• The Korean Journal of Physiology and Pharmacology
• /
• v.13 no.6
• /
• pp.511-516
• /
• 2009

A series of substituted 2-arylnaphthyridin-4-one analogues, which were previously synthesized in our laboratory, were evaluated for their in vitro cytotoxic activity against human lung cancer A549 and human renal cancer Caki-2 cells using MTT assay. Some compounds (11, 12, and 13) showed stronger cytotoxicity than colchicine against both tumor cell lines, and compound 13 exhibited the most potent activity with $IC_{50}$ values of 2.3 and $13.4\;{\mu}M$, respectively. Three-dimensional quantitative structure activity relationship (3D-QSAR) studies of comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed. Predictive 3D-QSAR models were obtained with $q^2$ values of 0.869 and 0.872 and $r^2_{ncv}$ values of 0.983 and 0.993 for CoMFA and CoMSIA, respectively. These results demonstrate that CoMFA and CoMSIA models could be reliably used in the design of novel cytotoxic agents.

• ALGAE
• /
• v.18 no.4
• /
• pp.311-320
• /
• 2003

The community structure of benthic marine algae was investigated at Taean Thermal Power Plant and other places around Taean Peninsula, the west coast of Korea. Total of 100 species including 3 Cyanophyta, 14 Chlorophyta, 18 Phaeophyta, and 65 Rhodophyta were identified. The number of species was highest with 78 species at the Power Plant intake, followed by 61 at the discharge, 56 at Bunjeondo, and 50 at Maoe. It was noteworthy that a subtropical species Caulerpa okamurae was collected at the intake in autumn and it was the first observation in the west coast of Korea. The pattern of vertical algal distribution showed Gloiopeltis furcata occurred in the upper intertidal zone, Sargassum thunbergii and Corallina spp. in the middle and lower zone and Enteromorpha spp. in the lower middle zone. These were all dominant species except for Enteromopha spp., which was subdominant species. Other subdominant species were Chondrus ocellatus and Neorhodomela aculeata. The average diversity indices were between 0.70 and 1.20 at each area based on their dry weight. The similarity index was 0.79 between the algal flora of this study and that of 1987, indicating that the condition of the benthic environment remained unchanged since then. This area maintained its environmental quality, so the algal community remained same with similar structure. This study area seemed a suitable place for long term monitoring of the benthic environment where industrial facilities such as a power plant might affect the benthic algal community.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.11
• /
• pp.2739-2748
• /
• 2009

Hologram and three dimensional quantitative structure activity relationship (3D QSAR) studies for a series of anilinobipyridine JNK3 inhibitors were performed using various alignment-based comparative molecular field analysis (COMFA) and comparative molecular similarity indices analysis (CoMSIA). The in vitro JNK3 inhibitory activity exhibited a strong correlation with steric and electrostatic factors of the molecules. Using four different types of alignments, the best model was selected based on the statistical significance of CoMFA ($q_2\;=\;0.728,\;r_2\;=\;0.865$), CoMSIA ($q_2\;=\;0.706,\;r_2\;=\;0.960$) and Hologram QSAR (HQSAR: $q_2\;=\;0.838,\;r_2\;=\;0.935$). The graphical analysis of produced CoMFA and CoMSIA contour maps in the active site indicated that steric and electrostatic interactions with key residues are crucial for potency and selectivity of JNK3 inhibitors. The HQSAR analysis showed a similar qualitative conclusion. We believe these findings could be utilized for further development of more potent and selective JNK3 inhibitors.

• Journal of the Korean Institute of Landscape Architecture
• /
• v.19 no.2
• /
• pp.75-91
• /
• 1991

This study is one of studies on the analysis of vegetation spatial image and visual preference of roadside slopes in Chi-Ri Mt. national park. In this article, we analized the soil characteristics and the actual vegetation within slopes and forest lands contiguous to those. The results obtained were summarized as follows; The physical and chemical properties of soil in forest lands were better than slopes and Cheoneun temple - Seongsam pass was the best fertilized among 3 sector. In the structure of woody plants in forest lands, the high importance value species were Pinus denciflora, Quercus aliena within Ukmojeong-Deokdong sector, Q. aliena, Q. varabilis, Q. serrata within Banseon-Seongsam pass sector, and P. denciflora, Q. dentata within Cheoneun temple-Seongsam pass sector. And also, Aster scaber, Arundinella hirta, Pteridium aquilinum were the high importance value herbs within all sector. In slopes, the species diversity indices of woody plants were low, but that of herbs showed slightly high. By the cluster analysis used in similarity index, it was observed that woody plants structure between slopes and forest lands made little, but the herbs made slightly higher than woody plants.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2005.09a
• /
• pp.249-255
• /
• 2005

Angiotensin-converting enzyme (ACE) is primarily responsible for human hypertension. Current ACE drugs show serious cough and angiodema health problems due to the un-specific activity of the drug to ACE protein. The availability of ACE crystal structure (1UZF) provided the plausible biological orientation of inhibitors to ACE active site (C-domain). Three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecula. field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for a series of 28 ACE inhibitors. Alignment for CoMFA obtained by docking ligands to 1UZF protein using FlexX program showed better statistical model as compared to superposition of corresponding atoms. The statistical parameters indicate reasonable models for both CoMFA (q$^2$ = 0.530, r$^2$ = 0.998) and CoMSIA (q$^2$= 0.518, r$^2$ = 0.990). The 3D-QSAR analyses provide valuable information for the design of ACE inhibitors with potent activity towards C-domain of ACE. The group substitutions involving the phenyl ring and carbon chain at the propionyl and sulfonyl moieties of captopril are essential for specific activity to ACE.

• KSBB Journal
• /
• v.27 no.2
• /
• pp.121-126
• /
• 2012

In order to explore structural features of minoxidil analogs with a view of enhancing lysyl hydroxylase (LH) inhibitory activity, molecular holographic QSAR (HQSAR) and CoMSIA (comparative molecular similarity indices analysis) were performed. The results from the atomic contributions with optimized the HQSAR 6-2 model indicated that, in case of pyrimidine-1-N-oxide substituent, C2 atom of pyrimidine ring and C'3-C'4 bond of 4-piperidinol group showed the highest impact on the inhibitory activity towards LH enzyme. It was also evident from the information of the optimized CoMSIA F5 model that the inhibitory activity mainly depended on the hydrophobic field contribution (36%) and the hydrogen bond (H-bond) field contribution (49.2%) of substrate molecule. Particularly, it is predicted that the functional groups which disfavor H-bond acceptors in large space around the piperidinol group and also the functional groups which favor the H-bond acceptors at C'4 (& C'5) atom in $R_5$ group play a role for increased inhibitory activity. With this in mind, it is likely that a novel candidate having more improved inhibitory activity on hair growth could be designed in the future.

• Bulletin of the Korean Chemical Society
• /
• v.35 no.7
• /
• pp.2065-2071
• /
• 2014

${\beta}$-Secretase (beta-amyloid converting enzyme 1 [BACE1]) is involved in the first and rate-limiting step of ${\beta}$-amyloid ($A{\beta}$) peptides production, which leads to the pathogenesis of Alzheimer's disease(AD). Therefore, inhibition of BACE1 activity has become an efficient approach for the treatment of AD. Ligand-based and docking-based 3D-quantitative structure-activity relationship (3D-QSAR) studies of acyl guanidine analogues were performed with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) to obtain insights for designing novel potent BACE1 inhibitors. We obtained highly reliable and predictive CoMSIA models with a cross-validated $q^2$ value of 0.725 and a predictive coefficient $r{^2}_{pred}$ value of 0.956. CoMSIA contour maps showed the structural requirements for potent activity. 3D-QSAR analysis suggested that an acyl guanidine and an amide group in the $R_6$ substituent would be important moieties for potent activity. Moreover, the introduction of small hydrophobic groups in the phenyl ring and hydrogen bond donor groups in 3,5-dichlorophenyl ring could increase biological activity.

• Bulletin of the Korean Chemical Society
• /
• v.25 no.12
• /
• pp.1801-1806
• /
• 2004

Ligand-based quantitative structure-activity relationship (QSAR) studies were performed on indolinones derivatives as a potential inhibitor of the protein tyrosine kinase of fibroblast growth factor receptor (FGFR) by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) implemented in the SYBYL packages. The initial X-ray structure of docked ligand (Su5402) to FGFR was used to minimize the 27 training set molecules using TRIPOS force field. Seven models were generated using CoMFA and CoMSIA with grid spacing 2 ${\AA}$. After the PLS analysis the best predicted CoMSIA model with hydrophobicity, hydrogen bond donor and acceptor property showed that a leave-one out(LOO) cross validated value $({r^2}_{cv})^$ and non-cross validated conventional value $({r^2}_{ncv})^$ are 0.543 and 0.938, respectively.

• Korean Journal of Environmental Biology
• /
• v.42 no.2
• /
• pp.207-218
• /
• 2024

Food webs have received global attention as next-generation biomonitoring tools; however, it remains challenging because revealing trophic links between species is costly and laborious. Although a link-extrapolation method utilizing published trophic link data can address this difficulty, it has limitations when applied to construct food webs in domestic streams due to the lack of information on endemic species in global literature. Therefore, this study aimed to develop a link extrapolation-based food web model adapted to Korean stream ecosystems. We considered taxonomic similarity of predation and dominance of generalists in aquatic ecosystems, designing taxonomically higher-level matching methods: family matching for all fish (Family), endemic fish (Family-E), endemic fish playing the role of consumers (Family-EC), and resources (Family-ER). By adding the commonly used genus matching method (Genus) to these four matching methods, a total of five matching methods were used to construct 103 domestic food webs. Predictive power of both individual links and food web indices were evaluated by comparing constructed food webs with corresponding empirical food webs. Results showed that, in both evaluations, proposed methods tended to perform better than Genus in a data-poor environment. In particular, Family-E and Family-EC were the most effective matching methods. Our model addressed domestic data scarcity problems when using a link-extrapolation method. It offers opportunities to understand stream ecosystem food webs and may provide novel insights into biomonitoring.

• YAKHAK HOEJI
• /
• v.54 no.4
• /
• pp.288-294
• /
• 2010

Three dimensional quantitative-structure relationships (3D-QSARs) models between structures of phenoxy, phenylthio or benzyloxy substituted quinolone analogues and their antitrypanosomal activity against Chagas disease (Trypanosoma cruzi) were derived and discussed quantitatively using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. The optimized CoMFA 1 model ($q^2$=0.528 and $r^2$=0.964) showed the best statistical results. According to the optimized CoMFA 1 model, the antitrypanosomal activities were dependent on the steric (60.0%) and electrostatic (36.2%) factors of quinolone derivatives. From the contour maps, it is predicted that the activity will be increased when sterically favored groups were located in $R_4$ and $R_5$ position and sterically disfavored groups were located in $R_2$ position. Also, the positively charged groups on $R_2$ would be able to increase the antitrypanosomal activities.