• Bulletin of the Korean Chemical Society
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• 제28권12호
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• pp.2248-2252
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• 2007

SOMT-9 is an O-methyltransferase that utilizes quercetin to produce 3'-methoxy quercetin. In order to determine which amino acids of SOMT-9 are important for this reaction and its regioselectivity, molecular docking experiments followed by site directed mutagenesis were performed. Molecular modeling and molecular docking experiments identified several amino acid residues involved in metal binding, AdoMet binding, and substrate binding. Site-directed mutagenesis showed that Asp188 is critical for metal binding and that Lys165 assists other metal binding residues in maintaining quercetin in the proper position during the reaction. In addition, Tyr207 was shown to play an important role in the determination of the regioselectivity and Met60 was shown to be involved in formation of the hydrophobic pocket necessary for substrate binding. The molecular modeling and docking experiments discussed in this study could be applicable to future research including prediction of substrate binding and regioselectivity of an enzyme.

• 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.

• Bulletin of the Korean Chemical Society
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• 제35권1호
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• pp.62-68
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• 2014

Coptis chinensis 3'-hydroxy-N-methylcoclaurine 4'-O-methyltransferase (HOMT), an essential enzyme in the berberine biosynthetic pathway, catalyzes the methylation of 3'-hydroxy-N-methylcoclaurine (HMC) producing reticuline. A 3D model of HOMT was constructed by homology modeling and further subjected to docking with its ligands and molecular dynamics simulations. The 3D structure of HOMT revealed unique structural features which permitted the methylation of HMC. The methylation of HMC was proposed to proceed by deprotonation of the 4'-hydroxyl group via His257 and Asp258 of HOMT, followed by a nucleophilic attack on the SAM-methyl group resulting in reticuline. HOMT showed high substrate specificity for methylation of HMC. The study evidenced that Gly117, Thr312 and Asp258 in HOMT might be the key residues for orienting substrate for specific catalysis.

• 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.

• Bulletin of the Korean Chemical Society
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• 제34권8호
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• pp.2466-2472
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• 2013

Human immunodeficiency virus type-1 (HIV-1) is a causative agent of Acquired immunodeficiency syndrome (AIDS), which has affected a large population of the world. Viral envelope glycoprotein (gp120) is an intrinsic protein for HIV-1 to enter into human host cells. Molecular docking guided molecular dynamics (MD) simulation was performed to explore the interaction mechanism of heterobiaryl derivative with gp120. MD simulation result of inhibitor-gp120 complex demonstrated stability. Our MD simulation results are consistent with most of the previous mutational and modeling studies. Inhibitor has an interaction with the CD4 binding region. Van der Waals interaction between inhibitor and Val255, Thr257, Asn425, Met426 and Trp427 were important. This preliminary MD model could be useful in exploiting heterobiaryl-gp120 interaction in greater detail, and will likely to shed lights for further utilization in the development of more potent inhibitors.

• 한국해양공학회지
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• 제34권6호
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• pp.377-386
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• 2020

This paper discusses the effectiveness of onboard measurements and data extracted from weather information for speed-power analysis. Furthermore, validation results of hull and propeller cleaning and painting during dry-docking are discussed. Wind and wave information can be obtained from onboard measurements or weather information from the National Oceanic and Atmospheric Administration (NOAA). The weather information of a specified position and time is extracted from NOAA weather data and compared with onboard measurements. In addition, to validate the effects of hull cleaning and painting during dry-docking, speed-power analysis results of before and after dry-docking are compared. The results show that both onboard measurements and weather information show acceptable reliability when added resistance and speed-power analysis results are compared with each other. Moreover, the ship performance analysis (SPA) software clearly shows the effects of hull cleaning and painting, and it can provide reliable analysis results with either onboard measurements or weather information. In conclusion, it is confirmed that the analysis method and SPA software used in this study are effective in analyzing the ship's speed-power performance.

• 대한화학회지
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• 제66권3호
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• pp.194-201
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• 2022

A simple, efficient, and cost-effective method has been employed for the synthesis of 2,4,5-trisubstituted imidazole derivatives (3a-j) containing quinoline substituent at 2^nd position. Title compounds were obtained by multicomponent reaction (MCR), involving aryl substituted 1,2-diketone, quinoline carbaldehyde and ammonium acetate in the presence of acetic acid solvent under mild reaction conditions. The newly synthesized quinoline containing imidazole derivatives were confirmed through FT-IR, ¹H-NMR, ¹³C-NMR and mass spectral analysis. In-vitro microplate alamar blue assay (MABA) to determine the MIC (minimum inhibitory concentration) values against Mycobacterium tuberculosis H37Rv was performed for the synthesized compounds. The synthesized compounds exhibited activity against Mycobacterium tuberculosis and among which compounds, 3d, 3f and 3i showed good activity. The highest activity was showed with compound 3i. The anti-mycobacterial activity results are well correlated with the computational molecular docking analysis, which was performed for the synthesized compounds prior to the evaluation of the activity.

• 통합자연과학논문집
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• 제15권4호
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• pp.145-152
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• 2022

Colon rectal cancer is one of the frequently diagnosed cancers worldwide. In recent times the drug discovery for colon cancer is challenging because of their speedy metastasis and morality of these patients. C-jun N-terminal kinase signaling pathway controls the cell cycle survival and apoptosis. Evidence has shown that JNK1 promotes the tumor progression in various types of cancers like colon cancer, breast cancer and lung cancer. Recent study has shown that inhibiting, JNK1 pathway is identified as one of the important cascades in drug discovery. One of the recent approaches in the field of drug discovery is drug repurposing. In drug repurposing approach we have virtually screened ChEMBL dataset against JNK1 protein and their interactions have been studied through Molecular docking. Cross docking was performed with the top compounds to be more specific with JNK1 comparing the affinity with JNK2 and JNK3.The drugs which exhibited higher binding were subjected to Conceptual - Density functional theory. The results showed mainly Entrectinib and Exatecan showed better binding to the target.

• Bulletin of the Korean Chemical Society
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• 제32권7호
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• pp.2222-2226
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• 2011

Amylase is a digestive enzyme that catalyses the starch into sugar. It has been reported that the green tea flavonoid (or polyphenols) (-)-epigallocatechin 3-gallate (EGCG) inhibits human salivary ${\alpha}$-amylase (HSA) and induced anti-nutritional effects. In this study, we performed docking study for seven EGCG-like flavonoids and HSA to understand the interaction mechanism of HSA and EGCG and suggest new possible flavonoid inhibitors of HSA. As a result, EGCG and (-)-epicatechin gallate (ECG) bind to HSA with complex hydrogen bonding interactions. These hydrogen bonding interactions are important for inhibitory activity of EGCG against HSA. We suggested that ECG can be a potent inhibitor of HSA. This study will be helpful to understand the mechanism of inhibition of HSA by EGCG and give insights to develop therapeutic strategies against diabetes.

• Bulletin of the Korean Chemical Society
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• 제29권7호
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• pp.1311-1314
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• 2008

Bacillus halodurans O-methyltransferase (BhOMT) is an S-adenosylmethionine dependent methyltransferase. In our previous study, three dimensional structure of the BhOMT has been determined by comparative homology modeling and automated docking study showed that two hydroxyl groups at 3'- and 4'-position in Bring and structural rigidity of C-ring resulting from the double bond characters between C2 and C3 of flavonoid, were key factors for interaction with BhOMT. In the present study, BhOMT was cloned and expressed. Binding assay was performed on purified BhOMT using fluorescence experiments and binding affinity of luteolin, quercetin, fisetin, and myricetin were measured in the range of $10^7$. Fluorescence quenching experiments indicated that divalent cation plays a critical role on the metal-mediated electrostatic interactions between flavonoid and substrate binding site of BhOMT. Fluorescence study confirmed successfully the data obtained from the docking study and these results imply that hydroxyl group at 7-position of luteolin, quercetin, fisetin, and myricetin forms a stable hydrogen bonding with K211 and carboxyl oxygen of C-ring forms a stable hydrogen bonding with R170. Hydroxyl group at 3'-and 4'-position in the B-ring also has strong $Ca^{2+}$ mediated electrostatic interactions with BhOMT.