• Bulletin of the Korean Chemical Society
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• v.33 no.4
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• pp.1303-1309
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• 2012

A novel ligand N,N'-(2,6-pyridinedicarbonyl)bis[N-(carboxymethyl)] (L1) was designed and synthesized. Four co-luminescence groups of Sm-La-pyridyl carboxylic acids systems were researched, which are $K_4Sm_{(1-x)}-La_x(L_1)Cl_3{\cdot}y_1H_2O$, $K_4Sm_{(1-x)}La_x(L_2)Cl_3{\cdot}y_2H_2O$, $K_6Sm_{2(1-x)}La_{2x}(L_3)Cl_6{\cdot}y_3H_2O$, $K_4Sm_{(1-x)}La_x(L_4)Cl_3{\cdot}y_4H_2O$. The results indicated the addition of La(III) could sensitize the luminescence of Sm(III) obviously in a certain range, enhancing emission intensity of Sm-pyridyl carboxylic acids relative to the undoped ones. The optimal mole percentages of La(III) in the mixed ions for $L_1$, $L_2$, $L_3$, $L_4$ were confirmed to be 0.6, 0.5, 0.3, 0.6, respectively. The mechanism of the fluorescence enhancement effect was discussed in detail. Furthermore, the binding interaction of $K_4Sm_{0.4}La_{0.6}(L_4)Cl_3{\cdot}5H_2O$ with bovine serum albumin (BSA) have been investigated due to its potential biological activity. The binding site number n was equal to 1.0 and binding constant $K_a$ was about $2.5{\times}10^5\;L{\cdot}mol^{-1}$.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.770-774
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• 2012

Protein loops are often involved in diverse biological functions, and some functional loops show conformational changes upon ligand binding. Since this conformational change is directly related to ligand binding pose and protein function, there have been numerous attempts to predict this change accurately. In this study, we show that it is plausible to obtain meaningful ensembles of loop conformations for flexible, ligand-binding protein loops efficiently by applying a loop modeling method. The loop modeling method employs triaxial loop closure algorithm for trial conformation generation and conformational space annealing for global energy optimization. When loop modeling was performed on the framework of ligand-free structure, loop structures within $3\AA$ RMSD from the crystal loop structure for the ligand-bound state were sampled in 4 out of 6 cases. This result is encouraging considering that no information on the ligand-bound state was used during the loop modeling process. We therefore expect that the present loop modeling method will be useful for future developments of flexible protein-ligand docking methods.

• Bulletin of the Korean Chemical Society
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• v.31 no.2
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• pp.435-441
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• 2010

We report the preparation and characterization of a new and water soluble complex of palladium(II) with 1,10- phenanthroline and butyldithiocarbamate ligands. This compound has been studied through spectroscopic techniques, $^1H$ NMR, IR, electronic spectra and elemental analysis and conductivity measurements. The complex shows 50% cytotoxic concentration ($Ic_{50}$) value against chronic myelogenous leukemia cell line, K562, much lower than that of cisplatin. Thus the mode of binding of this complex to calf thymus DNA have been extensively investigated by isothermal titration UV-visible spectrophotometry, fluorescence, gel filteration and other methods. UV-visible studies show that the complex exhibits cooperative binding with DNA and remarkably denatures the DNA at extremely low concentration ($~13\;{\mu}M$). Fluorescence studies indicate that the complex intercalate into DNA. Gel filtration studies suggest that the binding of Pd(II) complex with DNA is strong enough that it does not readily break. In these interaction studies, several thermodynamic and binding parameters are also determined which may reflect the mechanism of action of this type of compound with DNA.

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2753-2757
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• 2014

INtegrase Interactor 1 protein (INI1/hSNF5) or BRG1-associated factor 47 (BAF47) is a SWI/SNF-related matrix associated actin dependent regulator of chromatin subfamily B member. DNA binding domain of INI1/hSNF5 is cloned into E.coli expression vectors, pET32a and purified as a monomer using size exclusion chromatography. NMR data show that $INI1^{DBD}$ has folded state with high population of ${\alpha}$-helices. By fluorescence-quenching experiments, binding affinities between $INI1^{DBD}$ and two double stranded DNA fragments were determined as $29.9{\pm}2.6{\mu}M$ (GAL4_1) and $258.7{\pm}5.8$ (GAL4_2) ${\mu}M$, respectively. Our data revealed that DNA binding domain of INI1/hSNF5 binds to transcriptional DNA sequences, and it could play an important role as a transcriptional regulator.

• Journal of the Korean Chemical Society
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• v.52 no.3
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• pp.322-327
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• 2008

The geometrical structure, binding energy and vibrational frequencies of HOOCl-H2O cluster were investigated with MP2/6-311G(d,p) and MP2/6-311G(2d,2p) methods. The most stable conformer is skew HOOCl-H2O cluster and the binding energy was 46~48kJ/mol. The trans HOOCl-H2O cluster is less stable than skew form, but the binding energy is big enough to stablize the complex. The vibrational frequencies of skew and trans HOOCl-H2O cluster were calculated and compared with the spectrum of HOOCl.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.751-756
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• 2003

We have investigated the solvent effects on Δlog $K_s$ (the difference of stability constant of binding) and the relative free energies of binding of $La^{3+} and Nd^{3+}$ ions to 18-crown-6 by a Monte Carlo simulation of statistical perturbation theory (SPT) in diverse solvents. We compared relative binding Gibbs free energies and the differences in stability constant (Δlog $K_s$) of binding of $La^{3+} and Nd^{3+}$ ions to 18-crown-6 in $CH_3OH$ in this study with the experimental. There is a good agreement between our study and the experimental. We noted that Borns function of the solvents, the electron pair donor properties of the solvent, the radii of host and guest and the differences in solvation dominate the differences in the stability constant (Δlog $K_s$) as well as the relative free energies of binding of TEX>$La^{3+} to Nd^{3+}$ ions to 18-crown-6. The results of this study appear promising for providing the association properties of crown ethers with alkaline earth metals among polar solvents and the less polar or non-polar solvents.

• Bulletin of the Korean Chemical Society
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• v.32 no.2
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• pp.455-458
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• 2011

In previous report, with the aid of receptor-oriented pharmacophore-based in silico screening, we characterized three novel hPNMT inhibitors (YPN010, YPN016, and YPN017) and proposed that the hydrogen bonding interaction between inhibitors and side chain of Lys57 is very important to inhibitory activity of hPNMT. To confirm the importance of Lys57, mutant with substitution of Lys57 with Ala was cloned and binding study was performed for a K57A mutant of hPNMT using STD-NMR and fluorescence experiments. The binding constants for three novel inhibitors with mutant hPNMT were dramatically decreased compared to those with wild-type protein. K57A mutant-induced conversion of noradrenaline to adrenaline was suppressed about 95 % compared to wild-type hPNMT. Mutagenic analysis using a K57A mutant confirmed the importance of the Lys57 residue in binding of the inhibitor candidate to hPNMT as well as enzymatic activity of hPNMT, implying that these results are consistent with our binding model.

• Journal of the Korean Chemical Society
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• v.28 no.3
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• pp.185-193
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• 1984

At the spermine concentration to cover the number of the binding site of spermine 0.016 per nucleotide, the Hill coefficient of the ethidium binding to the calf thymus DNA was 1.7, while the value was 0.38 in the absence of the spermine. On the basis of the data, together with other present data on the viscometric titration of the DNA with spermine and anomalous absorbance-temperature profile at 260nm and viscosity-temperature profile, it can be speculated that allosteric propagation of the conformational transition induced by the binding of the spermine may be involved in the monomolecular collapse of the DNA to a condensed structure.

• Bulletin of the Korean Chemical Society
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• v.24 no.9
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• pp.1256-1260
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• 2003

Two O-methyltransferases, OMTII-1 and OMTII-4 of meadow rue Thalictrum tuberosum showed a high sequence identity. Of 364 amino acids only one residue is not the same, which is Tyr21 or Cys21. Even if the 21st residues in these OMTs are not included in the binding sites of the enzymes, binding affinities of the enzyme homodimers over the same substrate are very different. While the binding affinity of one homodimer over caffeic acid is 100%, that of the other is 25%. Authors tried to predict the three-dimensional structures of Thalictrum tuberosum O-methyltransferases using homology-based modelling by a comparison with caffeic acid O-methyltransferase, and explain the reason of the phenomenon mentioned above based on their three dimensional structural studies. In the enzyme homodimer, the better binding affinity may be caused by the shorter distance between the 21st residue and the binding site of the other monomer.

• Bulletin of the Korean Chemical Society
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• v.32 no.3
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• pp.768-778
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• 2011

Calixpyrroles and related macrocycles are non-planer synthetic anion receptors that have attracted considerable attentions in recent years. Although the synthesis of calix[4]pyrrole (known as meso-octamethylporphyrinogen) was reported more than 100 years ago, the anion binding properties were first discovered in 1996. The simple calix[4]pyrroles can be synthesized in single step in high yield by condensation of pyrrole with acetone. The compounds showed preferential binding for halide anions including fluoride, phosphate, carboxylate, and chloride in organic media. Efforts to improve the anion affinity of calix[4]pyrrole and to enhance its selectivity have led to the synthesis of a variety of new calixpyrrole derivatives. Among the various modifications, introduction of straps on one side of the calix[4]pyrroles are the most effective. Incorporation of aromatic rings other than pyrroles also exhibited interesting binding behaviour. Introduction of signalling units as part of the strapping element enable to detect the anions on chromogenic or fluorogenic fashion. Finding of the anion transport properties across the membrane and cytotoxic effects of the calix[4]pyrroles open new window for calixpyrrole-related research. The polymer-incorporated systems have also been employed as anion complexants in solvent-solvent extraction. These old, yet easy-to-make macrocycles have well advanced more recently with the discovery of the ion-pair complexation properties. In this review, the synthetic developments and anion binding properties of calixpyrroles for the last decades will be discussed and will cover the advances in calixpyrrole chemistry.