• Title/Summary/Keyword: CoMSIA

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Comparative Molecular Similarity Indices Analyses (CoMSIA) on the Herbiridal Activities of New 5-benzofuryl-2-[1-(alkoxy-imino)alkyl]-3-hydroxycyclo-hex-2-en-1-one Derivatives (새로운 5-benzofuryl-2-[1-(alkoxyimino)alkyl]-3-hydroxycyclo-hex-2-en-1-one 유도체들의 제초활성에 관한 비교분자 유사성지수 분석)

  • Sung, Nack-Do;Jung, Ki-Sung;Jung, Hoon-Sung;Chung, Young-Ho
    • The Korean Journal of Pesticide Science
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    • v.10 no.1
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    • pp.7-14
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    • 2006
  • Three-dimensional quantitative structure-activity relationships (3D-QSARs) on the herbicidal activities against in-vitro pre-emergence rice plant (Oryza sativa L.) and barnyard grass (Echinochloa crus-galli) by new 5-benzofuryl-2-[1-(alkoxyimino)alkyl]-3-hydroxycyclohex-2-en-1-one derivatives were studied quantitatively using comparative molecular similarity indices analysis (CoMSIA) methodology. The optimized CoMSIA model(A5: $r^2_{cv.}=0.569$ & $r^2_{ncv.}=0.941$) for rice plant exhibited a good correlation with steric (31.6%) and hydrophobic (39.7%) factors of the substrate molecules, and the model (B4: $r^2_{cv.}=0.569$ & $r^2_{ncv.}=0.941$) for barnyardgrass exhibited a good correlation with electrostatic (46.7%) and H-bond acceptor field (30.8%), respectively. The predicted $R_1=SF_5,\;R_2=R_3=R_4=H(P1)$ substituent (Rice plant: $pI_{50}=4.84$ & Barnyardgrass: $pI_{50}=7.21$, ${\Delta}pI_{50}=2.37$) by the model (B4) not only exhibited to the highest herbicidal activity against barnyardgrass, but also exhibited to the highest selecticity between two plants.

Pharmacophore-Based Comparative Molecular Similarity Indices Analysis of CRTh2 Antagonists

  • Babu, Sathya
    • Journal of Integrative Natural Science
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    • v.8 no.4
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    • pp.273-284
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    • 2015
  • Chemoattractant Receptor Homologous molecule expressed on Th2 cells (CRTh2) is a chemoattractant receptor with seven transmembrane helices targeted for inflammatory diseases such as asthma and allergic rhinitis. In this study, pharmacophore based Comparative Molecular Similarity Indices Analysis (CoMSIA) were performed on the series of 2-(2-(benzylthio)-1H-benzo[d]imidazol-1-yl) acetic acids derivatives. Initially, GASP module was used for generation of pharmacophore models using five highly active compounds from the dataset. Among the generated pharmacophores, the best pharmacophore model was selected based on fitness score and was used as template for the alignment of compounds which was used for CoMSIA analysis. The best predictions were obtained utilizing steric, hydrophobic and H-bond acceptor parameters showing a $q^2$=0.559 and $r^2$=0.730. 15 test set compounds was used to investigate the predictive ability of the CoMSIA model. Contour maps suggested that presence of bulky substituents and H-bond acceptor atoms at $5^{th}$ position of benzene ring will increase the activity of the compounds. The results obtained from this study will be useful to design more potent CRTh2 antagonists.

CoMSIA 3D-QSAR Analysis of 3,4-Dihydroquinazoline Derivatives Against Human Colon Cancer HT-29 Cells

  • Kwon, Gi Hyun;Cho, Sehyeon;Lee, Jinsung;Sohn, Joo Mi;Byun, Joon Seok;Lee, Kyung-Tae;Lee, Jae Yeol
    • 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.

Three Dimensional Quantitative Structure-Activity Relationship Analyses on the Fungicidal Activities of New Novel 2-Alkoxyphenyl-3-phenylthioisoindoline-1-one Derivatives Using the Comparative Molecular Similarity Indices Analyses (CoMSIA) Methodology Based on the Different Alignment Approaches (상이한 정렬에 따른 비교분자 유사성 지수분석(CoMSIA) 방법을 이용한 새로운 2-Alkoxyphenyl-3-phenylthioisoindoline-1-one 유도체들의 살균활성에 관한 3차원적인 정량적 구조와 활성과의 관계)

  • Sung, Nack-Do;Yoon, Tae-Yong;Song, Jong-Hwan;Jung, Hoon-Sung
    • 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.

3-D QSAR Studies on Thiazole and Triazole Antifungal Agents by CoMFA and CoMSIA

  • Thai, Khac-Minh;Tran, Thanh-Dao;Park, Hyun-Ju
    • Proceedings of the PSK Conference
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    • 2003.04a
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    • pp.249.2-250
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    • 2003
  • 3D-QSAR analyses by CoMFA and CoMSIA were conducted on a series of thiazole and triazole analogues with respect to their antifungal activities against Microsporum gypseum. A total of twenty analogues were used for the derivation of the 3D-QSAR models (training set). Thesuperposition of the compounds was performed by applying the FlexS with shape-based screening method. (omitted)

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3D-QSAR (CoMFA, CoMSIA) study of PPAR-$\gamma$ agonists.

  • Lee, Hye-Sun;Chae, Chong-Hak;Yoo, Sung-Eun;Yi, Kyu-Yang;Park, Kyung-Lae
    • Proceedings of the PSK Conference
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    • 2003.10b
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    • pp.181.3-181.3
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    • 2003
  • Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on 60 PPAR-g agonists. Partial Least Squars (PLS) analysis produced good predicted models with $q^2$ value of 0.62 (SDEP=0.33, F value=93.22, $r^2$=0.92) and 0.56 (SDEP=0.47 F value=27.65, $r^2$=0.86), respectivly. The key spatial properties were detected by careful analysis of the isocontour maps.

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Structural Characteristics that Influence on the Insecticidal Activity of 2-(n-Octyl)pseudothiourea Analogues against the Diamondback Moth (Plutella xylostella, L.)

  • Soung, Min-Gyu;Kil, Mun-Jae;Sung, Nack-Do
    • Bulletin of the Korean Chemical Society
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    • v.30 no.11
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    • pp.2749-2753
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    • 2009
  • Structural characteristics that influence on the insecticidal activity ($pI_{50}$) of 2-(n-octyl)isothiourea analogues (1-45) against the diamondback moth (Plutella xylostella, L.) based on three dimensional quantitative structure activity relationships (3D-QSARs) were discussed quantitatively using a comparative molecular field analysis (CoMFA) and a comparative molecular similarity indeces analysis (CoMSIA) methods. The statistical values of the CoMFA 2 model were better than those of the CoMSIA 1 model. The CoMFA 2 model was the optimized model with the correlativity (the training set: Ave. = 0.104 & PRESS = 0.613) and the predictability (the test set: Ave. = 0.086 & PRESS = 0.096). Insecticidal activities with the optimized CoMFA 2 model were dependent upon steric factors (79.4%) of $R_1-R_3$ substituents. From the analytical results of CoMFA contour maps, it is predicted that the R1 substituent of 1-45 which has a steric favor in a broad space, $R_2\;and\;R_3$ groups with a steric favor in a narrow space and a H-bond donor favor would have better the insecticidal activity.

Comparative Molecular Similarity Indices Analysis of Caspase-3 Inhibitors

  • Babu, Sathya;Madhavan, Thirumurthy
    • Journal of Integrative Natural Science
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    • v.7 no.4
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    • pp.227-233
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    • 2014
  • Caspases, a family of cysteinyl aspartate-specific proteases plays a central role in the regulation and the execution of apoptotic cell death. Activation of caspases-3 stimulates a signaling pathway that ultimately leads to the death of the cell. Hence, caspase-3 has been proven to be an effective target for reducing the amount of cellular and tissue damage. In this work, comparative molecular similarity indices analysis (CoMSIA) was performed on a series of 3,4-dihydropyrimidoindolones derivatives which are inhibitors of caspase-3. The best predictions were obtained for CoMSIA model ($q^2$ = 0.586, $r^2$ = 0.955). The predictive ability of test set ($r^2_{pred}$) was 0.723. Statistical parameters from the generated QSAR models indicated the data is well fitted and have high predictive ability. Our theoretical results could be useful to design novel and more potent caspase-3 derivatives.

Comparative Molecular Similarity Indices Analysis of CXCR-2 Inhibitors

  • B, Sathya.
    • Journal of Integrative Natural Science
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    • v.9 no.3
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    • pp.177-184
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    • 2016
  • CXC chemokine receptor 2 (CXCR2) is a prominent chemokine receptor on neutrophils and it regulates the neutrophilic inflammation in the lung diseases. CXCR2 antagonist may reduce the neutrophil chemotaxis and alter the inflammatory response. Hence, in the present study, ligand based Comparative Molecular Similar Indices Analysis (CoMSIA) was performed on a series of CXCR2 antagonist named pyrimidine-5-carbonitrile-6-alkyl derivatives. The optimum CoMSIA model was obtained with statistically significant cross-validated coefficients ($q^2$) of 0.582 and conventional coefficients ($r^2$) of 0.987 with steric, electrostatic, hydrophobic, donor and acceptor fields. The contour maps suggest the important structural modifications and this study can be used to guide the development of potent CXCR2 antagonist.