Nano drugs phenomenal advances in nanotechnology and nanoscience have been accompanied by exciting progress in the de novo design of nano-sized drugs. Nanoparticles with their large space of structural amenability and excellent mechanical and electrical properties have become ideal candidates for high efficacy nanomedicines in both diagnostics and therapeutics. The therapeutic nanomedicines can be further categorized into nanoparticle drug delivery for conventional drugs and nano drugs and nanobots with direct curing of target diseases. Here we review some of the recent advances in the de novo design of nano drugs, with an emphasis on the molecular level understanding of their interactions with biological systems including key proteins and cell membranes. We also include some of the latest advances in the development of nanocarriers with both passive and active targeting for completeness. These studies may shed light on a better understanding of the molecular mechanisms behind these nano drugs, formulations of drugs, and also provide new insights and direction for the future design of nanomedicines.