• Journal of the East Asian Society of Dietary Life
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• v.15 no.3
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• pp.315-322
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• 2005

In this study we report on the estrogen activity of silkworm pupa and herb extracts in vitro. The estrogenic activity of these resources was investigated by competition binding assays with estrogen receptor $\alpha(ER{\alpha})\;or\;ER{\beta}$, and viability of MCF-7 cells, a human breast cancer cell line. Saturation ligand-binding analysis of $ER{\alpha}\;and\;ER{\beta}$ revealed that all plant extracts competed with estrogen ligand for binding to both ER subtypes with a similar preference and degree and competed stronger with ligand for binding to $ER{\beta}\;than\;to\;ER{\alpha}$. The highest $ER{\alpha}-binding$ sample was silkworm pupa aqueous extract The highest $ER{\beta}-binding$ sample was silkworm pupa oil. These samples were further tested for bioactivity based on their ability to regulate cell growth rate in ER(+) breast cancer cell line, MCF-7 cells. Our studies showed that silkworm pupa, soritae, sesame, yam, pueraria, malt, ginseng, Polygonum multiflorum, and Curcuma longa significantly stimulated the growth of MCF-7 cells (P<0.05). In summary, these results suggested that silkworm pupa and herbs might be useful as potential phytoestrogens.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3658-3662
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• 2010

A new bis-Ru(II) complex, in which two [Ru(1,10-phenanthroline)$_2$dipyrido[3,2-a:2',3'-c]phenazine]$^{2+}$ were tethered by a 1,3-bis(4-pyridyl)propane linker, was synthesized and its binding mode and stoichiometry to DNA was investigated by optical spectroscopy including linear dichroism (LD) and fluorescence intensity measurement. The magnitude of the negatively reduced LD signal of the bis-Ru(II) complex in the dipyrido[3,2-a:2',3'-c]phenazine (DPPZ) ligand absorption region appeared to be similar compared to that in the DNA absorption region, which is considered to be a diagnostic for DPPZ ligand intercalation. The binding stoichiometry measured from its LD magnitude and enhanced fluorescence intensity corresponds to one ligand per three DNA bases, effectively violating the nearest neighbouring site exclusion model for classical DNA intercalation. This observation is in contrast with monomer analogue [Ru(1,10-phenanthroline)$_2$dipyrido[3,2-a:2',3'-c]phenazine]$^{2+}$, which is saturated at the DPPZ ligand to DNA base ratio of 0.25, or one DPPZ ligand per four nucleobases.

• Journal of Integrative Natural Science
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• v.3 no.1
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• pp.49-53
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• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• Journal of the Korean Magnetic Resonance Society
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• v.5 no.2
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• pp.130-137
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• 2001

Backbone dynamics of the catalytic residues in free and steroid-bound $\Delta$$^{5}$ -3- ketosteroid isomerase from Pseudomonas testosteroni has been examined by $^{15}$ N relaxation measurements. The relaxation data were analyzed using the model-free formalism to extract the model-free parameters (S$^2$, $\tau$$_{e}$, and R$_{ex}$). Tyr-34 and Asp-99 exhibit enhanced high-frequency (pico- to nanosecond) internal motions in the free enzyme, which are restricted upon ligand binding, while Asp-38 experiences severe restriction of the internal motions in the fee enzyme, suggesting that Tyr-14 and Asp-99 are more actively involved in the ligand binding than Asp-38. The results also indicate that the H-bond network in the catalytic cavity might be slightly strengthened upon ligand binding, which may have some implications on the enzyme mechanism.he enzyme mechanism.m.

• Bulletin of the Korean Chemical Society
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• v.31 no.4
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• pp.829-834
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• 2010

Ligand variation was carried out on a cobalt(III) complex of Salen-type ligand comprised of 1,2-cyclohexenediamine and salicylaldehyde bearing a methyl substituent on 3-position and -[$CMe(CH_2CH_2CH_2N^+Bu_3)_2$] on 5-position, which is a highly active catalyst for $CO_2$/propylene oxide copolymerization. Replacement of the methyl substituent with bulky isopropyl group resulted in alteration of the binding mode, consequently lowering turnover frequency significantly. Replacement with an ethyl group preserved binding mode and activity. Replacement of the tributylammonium unit with trihexylammonium or trioctylammonium, or replacement of 1,2-cyclohexenediamino unit with -$NC(Me)_2CH_2N$- decreased activity, even though the binding mode was unaltered.

• Clinical and Experimental Reproductive Medicine
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• v.13 no.2
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• pp.187-193
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• 1986

The purpose of this study was to establish optimal conditions for progesterone receptor assay using rat uterus, therby applying this system to understand action mechanism of progesterone in female reproductive organ and to evaluate physiological and pathological conditions in female reproduction. The results obtained were as follows 1. $^3H-R5020$ seemed to be more stable than 3H-progesterone as a ligand. 2. Optimal incubation time for ligand and receptor binding was 4-5 hrs at $4^{\circ}C$. 3. For the separation of bond and free ligand, optimal charcoal incubation time was 20 mins. 4. 2-3 mg cytosolic protein/ml was optimal for the binding of ligand. 5. Endogenous progesterone did not influence binding of ligand and receptor unless endogenous progesterone levels were extremely high as in case of pregnancy. 6. Dissociation rate for progesterone receptor was 1.22 nM. 7. $^3H-R5020$ did not bind to corticoid binding globulin (CBG), suggesting that addition of cortisol is saturate CBG was, not necessary as far as $^3H-R5020$ was used as a radioligand. It is, therefore, considered that this assay system established with these conditions might be used for the research as well as clinical routine purposes.

• Food Science and Biotechnology
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• v.17 no.6
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• pp.1146-1150
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• 2008

Peroxisome proliferator-activated receptor-gamma ($PPAR_{\gamma}$), a member of the nuclear receptor of ligand-activated transcription factors, plays a key role in lipid and glucose metabolism or adipocytes differentiation. A lignan compound was isolated from mace (the aril of Myristica fragrans Houtt.) as a $PPAR_{\gamma}$ ligand, which was identified as fragrin A or 2-(4-allyl-2,6-dimethoxyphenoxy)-1-(4-hydroxy-3-methoxyphenyl)-propane. To ascertain whether fragrin A has $PPAR_{\gamma}$ ligand-binding activity, it was performed that GAL-4/$PPAR_{\gamma}$ transactivation assay. $PPAR_{\gamma}$ ligand-binding activity of fragrin A increased 4.7, 6.6, and 7.3-fold at 3, 5, and $10{\mu}M$, respectively, when compared with a vehicle control. Fragrin A also enhanced adipocytes differentiation and increased the expression of $PPAR_{\gamma}$ target genes such as adipocytes fatty acid-binding protein (aP2), lipoprotein lipase (LPL), and phosphoenol pyruvate carboxykinase (PEPCK). Furthermore, it significantly increased the expression level of glucose transporter 4 (GLUT4). These results indicate that fragrin A can be developed as a $PPAR_{\gamma}$ agonist for the improvement of insulin resistance associated with type 2 diabetes.

• Journal of the Korean Magnetic Resonance Society
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• v.16 no.2
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• pp.133-146
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• 2012

Three different derivatives were obtained in the synthesis of cobalt-binding BLM-A2 and characterized by NMR and Mass spectrometry. It was found that Component 1 is Co(II)($2H_2O$)(BLM-A2), component 2 is Co(III)($OOH^-$)(BLM-A2) and component 3 is Co(III)($H_2O$)($OH^-$)(BLM-A2), respectively. Component 2 and 3 were interestingly dominated when CoBLM-A2 complex was synthesized under basic condition. In this experiment, it was revealed newly that the brown form (component 1) was 6-coordinated structure composed with not 5 ligands but 4 ligands from BLM-A2 and with $2H_2O$ as the axial ligands. The component 3 exhibiting a novel ligand configuration is found, and the structure of component 3 was observed to be very similar to that of component 1 in the kind of their ligands but one of the axial ligand is $OH^-$ instead of $H_2O$. These ligand configurations are different from the green form (component 2) exhibiting 6-coordinate structure composed of 5 ligands from BLM-A2 and one ligand of $OOH^-$, being consistent with former studies.

• YAKHAK HOEJI
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• v.58 no.1
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• pp.16-20
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• 2014

KR-31064 was developed for the strong angiotensin II receptor antagonist among the one of pyridyl imidazol series compounds. To investigate the receptor-ligand binding characteristics of this nonpeptide antagonist, binding experiments were deployed in various conditions and ex vivo contractile responses were tested toward the standard compound, losartan. Receptor binding experiments with radiolabeled angiotensin II, the $IC_{50}$ value for KR-31064 resulted 0.67 nM without any activities toward type 2 angiotensin II receptor. The comparative potency against losartan was more than 18 fold and the specific activity in type 1 angiotensin II receptor was more than 10,000 fold comparing to the type 2 receptor. Scatchard analysis of saturation binding data showed KR-31064 acted on the receptor in a competitive mode. KR-31064 inhibited the contractile response derived by angiotensin II ($pK_B$: 9.86) similar to that of losartan with decreased maximum signals. As a potent and specific type 1 angiotensin II receptor antagonist, KR-31064 may have possibilities for the development of diagnostic ligands that can be used as tools for various biochemical research experiments and non-invasive diagnostics.

• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.13-24
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• 2013

Dopamine agonists and antagonists and its receptor play a critical role in the information transfer in the nervous system, and dopamine receptor-ligands interactions are deeply related to Parkinson's disease, schizophrenia and some other mental diseases. However, the only experimental 3D structure available for dopamine receptors is human D3 dopamine receptor. Therefore, it is important to create model of subtype dopamine receptor-ligands interactions. We report here the 3D structures of the human D1 and D2 dopamine receptor predicted by using GalaxyTBM, and its predicted binding site determined by using GalaxyDock. The highly conserved Asp on TM 3 and Phe on TM 6 have critical role in ligand binding. Also, highly conserved serines on TM 5 are essential for binding agonists and some kinds of antagonists. We identify differences between binding sites of agonists and antagonists of human D1 and D2 dopamine receptor, and find the reasons of selective binding of antagonists.