In the past, drugs have been identified by screening vast libraries of small molecules against whole tissues or animals in order to find one which affects the disease under investigation. As a generalisation, diseases are caused by proteins which are either overworking, underworking or incorrectly working. There are, of course, other causes for specific diseases, but the majority result from the first example.
The majority of pharmaceutical drugs are small molecule compounds which bind to a specific
protein and inhibit it from functioning properly. Classical pharmaceutical research involved
screening vast libraries of small molecule compounds across tissues or even entire organisms
and hoping to observe an effect. Modern research focuses on a specific protein target, allowing researchers to identify more specific compounds, ones with greater potency and fewer side effects. To visualise it easier: a protein and its normal substrate can be considered a lock and a
key – the substrate fits exactly in the three dimensional shape of the protein. A small molecule which can also fit the lock will block it, thereby inhibiting the protein. The better the fit in the lock, the stronger the inhibition and the more specific the compound is for this particular protein. Knowing the exact three dimensional structure of the protein is, therefore, a great tool in helping to design more specific drugs.