• The Korean Journal of Pesticide Science
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• v.6 no.3
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• pp.209-217
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• 2002

Two different QSAR methods, the comparative molecular similarity indices analyses (CoMSIA) and hologram quantitative structure activity relationship (HQSAR) are studied for the fungicidal activities ($pI_{50}$) of 2-N-benzyl-5-phenoxy-3-isothiazolone derivatives against sensitive (SPC: 95CC7105) and resisitive (RPC: 95CC7303) phytophthora blight fungus (Phytaphthora capsici). According to the findings from these QSAR investigation, the cross-validation value, $q^2$ and Pearson correlation coefficient, $r^2$ in the two methods were CoMSIA: RPC; $q^2=0.675,\;r^2=0.942$, SPC; $q^2=0.350,\;r^2=0.876$ and HQSAR: RPC; $q^2=0.519,\;r^2=0.869$, SPC; $q^2=0.483,\;r^2=0.990$, respectively. Therefore, the two models of comparative statistical significance were obtained. From the CoMSIA contour maps, the important factors for selective fungicidal activity against RPC are to be expected that the lower hydrophobic and not bulkiness substituent as hydrogen bonding acceptor have to introduce to meta and para-position (C1-C6) on the phenoxy moiety. And the results of prediction suggest that HQSAR method showed higher fungicidal activity than CoMSIA method.

• Journal of Integrative Natural Science
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• v.9 no.2
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• pp.113-120
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• 2016

Monopolar spindle 1 (Mps1) is an attractive cancer target due to its high expression levels in a wide range of cancer cells. Mps1 is a dual specificity kinase. It plays an essential role in mitosis. The high expression od Mps1 was observed in various grades of breast cancers. In the current study, we have developed a CoMFA model of pyridazine derivatives as Mps1 kinase inhibitors. The developed CoMFA model ($q^2=0.797$; ONC=6; $r^2=0.992$) exhibited a good predictive ability. The model was then validated by Leave out five, progressive sampling and bootstrapping and found to be robust. The analysis of the CoMFA contour maps depicted favorable and unfavorable regions to enhance the activity. Bulky positive substitution at $R^3$ position and Negative substitution in $R^1$ position is favored could increase the activity. In contrast, bulky substitution in $R^1$ position is not favored. Our results can be used in designing a potent Mps1 (TTK) inhibitor.

• Environmental Analysis Health and Toxicology
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• v.24 no.2
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• pp.79-93
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• 2009

오염물질에 대한 생태위해성평가(ecological risk assessment)를 위해서는 노출평가(exposure assessment)와 함께 생물영향에 대한 평가(effect assessment)를 수행해야 한다. 노출평가의 경우는 지화학적 과정에 대한 이해를 바탕으로 환경농도를 예측하기 위한 화학평형모델이나 다매체환경거동모델 등 다양한 평가 및 예측모델을 활용해 왔다. 이와 달리 생물영향평가는 실험실 조건에서 제한된 독성자료를 대상으로 외부노출농도에 기반한 농도-반응관계를 통계적 방법을 통해서 추정하는 '경험적 모델(empirical model)'에 주로 의존해 왔다. 최근에 와서 생체 내 잔류량을 기반으로 농도-시간-반응관계를 기술하고 예측하는 독성동태학 및 독성역학 모델(toxicokinetic-toxicodynamic model)과 같은 독성작용에 기반한 모델(processbased model)들이 개발되어 활용되고 있다. 본 논문에서는 여러 종류의 독성동태학 및 독성역학 모델을 소개하고, 이를 통계적 추론에 기반한 전통적인 독성학 모델과 비교하였다. 서로 다른 종류의 독성동태학 및 독성역학 모델로부터 도출된 노출농도-시간 -반응관계식을 비교하고, 동일 독성기작을 보이는 오염물질 그룹 내에서 미측정 오염물질의 독성을 예측할 수 있게 해주는 구조-활성관계(Quantitative Structure-Activity Relationship, QSAR) 모델을 여러 독성동태 및 독성역학모델로부터 유도하였다. 마지막으로 독성동태학 및 독성역학 파라미터를 추정하기 위한 실험계획을 제안하였고, 앞으로 독성동태학 및 독성역학 모델을 생태계 위해성평가에 활용하기 위해서 해결해야 될 연구과제를 검토하였다.

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

• Journal of Integrative Natural Science
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• v.11 no.2
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• pp.93-100
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• 2018

Caspases, a family of cysteinyl aspartate-specific proteases plays a central role in the regulation and the execution of apoptotic cell death. Caspase-3 has been proven to be an effective target for reducing the amount of cellular and tissue damage because the activation of caspases-3 stimulates a signalling pathway that ultimately leads to the death of the cell. In this study, Hologram based Quantitative Structure Activity Relationship (HQSAR) models was generated on a series of Caspase-3 inhibitors named 3, 4-dihydropyrimidoindolones derivatives. The best HQSAR model was obtained using atoms, bonds, and hydrogen atoms (A/B/H) as fragment distinction parameter using hologram length 61 and 3 components with fragment size of minimum 5 and maximum 8. Significant cross-validated correlation coefficient ($q^2=0.684$) and non cross-validated correlation coefficients ($r^2=0.754$) were obtained. The model was then used to evaluate the eight external test compounds and its $r^2_{pred}$ was found to be 0.559. Contribution map show that presence of pyrrolidine sulfonamide ring and its bulkier substituent's makes big contributions for improving the biological activities of the compounds.

• Journal of Integrative Natural Science
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• v.10 no.3
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• pp.141-147
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• 2017

Vascular endothelial growth factor (VEGF) is an important signaling protein involved in angiogenesis, which is the formation of new blood vessels from pre-existing vessels. Consequently, blocking of the vascular endothelial growth factor receptor (VEGFR-2) by small molecule inhibitors leads to the inhibition of cancer induced angiogenesis. In this study, we performed a two dimensional quantitative structure activity relationship (2D-QSAR) study of 38 N-Phenyl-N'-{4-(4-quinolyloxy) phenyl} urea derivatives as VEGFR-2 inhibitors based on hologram quantitative structure-activity (HQSAR). The model developed showed reasonable $q^2=0.521$ and $r^2=0.932$ values indicating good predictive ability and reliability. The atomic contribution map analysis of most active compound (compound 7) indicates that hydrogen and oxygen atoms in the side chain of ring A and oxygen atom in side chain of ring C contributes positively to the activity of the compounds. The HQSAR model developed and the atomic contribution map can serve as a guideline in designing new compounds for VEGFR-2 inhibition.

• The Korean Journal of Pesticide Science
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• v.8 no.3
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• pp.151-161
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• 2004

Three dimensional quantitative structure-activity relationships (3D-QSAR) studies for the protox inhibition activities against root and shoot of rice plant (Orysa sativa L.) and barnyardgrass (Echinochloa crus-galli) by a series of new A=3,4,5,6-tetrahydrophthalimino, B=3-chloro-4,5,6,7-tetrahydro-2H-indazolyl and C=3,4-dimethylmaleimino group, and R-group substituted on the phenyl ring in 1-(5-methyl-3-phenylisoxazolin-5-yl)methoxy-2chloro-4-fluorobenzene derivatives were performed using comparative molecular field analyses (CoMFA) methodology with Gasteiger-Huckel charge. Four CoMFA models for the protox inhibition activities against root and shoot of the two plants were generated using 46 molecules as training set and the predictive ability of the each models was evaluated against a test set of 8 molecules. And the statistical results of these models with combination (SIH) of standard field, indicator field and H-bond field showed the best predictability of the protox inhibition activities based on the cross-validated value $r^2_{cv.}$ $(q^2=0.635\sim0.924)$, conventional coefficient $(r^2_{ncv.}=0.928\sim0.977)$ and PRESS value $(0.091\sim0.156)$, respectively. The activities exhibited a strong correlation with steric $(74.3\sim87.4%)$, electrostatic $(10.10\sim18.5%)$ and hydrophobic $(1.10\sim8.30%)$ factors of the molecules. The steric feature of molecule may be an important factor for the activities. We founded that an novel selective and higher protox inhibitors between the two plants may be designed by modification of X-subsitutents for barnyardgrass based upon the results obtained from CoMFA analyses.

• Bulletin of the Korean Chemical Society
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• v.32 no.1
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• pp.251-262
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• 2011

Human ether-a-go-go related gene (hERG) potassium channel blockade, an undesirable side effect which might cause sudden cardiac death, is one of the major concerns facing the pharmaceutical industry. The purpose of this study is to develop an in silico QSAR model which uncovers the structural parameters of T-type calcium channel blockers to reduce hERG blockade. Comparative molecular similarity indices analysis (CoMSIA) was conducted on a series of piperazine and benzimidazole derivatives bearing methyl 5-(ethyl(methyl)amino)-2-isopropyl-2-phenylpentanoate moieties, which was synthesized by our group. Three different alignment methods were applied to obtain a reliable model: ligand based alignment, pharmacophore based alignment, and receptor guided alignment. The CoMSIA model with receptor guided alignment yielded the best results : $r^2$ = 0.955, $q^2$ = 0.781, $r^2_{pred}$ = 0.758. The generated CoMSIA contour maps using electrostatic, hydrophobic, H-bond donor, and acceptor fields explain well the structural requirements for hERG nonblockers and also correlate with the lipophilic potential map of the hERG channel pore.

• Applied Biological Chemistry
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• v.42 no.3
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• pp.252-255
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• 1999

Inhibition activities$(pI_{50})$ of chalcone derivatives as substrate with farnesyl protein transferase(FPTase) were determined in vitro. The structure activity relationships(SAR) between the activity and physicochemical parameters of X & Y-substituents on the phenyl groups were analyzed by Free-Wilson and Hansch method. X-substituents on the benzoyl group have the more important role to inhibition activity than Y-substituents on the styryl group. Among them, none substituent, 8 showed the highest FPTase inhibition activity$(pI_{50}=4.30)$. Particularly, the SAR equation could be formulated, showing a parabolic relationship between the activity and hydrophobicity(logP) where the optimal value$({\Sigma}logP)_{opt}$ was 3.915. And also the activity depends on the steric effect(Es > 0) with X-substituent and the resonance effect(R < 0) with electron donating Y-substituents. Based on the results of SAR analyses, the interactions between substrates and receptor, FPTase, could be assumed.

• Environmental Analysis Health and Toxicology
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• v.19 no.2
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• pp.141-151
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• 2004

We exposed juvenile puffer fish, Takifugu obscurus(30 days after hatching) to various aqueous pollutants including 4 kinds of inorganic metals (Ag, Cd, Cu and Hg), 2 organotin compound.; (tributyltin ［TBT］ and triphenyltin［TPhT］) and 5 polycyclic aromatic hydrocarbon (PAH) compounds (chrysene, fluoranthene, naphthalene, phenanthrene and pyrene) to estimate median lethal concentrations (LC50s) of each pollutant after the 96-hour acute exposure. Among the inorganic metals, Hg (52 $\mu\textrm{g}$/L; 96-h LC50) was most toxic to test animals and followed by Ag (164 $\mu\textrm{g}$/L), Cu (440 $\mu\textrm{g}$/L) and Cd (1180 $\mu\textrm{g}$/L). Aqueous TBT was more toxic between the two organotins; the 96-h LC50 for TBT (5.1 $\mu\textrm{g}$/L) was 3 times lower than that of TPhT (17.3 $\mu\textrm{g}$/L). The acute toxicity of PAH compounds was highest for chrysene (1.5 $\mu\textrm{g}$/L; 96-h LC50) and decreased in the order of pyrene (65 $\mu\textrm{g}$/L) > fluoranthene (158 $\mu\textrm{g}$/L) > phenanthrene (432 $\mu\textrm{g}$/L) > naphthalene (8690 $\mu\textrm{g}$/L). The toxicity of PAH compounds wat closely related to their physico-chemical characteristics such as $K_{ow}$ and water solubility, and well explained by simple QSAR relationship. The sensitivity of puffer fish to various inorganic and organic pollutants was generally comparable to various fish species widely used as standard test species in previous studies and further evaluation should be conducted to develop adequate testing procedure for T. obscurus when used in various toxicity tests.