Growth factor receptors and enzymes are essential proteins that link extracellular signals with intracellular signaling pathways and support many phases of the development of cancer. Vascular endothelial growth factor receptor (VEGFR2) is a dominant player in the angiogenesis process of malignant cells and Sterol O-acyltransferase (SOAT1) is emerging as a new oncogenic enzyme in the development and progression of cancer. In this study we selected three plant-derived compounds Indigoferin A (compound 1), Indigoferin B (compound 2) and Indigoferin C (compound 3) as ligands and investigated their binding affinity and simulation energy with prospective targets VEGFR2 and SOAT1. Indigofera Giardiana is a shrub and is found in northern hilly areas of Pakistan and India. It has medicinal uses in conventional medicine for treating skin infections and stomach spasms. In the current work, ligand-receptor complexes were subjected to molecular dynamics and simulation analysis. Compounds Indigoferin A, B and C all have good binding affinity with the three selected targets (VEGFR2, SOAT1 and p53Mapkinase). In terms of metrics generated from molecular dynamics simulations, such as root mean square deviation and fluctuation, the ligand and receptor complexes were found stable. The molecules Indigoferin A, B, and C exhibit different protonation states that interact significantly with the target proteins' active site residues, as shown by the results of molecular dynamics and simulation analysis. The relative binding free energies have been precisely calculated using the MM-GBSA method. Preventing cell growth is an important strategy for treating cancer and these three compounds have the potential to inhibit the targeted enzyme (SOAT1) and receptor proteins (VEGFR2, p53 Map Kinase) thus helping to find novel compounds that could successfully restrain the growth of malignant cells.