IMPORTANT TYPES OF MOLECULAR ALTERATION 255 



are not known, since for two inhibitors: 



AF, — AF, = 1.422 log [' il ~ \'l (2-10) 



ii (1 —I2) 



if(Ij) = (l2)- 



It is easy to derive an expression for the relationship between the true 



AF difference and the apparent JF difference for two inhibitors when the 



sole factor involved is the ionization of the inhibitors. If we designate the 



true free energy of binding as AF and the apparent free energy of binding 



as AF', the difference in the true binding energies for the two inhibitors 



will be AFi — AF^, and the difference in the apparent binding energies 



will be AF^ — AF^'. The relationship between these for analogs that are 



singly ionizing weak acids is: 



(AF, - AF,) = {AF,' - AF,') - 1.422 log \ + [|h^)/^?] ^^'^^^ 



It is therefore possible to correct for the pH effect if the p/C^'s of the inhibi- 

 tors are known and the true interaction energy difference may be obtained. 



IMPORTANT TYPES OF MOLECULAR ALTERATION 

 PRODUCING INHIBITING ANALOGS 



A substrate or coenzyme might generally be considered to have three 

 different types of molecular region: (1) groups involved primarily in the 

 binding to the enzyme, (2) groups involved in the catalytic reaction, and 

 (3) groups or regions not directly involved in either binding or reaction. 

 There is overlap between these in some cases, of course, because the groups 

 undergoing chemical change usually participate to a certain extent in the 

 binding. Furthermore, some substrates, such as succinate, do not possess 

 the third type of group, all of the molecule being directly involved in bind- 

 ing and reaction. The properties of a substance produced by altering a single 

 group or region of a substrate wiU depend on the type of group or region 

 that is modified, that is, its function in the reaction of the substrate with 

 the enzyme. A change in a binding group will usually alter the interaction 

 energy in the combination of the substance with the enzyme and may or 

 may not affect the susceptibility to chemical reaction, whereas a change in 

 a group directly involved in the catalysis will generally reduce the reactivity 

 without necessarily modifying the binding to the enzyme. It is also evident 

 that a change in the third type of neutral group will not be so likely to 

 alter the behavior of the substrate, unless such a change in some way 

 secondarily modifies the interactions of the other groups. The aim in the 

 design of analogs for enzyme inhibition is to produce a compound which 

 will bind reasonably tightly to the enzyme (preferably more tightly than 



