simulation studies revealed considerable flexibility for the BC and CT domains in the BCCP-bound forms, thus indicating the adaptive behaviour of BCCP. Further, principal component analysis revealed that in the presence of BCCP, the BC and CT domains exhibited an open-state conformation via the outward clockwise rotation of the binding helices. These conformational changes might be responsible for binding of BCCP domain and its translocation to the respective active sites. Various rearrangements of inter-domain hydrogen bonds (H-bonds) contributed to conformational changes in the structures. H-bond interactions between the interacting residue pairs involving Glu201BCCP/Arg255BC and Asp224BCCP/Gln228CT were found to be essential for the intermolecular assembly. The present findings are consistent with previous biochemical studies.     

Molecular Recognition and Cooperative Binding Ability of Fluorescent Dyes by Bridged Bisβ-cyclodextrin)s Tethered with Aromatic Diamine

A novel bridged bis(β-cyclodextrin),m-phenylenediimino-bridged bis(6-imino-6-deoxy-β-cyclodextrin) (2), was synthesized by the reaction of m-phenylenediamine and 6-deoxy-6-formyl-β-cyclodextrin. The inclusion complexation behavior of the novel bridged bis(β-cyclodextrin) 2,as well as native β-cyclodextrin (1),p-phenylenediamino-bridged bis(6-amino-6-deoxy-β-cyclodextrin) (3) and 4,4'-bianilino-bridged bis(6-amino-6-deoxy-β-cyclodextrin) (4) with representative fluorescent dye molecules, i.e., acridine red (AR), neutral red (NR), Rhodamine B (RhB), ammonium 8-anilino-1-naphthalenesulfonate (ANS) and sodium 6-toluidino-2-naphthalenesulfonate (TNS), was investigated at 25 °C in aqueous phosphate buffer solution (pH 7.20) by means of fluorescence, and circular dichroism, as well as 2D NMR spectrometry. The spectrofluorometric titrations have been performed to calculate the complex stability constants (K_S) and Gibbs free energy changes (Δ G°) for the stoichiometric 1 : 1 inclusion complexation of 1–4 with fluorescent dye molecules. The results obtained demonstrated that bis(β-cyclodextrin)s 2–4 showed much higher affinities toward these guest dyesthan native β-cyclodextrin 1. Typically, dimer 2 displayed the highest binding ability upon inclusion complexation with ANS, affording 35 times higher K_S value than native β-cyclodextrin. The significantlyenhanced binding abilities of these bis(β-cyclodextrin)s are discussed from thebinding mode and viewpoints of size/shape-fit concept and multiple recognition mechanism.     

Hierarchical enumeration of Kekulé’s benzenes,Ladenburg’s benzenes,Dewar’s benzenes,and benzvalenes by using combined-permutation representations

The group hierarchy for each skeleton of ligancy 6 is formulated to be: point group (PG \({\varvec{G}}_{\sigma }\)) \(\subseteq \) RS-stereoisomeric group (RS-SIG \({\varvec{G}}_{\sigma \widetilde{\sigma }\widehat{I}}\)) \(\subseteq \) stereoisomeric group (SIG \(\widetilde{{\varvec{G}}}_{\sigma \widetilde{\sigma }\widehat{I}}\)) \(\subseteq \) isoskeletomeric group (ISG \(\widetilde{\widetilde{{\varvec{G}}}}_{\sigma \widetilde{\sigma }\widehat{I}}\) = \({\varvec{S}}^{[6]}_{\sigma \widehat{I}}\)), where we start from the PG \({\varvec{G}}_{\sigma }\) = \({\varvec{D}}_{6h}\) for the Kekulé benzene skeleton, from the PG \({\varvec{G}}_{\sigma }\) = \({\varvec{D}}_{3h}\) for the Ladenburg benzene skeleton, from the PG \({\varvec{G}}_{\sigma }\) = \({\varvec{C}}_{2v}\) for the Dewar benzene skeleton, or from the PG \({\varvec{G}}_{\sigma }\) = \({\varvec{C}}_{2v}\) for the benzvalene skeleton. After these groups are constructed as combined-permutation representations, the calculation of the respective cycle indices with chirality fittingness (CI-CFs) and the introduction of ligand-inventory functions are conducted to give generation functions for 3D-based enumerations (for PGs and RS-SIGs) and 2D-based enumerations (for SIGs and ISGs). The enumeration results are discussed by means of isomer-classification diagrams, in which equivalence classes under enantiomerism (for PGs), RS-stereoisomerism (for RS-SIGs), stereoisomerism (for SIGs), and isoskeletomerism (for ISGs) are illustrated schematically. The implicit connotations of the conventional terms “skeletal isomerism”, “positional isomerism”, and “constitutional isomerism” are discussed, where the effects of the concept of isoskeletomerism are emphasized.     

Enantio-, Regio-, and Chemoselective Reduction of Aromatic a-Diketones by Baker’s Yeast

The enantio- and regioselective reduction of several symmetric and nonsymmetrically para-substituted benzil derivatives (21–92%) was achieved by means of Saccharomyces cerevisiae (bakers yeast). After modification of the reaction conditions reduction of nonsymmetric -diketones led chemoselectively to chiral -hydroxy ketones with up to 82% ee.     

Molecular docking studies of coumarin hybrids as potential acetylcholinesterase,butyrylcholinesterase, monoamine oxidase A/B and β-amyloid inhibitors for Alzheimer’s disease

Coumarins are the phytochemicals, which belong to the family of benzopyrone, that display interesting pharmacological properties. Several natural, synthetic and semisynthetic coumarin derivatives have been discovered in decades for their applicability as lead structures as drugs. Coumarin based conjugates have been described as potential AChE, BuChE, MAO and β-amyloid inhibitors. Therefore, the objective of this review is to focus on the construction of these pharmacologically important coumarin analogues with anti-Alzheimer’s activities, highlight their docking studies and structure–activity relationships based on their substitution pattern with respect to the selected positions on the chromen ring by emphasising on the research reports conducted in between year 1968 to 2017.

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Enantio-, Regio-, and Chemoselective Reduction of Aromatic α-Diketones by Baker’s Yeast

Summary. The enantio- and regioselective reduction of several symmetric and nonsymmetrically para-substituted benzil derivatives (21–92%) was achieved by means of Saccharomyces cerevisiae (bakers yeast). After modification of the reaction conditions reduction of nonsymmetric -diketones led chemoselectively to chiral -hydroxy ketones with up to 82% ee.Received December 16, 2002; accepted (revised) January 9, 2003 Published online July 28, 2003     

Synthesis and Dynamic NMR Study of New Stable Ylides Derived from the Reaction of Triphenylphosphine,Dialkyl Acetylenedicarboxylates,and 5-ACYL Meldrum’s Acid

Abstract

Triphenylphosphine and dialkyl acetylenedicarboxylate react smoothly in the presence of 5-acyl Meldrum's acid in dichloromethane at room temperature and lead to synthesis of new stable ylide derivatives of dimethyl (5-acetyl-2,2-dimethyl-4,6-dioxo-1,3-dioxane-5-yl)-3-(triphenyl-λ⁵-phosphanylidene) succinate. Dynamic NMR study results of rotamers are reported and compared with the previous-related reports.     

Analysis of multicomponent mixture and simultaneous enantioresolution of proteinogenic and non-proteinogenic amino acids by reversed-phase high-performance liquid chromatography using chiral variants of Sanger’s reagent

Four chiral derivatizing reagents (CDR 1–4), namely, FDNP-l-Ala, FDNP-l-Val, FDNP-l-Phe, and FDNP-l-Leu, were synthesized using microwave (MW) irradiation by substituting one of the fluorine atoms in difluoro dinitro benzene (DFDNB) with l-Ala, l-Val, l-Phe, and l-Leu (CDR 1–4). The other set of CDRs, namely, FDNP-l-Phe-NH₂, FDNP-l-Val-NH₂, and FDNP-l-Leu-NH₂, was also prepared. These reagents were used for synthesis of diastereomers of 18 proteinogenic and 08 non-proteinogenic amino acids, which were resolved by reversed-phase high-performance liquid chromatography using C18 column and gradient eluting mixture of aq.TFA and acetonitrile with UV detection at 340 nm. The reagents were used for resolution of a complex mixture of 18 racemic proteinogenic amino acids in a single chromatographic run of 65 min and to determine concentration of the d-amino acid in a solution of dl-amino acid. The resolution (R _S) and selectivity (α) obtained for the two sets of diastereomers were compared among themselves and among the two groups. The method was validated for accuracy, precision, limit of detection (LOD), and limit of quantification. LOD is 0.001% impurity of d-enantiomer.     

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.     

Evaluation of the Expression of Amyloid Precursor Protein and the Ratio of Secreted Amyloid Beta 42 to Amyloid Beta 40 in SH-SY5Y Cells Stably Transfected with Wild-Type,Single-Mutant and Double-Mutant Forms of the APP Gene for the Study of Alzheimer’s Disease Pathology

Neuroblastoma cell lines such as SH-SY5Y are the most frequently utilized models in neurodegenerative research, and their use has advanced the understanding of the pathology of neurodegeneration over the past few decades. In Alzheimer’s disease (AD), several pathogenic mutations have been described, all of which cause elevated levels of pathological hallmarks such as amyloid-beta (Aβ). Although the genetics of Alzheimer’s disease is well known, familial AD only accounts for a small number of cases in the population, with the rest being sporadic AD, which contains no known mutations. Currently, most of the in vitro models used to study AD pathogenesis only examine the level of Aβ42 as a confirmation of successful model generation and only perform comparisons between wild-type APP and single mutants of the APP gene. Recent findings have shown that the Aβ42/40 ratio in cerebrospinal fluid (CSF) is a better diagnostic indicator for AD patients than is Aβ42 alone and that more extensive Aβ formation, such as accumulation of intraneuronal Aβ, Aβ plaques, soluble oligomeric Aβ (oAβ), and insoluble fibrillar Aβ (fAβ) occurs in TgCRND8 mice expressing a double-mutant form (Swedish and Indiana) of APP, later leading to greater progressive impairment of the brain. In this study, we generated SH-SY5Y cells stably transfected separately with wild-type APP, the Swedish mutation of APP, and the Swedish and Indiana mutations of APP and evaluated the APP expression as well as the Aβ42/40 ratio in those cells. The double-mutant form of APP (Swedish/Indiana) expressed markedly high levels of APP protein and showed a high Aβ2/40 ratio compared to wild-type and single-mutant cells.     

Determination of Cu, Zn and Cd in water by FAAS after preconcentration by baker’s yeast (Saccharomyces cerevisiae) immobilized on sepiolite

By using the adsorbent Saccharomyces cerevisiae immobilized on sepiolite an adsorption-elution method was developed for the preconcentration of Cu, Zn, and Cd followed by flame atomic absorption spectrometry (FAAS). Recoveries were 98.3 ± 0.4% for Cu, 94.2 ± 0.3% for Zn, and 99.04 ± 0.04% for Cd at 95% confidence level obtained by the column method. The influence of sea water matrix elements on the separation of the trace elements was also assessed by using the column procedure. The breakthrough capacities were found to be 74 μmol/g for copper, 128 μmol/g for zinc and 97 μmol/g for cadmium. After optimization the proposed method was applied to the trace metal determination in sea and river water. Received: 8 June 1998 / Revised: 8 September 1998 / Accepted: 16 September 1998     

Determination of Cu, Zn and Cd in water by FAAS after preconcentration by baker’s yeast (Saccharomyces cerevisiae) immobilized on sepiolite

By using the adsorbent Saccharomyces cerevisiae immobilized on sepiolite an adsorption-elution method was developed for the preconcentration of Cu, Zn, and Cd followed by flame atomic absorption spectrometry (FAAS). Recoveries were 98.3 ± 0.4% for Cu, 94.2 ± 0.3% for Zn, and 99.04 ± 0.04% for Cd at 95% confidence level obtained by the column method. The influence of sea water matrix elements on the separation of the trace elements was also assessed by using the column procedure. The breakthrough capacities were found to be 74 μmol/g for copper, 128 μmol/g for zinc and 97 μmol/g for cadmium. After optimization the proposed method was applied to the trace metal determination in sea and river water.     

Molecular Engineering of Liquid Crystal Polymers by Living Polymerization. VIII. Influence of Molecular Weight on the Phase Behavior of Poly {ω-[(4-Cyano-4′-biphenyl)-oxy]alkyl Vinyl Ether}s with Ethyl,Propyl, and Butyl Alkyl Groups

The synthesis and living cationic polymerization of 2-[4-cyano-4′-biphenyl)oxy]ethyl vinyl ether (6–2), 3-[4-cyano-4′-biphenyl)oxy]-propyl vinyl ether (6-3), and 4-[4-cyano-4′-biphenyl)oxy]butyl vinyl ether (6-4) are described. The mesomorphic behaviors of poly(6–2), poly(6-3), and poly(6-4) with different degrees of polymerization and narrow molecular weight distributions were compared to those of 6–2, 6–3, and 6–4 and of 2-[(4-cyano-4′-biphenyl)oxy]ethyl ethyl ether (8–2), 3-[(4-cyano-4′-biphenyl)oxy]propyl ethyl ether (8–3), and 4-[4-cyano-4′-biphenyl)oxy]butyl ethyl ether (8–4) which are model compounds of the monomeric structural units of poly(6–2), poly(6–3), and poly(6–4). In the first heating scan, all three polymers exhibit an x (unidentified) mesophase which overlaps the glass transition temperature, and an enantiotropic nematic mesophase. In the second and subsequent heating and cooling scans, poly(6–3) and poly(6–4) display only the enantiotropic nematic mesophase. Both in the first and subsequent scans, only poly(6–2) with degrees of polymerization lower than 4 exhibits an enantiotropic nematic mesophase.     

History of individuals of the 18th/19th centuries stored in bones,teeth, and hair analyzed by LA–ICP–MS—a step in attempts to confirm the authenticity of Mozart’s skull

A cranium stored in the Stiftung Mozarteum in Salzburg/Austria which is believed to be that of Mozart, and skeletal remains of suspected relatives which have been excavated from the Mozart family grave in the cemetery in Salzburg, have been subjected to scientific investigations to determine whether or not the skull is authentic. A film project by the Austrian television ORF in collaboration with Interspot Film on this issue was broadcast at the beginning of the “Mozart year 2006”. DNA analysis could not clarify relationships among the remains and, therefore, assignment of the samples was not really possible. In our work this skull and excavated skeletal remains have been quantified for Pb, Cr, Hg, As, and Sb content by laser ablation-inductively coupled plasma-mass spectrometry (LA–ICP–MS) to obtain information about the living conditions of these individuals. A small splinter of enamel (less than 1 mm³) from a tooth of the “Mozart cranium” was also available for investigation. Quantification was performed by using spiked hydroxyapatite standards. Single hair samples which are recorded to originate from Mozart have also been investigated by LA–ICP–MS and compared with hair samples of contemporary citizens stored in the Federal Pathologic–Anatomical Museum, Vienna. In general, Pb concentrations up to approximately 16 μg g⁻¹ were found in the bone samples of 18th century individuals (a factor of 7 to 8 higher than in recent samples) reflecting elevated Pb levels in food or beverages. Elevated Pb levels were also found in hair samples. The amount of Sb in the enamel sample of the “Mozart cranium” (approx. 3 μg g⁻¹) was significantly higher than in all the other tooth samples investigated, indicating possible Sb ingestion in early childhood. Elevated concentrations of elements in single hair samples gave additional information about possible exposure of the individuals to heavy metals at a particular point in their life.