Drug development is the process of bringing a new drug to market after a lead chemical has been identified through drug discovery. Before a medicine is available for clinical use, the drug development process can take up to 20 years and cost as much as $3 billion USD. Finding a single molecule for multiple targets, also known as polypharmacology or multitarget drug (MTD), can be a time- and cost-efficient technique for drug development. In addition, the application of computer-aided drug design techniques in drug development can reduce drug development expenditures and shorten the drug development cycle in comparison to conventional drug development. This chapter focused on methods for identifying polypharmacological compounds with multiple targets. A step-by-step case study for identifying a multitarget drug to treat breast cancer is also provided.