An enzyme generally binds moderately well to its substrate(s), and it may or may not bind well to its product(s).
But an enzyme will generally bind really, really well to substrates that are partway to being converted into products.
In other words, an enzyme preferentially binds to its substrates/products that are in a transition state.
Strong binding to the transition state serves to stabilize the transition state and to lower the activation energy of the reaction that the enzyme catalyzes, as in the image
The recognition that enzymes preferentially bind to ligands in their transition state has been extremely useful in the development of transition state analogs that target specific steps in bacterial or viral metabolism. Transition state analog inhibitors used as drugs include the neuraminidase inhibitor oseltamivir (used in treatment of flu) and the HIV protease inhibitor saquinavir (used in the treatment of AIDS).
The following illustration on the left shows the transition state in the enzymatic action of , which is an important target for drug discovery because it is specific to bacteria. The transition state has a particular configuration of 5'-methylthioadenosine and S-adenosylhomocysteine, the geometry and/or electronic configuration of which can be mimicked by transition state analogs
