• Title, Summary, Keyword: comparative molecular field analysis (CoMFA)

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Comparison of QSAR Methods (CoMFA, CoMSIA, HQSAR) of Anticancer 1-N-Substituted Imidazoquinoline-4,9-dione Derivatives

  • Suh, Myung-Eun;Park, So-Young;Lee, Hyun-Jung
    • Bulletin of the Korean Chemical Society
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    • v.23 no.3
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    • pp.417-422
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    • 2002
  • Comparison studies of the Quantitative Structure Activity Relationship (QSAR) methods with new imidazo-quinolinedione derivatives were conducted using Comparative Molecular Field Analysis (CoMFA), Comparative Molecular Similarity Indices Analysis (CoMSIA), and the Hologram Quantitative Structure Activity Relationship (HQSAR). When the CoMFA crossvalidation value, q2, was 0.625, the Pearson correlation coefficient, r2, was 0.973. In CoMSIA, q2 was 0.52 and r2 was 0.979. In the HQSAR, q2 was 0.501 and r2 was 0.924. The best result was obtained using the CoMSIA method according to a comparison of the calculated values with the real in vitro cytotoxic activities against human ovarian cancer cell lines.

Development of new agrochemicals by quantitative structure-activity relationship (QSAR) methodology. III. 3D QSAR methodologies and computer-assisted molecular design (CAMD) (정량적인 구조-활성상관 (QSAR) 기법에 의한 새로운 농약의 개발. III. 3D QSAR 기법들과 컴퓨터를 이용한 분자설계(CAMD))

  • Sung, Nack-Do
    • The Korean Journal of Pesticide Science
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    • v.7 no.1
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    • pp.1-11
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    • 2003
  • Acoording to improvement of HTOS (high throughput organic synthesis) and HTS (high throughput screening) technique, the CoMFA (comparative molecular field analysis), CoMSIA (comparative molecular similarity indeces analysis) and molecular HQSAR (hologram quantitative structure-activity relationship) analysis techniques as methodology of computer assisted molecular design (CAMD) were introduced generally and summarized for some application cases.

Molecular Docking, 3D QSAR and Designing of New Quinazolinone Analogues as DHFR Inhibitors

  • Yamini, L.;Kumari, K. Meena;Vijjulatha, M.
    • Bulletin of the Korean Chemical Society
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    • v.32 no.7
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    • pp.2433-2442
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    • 2011
  • The three dimensional quantitative structure activity relationship (3D QSAR) models were developed using Comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and docking studies. The fit of Quinazolinone antifolates inside the active site of modeled bovine dihydrofolate reductase (DHFR) was assessed. Both ligand based (LB) and receptor based (RB) QSAR models were generated, these models showed good internal and external statistical reliability that is evident from the $q^2_{loo}$, $r^2_{ncv}$ and $r^2_{pred}$. The identified key features enabled us to design new Quinazolinone analogues as DHFR inhibitors. This study is a building bridge between docking studies of homology modeled bovine DHFR protein as well as ligand and target based 3D QSAR techniques of CoMFA and CoMSIA approaches.

Comparative Molecular Field Analysis of Dioxins and Dioxin-like Compounds

  • Ashek, Ali;Cho, Seung-Joo
    • Molecular & Cellular Toxicology
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    • v.1 no.3
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    • pp.157-163
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    • 2005
  • Because of their widespread occurrence and substantial biological activity, halogenated aromatic hydrocarbons are one of the important classes of contaminants in the environment. We have performed comparative molecular field analysis (CoMFA) on structurally diverse ligands of Ah (dioxin) receptor to explore the physico-chemical requirements for binding. All CoMFA models have given $q^{2}$ value of more than 0.5 and $r^{2}$ value of more than 0.83. The predictive ability of the models was validated by an external test set, which gave satisfactory predictive $r^{2}$ values. Best predictions were obtained with CoMFA model of combined modified training set ($q^{2}=0.631,\;r^{2}=0.900$), giving predictive residual value = 0.002 log unit for the test compound. We have suggested a model comprises of four structurally different compounds, which offers a good predictability for various ligands. Our QSAR model is consistent with all previously established QSAR models with less structurally diverse ligands. The implications of the CoMFA/QSAR model presented herein are explored with respect to quantitative hazard identification of potential toxicants.

Theoretical Study on the [3,3]-Sigmatropic Rearrangement of Allylic Esters by Comparative Molecular Field Analysis (CoMFA)

  • Yoo, Sung-Eun;Cha, OKJa
    • Bulletin of the Korean Chemical Society
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    • v.15 no.10
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    • pp.889-890
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    • 1994
  • A comparative molecular field analysis (CoMFA) on the substituent effect of the palladium(Ⅱ) catalyzed [3,3]-sigmatropic rearrangement of allylic esters was studied to show a good correlation between the electrostatic property of substituents and the reaction rate. The CoMFA result suggests that the reaction rate will increase as the electron-donating ability of substituents increases.

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Prediction of Lipophilicity of Orthopramides by Comparative Molecular Field Analysis (CoMFA)

  • 유성은;신영아
    • Bulletin of the Korean Chemical Society
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    • v.16 no.12
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    • pp.1189-1193
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    • 1995
  • The comparative molecular field analysis (CoMFA) method has been employed to correlate the apparent lipophilicity (logkw) and global lipophilicity (logP) for orthopramide derivatives. This study demonstrated that CoMFA is an excellent method in predicting the complex properties of molecules such as apparent lipophilicity (logkw) or lipophilicity (logP). The better predictability of lipophilicity by introducing logkw as an independent descriptor suggests that the HPLC capacity factor measured in a buffer of pH 7.5 (logkw) can be effectively utilized in the prediction of global lipophilicity.

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CoMFA and CoMSIA 3D QSAR Studies on Pimarane Cyclooxygenase-2 (COX-2) Inhibitors

  • Suh, Young-Ger;Lee, Kwang-Ok;Park, Hyun-Ju;Kim, Young-Ho;Moon, Sung-Hyun
    • Proceedings of the PSK Conference
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    • pp.250.1-250
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    • 2003
  • In this work, we have conducted 3D-QSAR studies on a series of acanthonic acid derivatives that act as COX-2 inhibitors, using two different methods: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). CoMFA and CoMSIA analysis of twenty five pimarane analogues produced good models with high predictive abilities. (omitted)

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Correlation between the Reactant Complex or Transition State Conformations and the Reactivity of 4-Nitrophenyl Benzoate and Its Sulfur Analoguew with Anoinic Nucleophiles by Comparative Molecular Field Analysis (CoMFA)

  • 유성은;차옥자
    • Bulletin of the Korean Chemical Society
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    • v.17 no.7
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    • pp.653-655
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    • 1996
  • A comparative molecular field analysis (CoMFA) was carried out for the correlation of the transition state structures and the reaction rates for the SN2 reaction of 4-nitrophenyl benzoate and its sulfur analogs with anionic nucleophiles. The CoMFA analysis showed that both steric and electrostatic effects are important, and the steric contribution increased when nucleophiles are alkoxides or arylsulfides. In this study, we have demonstrated that the CoMFA analysis can be expanded beyond the scope of dealing with reactants and products. The reactant complex and transition state conformations generated along the reaction path can be more appropriately used for the correlation of structures and reaction rates.

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Pharmacophore Based Comparative Molecular Field Analysis of CRTh2 Antagonists

  • Babu, Sathya;Madhavan, Thirumurthy
    • Journal of the Chosun Natural Science
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    • v.8 no.2
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    • pp.89-98
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    • 2015
  • Chemoattractant receptor homologous molecule expressed on Th2 cells (CRTh2) is a G-protein coupled receptor targeted for inflammatory diseases such as asthma, allergic rhinitis and atopic dermatitis. In this study, pharmacophore modeling and comparative molecular field analysis (CoMFA) were performed on the series of 2-(2-(benzylthio)-1H-benzo[d]imidazol-1-yl) acetic acids derivatives. Five highly active compounds were used for generation of pharmacophore models using GASP module. The best pharmacophore model was selected and used as template for the alignment of compounds which was used for CoMFA analysis. The best predictions obtained for CoMFA was $q^2=0.545$, $r^2=0.756$. The predictive ability of the model was investigated using 15 test set compounds. Contour maps suggested that presence of bulky substituents at $5^{th}$ position of benzene ring connected to suphur atoms attached to imidazol ring will increase the activity of the compounds. The results obtained from this study will be useful to design more potent CRTh2 antagonists.

3D-QSAR of Non-peptidyl Caspase-3 Enzyme Inhibitors Using CoMFA and CoMSIA

  • Lee, Do-Young;Hyun, Kwan-Hoon;Park, Hyung-Yeon;Lee, Kyung- A.;Lee, Bon-Su;Kim, Chan-Kyung
    • Bulletin of the Korean Chemical Society
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    • v.27 no.2
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    • pp.273-276
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    • 2006
  • Three dimensional quantitative structure-activity relationship studies for a series of isatin derivatives as a nonpeptidyl caspase-3 enzyme inhibitor were investigated using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The first approach of non-peptidyl small molecules by 3D QSAR may be useful in guiding further development of potent caspase-3 inhibitors.