• Proceedings of the PSK Conference
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• 2001.10a
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• pp.311.2-312
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• 2001

• Bulletin of the Korean Chemical Society
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• v.24 no.12
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• pp.1757-1762
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• 2003

The interrelation between retention factors of several L-amino acids and their physico-chemical and structural properties can be determined in chromatographic research. In this paper we describe a predictor for retention factors with various properties of the L-amino acids. Eighteen L-amino acids are included in this study, and retention factors are measured experimentally by RP-HPLC. Binding energy ($E_b$), hydrophobicity (log P), molecular refractivity (MR), polarizability (${\alpha}$), total energy ($E_t$), water solubility (log S), connectivity index (${\chi}$) of different orders and Wiener index (w) are theoretically calculated. Relationships between these properties and retention factors are established, and their predictive and interpretive ability are evaluated. The equation of the relationship between retention factors and various descriptors of L-amino acids is suggested as linear and multiple linear form, and the correlation coefficients estimated are relatively higher than 0.90.

• Bulletin of the Korean Chemical Society
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• v.27 no.12
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• pp.1969-1975
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• 2006

3D-QSAR model that correlates the biological activities with the chemical structures of quipazine derivatives acting on the serotonine transporter (SERT) was developed by comparative molecular field analysis (CoMFA). Total 8 models were constructed and a more accurate model, using close 1 $\AA$ grid spacing and StDev*Coefficients weight value gave better results. The contour maps with the best model, the resulting cross-validated correlation ($q^2$ : 0.744), and non-cross-validated correlation ($r^2$ : 0.966) indicate the steric and electrostatic environment of inhibitors in the SERT binding pocket. This study can be used as a putative picture of the pharmacophore in the design of novel and potent inhibitors.

• Bulletin of the Korean Chemical Society
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• v.33 no.7
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• pp.2365-2368
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• 2012

The $11{\beta}$-hydroxysteroid dehydrogenase type 1 ($11{\beta}$-HSD1) enzyme is involved in modulation of glucocorticoid activity within target tissues. This enzyme may contribute to obesity and/or metabolic disease through its action in adipose or liver tissue. Inhibition of $11{\beta}$-HSD1 has major therapeutic potential for glucocorticoid-associated diseases, including obesity, diabetes (wound healing), and muscle atrophy. To develop such therapeutics, we performed a pharmacophore-based virtual screening (VS) for identification of novel $11{\beta}$-HSD1 inhibitors and found that the VS hit compounds show potent inhibition of $11{\beta}$-HSD1 enzyme activity. Further, we present a binding model for active compounds. The proposed pharmacophore may serve as a useful guideline for future design of new chemical entities as $11{\beta}$-HSD1-targeted antidiabetic agents.

• Journal of the Korean Chemical Society
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• v.57 no.1
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• pp.35-39
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• 2013

The chemical bonding and elastic properties of $Ti_2AC$ (A = Ga, Tl) have been investigated by means of extended H$\ddot{u}$ckel tight-binding band structure calculations. The bulk modulus of $Ti_2AC$ decreases as Ga is replaced with Tl at the A sites. This can be understood by considering the relative strength of Ti-A bonds resulting from the different atomic size of 3A-group elements. The analysis of the projected density of states (PDOS) and the crystal orbital overlap population (COOP) for the respective phases shows that Ti-Ga bonds in $Ti_2GaC$ are stronger than Ti-Tl bonds in $Ti_2TlC$.

• Journal of the Mineralogical Society of Korea
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• v.4 no.2
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• pp.90-98
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• 1991

This study introduces a new structural model of 1M 2:1 trioctahedral clay minerals or, more generally, 2:1 trioctahedral phyllosilicates. The structural model requires only the chemical formulae of the clay minerals as an input and uses the regression relation (Radoslovich, 1962) to calculate the a- and b-dimensions of the phyllosilicates with the given chemical formulae. The atomic coordinates of the constituent atoms are geometrically calculated for C2/m space group under the assumption that the interatomic distances are constant. To determine the c-dimension, this study calculates the binding energies of 1M 2:1 trioctahedral phyllosilicates as a function of d(001) and find the minimum energy producing d(001). The structural model generates the cell dimensions, interaxial angles, interatomic distances, octahedral, tetrahedral and interlayer thickness, polyhedron deformation angles and atomic coordinates in the unit cell. The simulated structural parameters of phlogopite and annite are very close to the reported data by Hazen and Burnham (1973), suggesting that the structure simulation using only the chemical formule is successful, and thus, that the structural model of this study overcomes the difficulties in the previous models by other investigators.

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.146.2-147
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• 2003

The benzoxathiol LYR-71 compound was discovered as an inhibitor of NF-kB transcriptional activity with an IC50 value of 5.4 uM. Furthermore, benzoxathiol LYR-71 compound inhibited the NF-kB binding activity to DNA in a dose-dependent manner, which was identified by EMSA with oligonucleotide corresponding to NF-kB consensus sequence. It is well known that NF-kB is an important transcription factor to regulate the expression of inflammatory enzymes (iNOS and COX-2) and cytokines (TNF, IL-1 and IL-6). (omitted)

• Journal of Environmental Health Sciences
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• v.28 no.5
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• pp.65-70
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• 2002

Recently, surfactants were frequently used in order to desorb the hydrophobic organic compounds (HOCs) from soil and to enhance the bioavailability. Among them, -cyclodextrin ($\beta$-CD) is one of those. This study was performed to investigate the binding characteristics between benzene and $\beta$-CD and to examine the bioavailability of benzene. First, we investigated binding characteristics between benzene and $\beta$-CD in water and water/soil system. Then, we examined the effect of $\beta$-CD on the biodegradation of benzene in water and water/soil system. Experimental results on the binding characteristics showed that $\beta$-CD resulted in an efficient complex formation with benzene. As -CD concentration increased, the benzene concentration complexed with $\beta$-CD rapidly increased to 30-40% initial benzene added, and reached the equilibrium. We also investigated the effect of $\beta$-CD on the desorption of benzene from soil in the water/soil system. As $\beta$-CD concentration increased, benzene concentration desorbed into water increased up to 90%. How-ever, in its application to biodegradation of benzene in water and water/soil system, the biodegradation rate of benzene did not improved in the presence of $\beta$-CD compared with in the absense of $\beta$-CD. This result indicated that $\beta$-CD was more preferentially used as a carbon source than benzene. Therefore, for remediation of benzene contaminated soils, $\beta$-CD can be used as a surfactant to desert benzene from soil, and then ex-situ chemical treatment can be applied for the remediation.

• Journal of Ginseng Research
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• v.44 no.5
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• pp.690-696
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• 2020

Background: As the main metabolites of ginsenosides, 20(S, R)-protopanaxadiol [PPD(S, R)] and 20(S, R)-protopanaxatriol [PPT(S, R)] are the structural basis response to a series of pharmacological effects of their parent components. Although the estrogenicity of several ginsenosides has been confirmed, however, the underlying mechanisms of their estrogenic effects are still largely unclear. In this work, PPD(S, R) and PPT(S, R) were assessed for their ability to bind and activate human estrogen receptor α (hERα) by a combination of in vitro and in silico analysis. Methods: The recombinant hERα ligand-binding domain (hERα-LBD) was expressed in E. coli strain. The direct binding interactions of ginsenosides with hERα-LBD and their ERα agonistic potency were investigated by fluorescence polarization and reporter gene assays, respectively. Then, molecular dynamics simulations were carried out to simulate the binding modes between ginsenosides and hERα-LBD to reveal the structural basis for their agonist activities toward receptor. Results: Fluorescence polarization assay revealed that PPD(S, R) and PPT(S, R) could bind to hERα-LBD with moderate affinities. In the dual luciferase reporter assay using transiently transfected MCF-7 cells, PPD(S, R) and PPT(S, R) acted as agonists of hERα. Molecular docking results showed that these ginsenosides adopted an agonist conformation in the flexible hydrophobic ligand-binding pocket. The stereostructure of C-20 hydroxyl group and the presence of C-6 hydroxyl group exerted significant influence on the hydrogen bond network and steric hindrance, respectively. Conclusion: This work may provide insight into the chemical and pharmacological screening of novel therapeutic agents from ginsenosides.

• Korean Journal of Environmental Agriculture
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• v.17 no.3
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• pp.246-253
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• 1998

Heavy metal-tolerant microorganisms, such as Pseudomonas putida, P. aeruginosa, P. chlororaphis and P. stutzeri which possessed the ability to accumulate cadmium, lead, zinc and copper, respectively, were isolated from industrial wastewaters and mine wastewaters polluted with various heavy metals. The binding sites of heavy metal in the cells were investigated by chemical modification of functional groups the cell walls. To determine the binding sites of heavy metal in the cells, electrochemical charge of amine and carboxyl groups in the cell walls of heavy metal-tolerant microorganisms were chemically modified. Chemical modifications of amine groups did not affect the heavy metal uptake as compared to native cell walls. In contrast, modifications of carboxyl groups drastically decreased heavy metal uptake as compared to native cell walls, and electron microscopy confirmed that the form and structure of the heavy metal uptake were different from those of native cell walls. The results suggested that the carboxyl groups were the major sites of heavy metal uptake in the heavy metal-tolerant microorganism cell.