A correlated force-optical study on the self-assembly behavior of annexin V on model membranes: effect of dye conjugation

We have examined the self-assembled membrane-bound aggregates of two annexin V (A5) dye conjugates and compared them to those from native A5. Native A5 and FITC-labeled A5 (A5-FITC) both formed discrete well-defined crystalline monolayer domains of p6 symmetry. However, A5-FITC also showed additional domains with a corrugated appearance not observed in native A5. In contrast, Cy3-labeled A5 (A5-Cy3) showed a mixture of crystalline monolayer and irregular multilayered domains, with the ratio of the two types varying significantly from sample to sample, and also required a much longer incubation time than native A5 and A5-FITC. When A5-FITC and A5-Cy3 were co-incubated on the same bilayer, well-defined crystalline monolayer domains containing both A5-FITC and A5-Cy3 were consistently observed at a much shorter incubation time than that of pure A5-Cy3 alone, indicating that A5-FITC facilitates the inclusion of A5-Cy3. These results suggest that dye labels can affect A5 2D self-assembly and crystal formation on membrane surfaces.     

Effect of the sarcosine residue on sequence scrambling in peptide b5 ions

The effect of N‐methylation on sequence scrambling in the fragmentation of b₅ ions has been investigated by studying a variety of peptides containing sarcosine (N‐methylglycine). The product ion mass spectra for the b₅ ions derived from Sar‐A‐A‐A‐Y‐A and Sar‐A‐A‐Y‐A‐A show only minor signals for non‐direct sequence ions the major fragmentation reactions occurring from the unrearranged structures. This is in contrast to the b₅ ions where the Sar residue is replaced by Ala and sequence scrambling occurs. The b₅ ion derived from Y‐Sar‐A‐A‐A‐A shows a product ion mass spectrum essentially identical to the spectrum of the b₅ ion derived from Sar‐A‐A‐A‐Y‐A, indicating that in the former case macrocyclization has occurred but the macrocyclic form shows a strong preference to reopen to put the Sar residue in the N‐terminal position. Similar results were obtained in the comparison of b₅ ions derived from A‐Sar‐A‐A‐Y‐A and Sar‐A‐A‐Y‐A‐A. The product ion mass spectra of the MH⁺ ions of Y‐Sar‐A‐A‐A‐A and A‐Sar‐A‐A‐Y‐A show substantial signals for non‐direct sequence ions indicating that fragmentation of the MH⁺ ions channels extensively through the respective b₅ ions and further fragmentation of these species. Copyright © 2014 John Wiley & Sons, Ltd.     

Amyloid-β peptide structure in aqueous solution varies with fragment size

Various fragment sizes of the amyloid-β (Aβ) peptide have been utilized to mimic the properties of the full-length Aβ peptide in solution. Among these smaller fragments, Aβ16 and Aβ28 have been investigated extensively. In this work, we report the structural and thermodynamic properties of the Aβ16, Aβ28, and Aβ42 peptides in an aqueous solution environment. We performed replica exchange molecular dynamics simulations along with thermodynamic calculations for investigating the conformational free energies, secondary and tertiary structures of the Aβ16, Aβ28, and Aβ42 peptides. The results show that the thermodynamic properties vary from each other for these peptides. Furthermore, the secondary structures in the Asp1-Lys16 and Asp1-Lys28 regions of Aβ42 cannot be completely captured by the Aβ16 and Aβ28 fragments. For example, the β-sheet structures in the N-terminal region of Aβ16 and Aβ28 are either not present or the abundance is significantly decreased in Aβ42. The α-helix and β-sheet abundances in Aβ28 and Aβ42 show trends--to some extent--with the potential of mean forces but no such trend could be obtained for Aβ16. Interestingly, Arg5 forms salt bridges with large abundances in all three peptides. The formation of a salt bridge between Asp23-Lys28 is more preferred over the Glu22-Lys28 salt bridge in Aβ28 but this trend is vice versa for Aβ42. This study shows that the Asp1-Lys16 and Asp1-Lys28 regions of the full length Aβ42 peptide cannot be completely mimicked by studying the Aβ16 and Aβ28 peptides.     

Simultaneous determination of ascorbic acid,uric acid and dopamine at modified electrode based on hybrid nickel hexacyanoferrate/poly(1,5-diaminonaphthalene)

A novel modified electrode was fabricated by a mixed-valent nickel hexacyanoferrate (NiHCF) and poly 1,5-diaminonaphthalene (PDAN) hybrid at glassy carbon (GC) electrode. The obtained NiHCF/PDAN/GC modified electrode was characterized using cyclic voltammetry (CV) technique and scanning electron microscope (SEM). This electrode showed excellent catalytic properties toward the electrooxidation of ascorbic acid (A.A), dopamine (D.A) and uric acid (U.A) in 0.1 M NaCl solution using CV and square wave voltammetry (SWV) techniques. The NiHCF/PDAN/GC modified electrode exhibits high sensitivity, selectivity and stability making it a suitable sensor for the simultaneous detection of A.A, U.A and D.A in single and ternary mixture solutions. Different analytical parameters such as low detection limit (LOD), low quantification limit, correlation coefficient (R) and linear dynamic range were reported and discussed. The NiHCF/PDAN/GC modified electrode exhibits linear responses to A.A, D.A and U.A in the range 600–1000, 600–1000 and 600–1000 µM, respectively. The LOD for A.A, D.A and U.A were 0.036, 0.034 and 0.037 µM, respectively. The analytical behavior of this sensor had been evaluated for the detection of A.A and U.A in human serum and urine samples with satisfactory results.     

Synthesis and evaluation of adenosine antagonist activity of a series of [1,2,4]triazolo[1,5-c]quinazolines

A series of [1,2,4]triazolo[1,5-c]quinazolines were prepared in satisfactory yields by reaction of some derivatives of 2-aminobenzohydrazide with several hydrochlorides of aromatic amidines, and their binding affinities for the recombinant human adenosine A2A and A2B receptors were determined. None of the new compounds showed noteworthy affinity for these receptors, though a very high affinity for the A2A receptor and, consequently, a high level of A2A/A2B selectivity was revealed for one of the synthesized compounds.     

Molecular modeling of A1 and A2A adenosine receptors: comparison of rhodopsin- and beta2-adrenergic-based homology models through the docking studies

Adenosine receptors (ARs) are members of the superfamily of G protein-coupled receptors. The homology models of adenosine A1 and A2A receptors were constructed. The high-resolution X-ray structure of bovine rhodopsin and crystal structure of beta2-adrenergic receptor were used as templates. The binding sites of the A1 and A2A ARs were constructed by using data obtained from mutagenesis experiments as well as docking simulations of the respective AR antagonsists DPCPX and XAC. To compare rhodopsin- and beta2-adrenergic-based models, the binding mode of A1 (KW-3902, LUF-5437) and A2A (KW-6002, ZM-241385) ARs antagonists were also examined. The differences in the binding ability of both models were noted during the study. The beta2-adrenergic-based A2A AR model was much more capable to stabilize the ligand in the binding site cavity than the corresponding rhodopsin-based A2A AR model, however, such differences were not so clear in case of A1 AR models. It was suggested that for the A1 AR it is possible to use the crystal structure of rhodopsin as a template as well as beta2-adrenergic receptor, but for A2A AR, with the now available beta2-adrenergic receptor X-ray structure, docking studies should be avoided on the rhodopsin-based model. However, taking into account that the beta2AR shares about 31% of the residues with the AR in comparison to 21% in case of bRho, we suggest using beta2-adrenergic-based models for the A1 and A2A ARs for further in silico ligand screening also because of their generally better ability to stabilize ligands inside the binding pocket.     

3D-pharmacophore models for selective A2A and A2B adenosine receptor antagonists

Three-dimensional pharmacophore models were generated for A2A and A2B adenosine receptors (ARs) based on highly selective A2A and A2B antagonists using the Catalyst program. The best pharmacophore model for selective A2A antagonists (Hypo-A2A) was obtained through a careful validation process. Four features contained in Hypo-A2A (one ring aromatic feature (R), one positively ionizable feature (P), one hydrogen bond acceptor lipid feature (L), and one hydrophobic feature (H)) seem to be essential for antagonists in terms of binding activity and A2A AR selectivity. The best pharmacophore model for selective A2B antagonists (Hypo-A2B) was elaborated by modifying the Catalyst common features (HipHop) hypotheses generated from the selective A2B antagonists training set. Hypo-A2B also consists of four features: one ring aromatic feature (R), one hydrophobic aliphatic feature (Z), and two hydrogen bond acceptor lipid features (L). All features play an important role in A2B AR binding affinity and are essential for A2B selectivity. Both A2A and A2B pharmacophore models have been validated toward a wide set of test molecules containing structurally diverse selective antagonists of all AR subtypes. They are capable of identifying correspondingly high potent antagonists and differentiating antagonists between subtypes. The results of our study will act as a valuable tool for retrieving structurally diverse compounds with desired biological activities and designing novel selective adenosine receptor ligands.     

Thin-layer chromatographic study of the metabolites of erythromycins in the Wistar rat

The metabolites of erythromycin A, anhydroerythromycin A, N-demethylerythromycin A and erythromycin B in the Wistar rat were studied by thin-layer chromatography. In some experiments germ-free rats, rats with a cannulated bile duct and a gastrectomized rat were used. The erythromycins examined were shown to undergo two principal changes, N-demethylation and acid-catalysed degradation. It was demonstrated that the stomach and the liver are not the sole sites of acid degradation and demethylation of erythromycins, respectively. Erythromycin A gives three principal metabolites, anhydroerythromycin A, anhydro-N-demethylerythromycin A and N-demethylerythromycin A, and erythromycin A enol ether and N-demethylerythromycin A enol ether are present to a minor extent. 5-O-Desosaminylerythronolide A was also identified, suggesting the presence of an erythromycin glycosidase.     

Synthesis and Characterization of Water‐Soluble Conjugated Glycopolymer for Fluorescent Sensing of Concanavalin A

A neutral polyfluorene derivative that contains 20 mol % 2,1,3‐benzothiadiazole (BT) is synthesized by Suzuki cross‐coupling polymerization. A cationic conjugated polymer A and an α‐mannose‐bearing polymer B are subsequently obtained through different post‐polymerization methods. As a result of the charged pendant groups or sugar‐bearing groups attached to the polymer side chains, both A and B show good water‐solubility. The titration of Concanavalin A (Con A) into polymer aqueous solution leads to different fluorescent responses for polymers A and B . Polymer A does not show any obvious fluorescence change upon interaction with Con A, whereas polymer B shows fluorescence increase in BT emission intensity when Con A is added. This is because of the specific interaction between α‐mannose and Con A, which induces polymer aggregation, and then facilitates energy transfer from the phenylene–fluorene segments to the BT units. A practical calibration curve ranging from 1 nM to 250 nM is obtained by correlating the changes in BT emission intensity with Con A concentration. The advantage of polymer B ‐based Con A macromolecular probe is that it shows signal increase upon Con A recognition, which is significantly different from other conjugated polymer‐based fluorescence quenching assays.     

Two-dimensional lattice Monte Carlo simulation of the compatibility of A/B/functionalized A ternary polymer mixtures coupled with chemical reaction

Compatibility of A/B and functionalized A ternary polymer mixtures was studied by Monte Carlo simulation in a two-dimensional lattice. Polymer A was a nonreactive polymer, whereas polymer B was a reactive polymer and immiscible with polymer A. Functionalized polymer A could react with the end group of polymer B, leading to the formation of block copolymers. Simulation results showed the phase domain sizes dropped considerably with increasing functionalized polymer A content, indicating that the compatibility between polymer A and B could be markedly improved with the introduction of functionalized polymer A. Moreover, it was shown that the resulting block copolymers tended to distribute at the phase interface between polymer A and B, and the block copolymer conformation depended on the structures of polymer B and functionalized polymer A. In case 1, i.e., both polymer B and functionalized polymer A were with single end group, it could be found that the block A and block B of resulting A–B copolymer inserted into polymer A and polymer B phase domains, respectively. In case 2, i.e., functionalized polymer A was with single end group and polymer B was with double end groups, it was found that the resulting A–B–A triblock copolymer tended to connect two neighbor separated polymer A phase domains. However, in case 3, namely functionalized polymer A was with double end groups and polymer B was with single end group, it was found that the resulting B–A–B triblock copolymer was likely to form a folding conformation. These lead to the different compatibilizing effects for different polymer structures. Comparing with case 1 and case 2, functionalized polymer A with double end groups (case 3) had less effective to compatibilize the A/B polymer blends. For the purpose of comparison, same simulations were carried out in a three-dimensional lattice. The results showed the compatibility behavior of the mixtures was similar to those in the two-dimensional lattice with the addition of functionalized polymer A. However, the conformation of the resulting block copolymers was different from that in the two-dimensional lattice.     

Bioinspired Total Synthesis of Complex Nucleoside Antibiotics A201A,A201D and A201E

Herein, bioinspired total syntheses of A201A, A201D, and A201E based on a previously reported biosynthetic pathway are presented. The challenging 1,2-cis-furanoside, a core structure of the A201 family, was obtained by remote 2-quinolinecarbonyl-assisted glycosylation. We accomplished the total synthesis of A201A and A201E based on the critical 1,2-cis-furanoside moiety through late-stage glycosylation without any interference from basic dimethyl adenosine. We also confirmed the absolute configuration of A201E by total synthesis. This modular synthesis strategy enables efficient preparation of A201 family antibiotics, allowing the study of their structure–activity relationships and mode of action. This study satisfies the increasing demand for developing novel antibiotics inspired by the A201 family.     

Aβ40 and Aβ42 amyloid fibrils exhibit distinct molecular recycling properties

A critical aspect to understanding the molecular basis of Alzheimer's disease (AD) is the characterization of the kinetics of interconversion between the different species present during amyloid-β protein (Aβ) aggregation. By monitoring hydrogen/deuterium exchange in Aβ fibrils using electrospray ionization mass spectrometry, we demonstrate that the Aβ molecules comprising the fibril continuously dissociate and reassociate, resulting in molecular recycling within the fibril population. Investigations on Aβ40 and Aβ42 amyloid fibrils reveal that molecules making up Aβ40 fibrils recycle to a much greater extent than those of Aβ42. By examining factors that could influence molecular recycling and by running simulations, we show that the rate constant for dissociation of molecules from the fibril (k(off)) is much greater for Aβ40 than that for Aβ42. Importantly, the k(off) values obtained for Aβ40 and Aβ42 reveal that recycling occurs on biologically relevant time scales. These results have implications for understanding the role of Aβ fibrils in neurotoxicity and for designing therapeutic strategies against AD.     

Synthesis of the proposed structure of plakevulin A: revised structure of plakevulin A

A total synthesis of the proposed structure of plakevulin A was accomplished. However, the NMR spectral data of the synthetic plakevulin A were not identical of those of the reported compound. We next converted the synthetic plakevulin A into 1-dihydrountenone A. The ¹H and ¹³C NMR spectral data of 1-dihydrountenone A were identical with those of reported plakevulin A except for the peaks derived from levulinic acid. Thus, we repurified sample of the natural product and confirmed that the natural sample contained 1-dihydrountenone A and levulinic acid in the ratio of one to one. We also found that not plakevulin A but 1-dihydountenone A possessed the inhibitory activity against mammalian DNA polymerases α and β.     

Molecular dynamics simulations of low-ordered alzheimer β-amyloid oligomers from dimer to hexamer on self-assembled monolayers

Accumulation of small soluble oligomers of amyloid-β (Aβ) in the human brain is thought to play an important pathological role in Alzheimer's disease. The interaction of these Aβ oligomers with cell membrane and other artificial surfaces is important for the understanding of Aβ aggregation and toxicity mechanisms. Here, we present a series of exploratory molecular dynamics (MD) simulations to study the early adsorption and conformational change of Aβ oligomers from dimer to hexamer on three different self-assembled monolayers (SAMs) terminated with CH(3), OH, and COOH groups. Within the time scale of MD simulations, the conformation, orientation, and adsorption of Aβ oligomers on the SAMs is determined by complex interplay among the size of Aβ oligomers, the surface chemistry of the SAMs, and the structure and dynamics of interfacial waters. Energetic analysis of Aβ adsorption on the SAMs reveals that Aβ adsorption on the SAMs is a net outcome of different competitions between dominant hydrophobic Aβ-CH(3)-SAM interactions and weak CH(3)-SAM-water interactions, between dominant electrostatic Aβ-COOH-SAM interactions and strong COOH-SAM-water interactions, and between comparable hydrophobic and electrostatic Aβ-OH-SAM interactions and strong OH-SAM-water interactions. Atomic force microscopy images also confirm that all of three SAMs can induce the adsorption and polymerization of Aβ oligomers. Structural analysis of Aβ oligomers on the SAMs shows a dramatic increase in structural stability and β-sheet content from dimer to trimer, suggesting that Aβ trimer could act as seeds for Aβ polymerization on the SAMs. This work provides atomic-level understanding of Aβ peptides at interface.     

Synthesis of lipid A derivatives and their interactions with polymyxin B and polymyxin B nonapeptide

Lipid A is the causative agent of Gram-negative sepsis, a leading cause of mortality among hospitalized patients. Compounds that bind lipid A can limit its detrimental effects. Polymyxin B, a cationic peptide antibiotic, is one of the simplest molecules capable of selectively binding lipid A and may serve as a model for further development of lipid A binding agents. However, association of polymyxin B with lipid A is not fully understood, primarily due to the low solubility of lipid A in water and inhomogeneity of lipid A preparations. To better understand lipid A-polymyxin B interaction, pure lipid A derivatives were prepared with incrementally varied lipid chain lengths. These compounds proved to be more soluble in water than lipid A, with higher aggregation concentrations. Isothermal titration calorimetric studies of these lipid A derivatives with polymyxin B and polymyxin B nonapeptide indicate that binding stoichiometries (peptide to lipid A derivative) are less than 1 and that affinities of these binding partners correlate with the aggregation states of the lipid A derivatives. These studies also suggest that cooperative ionic interactions dominate association of polymyxin B and polymyxin B nonapeptide with lipid A.     

Bioinspired Total Synthesis of Complex Nucleoside Antibiotics A201A,A201D and A201E

Herein, bioinspired total syntheses of A201A, A201D, and A201E based on a previously reported biosynthetic pathway are presented. The challenging 1,2-cis-furanoside, a core structure of the A201 family, was obtained by remote 2-quinolinecarbonyl-assisted glycosylation. We accomplished the total synthesis of A201A and A201E based on the critical 1,2-cis-furanoside moiety through late-stage glycosylation without any interference from basic dimethyl adenosine. We also confirmed the absolute configuration of A201E by total synthesis. This modular synthesis strategy enables efficient preparation of A201 family antibiotics, allowing the study of their structure–activity relationships and mode of action. This study satisfies the increasing demand for developing novel antibiotics inspired by the A201 family.     

Synthesis of indole-based oxadiazoles and their interaction with bacterial peptidoglycan and SARS-CoV-2 main protease: In vitro,molecular docking and in silico ADME/Tox study

In the present study, Indole-based-oxadiazole (1A-17A) compounds were successfully synthesized. The structures of all synthesized compounds were fully characterized by different sophisticated spectroscopic techniques such 1H NMR, 13C NMR, and HREI-MS. Further, the synthesized compounds were explored to investigate their broad-spectrum antibacterial and antibiofilm potential against multidrug resistant Pseudomonas aeruginosa (MDR-PA) and methicillin resistant Staphylococcus aureus (MRSA). The compounds possessed a broad spectrum of antibacterial activity having MIC values of values 1–8 mg/ml against the tested microorganisms. Compound A6 and A7 shows maximum antibacterial activity against MDR-PA, whereas A6, A7 and A11 shows highest activity against MRSA. Furthermore, antibiofilm assay shows that A6, A7 and A11 showed maximum inhibition of biofilm formation and it was found that at 4 mg/ml; A6, A7 and A11 inhibit MRSA biofilm formation by 81.1, 77.5 and 75.9%, respectively; whereas in case of P. aeruginosa; A6 and A7 showed maximum biofilm inhibition and inhibit biofilm formation by 81.5 and 73.7%, respectively. Molecular docking study showed that compounds A6, A7, A8, A10, and A11 had high binding affinity to bacterial peptidoglycan, indicating their potential inhibitory activity against tested bacteria, whereas A6 and A11 were found to be the most effective inhibitors of SARS CoV-2 main protease (3CLpro), with a binding affinity of ? 7.78 kcal/mol. Furthermore, SwissADME and pkCSM-pharmacokinetics online tools was applied to calculate the ADME/Tox profile of the synthesized compounds and the toxicity of these chemicals was found to be low. The Lipinski, Veber, Ghose, and Consensus LogP criteria were also used to predict drug-likeness levels of the compounds. Our findings imply that the synthesized compounds could be a useful for the preventing and treating biofilm-related microbial infection as well as SARS-CoV2 infections.     

Fabrication and electron transport properties of epitaxial films of electron-doped 12CaO·7Al2O3 and 12SrO·7Al2O3

Epitaxial growth and electron doping of 12CaO·7Al₂O₃ (C12A7) and 12SrO·7Al₂O₃ (S12A7) are reported. The C12A7 films were prepared on Y₃Al₅O₁₂ (YAG) single-crystal substrates by pulsed laser deposition at room temperature and subsequent thermal crystallization. X-ray diffraction patterns revealed the films were grown epitaxially with the orientation relationship of (001)[100] C12A7 || (001)[100] YAG. For S12A7, pseudo-homoepitaxial growth was attained on the C12A7 epitaxial layer. Upon electron doping, metallic conduction was achieved in the C12A7 film and the S12A7/C12A7 double-layered films. Analyses of optical absorption spectra for the S12A7/C12A7 films provided the densities of free electrons in each layer separately. Hall measurements exhibited larger electron mobility in the S12A7/C12A7 film than those in C12A7 and S12A7 films, suggesting free electrons may be accumulated at the S12A7/C12A7 interface due presumably to a discontinuity of the cage conduction bands.     

Structures of americanol A and isoamericanol A having a neurotrophic property from the seeds of Phytolacca americana.

The structures of new neo-lignans, isoamericanol A (1) and americanol A (2) isolated from the seeds of Phytolacca americana have been elucidated on the basis of spectroscopic data and then confirmed by chemical correlation with the previously known isoamericanin A (3) and americanin A (4). Isoamericanol A, americanol A, and americanin A have been found to enhance choline acetyltransferase activity at 10(-5) M in a cultured neuronal cell system derived from fetal rat hemisphere.     

小孔沸石微结构的CO_2吸附表征

以3种已知结构的小孔沸石3A、4A和5A为研究对象,以N2和CO2为吸附质,通过吸附数据测定,研究了小孔沸石微孔结构的吸附表征方法.结果表明,N2吸附无法检测4A沸石的孔,而CO2吸附可以检测.对于4A和5A沸石,在35s内CO2吸附就可以达到平衡.HK(Horvath-Kawazoe)柱状模型不能表征4A和5A沸石的孔结构,但是HK球形模型可以,基于最大吸附量、D-A(Dubinin-Astakhov)方程和Langmuir-Freundlich模型计算了4A和5A沸石的微孔孔容,其中根据最大吸附容量和D-A方程计算的微孔孔容与文献值最接近.