• Bulletin of the Korean Chemical Society
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• 제35권7호
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• pp.2097-2108
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• 2014

Chemical feature based quantitative pharmacophore models were generated using the HypoGen module implemented in DS2.5. The best hypothesis, Hypo1, which was characterized by the highest correlation coefficient (0.96), the highest cost difference (61.60) and the lowest RMSD (0.74), consisted of one hydrogen bond acceptor, one hydrogen bond donor, one hydrophobic and one ring aromatic. The reliability of Hypo1 was validated on the basis of cost analysis, test set, Fischer's randomization method and GH test method. The validated Hypo1 was used as a 3D search query to identify novel inhibitors. The screened molecules were further refined by employing ADMET, docking studies and visual inspection. Three compounds with novel scaffolds were selected as the most promising candidates for the designing of Mcl-1 antagonists. Finally, a 10 ns molecular dynamics simulation was carried out on the complex of receptor and the retrieved ligand to demonstrate that the binding mode was stable during the MD simulation.

• Natural Product Sciences
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• 제26권2호
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• pp.165-170
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• 2020

Carica papaya is a medicinal and fruit plant owing biological activities including antioxidant, antiviral, antibacterial and anticancer. The present study aims to investigate the acetyl (AChE) and butyryl (BChE) cholinesterase inhibitory potentials of C. papaya extracts as well as their chemical compositions. The chemical composition of the active extract was identified using a gas chromatography-mass spectrometry (GC-MS). Ellman enzyme inhibition assay showed that the alkaloid-enriched leaf extract of C. papaya possessed significant anti-BChE activity with an enzyme inhibition of 75.9%. GC-MS analysis showed that the alkaloid extract composed mainly the carpaine (64.9%) - a major papaya alkaloid, and some minor constituents such as aliphatic hydrocarbons, terpenes and phenolics. Molecular docking of carpaine revealed that this molecule formed hydrogen bond and hydrophobic interactions with choline binding site and acyl pocket. This study provides some preliminary findings on the potential use of C. papaya leaf as an herbal supplement for the prevention and treatment of Alzheimer's disease.

• 한국응용과학기술학회지
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• 제14권1호
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• pp.109-115
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• 1997

Fluorescent anionic oligo surfactants were synthesized by the condensing products of long chain alkylvinylether-maleic anhydride cooligomers and resorcinol including dye structures. Their various surface activities and dispersing action were studied on the aqueous solution. These oligo surfactants exhibited a remarkable surface tension lowering property, lower foaming and a large dispersing action for the particles of ${\alpha}-copper$ phthalocyanine blue. Further it was ascertained that the binding of oligo surfactant onto the pigment surface caused the deviation towards lower wavelengths at the maximum fluorescent intensity as compared with aqueous oligo surfactant solutions, These surface active properties of the oligo surfactants may be attributed to rigid and hydrophobic structure of dye groups, besides surface-active groups of alkylether groups and carboxylic group of the anionic oligo surfactants.

• Journal of Microbiology and Biotechnology
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• 제3권4호
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• pp.224-231
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• 1993

The nucleotide sequence of the xylanase gene (xynY) from alkalophilic Bacillus sp. YC-335 was determined and analyzed. An open reading frame of 1, 062 base pairs for xynY gene was observed and encoded for a protein of 354 amino acids with a molecular weight of 38, 915. S1 nuclease mapping showed that the transcription initiation sites of the xynY gene were different in Bacillus sp. YC-335 and Escherichia coli HB101 (pYS55). S1 mapping also showed that -10 region of the xynY gene recognized by RNA polymerases of E. coli and Bacillus sp. YC-335 were TACAGT and TATGAT , respectively. A ribosome binding site sequence with the free energy of -17.0 Kcal/mol was observed 9 base pairs upstream from the unusual initiation codon, TTG. The proposed signal sequence consisted of 27 amino acids, 2 of which were basic amino acid residues and 21 were hydrophobic amino acid residues. When the amino acid sequences of xylanases were compared, Bacillus sp. YC-335 xylanase showed more than 50% homology with xylanases from B. pumilus, B. subtilis, and B. circulans.

• Applied Biological Chemistry
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• 제37권3호
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• pp.189-193
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• 1994

이온성 계면활성제인 sodium laurylsulfate(NaLs)와 cetyltrimethylammonium bromide(CTABr)의 존재하에서 항균성 N-[1-(benzotriazol-1-yl)benzyl]aniline(BBA)분자의 가수 분해 반응에 미치는 미셀효과를 검토한 바, NaLs가 존재하는 높은 pH에서 미셀 촉매효과가 나타났으며 결합상수(Ks)는 $1.45{\times}10^4M^{-1}$이었다. 이와 같은 미셀 촉매효과는 (BBA)의 소수성(${\pi}$: 4.93)보다 전이상태에서 생성되는 carbocation이 음이온성 미셀에 의한 정전기적 안정화에 기인한 결과로 보여진다.

• 한국염색가공학회지
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• 제20권1호
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• pp.8-15
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• 2008

We presented the modified decal-transfer lithography (DTL) and light stamping lithography (LSL) as new powerful methods to generate patterns of poly(dimethylsiloxane) (PDMS) on the substrate. The microstructures of PDMS fabricated by covalent binding between PDMS and substrate had played as barrier to locally control wettability. The transfer mechanism of PDMS is cohesive mechanical failure (CMF) in DTL method. In the LSL method, the features of patterned PDMS are physically torn and transferred onto a substrate via UV-induced surface reaction that results in bonding between PDMS and substrate. Additionally we have exploited to generate the patterning of rhodamine B and quantum dots (QDs), which was accomplished by hydrophobic interaction between dyes and PDMS micropatterns. The topological analysis of micropatterning of PDMS were performed by atomic force microscopy (AFM), and the patterning of rhodamine B and quantum dots was clearly shown by optical and fluorescence microscope. Furthermore, it could be applied to surface guided flow patterns in microfluidic device because of control of surface wettability. The advantages of these methods are simple process, rapid transfer of PDMS, modulation of surface wettability, and control of various pattern size and shape. It may be applied to the fabrication of chemical sensor, display units, and microfluidic devices.

• Journal of Microbiology and Biotechnology
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• 제15권2호
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• pp.296-301
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• 2005

The effect of aqueous methanol on the catalytic properties of porcine pancreatic lipase has been investigated. The k$_{CAT}$, values for the hydrolysis of N$^{alpha}$-benzyloxycarbonyl-L­lysine p-nitrophenyl ester at 0$^{circ}$C increased in a linear manner with increasing methanol concentration. However, the K$_{M}$ values were not influenced at methanol concentrations lower than $30\%$ and then began to increase at higher concentrations in an exponential fashion. Based on product analysis, the increase in k$_{CAT}$, with increasing methanol concentration can be accounted for by nucleophilic competition of methanol for the acyl enzyme intermediate, indicating that the rate-limiting step of the porcine pancreatic lipase-catalyzed reaction is deacylation under current experimental conditions. The exponential increase in K$_{M}$ at methanol concentrations higher than $30\%$ is attributed to the hydrophobic partitioning effect on substrate binding. There was no loss of lipase activity over a 4 h period in $60\%$ methanol concentration at pH$^{circ}$ 5.5 and 0$^{circ}$C. By monitoring the intrinsic fluorescence and absorbance, no evidence for structural changes by methanol was observed.

• Bulletin of the Korean Chemical Society
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• 제35권1호
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• pp.250-252
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• 2014

Lipoprotein-associated phospholipase A2 (Lp-$PLA_2$) is a crucial enzyme in atherosclerosis as a potential drug target. The most remarkable Lp-$PLA_2$ inhibitory drug is Darapladib. We determined the binding pose of Darapladib to Lp-$PLA_2$ through docking study. Darapladib formed two hydrogen bonding interactions with the side chain of Tyr160 and Gln352 and several pi-pi interactions with aromatic and aliphatic hydrophobic residues of Lp-$PLA_2$. It is known that the dietylpropan-amine moiety of Darapladib has influence on the improvement of its oral bioavailability and we supposed this in our docking results.

• 한국결정학회:학술대회논문집
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• 한국결정학회 2002년도 정기총회 및 추계학술연구발표회
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• pp.24-24
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• 2002

HtrA (high temperature requirement A), a periplasmic heat shock protein, is known to have molecular chaperone function at low temperatures and proteolytic activity at elevated temperatures. To investigate the mechanism of functional switch to pretense, we have determined the crystal structure of the N-terminal protease domain (PD) of HtrA from Thermotoga maritima. HtrA PD shares the same fold with chymotrypsin-like serine professes. However, crystal structure suggests that HtrA PD is not an active pretense at current state since its active site is not formed properly and blocked by an additional helical lid. On the surface of the lid, HtrA PD has hydrophobic patches that could be potential substrate binding sites for molecular chaperone activity. Present structure suggests that the activation of the proteolytic function of HtrA PD at elevated temperatures might occur by the conformational change.

• Molecules and Cells
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• 제25권3호
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• pp.352-357
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• 2008

Osteoprotegerin (OPG) is a soluble decoy receptor that inhibits osteoclastogenesis and is closely associated with bone resorption processes. We have designed and determined the solution structures of potent OPG analogue peptides, derived from sequences of the cysteine-rich domain of OPG. The inhibitory effects of the peptides on osteoclastogenesis are dose-dependent ($10^{-6}M-10^{-4}M$), and the activity of the linear peptide at $10^{-4}M$ is ten-fold higher than that of the cyclic OPG peptide. Both linear and cyclic peptides have a ${\beta}$-turn-like conformation and the cyclic peptide has a rigid conformation, suggesting that structural flexibility is an important factor for receptor binding. Based on structural and biochemical information about RANKL and the OPG peptides, we suggest that complex formation between the peptide and RANKL is mediated by both hydrophobic and hydrogen bonding interactions. These results provide structural insights that should aid in the design of peptidyl-mimetic inhibitors for treating metabolic bone diseases caused by abnormal osteoclast recruitment.