• Bulletin of the Korean Chemical Society
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• v.17 no.7
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• pp.653-655
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• 1996

A comparative molecular field analysis (CoMFA) was carried out for the correlation of the transition state structures and the reaction rates for the SN2 reaction of 4-nitrophenyl benzoate and its sulfur analogs with anionic nucleophiles. The CoMFA analysis showed that both steric and electrostatic effects are important, and the steric contribution increased when nucleophiles are alkoxides or arylsulfides. In this study, we have demonstrated that the CoMFA analysis can be expanded beyond the scope of dealing with reactants and products. The reactant complex and transition state conformations generated along the reaction path can be more appropriately used for the correlation of structures and reaction rates.

• Bulletin of the Korean Chemical Society
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• v.31 no.9
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• pp.2497-2502
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• 2010

Arg13 is a conserved active-site residue in all known Pi class glutathione S-transferases (GSTs) and in most Alpha class GSTs. To evaluate its contribution to substrate binding and catalysis of this residue, three mutants (R13A, R13K, and R13L) were expressed in Escherichia coli and purified by GSH affinity chromatography. The substitutions of Arg13 significantly affected GSH-conjugation activity, while scarcely affecting glutathione peroxidase or steroid isomerase activities. Mutation of Arg13 into Ala largely reduced the GSH-conjugation activity by approximately 85 - 95%, whereas substitutions by Lys and Leu barely affected activity. These results suggest that, in the GSH-conjugation activity of hGST P1-1, the contribution of Arg13 toward catalytic activity is highly dependent on substrate specificities and the size of the side chain at position 13. From the kinetic parameters, introduction of larger side chains at position 13 results in stronger affinity (Leu > Lys, Arg > Ala) towards GSH. The substitutions of Arg13 with alanine and leucine significantly affected $k_{cat}$, whereas substitution with Lys was similar to that of the wild type, indicating the significance of a positively charged residue at position 13. From the plots of log ($k_{cat}/{K_m}^{CDNB}$) against pH, the $pK_a$ values of the thiol group of GSH bound in R13A, R13K, and R13L were estimated to be 1.8, 1.4, and 1.8 pK units higher than the $pK_a$ value of the wild-type enzyme, demonstrating the contribution of the Arg13 guanidinium group to the electrostatic field in the active site. From these results, we suggest that contribution of Arg13 in substrate binding is highly dependent on the nature of the electrophilic substrates, while in the catalytic mechanism, it stabilizes the GSH thiolate through hydrogen bonding.

• Bulletin of the Korean Chemical Society
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• v.29 no.3
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• pp.647-655
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• 2008

Microsomal prostaglandin E2 synthase (mPGES-1) is a potent target for pain and inflammation. Various QSAR (quantitative structure activity relationship) analyses used to understand the factors affecting inhibitory potency for a series of MK886 analogues. We derived four QSAR models utilizing various quantum mechanical (QM) descriptors. These QM models indicate that steric, electrostatic and hydrophobic interaction can be important factors. Common pharmacophore hypotheses (CPHs) also have studied. The QSAR model derived by best-fitted CPHs considering hydrophobic, negative group and ring effect gave a reasonable result (q2 = 0.77, r2 = 0.97 and Rtestset = 0.90). The pharmacophore-derived molecular alignment subsequently used for 3D-QSAR. The CoMFA (Comparative Molecular Field Analysis) and CoMSIA (Comparative Molecular Similarity Indices Analysis) techniques employed on same series of mPGES-1 inhibitors which gives a statistically reasonable result (CoMFA; q2 = 0.90, r2 = 0.99. CoMSIA; q2 = 0.93, r2 = 1.00). All modeling results (QM-based QSAR, pharmacophore modeling and 3D-QSAR) imply steric, electrostatic and hydrophobic contribution to the inhibitory activity. CoMFA and CoMSIA models suggest the introduction of bulky group around ring B may enhance the inhibitory activity.

• Bulletin of the Korean Chemical Society
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• v.31 no.2
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• pp.453-456
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• 2010

The structural and energetic preferences of thiacalix[4]biscrown-5 with and without alkali metal ions ($Na^+$, $K^+$, $Rb^+$, and $Cs^+$) have been theoretically investigated for the first time using molecular dynamic (MD) simulations and density functional theory (MPWB1K/6-31G(d)//B3LYP/6-31G(d)) methods. The formation of the metal ion complex by the host is mainly driven by the electrostatic attraction between crown-5 oxygens and a cation together with the minor contribution of the cation-$\pi$ interaction between two facing phenyl rings around the cation. The computed binding energies and the atomic charge distribution analysis for the metal binding complexes indicate the selectivity toward a potassium ion. The theoretical results herein explain the experimentally observed extractability order by this host towards various alkali metal ions. The physical nature and the driving forces for cation recognition by this host are discussed in detail.

• Journal of the Korean Ceramic Society
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• v.36 no.2
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• pp.210-219
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• 1999

The fundamental dispersion property of Si2N4 and a combination of AlN and Nd2O3 as sintering additives in a variety of organic solvents such as alcohols, hydrocarbons, ketones, and ethers was investigated. The stabilization mechanism and interaction between organic functional groups of the various organic additives were studied to clarify the dispersibility of the ceramic particles in the nonaqueous suspending medium. characterization of the suspensions was based mainly on electrokinetic sonic amplitude(ESA) measurements and the flow curves obtained from the rheological studies as well as estimated Hamaker constants. It was found that the contribution of electrostatic repulsive forces to the Si3N4, AlN and Nd2O3 stabilization in organic media is appreciably greater than anticipated and is dependent on the physicochemical properties of organic solvents.

• Applied Biological Chemistry
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• v.50 no.3
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• pp.192-197
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• 2007

3D-QSARs on the fungicidal activity of N-phenylbenzenesulfonamide and N-phenyl-2-thienylsulfonamide analogues (1-37) against Phytophthora blight (Phytophthora capsici) were studied quantitatively using CoMFA and CoMSIA methods. The statistical results of the optimized CoMFA (2) model ($r^2_{cv.}(q^2)$ = 0.692 & $r^2_{ncv.}$= 0.965) show better predictability and fitness than CoMSIA (2) model ($r^2_{cv.}(q^2)$ = 0.796 & $r^2_{ncv.}$= 0.958). The fungicidal activities according to the information of the optimized CoMFA (2) model were dependent upon the steric and electrostatic fields of the molecules. Therefore, from the contribution contour maps of CoMFA (2) model, it is expected that 63% contribution was caused by the steric bulk of meta-substituent ($R_1$) on the S-phenyl ring. Also, the other contribution level of 32.9% was represented by the positive charged $R_4-group$ ($R_1$) on the N-phenyl ring and para-substituent ($R_1$) on the S-phenyl ring. A series of higher active compounds, $R_1$= 3-decyl substituent ($pred.pI_50$= 5.88) etc. were predicted based on the findings.

• Journal of Applied Biological Chemistry
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• v.53 no.2
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• pp.99-104
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• 2010

The influences on antioxidant activities of the substituents ($R_1-R_4$) on benzo ring in 4-Methyl-2H-benzopyran-2-one analogues (1-23) were discussed quantitatively using three dimensional quantitative structure-activity relationships (3D-QSARs: Comparative molecular field analyses (CoMFA) and Comparative molecular similarity indice analyses (CoMSIA)) methods. The statistical qualities of CoMSIA models were better than those of CoMFA models and the CoMSIA 2 model was optimized model ($q^2$=0.700 & $r^2$=0.979). Also, the contribution ratios (%) of the optimized CoMSIA 2 model were H-bond donor field 43.5%, electrostatic field 41.8% and steric field 14.7% so that the antioxidant activity exhibited a strong correlation with H-bond donor and electrostatic factor of molecules. From the analytical results of the CoMSIA contour maps, if the positive charge favor group and H-bond donor disfavor group were placed in the $R_1-R_4$ positions on the benzo ring, it was predicted that the groups would raised the antioxidant activity.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.103-108
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• 2006

Computational prediction of protein-ligand binding has been widely used as a tool to discover lead compounds fur new drugs. Prediction accuracy is determined in part by the scoring function used in docking calculations. Diverse scoring functions are available, and these can be classified into force-field based, empirical, and knowledge-based functions depending upon the basic assumptions made in development. Among these, force-field based functions consider physical interactions the most in detail. However, the force-field based functions have the drawback of not including the entropic effect while considering only the energy contribution such as dispersion or electrostatic forces. In this article, a method to take into account of the entropic effect using the colony energy is suggested when force-field based scoring functions is used by extracting conformational information obtained from the pre-existing docking program. An improved result for decoy discrimination is illustrated when the method is applied to the DOCK scoring function, and this implies that more accurate docking calculation is possible.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.911-916
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• 2012

Ion selectivity in a simple cyclic peptide nanotube, composed of four cyclo[-(D-Ala-Glu-D-Ala-Gln)$_2-$] units, is investigated by calculating the PMF profiles of $Na^+$, $K^+$, and $Cl^-$ ions permeating through the peptide nanotube in water. The final PMF profiles of the ions obtained from the umbrella sampling (US) method show an excellent agreement with those from the thermodynamic integration (TI) method. The PMF profiles of $Na^+$ and $K^+$ display free energy wells while the PMF curve of $Cl^-$ features free energy barriers, indicating the selectivity of the cyclic peptide nanotube to cations. Decomposition of the total mean force into the contribution from each component in the system is also accomplished by using the TI method. The mean force decomposition profiles of $Na^+$ and $K^+$ demonstrate that the dehydration free energy barriers by water molecules near the channel entrance and inside the channel are completely compensated for by attractive electrostatic interactions between the cations and carbonyl oxygens in the nanotube. In the case of $Cl^-$, the dehydration free energy barriers are not eliminated by an interaction between the anion and the peptide nanotube, leading to the high free energy barriers in the PMF profile. Calculations of the coordination numbers of the ions with oxygen atoms pertaining to either water molecules or carbonyl groups in the peptide nanotube reveal that the stabilization of the cations in the midplane regions of the nanotube arises from the favorable interaction of the cations with the negatively charged carbonyl oxygens.

• Journal of Microbiology and Biotechnology
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• v.15 no.3
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• pp.587-594
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• 2005

The contribution of electrostriction of water molecules to the stabilization of the negatively charged tetrahedral transition state of a lipase-catalyzed reaction was examined by means of kinetic studies involving high-pressure and solvent dielectric constant. A good correlation was observed between the increased catalytic efficiency of lipase and the decreased solvent dielectric constant. When the dielectric constant of solvents was lowered by 5.00 units, the losses of activation energy and free energy of activation were 7.92 kJ/mol and 11.24 kJ/mol, respectively. The activation volume for $k_{cat}$ decreased significantly as the dielectric constant of solvent decreased, indicating that the degree of electrostriction of water molecules around the charged tetrahedral transition state has been enhanced. These observations demonstrate that the increase in the catalytic efficiency of the lipase reaction with decreasing dielectric constant resulted from the stabilization of electrostatic energy for the formation of an oxyanion hole, and that this stabilization was caused by the increase of electrostricted water around the charged tetrahedral transition state. Therefore, we conclude that the control of solvent dielectric constant can stabilize the tetrahedral transition state, thus lowering the activation energy.