• Journal of Integrative Natural Science
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• v.7 no.1
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• pp.45-49
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• 2014

The (c-Jun N-terminal kinase 3) JNK3 is a potential therapeutic target for various neurological disorders. Here, a three dimensional quantitative structure-activity relationship (3D-QSAR) study on phenoxypyridine as JNK3 inhibitors was performed to rationalize the structural requirements responsible for the inhibitory activity of these compounds. The comparative molecular field analysis (CoMFA) using different partial atomic charges, was employed to understand the structural factors affecting JNK3 inhibitory potency. The Gasteiger-Marsili yielded a CoMFA model with cross-validated correlation coefficient ($q^2$) of 0.54 and non-cross-validated correlation coefficient ($r^2$) of 0.93 with five components. Furthermore, contour maps suggested that bulky substitution with oxygen atom in $R^3$ position could enhance the activity considerably. The work suggests that further chemical modifications of the compounds could lead to enhanced activity and could assist in the design of novel JNK3 inhibitors.

• Bulletin of the Korean Chemical Society
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• v.35 no.11
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• pp.3181-3187
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• 2014

A series of 3,4-dihydroquinazoline derivatives with anti-cancer activities against human colon cancer HT-29 cell were subjected to three-dimensional quantitative structure-activity relationship (3D-QSAR) studies using the comparative molecular similarity indices analysis (CoMSIA) approaches. The most potent compound, BK10001 was used to align the molecules. As a result, the best prediction was obtained with CoMSIA combined electrostatic, hydrophobic, and hydrogen-bond acceptor fields ($q^2=0.648$, $r^2=0.882$). This model was validated by an external test set of six compounds giving satisfactory predictive $r^2$ values of 0.879. This model would guide the design of potent 3,4-dihydroquinazoline derivatives as anti-cancer agent for the treatment of human colon cancer.

• Archives of Pharmacal Research
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• v.27 no.10
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• pp.1001-1008
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• 2004

Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies on 59 cinnamaldehyde analogues as Farnesyl Protein Transferase (FPTase) inhibitors were investigated using comparative molecular field analysis (CoMFA) with the PLS region-focusing method. Forty-nine training set inhibitors were used for CoMFA with two different grid spacings, $2{\AA}\;and\;1{\AA}$ Ten compounds, which were not used in model generation, were used to validate the CoMFA models. After the PLS analysis, the best predictive CoMFA model showed that the cross-validated value $(r^2_{cv})$ and the non-cross validated conventional value$(r^2_{ncv})$ are 0.557 and 0.950, respectively. From the CoMFA contour maps, the steric and electrostatic properties of cinnamaldehyde analogues can be identified and verified.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1469-1473
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• 2010

Influences of alrylamino (R) substituents on the herbicidal activity ($pI_{50}$) of 1-(4-chloro-2-fluoro-5-propargyloxypheny)-3-(R)-thiourea analogues (1 ~ 35) against the barnyard grass (Echinochloa crusgalli) in the pre-emergence step were discussed quantitatively using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) as the three dimensional quantitative structure-activity relationship (3D-QSAR) method. The statistically most satisfactory CoMFA models for the herbicidal activity against the barnyard grass had the better predictability ($r^2{_{cv.}}$) and correlativity ($r^2{_{ncv.}}$) than those of CoMSIA models. The optimized CoMFA model 1($r^2{_{cv.}}$ = 0.531 & $r^2{_{ncv.}}$ = 0.931) with the sensitivity to the perturbation (${d_q}^{2'}{dr^2}_{yy'}$ = 1.081) and the prediction ($q^2$ = 0.475) produced by a progressive scrambling analyses were not dependent on chance correlation. And statistical qualities with the atom based fit alignment (AF) were slightly higher than those of the field fit alignment (FF). According to the optimized CoMFA model 1, the contribution ratio (%) of the steric field (76.9%) on the herbicidal activity of the Thioureas was three-fold higher than that of the electrostatic field (20.1%) and the hydrophobic field (3.0%) had the least influence. A steric favor group is on the vicinity of the nitrogen atom in alrylamino (R) substituent, and a steric disfavor group is on the outer side of alrylamino (R) substituent. Thus, as the size of alrylamino (R) substituent increases, so does the herbicidal activity of the substituent.

• The Korean Journal of Pesticide Science
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• v.8 no.3
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• pp.162-167
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• 2004

In recent years, the diamondback moth (DBM), Plutella xylostella has become one of the most important pests for cruciferous plants in the world. A new type of the thiophosphoryl pyrazole insecticide, called KH502. Its outstanding insecticidal activity could be effective alternative against DBM. We investigated, using the comparative molecular field analysis (CoMPA) method, The structure-activity relationship of various thiophosphorylpyrazole derivatives and structure requirement for insecticidal activity. We found, the key substructures in pyrazole derivatives, the trifluoro-methyl group and the thiophosphoryl group. Both play an important role in insecticidal activity with the binding site. The three dimensional Quantitative Structure Activity Relationship (QSAR) analysis could provide useful information for the structural requirements of pyrazole insecticide as an insecticidal and the design of a new insecticide.

• Bulletin of the Korean Chemical Society
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• v.32 no.5
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• pp.1604-1612
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• 2011

We developed three-dimensional quantitative structure activity relationship (3D-QASR) models for 17 adamantyl derivatives as P-glycoprotein (P-gp) inhibitors. Eighteen different partial charge calculation methods were tested to check the feasibility of the 3D-QSAR models. Best predictive comparative molecular field analysis (CoMFA) model was obtained with the Austin Model 1-Bond Charge Correction (AM1-BCC) atomic charge. The 3D-QSAR models were derived with CoMFA and comparative molecular similarity indices analysis (CoMSIA). The final CoMFA model ($q^2$ = 0.764, $r^2$ = 0.988) was calculated with an AM1-BCC charge and electrostatic parameter, whereas the CoMSIA model ($q^2$ = 0.655, $r^2$ = 0.964) was derived with an AM1-BCC charge and combined steric, electrostatic, hydrophobic and HB-acceptor parameters. Leave-five-out (LFO) cross-validation was also performed, which yielded good correlation coefficient for both CoMFA (0.801) and CoMSIA (0.656) models. Robustness of the developed models was checked further with 1000 run bootstrapping analyses, which gave an acceptable correlation coefficient for CoMFA (BS-$r^2$ = 0.997, BS-SD = 0.003) and CoMSIA (BS-$r^2$ = 0.996, BS-SD = 0.018).

• Bulletin of the Korean Chemical Society
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• v.34 no.8
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• pp.2387-2393
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• 2013

Benzotriazole is an important synthetic auxiliary for potential clinical applications. A series of benzotriazoles as potential antiproliferative agents by inhibiting histone deacetylase (HDAC) were recently reported. Three-dimensional quantitative structure-activity relationship (3D-QSAR), including comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), were performed to elucidate the 3D structural features required for the antiproliferative activity. The results of both ligand-based CoMFA model ($q^2=0.647$, $r^2=0.968$, ${r^2}_{pred}=0.687$) and CoMSIA model ($q^2=0.685$, $r^2=0.928$, ${r^2}_{pred}=0.555$) demonstrated the highly statistical significance and good predictive ability. The results generated from CoMFA and CoMSIA provided important information about the structural characteristics influence inhibitory potency. In addition, docking analysis was applied to clarify the binding modes between the ligands and the receptor HDAC. The information obtained from this study could provide some instructions for the further development of potent antiproliferative agents and HDAC inhibitors.

• The Korean Journal of Pesticide Science
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• v.9 no.2
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• pp.140-145
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• 2005

Quantitative Structure Activity Relationship (QSAR) assumes the relatedness between physical property and biological activity. However, activity data measured at single concentration such as percent activity have not been used extensively for modeling purpose. This probably comes from the fact that these values are qualitative instead of quantitative. To utilize percent activity data for molecular modeling, we classified the whole data into two classes. One class represents the active while the other signifies the inactive. The percent activity data of ${\beta}$-Ketoacetoanilides measured for TLB (Tomato Late Blight) were investigated. CoMFA (Comparative Molecular Field Analysis) was used as a discriminant function. Using CoMFA provides 3D (three dimensional) information, which is crucial for chemical insight. It can also serve as a predictive model. The resultant model classified the given data correctly (98%). When LOO (leave-one-out) crossvalidation procedure was applied, the classification accuracy was 69%. Therefore two class approximation of percent activity data with CoMFA can be utilized to understand the relationship between chemical structure and biological activity and design subsequent chemical analogs.

• Bulletin of the Korean Chemical Society
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• v.34 no.12
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• pp.3553-3558
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• 2013

The three dimensional-quantitative structure activity relationship (3D-QSAR) studies on chemical features of pyridine-2-amines in the external region of c-Met active site (ER chemical features of pyridine-2-amines) were conducted by docking, comparative molecular field analysis (CoMFA), and topomer CoMFA methods. The CoMFA model obtained the partial least-squares (PLS) statistical results, cross-validated correlation coefficient ($q^2$) of 0.703, non cross-validated correlation coefficient ($r^2$) of 0.947 with standard error of estimate (SEE) of 0.23 and the topomer CoMFA obtained $q^2$ of 0.803, $r^2$ of 0.940, and SEE of 0.24. Further, the test set was applied to validate predictive abilities of models, where the predictive $r^2$ ($r{^2}_{pred}$) for CoMFA and topomer CoMFA models were 0.746 and 0.608, respectively. Each contribution of ER chemical features of pyridine-2-amines to the inhibitory potency showed correlation coefficients, $r^2$ of 0.670 and 0.913 for two core parts, 3-(benzo[d]oxazol-2-yl)pyridine-2-amine and 3-(1-(2,6-dichloro-3-fluorophenyl)ethoxy) pyridine-2-amine, respectively, with corresponding experimental $pIC_{50}$.

• The Korean Journal of Pesticide Science
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• v.9 no.1
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• pp.26-34
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• 2005

3D-QSAR studies for the fungicidal activities against resistance phytophthora blight (RPC; 95CC7303) and sensitive phytophthora blight (Phytopthora capsici) (SPC; 95CC7105) by a series of new 2-alkoxyphenyl-3-phenylthioisoindoline-1-one derivatives (A & B) were studieded using comparative molecular similarity indices analyses (CoMSIA) methodology. From the based on the results, the two CoMSIA models, R5 and S1: as the best models were derivated. The statistical results of the models showed the best predictability and fitness for the fungicidal activities based on the cross- validated value ($q^2=0.714{\sim}0.823$) and non cross-validated, value ($r^2_{ncv.}=0.918{\sim}0.954$), respectively. The model R5 for fungicidal activity of RPC generated from the field fit alignment and combination of electrostatic field, H-bond acceptor field and LUMO molecular orbital field. The model S1 (or S5) for fungicidal activity of SPC generated from the atom based fit alignment and combination of steric field and HOMO molecular orbital field. The models also shows that inclusion of H-bond acceptor field (A) improved the statistical significance of the models. From the based graphical analyses of CoMSIA contribution maps, it was revealed that the novel selective character for fungicidal activities between the two fungi by modify of X-sub-stituent on the N-phenyl group and R-substituent on the S-phenyl group will be able to achivement.