Linear and nonlinear quantitative structure–property relationship models for solubility of some anthraquinone, anthrone and xanthone derivatives in supercritical carbon dioxide

A study on quantitative structure-activity relationship and molecular docking of metalloproteinase inhibitors based on L-tyrosine scaffold

Background

MMP-2 enzyme is a kind of matrix metalloproteinases that digests the denatured collagens and gelatins. It is highly involved in the process of tumor invasion and has been considered as a promising target for cancer therapy. The structural requirements of an MMP-2 inhibitor are: (1) a functional group that binds the zinc ion, and (2) a functional group which interacts with the enzyme backbone and the side chains which undergo effective interactions with the enzyme subsites.

Methods

In the present study, a QSAR model was generated to screen new inhibitors of MMP-2 based on L–hydroxy tyrosine scaffold. Descriptors generation were done by Hyperchem 8, DRAGON and Gaussian98W programs. SPSS and MATLAB programs have been used for multiple linear regression (MLR) and genetic algorithm partial least squares (GA-PLS) analyses and for theoretical validation. Applicability domain of the model was performed to screen new compounds. The binding site potential of all inhibitors was verified by structure-based docking according to their binding energy and then the best inhibitors were selected.

Results

The best QSAR models in MLR and GA-PLS were reported, with the square correlation coefficient for leave-one-out cross-validation (Q²_LOO) larger than 0.921 and 0.900 respectively. The created MLR and GA-PLS models indicated the importance of molecular size, degree of branching, flexibility, shape, three-dimensional coordination of different atoms in a molecule in inhibitory activities against MMP-2.

The docking study indicated that lipophilic and hydrogen bonding interactions among the inhibitors and the receptor are involved in a ligand-receptor interaction. The oxygen of carbonyl and sulfonyl groups is important for hydrogen bonds of ligand with Leu82 and Ala83. R₂ and R₃ substituents play a main role in hydrogen bonding interactions. R₁ is sited in the hydrophobic pocket. Methylene group can help a ligand to be fitted in the lipophilic pocket, so two methylene groups are better than one. The Phenyl group can create a π-π interaction with Phe86.

Conclusions

The QSAR and docking analyses demonstrated to be helpful tools in the prediction of anti-cancer activities and a guide to the synthesis of new metalloproteinase inhibitors based on L-tyrosine scaffold.

A study on quantitative structure–activity relationship and molecular docking of metalloproteinase inhibitors based on L-tyrosine scaffold

Background

MMP-2 enzyme is a kind of matrix metalloproteinases that digests the denatured collagens and gelatins. It is highly involved in the process of tumor invasion and has been considered as a promising target for cancer therapy. The structural requirements of an MMP-2 inhibitor are: (1) a functional group that binds the zinc ion, and (2) a functional group which interacts with the enzyme backbone and the side chains which undergo effective interactions with the enzyme subsites.

Methods

In the present study, a QSAR model was generated to screen new inhibitors of MMP-2 based on L–hydroxy tyrosine scaffold. Descriptors generation were done by Hyperchem 8, DRAGON and Gaussian98W programs. SPSS and MATLAB programs have been used for multiple linear regression (MLR) and genetic algorithm partial least squares (GA-PLS) analyses and for theoretical validation. Applicability domain of the model was performed to screen new compounds. The binding site potential of all inhibitors was verified by structure-based docking according to their binding energy and then the best inhibitors were selected.

Results

The best QSAR models in MLR and GA-PLS were reported, with the square correlation coefficient for leave-one-out cross-validation (Q2 LOO) larger than 0.921 and 0.900 respectively. The created MLR and GA-PLS models indicated the importance of molecular size, degree of branching, flexibility, shape, three-dimensional coordination of different atoms in a molecule in inhibitory activities against MMP-2.

The docking study indicated that lipophilic and hydrogen bonding interactions among the inhibitors and the receptor are involved in a ligand-receptor interaction. The oxygen of carbonyl and sulfonyl groups is important for hydrogen bonds of ligand with Leu82 and Ala83. R2 and R3 substituents play a main role in hydrogen bonding interactions. R1 is sited in the hydrophobic pocket. Methylene group can help a ligand to be fitted in the lipophilic pocket, so two methylene groups are better than one. The Phenyl group can create a π-π interaction with Phe86.

Conclusions

The QSAR and docking analyses demonstrated to be helpful tools in the prediction of anti-cancer activities and a guide to the synthesis of new metalloproteinase inhibitors based on L-tyrosine scaffold.

Fluorescence enhancement effect for the determination of adenosine 5'-monophosphate with 9-anthracene carboxylic acid-cetyl trimethyl ammonium bromide system

A fluorimetric method based on fluorescence enhancement effect was developed for the determination of adenosine 5'-monophosphate (AMP) with 9-anthracene carboxylic acid (9-ANCA)-cetyl trimethyl ammonium bromide (CTAB) system. Fluorescence intensity of 9-ANCA was decreased by the addition of CTAB but addition of AMP again rose the intensity of 9-ANCA gradually. The observed fluorescence enhancement is attributed to the competitive binding reaction of 9-ANCA and adenosine to CTAB. The enhancement in the fluorescence intensity was found proportional to the concentration of AMP over the range 2.0 × 10(-4) to 1.2 × 10(-3) mol dm(-3). The ion pair complex is formed spontaneously between 9-ANCA and CTAB. Since the binding interaction is larger for the adenosine-CTAB pair, the fluorophore 9-ANCA will be released. The quantum yield of free 9-ANCA is higher therefore its fluorescence observed at 417 nm wavelength is enhanced. This mechanism of competitive molecular interaction is further confirmed by conductometric measurements. The method was applied successfully for the determination of AMP from pharmaceutical sample. The method is more selective, sensitive and relatively free from interferences.