The problems faced by a medication designer are complex. First, the drug has to bypass the body's self-protective mechanisms. If a medicine is to be taken by mouth, it must somehow be insulated from the strongly acid environment of the stomach (in general, drugs must pass through the stomach before they can be absorbed; very few materials besides alcohol are taken up from the stomach itself). Some drugs are naturally stable in an acid environment, but many others need to be protected by a covering, which then must fall apart and release its contents once the drug reaches the alkaline intestine. Most drugs must then be absorbed through the wall of the intestine—another hurdle. And even after a medicine has passed through this wall, blood must carry it to the site where it is active. This is hard because many organs are protected by their own barriers.

Next, concentration of the drug at the target site must be high and sustained enough to be effective. Meanwhile the body, desperate to protect itself against potentially toxic materials, is frantically trying to dump the medication overboard, usually via the kidneys or the liver. Finally, medication designers have to worry about cost, palatability, toxicity, side effects, and interactions with other medications.