Identification of novel potential HIF-prolyl hydroxylase inhibitors by in silico screening

Suppression of HIF-prolyl hydroxylase (PHD) activity by small-molecule inhibitors leads to the stabilization of hypoxia inducible factor and has been recognized as promising drug target for the treatment of ischemic diseases. In this study, pharmacophore-based virtual screening and molecular docking approaches were concurrently used with suitable modifications to identify target-specific PHD inhibitors with better absorption, distribution, metabolism, and excretion properties and to readily minimize false positives and false negatives. A customized method based on the active site information of the enzyme was used to generate a pharmacophore hypothesis (AAANR). The hypothesis was validated and utilized for chemical database screening and the retrieved hit compounds were subjected to molecular docking for further refinement. AAANR hypothesis comprised three H-bond acceptor, one negative ionizable group and one aromatic ring feature. The hypothesis was validated using decoy set with a goodness of fit score of 2 and was used as a 3D query for database screening. After manual selection, molecular docking and further refinement based on the molecular interactions of inhibitors with the essential amino acid residues, 18 hits with good absorption, distribution, metabolism, and excretion (ADME) properties were selected as excellent PHD inhibitors. The best pharmacophore hypothesis, AAANR, contains chemical features required for the effective inhibition of PHD. Using AAANR, we have identified 18 potential and diverse virtual leads, which can be readily evaluated for their potency as novel inhibitors of PHD. It can be concluded that the combination of pharmacophore, molecular docking, and manual interpretation approaches can be more successful than the traditional approach alone for discovering more effective inhibitors.     

Discovery of novel iron clusters in proteins by Mössbauer spectroscopy

Iron clusters are the catalytically active groups of many proteins. The basis building blocks of these clusters are few; they are all variants of three archetypal patterns: [Fe–O–Fe], [2Fe–2S], and [4Fe–4S]. Mössbauer spectroscopy, in conjunction with EPR spectroscopy, susceptometry and EXAFS, plays an important role in characterizing type, number, oxidation states and magnetic properties of such clusters in newly discovered proteins, and in detecting how valency and magnetism vary by passing through the catalytical cycle of these proteins. In this contribution we present the characterization of a novel iron cluster with unusual bridging and terminal ligands and metal coordinations.     

棱镜表面误差对波面面形的影响

本文讨论了棱镜表面误差（主要是局部误差）对波面面形的影响。给出了计算公式及其证明。并以直角棱镜和列曼棱镜为例进行了计算和讨论     

Differential production of superoxide by neuronal mitochondria

Background  

Mitochondrial DNA (mtDNA) mutations, which are present in all mitochondria-containing cells, paradoxically cause tissue-specific disease. For example, Leber's hereditary optic neuropathy (LHON) results from one of three point mutations mtDNA coding for complex I components, but is only manifested in retinal ganglion cells (RGCs), a central neuron contained within the retina. Given that RGCs use superoxide for intracellular signaling after axotomy, and that LHON mutations increase superoxide levels in non-RGC transmitochondrial cybrids, we hypothesized that RGCs regulate superoxide levels differently than other neuronal cells. To study this, we compared superoxide production and mitochondrial electron transport chain (METC) components in isolated RGC mitochondria to mitochondria isolated from cerebral cortex and neuroblastoma SK-N-AS cells.     

A novel graphical representation of proteins and its application

On the basis of three kinds of indices of physicochemical properties of twenty amino acids, a novel 3D graphical representation of protein sequences is presented. Then, the improved cumulative distance of the 3D graphical representations is defined in order to compare the proteins for similarity. Furthermore, the efficiency of our approach is illustrated by performing a comparison of similarities/dissimilarities among sequences of the ND5 proteins of nine different species. A correlation and significance analysis is provided to compare our results on similarities/dissimilarities and some other graphical representation results with the ClustalW results on similarities/dissimilarities. The comparison results show that our approach has better correlations with ClustalW for all nine species than other approaches.     

Computational design of proteins with novel structure and functions

Computational design of proteins is a relatively new field, where scientists search the enormous sequence space for sequences that can fold into desired structure and perform desired functions. With the computational approach, proteins can be designed, for example, as regulators of biological processes, novel enzymes, or as biotherapeutics. These approaches not only provide valuable information for understanding of sequence–structure–function relations in proteins, but also hold promise for applications to protein engineering and biomedical research. In this review, we briefly introduce the rationale for computational protein design, then summarize the recent progress in this field, including de novo protein design, enzyme design, and design of protein–protein interactions. Challenges and future prospects of this field are also discussed.     

Identification of pyrrolo-pyridine derivatives as novel class of antibacterials

Molecular Diversity - A series of 5-oxo-4H-pyrrolo[3,2-b]pyridine derivatives was identified as novel class of highly potent antibacterial agents during an extensive large-scale high-throughput...     

Identification of new novel scaffold for Aurora A inhibition by pharmacophore modeling and virtual screening

Aurora kinases belong to family of highly conserved serine/threonine protein kinases that are involved in diverse cell cycle events and play a major role in regulation of cell division. Abnormal expression of Aurora kinases may lead to cancer; hence, these are considered as a potential target in cancer treatment. In this research article, we identified three novel Aurora A inhibitors using modern computational tools. A four-point common 3D pharmacophore hypothesis of Aurora A (AurA) inhibitors was developed using a diverse set of 55 thienopyrimidine derivatives. A three-dimensional quantitative structure–activity relationship (3D-QSAR) study was carried out using atom-based alignment of diverse set of 55 molecules to evaluate the structure– activity relationships. Docking and 3D-QSAR studies were performed with the 3D structure of AurA to evaluate the generated pharmacophore. The pharmacophore model and 3D-QSAR results complemented the results of our docking study. The pharmacophore hypothesis, which yields the best results, was used to screen the Zinc ‘clean drug-like’ database. Various database filters such as 3D-arrangement of pharmacophoric features, predicted activity and binding interaction score were used to retrieve hits having potential AurA inhibition activity.     

Protein aggregation containing beta-amyloid,alpha-synuclein and hyperphosphorylated tau in cultured cells of hippocampus,substantia nigra and locus coeruleus after rotenone exposure

Background  

Protein aggregates containing alpha-synuclein, beta-amyloid and hyperphosphorylated tau are commonly found during neurodegenerative processes which is often accompanied by the impairment of mitochondrial complex I respiratory chain and dysfunction of cellular systems of protein degradation. In view of this, we aimed to develop an in vitro model to study protein aggregation associated to neurodegenerative diseases using cultured cells from hippocampus, locus coeruleus and substantia nigra of newborn Lewis rats exposed to 0.5, 1, 10 and 25 nM of rotenone, which is an agricultural pesticide, for 48 hours.     

Identification of novel Interleukin-2 inhibitors through computational approaches

Interleukin-2 (IL-2), is a 15.5-kDa cytokine that is now emerging as a target in drug discovery for novel therapeutic approaches in several autoimmune disorders. In an attempt to identify new inhibitors for the IL-2/IL-2R interaction, virtual screening (VS) was performed. Four different docking programs (GOLD, FlexX, Glide, and LigandFit) in combination with several scoring functions were used to identify novel IL-2/IL-2R interaction inhibitors. VS of a database of 6,000 compounds resulted in the identification of three novel and moderately active hits with IC $_{50}$ values ranging from 6.6 to 44.3  $\upmu $ M. Furthermore, the effect of these three compounds on the expression of IL-2R $\alpha $ was assessed. The three active hits showed dose-dependent inhibitory effects on the expression of IL-2R $\alpha $ with an IC $_{50}$ range of 5.8 to 140  $\upmu $ M. The cytotoxicity of these active hits was assessed using three normal cell-lines: bovine kidney cell-line (MDBK), mouse fibroblast cell-line (3T3), and rat hepatocytes cell-line (CC-1). The compounds were found to have negligible cytotoxicity compared to their IC $_{50}$ as IL-2/IL-2R interaction inhibitors. These results demonstrate that our VS protocol can identify novel inhibitors for IL-2/IL-2R interaction that effectively suppress IL-2 production, as well as the expression of IL-2R $\alpha $ . Optimization of these molecules could lead to improved and effective anti-inflammatory therapeutics.     

Polyphosphate-dependent nicotinamide adenine dinucleotide (NAD) kinase: A novel missing link in human mitochondria

Polyphosphate [poly(P)] is described as a homopolymer of inorganic phosphates. Nicotinamide adenine dinucleotide kinase (NAD kinase) catalyzes the phosphorylation of NAD⁺ to NADP⁺ in the presence of ATP (ATP-NAD kinase). Novel NAD kinase that explicitly phosphorylates NAD⁺ to NADP⁺ using poly(P), besides ATP [ATP/poly(P)-NAD kinase], was found in bacteria, in particular, Gram-positive bacteria, and the gene encoding ATP/poly(P)-NAD kinase was also newly identified in Mycobacterium tuberculosis H37Rv. Both NAD kinases required multi-homopolymeric structures for activity expression. The enzymatic and genetic results, combined with their primary and tertiary structures, have led to the discovery of a long-awaited human mitochondrial NAD kinase. This discovery showed that the NAD kinase is a bacterial type of ATP/poly(P)-NAD kinase. These pioneering findings, i.e., ATP/poly(P)-NAD kinase, NAD kinase gene, and human mitochondrial NAD kinase, have significantly enhanced research on the biochemistry, molecular biology, and evolutionary biology of NAD kinase, mitochondria, and poly(P), including some biotechnological knowledge applicable to NADP⁺ production.     

Design of novel SPEEK-based proton exchange membranes by self-assembly method for fuel cells

Fuel cell represents a new energy conversion device, which promises to provide clean source of power. Fuel cell [particularly proton exchange membrane fuel cell and direct methanol fuel cell (DMFC)] is a promising candidate for transportation and portable power source applications. In DMFC, there is a problem of methanol crossover. In order to reduce such a problem, there has been an intensive research activity in the modification of Nafion. In the present investigation, self-assembled membranes were fabricated with sulfonated polyether ether ketone as the core part of the membrane. Aminated polysulfone and sulfonated polysulfone were used as the layers in order to prevent the crossover of methanol. The assembled membranes were characterized by ion exchange capacity, water and methanol absorption, and durability. The methanol permeability and selectivity ratio proved a strong influence on DMFC application. Scanning electron microscopy proved smooth surface, which established strong cohesive force for the polymer chains. Among the synthesized self-assembled membranes, the membrane with two bilayers was the best in terms of power density in DMFC. The membrane electrode assembly with two bilayers showed higher performance (~61.05 mW/cm²) than sulfonated poly(ether ether ketone) and Nafion in DMFC.     

Property prices in urban areas affected by road traffic noise

This paper reports a revealed preference study into the different effects of road traffic noise on property values in residential areas with similarly high road traffic sound levels but with what appear to be important differences in the market for different types of residential property in each area. The results show significant differences in the revealed effects of noise on property prices between the three areas with in one case an increasing (and possibly misleading) relationship between higher monetary values and higher sound levels. A number of possible explanations for the findings are discussed in the paper.     

Specific binding of tubeimoside-2 with proteins in hepatocarcinoma HepG2 cells: investigation by molecular spectroscopy

In this study, we compared different binding interactions of TBMS2 with proteins both in hepatocarcinoma HepG2 cells and in normal embryo hepatic L02 cells by using fluorescence, absorption, and CD spectroscopy. The fluorescence data revealed that the fluorescence intensity of proteins in the HepG2 and L02 cells decreased in the presence of TBMS2 by 30.79% and 12.01%, respectively. Binding constants and thermodynamic parameters were obtained for systems of TBMS2 with the two kinds of cell proteins. The results indicated that HepG2 cell proteins had a higher TBMS2 binding activity than those in the L02 cells. Analysis of the TBMS2 cytotoxic activities showed that TBMS2 could selectively induce apoptosis of HepG2 cells by binding to them, while its apoptotic effect on L02 cells was relatively weaker.     

Adhesion and endothelialization of endothelial cells on the surface of endovascular stents by the novel rotational culture of cells

Recent researches indicate that the initial event in the implantation of endovascular stents involves mechanical injury to the vessel wall. Confluent endothelialization of vascular grafts in vitro before implantation has been suggested as a way to reduce injury of the blood vessel. The purpose of this study is to establish a useful way to improve the adhesion of endothelial cells and accelerate endothelialization on the surface of endovascular stents by a novel rotational culture device. Numerical simulation was used to predict the shear stress on the surface of stents. The number of cellular adhesion was calculated by cell counting, the cell growth was observed by scanning electron microscope and fluorescence microscope. Numerical simulation results showed that the stents was exposed to shear stress of 2.66 × 10⁻³ to 8.88 × 10⁻² Pa. Rotational culture of human umbilical vein endothelial cells could enhance the adhesion of cells and accelerate endothelialization on the surface of stents when the culture conditions for EC adhesion were intermediate rotation speed, higher dynamic incubation times, lower cell densities.     

"温度对扩散的影响"演示实验的改进

分析了教材和文献中"温度对扩散的影响"实验存在的弊端,并提出了"吸墨法"演示扩散现象,即利用注射器吸入墨水在下端与冷水和热水接触,通过墨水在冷热水中的不同扩散速度演示温度对扩散现象的影响,避免了重力对演示实验效果的影响.     

Elimination effects of toxic trans-crotonaldehyde in mitochondria of glioma by lithocholic acid

The purposes of this study were to explore the factors contributing to the generation of the toxic trans-crotonaldehyde in mitochondria of glioma and to look for the elimination effects of the toxic trans-crotonaldehyde by the lithocholic acid. Ultraviolet-visible absorption spectroscopy and mitochondrial isolation and extraction from glioma were used in this study. Research findings showed that the factors contributing to the generation of the toxic trans-crotonaldehyde were hydrogen peroxide, mitochondria of glioma, and their appropriate interaction, respectively. The appropriate quantity of the toxic trans-crotonaldehyde could be induced by hydrogen peroxide (0.16?mmol), mitochondria of glioma (3?mg protein/ml), and 30?min of their interaction, respectively. The most suitable conditions for the lithocholic acid to eliminate the toxic trans-crotonaldehyde were the weakly alkaline of mitochondria of glioma (pH 8.0), the lithocholic acid (0.15?mmol), and 15?min of interaction, respectively. The conclusion was that the lithocholic acid efficiently eliminated the toxic trans-crotonaldehyde in mitochondria of glioma in real time and opened up a new way to treat glioma.     

Equine estrogens differentially inhibit DNA fragmentation induced by glutamate in neuronal cells by modulation of regulatory proteins involved in programmed cell death

Background  

Recent data indicate that excitotoxicity of high levels of neurotransmitter glutamate may be mediated via programmed cell death (apoptosis) and that it can be prevented in HT22 mouse hippocampal cells by various equine estrogens with Δ⁸,17β-estradiol (Δ⁸,17β-E₂) being the most potent. In order to delineate the mechanism(s), glutamate-induced cell death of HT22 cells was assessed by measuring (a) DNA fragmentation in the presence or absence of 11 equine estrogens (components of the drug CEE); (b) cell death and (c) levels of anti-apoptotic (Bcl-2) and proapoptotic (Bax) proteins in the presence or absence of two equine estrogens, Δ⁸,17β-E₂ and 17β-estradiol (17β-E₂) by LDH release assay and Western blot analysis respectively.