Molecular docking and molecular dynamics studies of Millettia dielsiana phytochemicals with tumor necrosis factor-alpha (TNF-α)

TNF-alpha plays a crucial role in regulating immune responses and inducing inflammation. In this study, TNF alpha was selected as the primary target for in silico screening of phytochemicals from Millettia dielsiana using a combination of molecular docking and molecular dynamics simulations. The AutoDock Vina and GROMACS programs were employed in this study to perform calculations using the respective methods. The results indicated that the compounds trans-3-O-p-hydroxycinnamoyl ursolic acid (D15) and ichthynone (D19) were estimated to have stronger binding affinity than the reference inhibitor SPD304 in the binding site region of TNF alpha. These complexes were further subjected to MD simulations to evaluate structural stability, revealing that compound D19 is more stable than compound D15 and the reference inhibitor SPD304. However, the calculation of binding free energy using the MMGBSA method showed that the total Delta G value of compound D15 is better than that of the reference inhibitor SPD304. Therefore, compound D15 is considered the most promising candidate among the phytochemicals derived from M. dielsiana and provides direction for further biological experiments.