Computational modeling and study of the anti-cancer activity of novel NSAID 1-acyl-4-cycloalkyl/arylsemicarbazide and 1-acyl-5-benzyloxy/hydroxy carbamoylcarbazide derivatives using molecular docking and molecular dynamics simulations

Abstract

In this study, a series of NSAID 1-acyl-4-cycloalkyl/arylsemicarbazides and 1-acyl-5-benzyloxy/hydroxy carbamoylcarbazides possess anti-cancer activity against three human cancer cell lines L1210, CEM, and HeLa have been investigated using a combined approach including quantitative structure activity relationship (QSAR) study, molecular docking, and molecular dynamics (MD) simulations. First, different molecular descriptors were calculated for these compounds. Stepwise multiple linear regression (MLR) method was performed for selecting some common descriptors, including VEA1, hydration energy (HE), log P, and binding energy for all three cell lines. Then, other QSAR models were constructed using support vector regression (SVR) method. According to the results, SVR models were more efficient in predicting the anti-cancer activity. To better understand the mechanism of the binding interactions of NSAID 1-acyl-4-cycloalkyl/arylsemicarbazide and 1-acyl-5-benzyloxy/hydroxy carbamoylcarbazide derivatives with 5-lipoxygenase (5-LOX) protein, molecular docking studies were conducted. These studies have also been used to explore the effects of HE, log P, and binding energy on anti-cancer activity of the studied compounds. The results of molecular docking suggest that hydrophobic interactions of ligands with the active site of 5-LOX are responsible for their anti-cancer activities. Finally, molecular dynamics (MD) simulations using GROMACS package were used for evaluating the stability of 5-LOX in complex with NSAID 1-acyl-4-cycloalkyl/arylsemicarbazide and 1-acyl-5-benzyloxy/hydroxy carbamoylcarbazide derivatives. The results of MD simulations demonstrate stability of protein structure in complex with active compounds, 12 and 27.