• Environmental Analysis Health and Toxicology
• /
• v.30 no.sup
• /
• pp.7.1-7.10
• /
• 2015

Objectives For successful adoption of legislation controlling registration and assessment of chemical substances, it is important to obtain sufficient toxicological experimental evidence and other related information. It is also essential to obtain a sufficient number of predicted risk and toxicity results. Particularly, methods used in predicting toxicities of chemical substances during acquisition of required data, ultimately become an economic method for future dealings with new substances. Although the need for such methods is gradually increasing, the-required information about reliability and applicability range has not been systematically provided. Methods There are various representative environmental and human toxicity models based on quantitative structure-activity relationships (QSAR). Here, we secured the 10 representative QSAR-based prediction models and its information that can make predictions about substances that are expected to be regulated. We used models that predict and confirm usability of the information expected to be collected and submitted according to the legislation. After collecting and evaluating each predictive model and relevant data, we prepared methods quantifying the scientific validity and reliability, which are essential conditions for using predictive models. Results We calculated predicted values for the models. Furthermore, we deduced and compared adequacies of the models using the Alternative non-testing method assessed for Registration, Evaluation, Authorization, and Restriction of Chemicals Substances scoring system, and deduced the applicability domains for each model. Additionally, we calculated and compared inclusion rates of substances expected to be regulated, to confirm the applicability. Conclusions We evaluated and compared the data, adequacy, and applicability of our selected QSAR-based toxicity prediction models, and included them in a database. Based on this data, we aimed to construct a system that can be used with predicted toxicity results. Furthermore, by presenting the suitability of individual predicted results, we aimed to provide a foundation that could be used in actual assessments and regulations.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.12
• /
• pp.3553-3558
• /
• 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 $pIC_{50}$.

• Applied Biological Chemistry
• /
• v.33 no.3
• /
• pp.231-238
• /
• 1990

The structure-antifungal activity correlations between the structure of fourteen new 1-(phenoxymethyl)benzotriazoles (I) (Y=0), 1-(thiophenoxymethyl)benzotriazoles (ll) (Y=S) and 1-(azidomethyl)benzotriazole (III) derivatives were synthesized, and their activity, fifty percent inhibition of mycelial growth($pI_{50}$), in vitro against Pyricularia oryzae, Fusarium axysporum f.sp sesami, Valsa ceratosperma and Botrytis cinerea were investigated using a generalized QSAR method. The activity of (I) was superior In those of (II) and (III). The effect of the substituents (X) on the phenoxy group (I) was rationalized by a parabolic function of electronic (${\sigma}$), steric ($B_1$) and hydrophobic parameter(${\pi}$), and hydrogen bonding (HB). Where the optimal values of substituent on the fungicidal activity againt P. oryzae and F. axysporum f.sp.sesami are $B_1=1.40A;(H)$ and ${\pi}=0.07{\sim}0.15;(H)$, and those of substituent on the fungicidal activity against V. ceratosperma and B. cinerea are ${\sigma}=0.23{\sim}0.28;\;(C1),\;{\pi}=0.70;$ (C1), respectively. The most effective compound ( I a) and ( I d) were examined in this study.

• The Korean Journal of Pesticide Science
• /
• v.12 no.1
• /
• pp.18-23
• /
• 2008

3D-QSAR on the inhibitory activities of 6-bromobenzo-[4,5]imidazo[$1,2{\alpha}$]-pyridin-8,9-diones analogues as substrate molecule were studied quantitatively using CoMFA and CoMSIA methods. The statistical values of CoMFA model was better predictability and fitness than CoMSIA model. The inhibitory activities according to the optimized CoMFA 2 model were dependent on the steric field (90.4%). From the CoMFA contour maps, it is found that the branched side chain as R-group will be directly attached to the carbon atom (ipso carbon) of substituent, the inhibitory activities had expected to increase. The positive charge favor groups were placed in the position between imidazol ring and pyridine ring, the inhibitory activities would increase. And if the groups of liner type will be substituted, hydrophilic favor group would raise inhibitory activities.

• Applied Biological Chemistry
• /
• v.43 no.2
• /
• pp.95-99
• /
• 2000

A series of hetero ring (X) substitued chalcone derivatives with farnesyl protein transferase (FPTase) inhibition activities $(pI_{50})$ values determined in vitro is analyzed by modified Free-Wilson (F-W) and Hansch method for quantitative structure activity relationship (QSARs). On the basis of F-W analysis on the FPTase inhibitory activity of a training set of the compounds, none of the (X)-substituents were not contribute the activity. But the net charge of ${\alpha}$ carbon atom is contribute the activity than that of ${\beta}$ carbon atom. And the relative orders of the (Y)-substituents on the activity are ortho>meta>para-substituents. According to Hansch approach, the activities would depend largely on the optimal, $(R_{opt.}=-0.35)$ resonance effect with ortho substituted $(I_o>0)$ electron donating group (R<0) and STERIMOL parameter, $B_1$ constant. The inhibition activity between hetro ring substituents have been a proportioned with each others and none substituent(H), 45 showed the highest FPTase inhibition $(pI_{50}=4.30)$ activity.

• Journal of Integrative Natural Science
• /
• v.8 no.4
• /
• pp.258-266
• /
• 2015

Xanthine Oxidase is an enzyme, which oxidizes hypoxanthine to xanthine, and xanthine to uric acid. It is widely distributed throughout various organs including the liver, gut, lung, kidney, heart, brain and plasma. It is involved in gout pathogenesis. In this study, we have performed Comparative Molecular Field Analysis (CoMFA) on a series of 2-(indol-5-yl) thiazole derivatives as xanthine oxidase (XO) inhibitors to identify the structural variations with their inhibitory activities. Ligand based CoMFA models were generated based on atom-by-atom matching alignment. In atom-by-atom matching, the bioactive conformation of highly active molecule 11 was generated using systematic search. Compounds were aligned using the bioactive conformation and it is used for model generation. Different CoMFA models were generated using different alignments and the best model yielded a cross-validated $q^2$ of 0.698 with five components and non-cross-validated correlation coefficient ($r^2$) of 0.992 with Fisher value as 236.431, and an estimated standard error of 0.068. The predictive ability of the best CoMFA models was found to be $r^2_{pred}$0.653. The CoMFA study revealed that the $R_3$ position of the structure is important in influencing the biological activity of the inhibitors. Electro positive groups and bulkier substituents in this position enhance the biological activity.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.3
• /
• pp.899-906
• /
• 2013

Using generated conformations from docking analysis by Gold algorithm, some 3D-QSAR models; CoMFA and CoMSIA have been created on 39 N-benzoylated phenoxazines and phenothiazines, including their S-oxidized analogues. These molecules inhibit the polymerization of tubulin into microtubules and thus they have been studied for the development of antitumor drugs. Training set for the CoMFA and CoMSIA models using 30 docked conformations gives $q^2$ Leave one out (LOO) values of 0.756 and 0.617, and $r^2$ ncv values of 0.988 and 0.956, respectively. The ability of prediction and robustness of the models were evaluated by test set, cross validation (leave-one-out and leave-ten-out), bootstrapping, and progressive scrambling approaches. The all-orientation search (AOS) was used to achieve the best orientation to minimize the effect of initial orientation of the structures. The docking results confirmed CoMFA and CoMSIA contour maps. The docking and 3D-QSAR studies were thoroughly interpreted and discussed and confirmed the experimental $pIC_{50}$ values.

• The Korean Journal of Physiology and Pharmacology
• /
• v.17 no.3
• /
• pp.237-243
• /
• 2013

B13 is a ceramide analogue and apoptosis inducer with potent cytotoxic activity. A series of arylpropyl sulfonamide analogues of B13 were evaluated for their cytotoxicity using MTT assays in prostate cancer PC-3 and leukemia HL-60 cell lines. Some compounds (4, 9, 13, 14, 15, and 20) showed stronger activities than B13 in both tumor cell lines, and compound (15) gave the most potent activity with $IC_{50}$ values of 29.2 and 20.7 ${\mu}M$, for PC-3and HL-60 cells, respectively. Three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis was performed to build highly reliable and predictive CoMSIA models with cross-validated $q^2$ values of 0.816 and 0.702, respectively. Our results suggest that long alkyl chains and a 1R, 2R configuration of the propyl group are important for the cytotoxic activities of arylpropyl sulfonamides. Moreover, the introduction of small hydrophobic groups in the phenyl ring and sulfonamide group could increase biological activity.

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

• Journal of Integrative Natural Science
• /
• v.13 no.4
• /
• pp.170-180
• /
• 2020

Abnormal regulation, hyperphosphorylation, and aggregation of the tau protein are the hallmark of several types of dementia, including Alzheimer's Disease. Increased activity of Glycogen Synthase Kinase-3β (GSK-3β) in the Central Nervous System (CNS), increased the tau hyperphosphorylation and caused the neurofibrillary tangles (NFTs) formation in the brain cells. Over the last two decades, numerous adenosine triphosphate (ATP) competitive inhibitors have been discovered that show inhibitory activity against GSK-3β. But these compounds exhibited off-target effects which motivated researchers to find new GSK-3β inhibitors. In the present study, we have collected the dataset of 31 C-Glycosylflavones derivatives that showed inhibitory activity against GSK-3β. Among the dataset, the most active compound was docked with the GSK-3β and molecular dynamics (MD) simulation was performed for 50 ns. Based on the 50 ns MD pose of the most active compound, the other dataset compounds were sketched, minimized, and aligned. The 3D-QSAR based Comparative Molecular Field Analysis (CoMFA) model was developed, which showed a reasonable value of q2=0.664 and r2=0.920. The contour maps generated based on the CoMFA model elaborated on the favorable substitutions at the R2 position. This study could assist in the future development of new GSK-3β inhibitors.