Multiple drug resistance and increased side effects due to allopathic drugs has warned scientific community with a global alarm to identify molecules from natural sources to combat diseases with minimum or no side effects. The present investigation was aimed to identify and isolate secondary metabolites from traditionally used Nerium indicum using conventional column chromatography which led to the isolation of two compounds, C-I (fractions NB4f1) and C-II (fractions NC13b1). Further characterized, it is elucidated using spectral data and identified as N-(4-hydroxy-phenyl)-2-methoxy-2-phenyl-acetamide, molecular formula C 15 H 15 NO 3 , and molecular weight 257.3 (C-I) and N-(4-hydroxy-phenyl)-2-phenyl-N-phenylacetyl-acetamide, molecular formula C 22 H 19 NO 3 , and molecular weight 345.4 (C-II). Further, the isolated compounds were investigated using in silico approach by Autodock tool with four different proteins specific for cancer and in vitro assessed cell proliferation, and apoptosis against human breast cancer MCF 7 cell line. The results of the in silico model demonstrated potent binding affinity of both compounds with the proteins representing that the isolated molecules could be a drug of choice for cancer. Further, the isolated compounds revealed significant inhibition of cell proliferation (IC 50 values 21 μg/mL for C-I, 19 μg/mL for C-II) with induced apoptosis with nuclear condensation effect on the MCF 7 cells in in vitro condition even at very low concentration. Compound treatment to MCF-7 cell line represented bright fetches indicating condensed chromatins and higher level of nuclear fragmentation with DAPI staining, indicating higher cell death due to induced apoptosis and confirmed using flow cytometry analysis representing inhibition of cell proliferation at S phase. Graphical abstract.