• Applied Biological Chemistry
• /
• v.48 no.3
• /
• pp.252-257
• /
• 2005

Three-dimensional quantitative structure-activity relationships (3D-QSARs) for the herbicidal activities against pre-emergence barnyard grass (Echinochloa crus-galli) by new 2-(4-(6-chloro-2-benzoxazolyloxy)phenoxy)-N-phenylpropion amide derivatives were studied quantitatively using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methodologies. The best CoMFA model (AI-2) and CoMSIA model (AII-4) were derived from an atom based fit alignment and a combination of CoMFA fields. The herbicidal activities from CoMFA and CoMSIA contour maps showed that the activity will be able to be increased according to the substituents variation on the N-phenyl ring.

• 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 $pIC_{50}$.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.12
• /
• pp.3755-3761
• /
• 2013

This study aims to assess the ecological risk of the hazardous air pollutants (HAPs) emitted in the semiconductor manufacturing processes in Korea by using Quantitative Structure Activity Relationship (QSAR, EPA, US, EPI $Suite^{TM}$ 4.1). Owing to the absence of environmental standards of hazardous air pollutants in the semiconductor manufacturing processes in Korea, 18 HAPs in the semiconductor field included in both the US EPA NESHAPs and the hazardous air pollutant list of Ministry of Environment in Korea were selected. As a results 8 chemicals (44.4%) of the selected 18 HAPs were VOCs. Cyanides (cyanides) and ethylene oxides (epoxy resins), and tetrachloro-ethylene (aliphatic compounds, halides) showed long half-lives. Cyanide HAPs especially had the highest half-life with the estimated value of 356.533 days. Nickel compounds (heavy metal compounds) possessed the highest water solubility followed by acetaldehyde (aldehyde compounds), ethylene oxides, and 1,4-dioxanes. The halides, including tetrachloro-ethylenes, carbon tetra-chlorides, benzene (aromatic compounds), and lead (heavy metals), are estimated to take the longest time for biodegradation. Tetrachloroethylene, with the acute toxicity end point of 3.685-7.033 mg/L, was assessed to be the most highly toxic substance among the 18 HAPs. However, considering the absence of the HAPs in the common category of log $K_{ow}{\geq}4$and $BCF{\geq}500$, which indicates the standard of bioconcentration potentials, potentials of the bioconcentration are considered to be low.

• The Korea Journal of Herbology
• /
• v.21 no.4
• /
• pp.115-121
• /
• 2006

Objectives : For the purpose of developing new anti-HIV agents from natural sources, the extracts of Actinidia arguta were tested for their inhibitory effects on essential enzymes as the reverse transcriptase (RT), protease and ${\alpha}-\;glucosidase$. And we predicted inhibition activity of major compounds of Actinidia arguta using Quantitative Structure Activity Relationships (QSAR). Methods : In this assay the activity of HIV-1 reverse transcriptase is measured as the formation of a strand of copy-DNA (cDNA) using RNA as a template. The activity of HIV-1 protease is measured as the cleavage of an oligopeptide by HIV-1 protease. Results : In the anti-HIV-1 RT using Enzyme Linked Oligonucleotide Sorbent Assay (ELOSA) method, water extracts (100ug/ml) of stem and leaf showed strong activity of 93.9% and 91.9%, respectively. In the HIV-1 protease inhibition assay, aqueous stem extract inhibited the activity of the enzyme to cleave an oligopeptide, resembling one of the cleavage sites in the viral polyprotein which can only be processed by HIV-1 protease with 56.8%. In the ${\alpha}-glucosidase$ inhibition assay, aqueous stem extract showed activity of 73.1%. Conclusion : We found out this result, for these samples it is possible that the inhibition of the viral replication in vitro is due to the inhibition at least one of RT and ${\alpha}-glucosidase$. It would be of great interest to identify the compounds which are responsible for this inhibition, since all therapeutically useful agent up to date are RT, PR and ${\alpha}-glucosidase$ inhibitors.

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

• 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.

• Applied Biological Chemistry
• /
• v.51 no.3
• /
• pp.171-176
• /
• 2008

The comparative molecular similarity indices analysis (CoMSIA) models between 3${\beta}$-Hydroxy-12-oleanen-28-oic acid (1-30) analogues as substrate molecule and their inhibitory activities ($pI_{50}$) against protein tyrosine phosphatase (PTP)-1B were derived and discussed quantitatively. Listing in order, the CoMFA>CoMSIA${\geq}$HQSAR>2D-QSAR model, these QSAR models had the better statistical values. The optimized CoMSIA F1 model at grid 3.0${\AA}$ had the best predictability and fitness ($q^2$=0.754 and $r^2$=0.976) by field fit alignment. The order of contribution ratio (%) of CoMSIA fields concerning the inhibitory activities was a H-bond acceptor (48.9%), steric field (25.8%) and hydrophobic field (25.4%), respectively. Therefore, the inhibitory activities of substrate molecules against PTP-1B were dependent upon H-bond acceptor field (A) of $R_4$-group. From the analytical results of CoMSIA contour maps, oleanolic acid derivatives will have better inhibition activities if $R_1$ group has H-bond acceptor disfavor, $R_3$group has steric disfavor and $R_4$ group has steric, hydrophobic, H-bond favor.

• 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.

• Reproductive and Developmental Biology
• /
• v.32 no.3
• /
• pp.141-146
• /
• 2008

To search a new porcine pheromonal odorant, the models of four type (2D-QSAR, HQSAR, CoMFA & CoMSlA) were derived from quantitative structure-activity relationship (QSAR) between tetrahydrofuran-2-yl family compounds and their observed binding affinity constants (Obs.p$[Od]_{50}$). The optimized CoMFA model (predictability; $r^{2}_{cv.}(q^2)$=0.886 & correlation coefficient: $r^{2}_{ncv.}$=0.984) from ligand based approaches was confirmed as the best model among them. The $N^{1}$-allyl-$N^{2}$-(tetrahydrofuran-2-yl)methyl)oxalamide (P1), 2-(4-trimethylammoniummethylcyclohexyloxy)tetrahydrofurane (P5) and 2-(3-trimethylammoniummethylcyclohexyloxy)tetrahydrofurane (P6) molecules predicted as porcine pheromonal odorant by the CoMFA model were showed relatively high binding affinity constant values (Pred.p$[Od]_{50}=8{\sim}10$) and very lower toxicity values against some sorts of toxicity.