• Asian Pacific Journal of Cancer Prevention
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• v.15 no.10
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• pp.4331-4338
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• 2014

$N^1$-(2, 5-dimethoxyphenyl)-$N^8$-hydroxyoctanediamide (N25) is a novel SAHA cap derivative of HDACi, with a patent (No. CN 103159646). This invention is a hydroxamic acid compound with a structural formula of $RNHCO(CH_2)6CONHOH$ (wherein R=2, 5dimethoxyaniline), a pharmaceutically acceptable salt which is soluble. In the present study, we investigated the effects of N25 with regard to drug distribution and molecular docking, and anti-proliferation, apoptosis, cell cycling, and $LD_{50}$. First, we designed a molecular approach for modeling selected SAHA derivatives based on available structural information regarding human HDAC8 in complex with SAHA (PDB code 1T69). N25 was found to be stabilized by direct interaction with the HDAC8. Anti-proliferative activity was observed in human glioma U251, U87, T98G cells and human lung cancer H460, A549, H1299 cells at moderate concentrations ($0.5-30{\mu}M$). Compared with SAHA, N25 displayed an increased antitumor activity in U251 and H460 cells. We further analyzed cell death mechanisms activated by N25 in U251 and H460 cells. N25 significantly increased acetylation of Histone 3 and inhibited HDAC4. On RT-PCR analysis, N25 increased the mRNA levels of p21, however, decreased the levels of p53. These resulted in promotion of apoptosis, inducing G0/G1 arrest in U251 cells and G2/M arrest in H460 cells in a time-dependent and dose-dependent manner. In addition, N25 was able to distribute to brain tissue through the blood-brain barrier of mice ($LD_{50}$: 240.840mg/kg). In conclusion, our findings demonstrate that N25 will provide an invaluable tool to investigate the molecular mechanism with potential chemotherapeutic value in several malignancies, especially human glioma.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.26-51
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• 2003

Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

• Journal of Microbiology and Biotechnology
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• v.26 no.10
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• pp.1708-1716
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• 2016

Glucose dehydrogenase (GDH) is an oxidoreductase enzyme and is used as a biocatalyst to regenerate NAD(P)H in reductase-mediated chiral synthesis reactions. In this study, the glucose 1-dehydrogenase B gene (gdhB) was cloned from Bacillus thuringiensis subsp. kurstaki, and wild-type (GDH-BT^WT) and His-tagged (GDH-BT^N-His, GDH-BT^C-His) enzymes were produced in Escherichia coli BL21 (DE3). All enzymes were produced in the soluble forms from E. coli. GDH-BT^WT and GDH-BT^N-His showed high specific enzymatic activities of 6.6 U/mg and 5.5 U/mg, respectively, whereas GDH-BT^C-His showed a very low specific enzymatic activity of 0.020 U/mg. These results suggest that the intact C-terminal carboxyl group is important for GDH-BT activity. GDH-BT^WT was stable up to 65℃, whereas GDH-BT^N-His and GDH-BT^C-His were stable up to 45℃. Gel permeation chromatography showed that GDH-BT^WT is a dimer, whereas GDH-BT^N-His and GDH-BT^C-His are monomeric. These results suggest that the intact N- and C-termini are required for GDH-BT to maintain thermostability and to form its dimer structure. The homology model of the GDH-BT^WT single subunit was constructed based on the crystal structure of Bacillus megaterium GDH (PDB ID 3AY6), showing that GDH-BT^WT has a Rossmann fold structure with its N- and C-termini located on the subunit surface, which suggests that His-tagging affected the native dimer structure. GDH-BT^WT and GDH-BT^N-His regenerated NADPH in a yeast reductase-mediated chiral synthesis reaction, suggesting that these enzymes can be used as catalysts in fine-chemical and pharmaceutical industries.

• Korean Journal of Environmental Agriculture
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• v.17 no.3
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• pp.279-285
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• 1998

Fenitrothion-degrading microorganisms were isolated from 124 sampling sites of paddy, upland, forest and polluted soil, and wastewater. A total of 1,071 strains were isolated from each selective medium supplemented with 50mg/l of fenitrothion - nutrient agar (NA) 601, potato dextrose agar (PDA) 201, Actinomycetes isolation agar (AIA) 168 and basal salt medium (BSM) 101, respectively. Twenty-eight effective strains of them, which showed more than 80% degradation of fenitrothion by the gasliquid chromatography(GLC) analysis. were successfully selected from each liquid culture supplemented with 50mg/l of fenitrothion - NB 12(upland soil 3, paddy soil 3, forest soil 2, polluted soil 4), PDB 8(upland soil 1, paddy soil 2, forest soil 2, polluted soil 3) and PSB 8(upland soil 1, forest soil 1, polluted soil 6), respectively. Four strains - NPal, NFol, PFol and BPol, which have the most powerful degradation activity were finally selected among 28 fenitrothion-degrading microorganisms based on the degradation rate at the concentration of 100mg/l fenitrothion in enrichment media.

• Journal of Pharmacopuncture
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• v.18 no.2
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• pp.7-18
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• 2015

Objectives: Lawsone (1,4 naphthoquinone) is a non redox cycling compound that can be catalyzed by DT diaphorase (DTD) into 1,2,4-trihydroxynaphthalene (THN), which can generate reactive oxygen species by auto oxidation. The purpose of this study was to evaluate the toxicity of the phytomarker 1,4 naphthoquinone and its metabolite THN by using the molecular docking program AutoDock 4. Methods: The 3D structure of ligands such as hydrogen peroxide ($H_2O_2$), nitric oxide synthase (NOS), catalase (CAT), glutathione (GSH), glutathione reductase (GR), glucose 6-phosphate dehydrogenase (G6PDH) and nicotinamide adenine dinucleotide phosphate hydrogen (NADPH) were drawn using hyperchem drawing tools and minimizing the energy of all pdb files with the help of hyperchem by $MM^+$ followed by a semi-empirical (PM3) method. The docking process was studied with ligand molecules to identify suitable dockings at protein binding sites through annealing and genetic simulation algorithms. The program auto dock tools (ADT) was released as an extension suite to the python molecular viewer used to prepare proteins and ligands. Grids centered on active sites were obtained with spacings of $54{\times}55{\times}56$, and a grid spacing of 0.503 was calculated. Comparisons of Global and Local Search Methods in Drug Docking were adopted to determine parameters; a maximum number of 250,000 energy evaluations, a maximum number of generations of 27,000, and mutation and crossover rates of 0.02 and 0.8 were used. The number of docking runs was set to 10. Results: Lawsone and THN can be considered to efficiently bind with NOS, CAT, GSH, GR, G6PDH and NADPH, which has been confirmed through hydrogen bond affinity with the respective amino acids. Conclusion: Naphthoquinone derivatives of lawsone, which can be metabolized into THN by a catalyst DTD, were examined. Lawsone and THN were found to be identically potent molecules for their affinities for selected proteins.

• Journal of Mushroom
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• v.17 no.4
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• pp.247-254
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• 2019

Trametes hirsuta, a white rot fungus, exhibits the ability to degrade synthetic aromatic dyes such as congo red (CR), methylene blue (MB), crystal violet (CV), and remazol brilliant blue R (RBBR). The mycelia of T. hirsuta degraded RBBR and CR more efficiently than CV and MB in the PDB liquid medium (supplemented with 0.01% 4 aromatic dyes). In these mycelia the activities of three ligninolytic enzymes-laccase, manganese peroxidase (MnP), and lignin peroxidase (LiP)-were observed. Among these, laccase was identified to be the major enzyme responsible for the degradation of the four aromatic dyes. The degradation of bisphenol A was also investigated by culturing the mycelia of T. hirsuta in YMG medium supplemented with 100 ppm bisphenol A. The mycelia of T. hirsuta were found to degrade bisphenol A by 71.3, 95.3, and 100 % within incubation periods of 12, 24, and 36 hr, respectively. These mycelia also showed ligninolytic enzyme-like activities including those similar to laccase, MnP, and LiP. Therefore, these results indicate that T. hirsuta could emerge as a potential tool for the remediation of environmental contamination by aromatic dyes and bisphenol A.

• Korean Journal of Microbiology
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• v.32 no.4
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• pp.264-270
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• 1994

A gene coding for a novel putative $\sigma$ factor of RNA polymerase has been identified from Streptomyces coelicolor A3(2) using Escherichia coli rpoS gene fragment as a probe. The 486 bp rpoS gene fragment was amplified from E. coli genomic DNA by PCR with two synthetic oligonucleotides, the sequences of which were deduced from the amino acid sequences in the regions 2.3 and 4.2 conserved among various bacterial factors. When E. coli genomic DNA fragments were hybridized with cloned rpoS probe, only one band corresponding to rpoS gene (3.2 kb PvuII fragment or 2.3 kb KpnI fragment) was detected. In S. coelicolor, however, two bands were detected both in PvuII digested DNA and SalI digested DNA. 3.5 kb PvuII fragment which binds the rpoS gene probe was cloned (pMS1) from the sublibrary, and the nucleotide sequences of 1.0 kb BamH'/HincII subclone (pBH2) was partially determined. The nucleotide sequences revealed extensive similarity to other $\sigma$ factor genes of S. coelicolor (hrdA, hrdB, hrdC, hrdD), S. aureofaciens (hrdA, hrdB, hrdC, hrdD), Synechococcus species, Pseudomonas aeruginosa, Stigmatella aurantiaca, and Anabaena species. The nucleotide sequences in regions 1.2 and 4 were compared with the corresponding regions of 5 known ${\sigma}$ factor genes of S. coelicolor by multiple alignment. It turned out that the cloned gene is most closely related to hrdA showing 88% amino acid similarity in region 1.2 and 75% in region 4.

• The Korean Journal of Malacology
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• v.30 no.1
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• pp.1-8
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• 2014

Oxygen isotope analysis was carried out on a oyster (Crassostrea gigas) from the neolithic age Gagok-ri shell midden site, Dangjin, Korea to determine the seasonality of shellfish gathering and site occupation. Isotope samples were taken from the hinge section of the left valve of the oyster. The isotope values of the shell range from -2.02‰ to -6.05‰ vs PDB. The isotope profile shows a seasonal temperature cycle, providing information related to seasonality of shellfish gathering. The isotope values towards the edge of the hinge are gradually increasing, suggesting progressively cooling and a fall period of shell gathering and site occupation. The result shows that the oxygen isotope analysis using oyster shell hinges can be used for archaeological seasonality studies.

• Journal of the Korean Society of Groundwater Environment
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• v.7 no.3
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• pp.116-124
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• 2000

Geochemical and isotopic analyses were carried out to investigate hydrochemical characteristics, source of carbon species in the carbonated waters in South Korea. Most Korean carbonated waters from different geologic settings are characterized by a Ca-HCO$_3$type with a relatively low pH range from 5.3 to 6.3 (avg. 6.0). The concentrations of cations and anions in the carbonate waters are in the order of Ca$^{2＋}$>Na$^{＋}$>Mg$^{2＋}$>Si$^{4＋}$>Fe$^{2＋}$>K$^{＋}$ and HCO$_3$$^{－}$>SO$_4$$^{2－}$>Cl$^{－}$, respectively. The HCO$_3$$^{－}$ ion is more enriched in the carbonated water from the sedimentary rock and granitic rock of Mesozoic age in the Gyungsang basin(GII) and the Precambrian metamorphic rock and Jurassic granitic rocks of the Gyunggj massif in the Gangwon province(GⅠ) than those of the meta-sedimentary rock and granite in the Ogcheon zone(GⅢ). Based on the oxygen and hydrogen isotopic data, the carbonated waters are derived from the meteoric water, showing apparent latitude and altitude effects. The $delta$$^{13}$C values of carbon species in the carbonated water are in between -6.23 and 0.0 $textperthousand$, suggesting inorganic source of carbon originated from the carbonate mineral and carbonate rock in the aquifer.

• Economic and Environmental Geology
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• v.32 no.2
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• pp.129-139
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• 1999

Hydrothermal gold deposits of the Trabong district in Vietnam occur as single-stage quartz $\pm$ calcite veins (0.3-1.2 m thick) which fill fault fractures in graphite-bearing gneiss and schist of the Chulai Complex and Kham Duc Formation of the Proterozoic age. Ore grades are 1.3 to 92.4 g/ton Au. Ore mineralogy is very simple, consisting mainly of pyrite with minor amounts of base-metal sulfides and electrum. Gold grains occur in two assemblages as follows: (1) early, Fe-rich (7.2-10.4 mole % FeS) sphalerite + electrum (50.4-64.3 atom % Au) assemblage occurring as inclusions in pyrite; (2) late, Fe-poor «4.7 mole % FeS) sphalerite + galena + electrum (47.6-81.7 atom % Au) assemblage occurring along fractures of pyrites. Based on fluid inclusion data and thermochemical considerations of ore mineral assemblages, ore minerals were formed at high temperatures (about $230^{\circ}C$ to $420^{\circ}C$) from $H_{2}O-CO_{2}(-CH_{4})$-NaCI fluids with the sulfur fugacity of about $10^{-6}$ to $10^{-10}$ atm. Fluid inclusion data also indicate that ore mineralization occurred mainly as a result of fluid unmixing accompanying $CO_2$ effervescence. Calculated oxygen and measured hydrogen isotope compositions of mineralizing waters (${\delta}^{18}O_{V-SMOW}$ values = 5.3 to 8.6$\textperthousand$, ${\delta}D_{V-SMOW}$ values = - 60 to - 52$\textperthousand$), along with the sulfur isotope compositions of vein sulfides (${\delta}^{34}S_{CDR}$ values = - 1.2 to 2.8$\textperthousand$) and carbon isotope compositions of inclusion $CO_2$ (${\delta}^{13}C_{PDB}$ values = - 4.7 to - 2.0$\textperthousand$) indicate that the high temperature (mesohypothermal) gold mineralization formed from a magmatic fluid.