• BMB Reports
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• 제31권5호
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• pp.459-467
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• 1998

A new set of functional group interaction energy descriptors relevant to the ACE (Angiotensin-Converting Enzyme) inhibitory peptide, QSAR (Quantitative Structure Activity Relationships), is presented. The functional group interaction energies approximate the charged interactions and distances between functional groups in molecules. The effective energies of the computationally derived geometries are useful parameters for deriving 3D-QSAR models, especially in the absence of experimentally known active site conformation. ACE is a regulatory zinc protease in the renin-angiotensin system. Therapeutic inhibition of this enzyme has proven to be a very effective treatment for the management of hypertension. The non bond interaction energy values among functional groups of six-feature of ACE inhibitory peptides were used as descriptor terms and analyzed for multivariate correlation with ACE inhibition activity. The functional group interaction energy descriptors used in the regression analysis were obtained by a series of inhibitor structures derived from molecular mechanics and semi-empirical calculations. The descriptors calculated using electrostatic and steric fields from the precisely defined functional group were sufficient to explain the biological activity of inhibitor. Application of the descriptors to the inhibition of ACE indicates that the derived QSAR has good predicting ability and provides insight into the mechanism of enzyme inhibition. The method, functional group interaction energy analysis, is expected to be applicable to predict enzyme inhibitory activity of the rationally designed inhibitors.

• Bulletin of the Korean Chemical Society
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• 제34권12호
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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 $pIC_{50}$.

• Bulletin of the Korean Chemical Society
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• 제32권4호
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• pp.1241-1248
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• 2011

Three dimensional quantitative structure-activity relationships (3D-QSARs) between new thiosemicarbazone analogues (1-31) as a substrate molecule and their inhibitory activity against tyrosinase as a receptor were performed and discussed quantitatively using CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis) methods. According to the optimized CoMSIA 2 model obtained from the above procedure, inhibitory activities were mainly dependent upon H-bond acceptor favored field (36.5%) of substrate molecules. The optimized CoMSIA 2 model, with the sensitivity of the perturbation and the prediction, produced by a progressive scrambling analysis was not dependent on chance correlation. From molecular docking studies, it is supposed that the inhibitory activation of the substrate molecules against tyrosinase (PDB code: 1WX2) would not take place via uncompetitive inhibition forming a chelate between copper atoms in the active site of tyrosinase and thiosemicarbazone moieties of the substrate molecules, but via competitive inhibition based on H-bonding.

• The Korean Journal of Physiology and Pharmacology
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• 제13권6호
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• pp.511-516
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• 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.

• Molecular & Cellular Toxicology
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• 제1권1호
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• pp.46-51
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• 2005

Mutagen X (MX) exists in our drinking water as the bi-products of chlorine disinfection. Being one of the most potent mutagen, it attracted much attention from many researchers. MX and its analogs are tested and modeled by quantitative structure activity relationship (QSAR) methods. As a result, factors affecting this class of compounds have been found to be steric and electrostatic effects. We tried to collect all the data available from the literature. The quantitative structure-activity relationship of a set of 29 MX was analyzed using Molecular Field Analysis (MFA) and Receptor Surface Analysis (RSA). The best models gave $q^{2}=0.918,\;r^{2}=0.949$ for MFA and $q^{2}=0.893,\;r^{2}=0.954$ for RSA. The models indicate that an electronegative group at C6 position of the furanone ring increases mutagenicity.

• 대한화학회지
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• 제56권2호
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• pp.236-245
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• 2012

The main mycobacterial infection in human is tuberculosis caused by Mycobacterium tuberculosis. Tuberculosis is the leading infectious cause of death in the world. Therefore there is continuing and compelling need for new and improved treatment for tuberculosis. The entire logic towards design of new compounds containing 4-hydroxy-N'-(1,3-thiazoldin- 2-yldene)benzohydrazide moiety is basically for superior antimycobacterial activity. The recent advances in QSAR and computer science have provided a systematic approach to design a structure of any compound and further, the biological activity of the compound can be predicted before synthesis. The 3D-QSAR studies for the set of 4-hydroxy-N'-(1,3-thiazoldin- 2-yldene)benzohydrazide and their derivatives were carried out by using V-life MDS (3.50). The various statistical methods such as Multiple Linear Regression (MLR), Partial Least Square Regression (PLSR), Principle Component Regression(PCR) and K nearest neighbour (kNN) were used. The kNN showed good results having cross validated $r^2$ 0.9319, $r^2$ for external test set 0.8561 and standard error of estimate 0.2195. The docking studies were carried out by using Schrodinger GLIDE module which resulted in good docking score in comparison with the standard isoniazid. The designed compounds were further subjected for synthesis and biological evaluation. Antitubercular evaluation of these compounds showed that (4.a), (4.d) and (4.g) found as potent inhibitor of H37RV.

• The Korean Journal of Physiology and Pharmacology
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• 제17권6호
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• pp.517-523
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• 2013

Naphthyridine compounds are important, because they exhibit various biological activities including anticancer, antimicrobial, and anti-inflammatory activity. Some naphthyridines have antimitotic effects or demonstrate anticancer activity by inhibiting topoisomerase II. These compounds have been investigated as potential anticancer agents, and several compounds are now part of clinical trials. A series of naphthyridine derivatives were evaluated for their in vitro cytotoxic activities against human cervical cancer (HeLa), leukemia (HL-60), and prostate cancer (PC-3) cell lines using an MTT assay. Some compounds (14, 15, and 16) were more potent than colchicine against all three human cancer cell lines and compound (16) demonstrated potency with $IC_{50}$ values of 0.7, 0.1, and $5.1{\mu}M$, respectively. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used for quantitative structure-activity relationship (QSAR) molecular modeling of these compounds. We obtained accurate and predictive three-dimensional QSAR (3D-QSAR) models as indicated by the high PLS parameters of the HeLa ($q^2$, 0.857; $r^2$, 0.984; $r^2\;_{pred}$, 0.966), HL-60 ($q^2$, 0.777; $q^2$, 0.937; $r^2\;_{pred}$, 0.913), and PC-3 ($q^2$, 0.702; $q^2$, 0.983; $r^2\;_{pred}$, 0.974) cell lines. The 3D-QSAR contour maps suggested that the C-1 NH and C-4 carbonyl group of the naphthyridine ring and the C-2 naphthyl ring were important for cytotoxicity in all three human cancer cell lines.

• Molecular & Cellular Toxicology
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• 제5권1호
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• pp.14-22
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• 2009

In vitro cytotoxicity of 23 alkyl phenols (APs) on human cervical cancer cell lines (HeLa) was determined using the lactate dehydrogenase (LDH) cytotoxicity assay. Two different sets of descriptors were used to construct the calibration model based on Genetic Algorithm-Multiple Linear Regression (GA-MLR) based on the experimental data. A statistically robust Structure-Activity Relationships (QSAR) model was achieved ($R^2$=95.05%, $Q^2_{LOO}$=91.23%, F=72.02 and SE= 0.046) using three Dragon descriptors based on Me (0D-Constitutional descriptor), BELp8 (2D-Burden eigenvalue descriptor) and HATS8p (3D-GETAWAY descriptor). However, external validation could not fully prove its validity of the selected QSAR in characterization of the cytotoxicity of APs towards HeLa cells. Nevertheless, the cytotoxicity profiles showed a finding that 4-n-octylphenol (4-NOP), 4-tert-octyl-phenol (4-TOP), 4-n-nonylphenol (4-NNP) had a more potent cytotoxic effect than other APs tested, inferring that increased length and molecular bulkiness of the substituent had important influence on the LDH cytotoxicity.

• Applied Biological Chemistry
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• 제48권3호
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• pp.252-257
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• 2005

새로운 2-(4-(6-chloro-2-benzoxazolyloxy)phenoxy)-N-phenylpropionamide 유도체들의 구조 변화에 따른 발아 전, 논피(Echinochloa crus-galli)에 대한 제초활성과의 3D-QSAR 관계를 상이한 정렬방법에 따라 비교 분자장 분석(CoMFA)과 비교분자 유사성 지수분석(CoMSIA) 방법으로 연구하였다. 가장 양호한 3D-QSAR 모델은 atom based fit 정렬과 CoMFA장과 CoMSIA장의 조합 조건에서 유도된 CoMFA 모델(AI-2)과 CoMSIA 모델(AII-4)이었다. CoMFA 및 CoMSIA 등고도로부터 제초활성은 N-phenyl 고리 상 치환기의 구조변화로 개선될 수 있었다.

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.2-2
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• pp.186.3-186.3
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• 2003

The three-dimensional quantitative structure-activity relationship (3D-QSAR) study using the comparative molecular field analysis (CoMFA) was performed on indolinones derivatives as an inhibitor of the protein tyrosine kinase of fibroblast growth factor receptor (FGFR). In the training set, twenty-four indolinone derivatives were aligned based on the indole fragment and the steric and electrostatic fields were included in the analysis. The best predicted model showed the cross-validated coefficient (r$^2$$\sub$cv/) of 0.804 and bib-cross validated coefficient (r$^2$) of 0.942. The CoMFA study can be used to predict several new inhibitors of the FGFR.