QSAR studies on diclofenac analogues as potent cyclooxygenase inhibitors using CoMFA and CoMSIA

Arvind, Kumar; Solomon, K. Anand; Rajan, S.S.

doi:10.1007/s00044-013-0771-5

Cited by 8 publications

(3 citation statements)

References 22 publications

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“…For the 3D-QSAR study, a brief comparative molecular field analysis (CoMFA) was performed using the SYBYL-X 2.0 program to investigate the relationship of structure and activity. , 28 compounds were selected as the training set and the other 7 compounds were selected as the test set. The most active compound, II-13 , was selected as the template for superposition, and the remaining molecules were superimposed on the common skeleton of compound II-13 using the Align Database program.…”

Section: Methodsmentioning

confidence: 99%

Design, Synthesis, Structure–Activity Relationship, Molecular Docking, and Herbicidal Evaluation of 2-Cinnamoyl-3-Hydroxycyclohex-2-en-1-one Derivatives as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors

Song

Zhao

Zhang

et al. 2021

J. Agric. Food Chem.

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Cinnamic acid, isolated from cinnamon bark, is a natural product with excellent bioactivity, and it effectively binds with cyclohexanedione to form novel 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors. According to the active sub-structure combination principle, a series of novel 3-hydroxy-2-cinnamoyl-2-en-1-one derivatives were designed and synthesized. The title compounds were characterized by infrared, 1H NMR, 13C NMR, and HRMS. The in vitro inhibitory activity of AtHPPD verified that compound II-13 showed the most activity with a half-maximal inhibitory concentration (IC50) value of 0.180 μM, which was superior to that of mesotrione (0.206 μM) in vitro. The preliminary herbicidal activity tests demonstrated that some compounds had good herbicidal activity especially compound II-13 at a concentration of 150 g ai/ha. The binding mode of AtHPPD through molecular docking indicated that two oxygens of compounds II-13 formed bidentate interactions with metal ions, and the benzene ring formed π-π accumulation effects with Phe-381 and Phe-424. The results of molecular dynamics simulations showed that compound II-13 exhibited a more stable binding ability with AtHPPD than mesotrione. This study provided insights into the development of natural and efficient herbicides in the future.

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Section: Methodsmentioning

confidence: 99%

Design, Synthesis, Structure–Activity Relationship, Molecular Docking, and Herbicidal Evaluation of 2-Cinnamoyl-3-Hydroxycyclohex-2-en-1-one Derivatives as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors

Song

Zhao

Zhang

et al. 2021

J. Agric. Food Chem.

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“…The activity range of the inhibitors was 0.029–5.571 μM. The structures of these compounds were built and optimized by SYBYL 6.9 to generate 3D structures with appropriate conformation (SYBYL, 2006; Arvind et al, 2014). Simulations were carried out by employing Tripos force field with energy termination of 0.005 kcal/mol, and a maximum of 1,000 iterations.…”

Section: Methodsmentioning

confidence: 99%

“…The optimum number of components (ONC) was calculated and the cross-validated coefficient ( Q 2 ) was obtained to evaluate the model. The model was followed by the non-cross-validation analysis and the coefficient of determination ( R 2 ), the standard error of estimate (SEE), and the F value were calculated based on the ONC originated from LOO (Arvind et al, 2014). The predicted correlation coefficient for the test set (Rpred2) was used to examine the predictive power of the model.…”

Section: Methodsmentioning

confidence: 99%

Quantitative Structure Activity Relationship Studies and Molecular Dynamics Simulations of 2-(Aryloxyacetyl)cyclohexane-1,3-Diones Derivatives as 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors

Liu

et al. 2019

Front. Chem.

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4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a significant enzyme in the biosynthesis of plastoquinone and tocopherol. Moreover, it is also a potential target to develop new herbicide. The technology of computer-aided drug design (CADD) is a useful tool in the efficient discovery of new HPPD inhibitors. Forty-three compounds with known activities were used to generate comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models based on common framework and molecular docking. The structural contribution to the activity was determined, which provided further information for the design of novel inhibitors. Molecular docking was used to explain the changes in activity caused by the binding mode between ligand and protein. The molecular dynamics (MD) results indicated that the electrostatic energy was the major driving force for ligand–protein interaction and the Phe403 made the greatest contribution to the binding. The present work has provided useful information for the rational design of novel HPPD inhibitors with improved activity.

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Estimating antiwear properties of esters as potential lubricant-based oils using QSTR models with CoMFA and CoMSIA

Wang

Yang

et al. 2017

Friction

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Abstract:Comparative molecular field analysis and comparative molecular similarity indices analysis were employed to analyze the antiwear properties of a series of 57 esters as potential lubricant-based oils. Predictive 3D-quantitative structure tribo-ability relationship models were established using the SYBYL multifit molecular alignment rule with a training set and a test set. The optimum models were all shown to be statistically significant with cross-validated coefficients q 2 > 0.5 and conventional coefficients r 2 > 0.9, indicating that the models are sufficiently reliable for activity prediction, and may be useful in the design of novel ester-based oils.

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QSAR studies on diclofenac analogues as potent cyclooxygenase inhibitors using CoMFA and CoMSIA

Cited by 8 publications

References 22 publications

Design, Synthesis, Structure–Activity Relationship, Molecular Docking, and Herbicidal Evaluation of 2-Cinnamoyl-3-Hydroxycyclohex-2-en-1-one Derivatives as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors

Design, Synthesis, Structure–Activity Relationship, Molecular Docking, and Herbicidal Evaluation of 2-Cinnamoyl-3-Hydroxycyclohex-2-en-1-one Derivatives as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors

Quantitative Structure Activity Relationship Studies and Molecular Dynamics Simulations of 2-(Aryloxyacetyl)cyclohexane-1,3-Diones Derivatives as 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors

Estimating antiwear properties of esters as potential lubricant-based oils using QSTR models with CoMFA and CoMSIA

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