• Bulletin of the Korean Chemical Society
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• 제35권9호
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• pp.2655-2659
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• 2014

Dual specificity protein phosphatase 4 (DUSP4) has been considered a promising target for the development of therapeutics for various human cancers. Here, we report the first example for a successful application of the structure-based virtual screening to identify the novel small-molecule DUSP4 inhibitors. As a consequence of the virtual screening with the modified scoring function to include an effective molecular solvation free energy term, five micromolar DUSP4 inhibitors are found with the associated $IC_{50}$ values ranging from 3.5 to $10.8{\mu}M$. Because these newly identified inhibitors were also screened for having desirable physicochemical properties as a drug candidate, they may serve as a starting point of the structure-activity relationship study to optimize the medical efficacy. Structural features relevant to the stabilization of the new inhibitors in the active site of DUSP4 are discussed in detail.

• Asian Pacific Journal of Cancer Prevention
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• 제14권12호
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• pp.7473-7482
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• 2013

The G-protein coupled receptor 87 (GPR87) is a recently discovered orphan GPCR which means that the search of their endogenous ligands has been a novel challenge. GPR87 has been shown to be overexpressed in squamous cell carcinomas (SCCs) or adenocarcinomas in lungs and bladder. The 3D structure of GPR87 was here modeled using two templates (2VT4 and 2ZIY) by a threading method. Functional assignment of GPR87 by SVM revealed that along with transporter activity, various novel functions were predicted. The 3D structure was further validated by comparison with structural features of the templates through Verify-3D, ProSA and ERRAT for determining correct stereochemical parameters. The resulting model was evaluated by Ramachandran plot and good 3D structure compatibility was evidenced by DOPE score. Molecular dynamics simulation and solvation of protein were studied through explicit spherical boundaries with a harmonic restraint membrane water system. A DRY-motif (Asp-Arg-Tyr sequence) was found at the end of transmembrane helix3, where GPCR binds and thus activation of signals is transduced. In a search for better inhibitors of GPR87, in silico modification of some substrate ligands was carried out to form polar interactions with Arg115 and Lys296. Thus, this study provides early insights into the structure of a major drug target for SCCs.

• Bulletin of the Korean Chemical Society
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• 제29권5호
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• pp.921-927
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• 2008

Discovery of $\alpha$-glucosidase inhibitors has been actively pursued with the aim to develop therapeutics for the treatment of diabetes and the other carbohydrate mediated diseases. As a method for the discovery of new novel inhibitors of $\alpha$-glucosidase, we have addressed the performance of the computer-aided drug design protocol involving the homology modeling of $\alpha$-glucosidase and the structure-based virtual screening with the two docking tools: FlexX and the automated and improved AutoDock implementing the effects of ligand solvation in the scoring function. The homology modeling of $\alpha$-glucosidase from baker’s yeast provides a high-quality 3-D structure enabling the structure-based inhibitor design. Of the two docking programs under consideration, AutoDock is found to be more accurate than FlexX in terms of scoring putative ligands to the extent of 5-fold enhancement of hit rate in database screening when 1% of database coverage is used as a cutoff. A detailed binding mode analysis of the known inhibitors shows that they can be stabilized in the active site of $\alpha$- glucosidase through the simultaneous establishment of the multiple hydrogen bond and hydrophobic interactions. The present study demonstrates the usefulness of the automated AutoDock program with the improved scoring function as a docking tool for virtual screening of new $\alpha$-glucosidase inhibitors as well as for binding mode analysis to elucidate the activities of known inhibitors.

• 대한화학회지
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• 제50권3호
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• pp.203-207
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• 2006

K+(C2H5OH)n, (n=1~5) 착물에 대한 구조와 결합에너지에 대하여 MP2/full gen 6d와 MP2/6-311G**의 방법으로 계산하였다. n이 증가함에 따라 착물의 형태는 선형, 삼각형, 정사면체, 삼각이중피라밋 형태를 갖는 것으로 나타났고 K+-O의 길이는 용매 분자수가 증가함에 따라 증가하고 ∠K+OC도 증가하며 ∠K+OH는 n이 증가함에 따라 감소함을 보였다. 결합에너지는 n이 증가함에 따라 증가하나 순차적으로 증가하는 폭은 n이 커질수록 감소함을 볼 수 있었고 이는 용매분자간의 상호작용이 많은 영향을 주고 있는 것으로 나타났다.

• Bulletin of the Korean Chemical Society
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• 제31권1호
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• pp.146-150
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• 2010

A distinguished class of hydrophobic ionic liquids bearing a Br${\o}$nsted acidic character derived from amide-like compounds were prepared by a neutralization reaction of N,N-diethylformamide, N,N-dibutylformamide, 1-formylpiperidine, and $\varepsilon$-caprolactam with trifluoroacetic acid and physical absorptions of $CO_2$ in these ionic liquids were demonstrated and evaluated. $CO_2$ solubilities in these ionic liquids were influenced by the molecular structure of the cation and were apparently increased with the molar volume. Comparison based on a volume unit reveals that $CO_2$ solubilities in these liquids are relatively higher than those in imidazolium-based ionic liquids. Henry's coefficients calculated from low-pressure solubility tests at 313 to 333 K were used to derive the thermodynamics quantities. Enthalpy and entropy of solvation may share equal contributions in solubility.

• 한국자기공명학회논문지
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• 제22권4호
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• pp.139-143
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• 2018

Short antimicrobial peptide, A4W, have been studied by molecular dynamics (MD) simulation in an explicit dodecylphosphocholine (DPC) micelle. Peptide was aligned with DPC micelle and transferred new peptide-micelle coordinates within the same solvent box using specific micelle topology parameters. After initial energy minimization and equilibration, the conformation and orientation of the peptide were analyzed from trajectories obtained from the RMD (restrained molecular dynamics) or the subsequent free MD. Also, the information of solvation in the backbone and the side chain of the peptide, hydrogen bonding, and the properties of the dynamics were obtained. The results showed that the backbone residues of peptide are either solvated using water or in other case, they relate to hydrogen bonding. These properties could be a critical factor against the insertion mode of interaction. Most of the peptide-micelle interactions come from the hydrophobic interaction between the side chains of peptide and the structural interior of micelle system. The interaction of peptide-micelle, electrostatic potential and hydrogen bonding, between the terminal residues of peptide and the headgroups in micelle were observed. These interactions could be effect on the structure and flexibility of the peptide terminus.

• Bulletin of the Korean Chemical Society
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• 제13권3호
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• pp.306-311
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• 1992

The stable structures of pure ethylene and mixed ethylene-ammonia cluster ions are studied using an electron impact ionization time-of-flight mass spectrometer. Investigations on the relative cluster ion distributions of $(C_2H_4)_n(NH_3)_m^+$ under various experimental conditions suggest that $(C_2H_4)_2(NH_3)_3^+$ and $(C_2H_4)_3(NH_3)_2^+$ ions have the enhanced structural stabilities, which give insight into the feasible structure of solvated ions. For the stable configurations of these ionic species, we report an experimental evidence that both $(C_2H4)_2^+(C_2H_4)_3^+$ clusters as the central cations provide three and two hydrogen-bonding sites, respectively, for the surrounding $NH_3$ molecules. This interpretation is based on the structural stability for ethylene clusters and the intracluster ion-molecular rearrangement of the complex ion under the presence of ammonia solvent molecules.

• Journal of Photoscience
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• 제9권2호
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• pp.122-125
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• 2002

Coherent oscillations in is fluorescence dynamics of W.-t. PYP and its site-directed mutants have been observed. Two oscillatory modes coupled with the ultrafast fluorescence due to the twisting of the excited chromophore were identified, a high ftequency mode (∼135 cm$\^$-1/) with ∼550 is damping time and a low frequency overdamped mode (-45 cm$\^$-1/) with ∼250 is damping time, respectively. Both modes disappear in the fluorescence dynamics of denatured PYP emphasizing the important role of the protein nanospace as the environment for photoreaction. The qualitative picture of fluorescence dynamics in site-directed mutants was rather similar to that in W.-t. PYP, i.e., similar oscillatory modes (∼130-140 cm$\^$-1/ and ∼40-70 cm$\^$-1/) have been observed. This indicates that the vibrational modes and electron-vibration couplings do not change dramatically due to the mutation though the damping time of low frequency mode a little decreases as the protein nanospace structure becomes looser and more disordered by mutation. On the other hand, in the case of some PYP analogues, the qualitative picture of fluorescence dynamics changes, showing the familiar picture of solvation effect whereas the oscillations are almost damped. Comparative analyses of these observations are presented.

• 한국신재생에너지학회:학술대회논문집
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• 한국신재생에너지학회 2011년도 추계학술대회 초록집
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• pp.114.1-114.1
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• 2011

Bioenergy production from lignocellulosic biomass and agriculture wastes have been attracted because of its sustainable and non-edible source. Especially, canola is considered as one of the best feedstock for renewable fuel production. Oil extracted canola and its agriculture residues are reuseable for bioethanol production. However, a pretreatment step is required before enzymatic hydrolysis to disrupt recalcitrant lignocellulosic matrix. To increase the sugar conversion, more efficient pretreatment process was necessary for removal of saccharification barriers such as lignin. Alkaline pretreatment makes the lignocellulose swollen through solvation and induces more porous structure for enzyme access. In our previous work, aqueous ammonia (1~20%) was utilized for alkaline reagent to increase the crystallinity of canola residues pretreatment. In this study, significant factors for efficient soaking in aqueous ammonia pretreatment on canola residues was optimized by using the response surface method (RSM). Based on the fundamental experiments, the real values of factors at the center (0) were determined as follows; $70^{\circ}C$ of temperature, 17.5% of ammonia concentration and 18 h of reaction time in the experiment design using central composition design (CCD). A statistical model predicted that the highest removal yield of lignin was 54% at the following optimized reaction conditions: $72.68^{\circ}C$ of temperature, 18.30% of ammonia concentration and 18.30 h of reaction time. Finally, maximum theoretical yields of soaking in aqueous ammonia pretreatment were 42.23% of glucose and 22.68% of xylose.

• 대한화학회지
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• 제32권2호
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• pp.85-93
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• 1988

등유전상수 용매로 취급되는 MeOH-nitromethane, MeOH-nitrobenzene 및 MeOH-ethylene glycol 혼합용매 하에서 t-butyl halides (X = Cl, Br, I)의 가용매 분해반응을 연구 하였다. MeOH-NM 및 MeOH-NB에서 t-butyl halide의 가메탄올 분해반응 속도는 40~100 % (v/v) MeOH 조성에서 최대치를 보였다. 최대속도 현상은 용매의 극성-편극성과 수소결합 주게능력의 협력적인 결과로 설명하였다. Y값의 변화로 부터 극성-편극성과 수소 결합 주게능력의 협력적인 결과로 설명하였다. Y값의 변화로 부터 극성-편극성과 수소결합 주게능력이 기질의 반응성에 미치는 효과를 논의 하였다. E.G.에서 기질의 반응성은 MeOH에 비해 20배 이상 빠름을 보였으며 이는 아마도 E.G.의 특이한 용매구조에 기인 한다고 여겨 진다.