We have studied several biosystems comprising a fibrous protein, namely type 1 collagen (COL), which co-assembles with an anti-cancer drug, such as 5-fluorouracil (FLU) or doxorubicin (DOX), to form ordered films on glass or mica substrate, as visualized by atomic force microscopy. The anti-cancer drugs appear to lead to supramolecular collagen structures, with a remarkable nanoscale order, that mimics natural protein assemblies. Direct incorporation of such small molecules into the collagen assemblies represents a step toward rational design of nanostructured materials for a wide range of applications in synthetic biology and medicine, including the design of new drug delivery systems.