Are there limits to enzyme-inhibitor binding discrimination? Inferences from the behavior of nucleoside deaminases

An enzyme can enhance the rate of a reaction only to the extent that it binds the altered substrate in the transition state (S not equal to) more tightly than it binds the substrate in the ground state. Inhibitors that resemble S not equal to can be used to stop an enzyme from working, probe its mechanism of action and obtain exact structural information about intermediates in catalysis. In S not equal to analog inhibitors of adenosine and cytidine deaminases, a single hydroxyl group appears to make extremely large contributions to binding affinity. The magnitude of this contribution becomes even more striking when differences in free energy of solvation by water are taken into account. Other results, obtained by deleting individual binding determinants, indicate the operation of remarkable levels of cooperativity and suggest that if every group is in exactly the right position and is part of an inflexible structure, then a single substituent or H-bond can produce very large increases in binding affinity. Some implications for inhibitor design are considered.