For many years, the "one target, one drug" paradigm has been the driving force behind developments in pharmaceutical research. With the recent advances in molecular biology and genomics technologies, the focus is shifting toward "drug-holistic" systems based approaches (i.e. systems pharmacology). The integration of large and diverse amount of data from chemistry and biology coupled with the development and the application of network-based approaches to cope with these data is the next paradigm of drug discovery. Systems pharmacology offers a novel way of approaching drug discovery by developing models that consider the global physiological environment of protein targets and their modification by drugs. Studying drug action across multiple scales of complexity from molecular and cellular to tissue and organism levels may help identify new druggable disease genes and to design new drugs with a better efficacy and clinical safety.