The objective of this study was to analyze the molecular characteristics of the podophyllotoxins and its derivatives with the metabolic enzymes and regulate the designing of therapeutic mechanism against malignant cells. One such inhibitor is podophyllotoxin with anticancer activity because of the capability to stop the metabolic enzymes. In this study, we undertook the in silico analysis with respect to molecular docking podophyllotoxin and its derivatives using the Patchdock server. Moreover, drug likeness of podophyllotoxin, etoposide, and teniposide was investigated using Lipinski filter and SwissADME. According to the molecular docking score, podophyllotoxin indicated that both derivatives (especially teniposide) showed a good binding affinity toward selected protein receptors.