Structure based drug design is the way drugs are developed nowadays.
In a nutshell, it requires a complete knowledge of the biochemical target: size, 3D conformation, functional groups, stereo-electronic properties, ect.
This gives you the opportunity, with the help of data-bases and specific computer programmes, to design a pharmacophore, which is not a lead molecule, but a 'backbone', a minimum structure: it just displays the fundamental functions for the linkage between the drug and the target and the spatial collocation of the functions.
Then from the pharmacophore you have to work out the molecule(s): syntheses are commonly based on the development of already-existing molecules, but there is also the
de novo design (it's Latin: you know, Americans love it!
)
De novo design means trying to invent a molecule only from the pharmacophore.