In recent years, the use of computers in chemistry have been developed greatly. The molecular docking, computer based drug designing, etc. has proved the efficiency of computers in computational chemistry. With the use of sophisticated computational tools and techniques the drugs discovery has been accelerated in the form of target based drug discovery rather than rational methods. In the current scenario the software used for drug designing are very expensive, so in this paper the power of internet and open source community has been used for performing SAR and Pharmacophore based drug design approaches as they are free to use. Using SAR and Pharmacophore study here some derivatives of Podophyllotoxin have been designed by understanding their toxicity, metabolic sites and drug like properties.