Once the empirical and molecular formulas of the active
compounds are determined, then their structural formulas
are sought. At that point, synthetic work can begin. The
chemist can identify compounds in the material that have
medicinal value and fi nd a way to synthesize them, or prepare
them in the laboratory, so that they can be made available
in large quantities.
In rational drug design, the chemist begins with the
tumor or organism that the drug is intended to eradicate.
Virtually all processes in living cells depend on specifi c
enzymes, types of proteins with very large molecules that
have specifi c shapes. Usually there is an active site on the
enzyme into which only specifi c molecules can fi t and
react. If the enzymes that control the growth of parasites
or bacteria can be identifi ed and their shapes known, compounds
that fi t into the active sites and block the reactions
can be designed. The chemist taking this route begins by
identifying key enzymes in the bacterium or parasite. Then
the molecular structure of the enzyme is determined. A
computer program is used to design molecules with structures
that fi t into the active site. Structure–activity relationships
(SAR) are investigated to fi nd out which aspects
of the structure are important to the activity of the drug.
The new compounds are synthesized, and their effects and
side effects are tested.