Natural products with their specific structural features deliver chemical starting points in drug discovery to develop innovative therapies for diseases for which no or only unsatisfactory treatments exist. The evolved function of natural products in regulating a plethora of diverse biological pathways in nature makes them to a biologically biased and complementary source of chemical probes to identify novel mechanisms of molecular interactions. As there is a high need for specific modulators of new targets, the identification of new natural products and the elucidation of their mechanism of action are gaining an increasing attraction in today’s drug research. The technological driving forces of synthetic biology, genome sequencing, and DNA-synthesis are currently changing the face of natural products research. Whole genome data and the identification of silent natural products pathways in-silico open the door to a so far inaccessible chemodiversity from natural sources. Selected examples will illustrate how the investigation of new chemotypes from natural products, natural products-inspired synthetics in phenotypic assays can be integrated to orthologous target identification technologies. The fragmentation of natural products is a further scientifically exciting example how the broad diversity of natural products can be leveraged in the science of drug discovery.