Modern medicine is not going to wait hundreds, let alone thousands, of years for the right fungus to fall on bacteria growing on a plate of agar accidentally left uncovered on a window-sill as happened to Fleming and led to the discovery of penicillin. Designing the drug the medical profession wants, to act in a particular way in the human body, can be so much surer and faster today, using a combination of chemistry and computers.
Enzymes control all functions within living organisms.
On each enzyme is an active site that is switched on by the presence of the enzyme's natural substrate, the substance upon which the enzyme acts. Blocking the active site inhibits the enzyme and this is how most drugs work. Groups of enzymes performing similar functions or analogous enzymes in different organisms have similar active sites, so a drug that is not specific enough blocks active sites on a whole range of enzymes, causing side-effects. Therefore, structure is critical in creating a drug molecule that fits the enzyme's active site like hand and glove. The designer drug, blocking only that enzyme and no other, is free of these side-effects.