The goal of chemotherapy is to exploit a biochemical difference between the disease process and the host tissue in order to interfere selectively with the disease process. Knowledge from x-ray crystallographic analysis of enzymes and molecular modeling with modern computer software allows scientists to design drugs that fit into important, specific regions of enzymes (such as the active site) and inactivate them.

5-Fluorodeoxyuridine monophosphate (FdUMP) is a mechanism-based inhibitor. Irreversible binding of the substance to thymidylate synthase occurs only in the presence of 5,10-methylenetetrahydrofolate, a cofactor for the reaction catalyzed by thymidylate synthase (Figure 22.18). Crystallographic analysis of thymidylate synthase with dUMP and an analog of 5,10-methylenetetrahydrofolate (that could not be acted on by the enzyme) revealed that thymidylate synthase normally makes a transient covalent bond in the process of catalyzing the reaction. Apparently the structure of FdUMP is similar enough to dUMP to form the covalent bond with the enzyme, but different enough that the covalent bond doesn't break down again. Thus, the enzyme is trapped in a form that cannot react with dUMP; its intended substrate traps the enzyme-substrate covalent bond and prevents it from breaking down.

Unfortunately, the 5-fluorouracil used to make FdUMP can be incorporated into RNA by salvage routes normally used for uracil, thereby interfering with the function of messenger RNA in both cancer and normal cells. As a result, molecular modeling is currently being employed to design coenzymes that replace 5,10-methylenetetrahydrofolate and cause dUMP's transient covalent bond to become trapped during catalysis.