New drugs are the products of a long drug development process, the first step of which is often the discovery of a new enzyme inhibitor. There are two principle approaches of discovering these inhibitors.
The first general method is rational drug design based on mimicking the transition state of the chemical reaction catalysed by the enzyme. The designed inhibitor often closely resembles the substrate, except that the portion of the substrate that undergoes chemical reaction is replaced by a chemically stable functional group that resembles the transition state. Since the enzyme has evolved to stabilise the transition state, transition state analogues generally possess higher affinity for the enzyme compared to the substrate, and therefore are effective inhibitors.
The second way of discovering new enzyme inhibitors is high-throughput screening of large libraries of structurally diverse compounds to identify hit molecules that bind to the enzyme. This method has been extended to include virtual screening of databases of diverse molecules using computers, which are then followed by experimental confirmation of binding of the virtual screening hits. Complementary approaches that can provide new starting points for inhibitors include fragment-based lead discovery and DNA Encoded Chemical Libraries (DEL).
Hits from any of the above approaches can be optimised to high affinity binders that efficiently inhibit the enzyme. Computer-based methods for predicting the binding orientation and affinity of an inhibitor for an enzyme such as molecular docking and molecular mechanics can be used to assist in the optimisation process. New inhibitors are used to obtain crystallographic structures of the enzyme in an inhibitor/enzyme complex to show how the molecule is binding to the active site, allowing changes to be made to the inhibitor to optimise binding in a process known as structure-based drug design. This test and improve cycle is repeated until a sufficiently potent inhibitor is produced.