Although academic science has always provided a fundamental understanding of the biological and clinical basis of disease, the opportunity and imperative for academics to contribute more directly to the discovery of new medicines continues to grow. Embedding medicinal chemists with cancer biologists creates collaborative opportunities for drug discovery and the design and synthesis of chemical biology tool compounds (chemical probes) to better elucidate the role of specific proteins and pathways in biology and disease. Two case studies are presented here: (1) the discovery of inhibitors of mer kinase to treat acute lymphoblastic leukemia in children and (2) the discovery of chemical probes targeting epigenetic regulators. These case studies provide lessons in target selection strategies, the requirement for iterative optimization of lead compounds (useful drugs/probes rarely come directly from a screen), and the value of mutually dependent collaborations between medicinal chemists and cancer biologists.