Reaction bisubstrate

Such a reaction is termed a bisubstrate reaction. In general, bisubstrate reactions proceed by one of two possible routes ... 

The modality of compounds that inhibit enzymes catalyzing bisubstrate reactions will differ with respect to the two substrates of the reaction, and the pattern of inhibition will depend on the reaction mechanism of the enzyme. Thus, when we use terms like competitive, noncompetitive, or uncompetitive inhibition, we must... 

The example of methotrexate points out that the inhibition modality of dead end inhibitors, with respect to a specific substrate, will depend on the reaction mechanism of the target enzyme. Thus a complete understanding of inhibition mechanism requires an understanding of the underlying reaction mechanism of the target enzyme. A comprehensive discussion of these issues has been provided by Segel (1975). Table 3.6 summarizes the pattern of dead-end inhibition observed for competitive inhibitors of one substrate in the common bisubstrate reaction mecha-... 

Table 3.6 Pattern of dead-end inhibition observed for bisubstrate reactions...

In this chapter we described the thermodynamics of enzyme-inhibitor interactions and defined three potential modes of reversible binding of inhibitors to enzyme molecules. Competitive inhibitors bind to the free enzyme form in direct competition with substrate molecules. Noncompetitive inhibitors bind to both the free enzyme and to the ES complex or subsequent enzyme forms that are populated during catalysis. Uncompetitive inhibitors bind exclusively to the ES complex or to subsequent enzyme forms. We saw that one can distinguish among these inhibition modes by their effects on the apparent values of the steady state kinetic parameters Umax, Km, and VmdX/KM. We further saw that for bisubstrate reactions, the inhibition modality depends on the reaction mechanism used by the enzyme. Finally, we described how one may use the dissociation constant for inhibition (Kh o.K or both) to best evaluate the relative affinity of different inhibitors for ones target enzyme, and thus drive compound optimization through medicinal chemistry efforts. 

We saw in Chapter 3 that bisubstrate reactions can conform to a number of different reaction mechanisms. We saw further that the apparent value of a substrate Km (KT) can vary with the degree of saturation of the other substrate of the reaction, in different ways depending on the mechanistic details. Hence the determination of balanced conditions for screening of an enzyme that catalyzes a bisubstrate reaction will require a prior knowledge of reaction mechanism. This places a necessary, but often overlooked, burden on the scientist to determine the reaction mechanism of the enzyme before finalizing assay conditions for HTS purposes. The importance of this mechanistic information cannot be overstated. We have already seen, in the examples of methotrexate inhibition of dihydrofolate, mycophenolic acid inhibiton of IMP dehydrogenase, and epristeride inhibition of steroid 5a-reductase (Chapter 3), how the [5]/A p ratio can influence one s ability to identify uncompetitive inhibitors of bisubstrate reactions. We have also seen that our ability to discover uncompetitive inhibitors of such reactions must be balanced with our ability to discover competitive inhibitors as well. 

The determination of bisubstrate reaction mechanism is based on a combination of steady state and, possibly, pre-steady state kinetic studies. This can include determination of apparent substrate cooperativity, as described in Chapter 2, study of product and dead-end inhibiton patterns (Chapter 2), and attempts to identify... 

Because mechanism-based inactivators behave as alternative substrates for the enzyme, they must bind in the enzyme active site. Binding of a mechanism-based inactivator is therefore mutually exclusive with binding of the cognate substrate of the normal enzymatic reaction (we say cognate substrate here because for bisubstrate reactions, the mechanism-based inactivator could be competitive with one substrate and noncompetitive or uncompetitive with the other substrate of the reaction, depending on the details of the reaction mechanism). Thus, as the substrate concentration is increased, the observed rate of inactivation should decrease (Figure 8.10) as... 

For bisubstrate reactions that conform to a ternary complex mechanism (see Chapter 3), inactivation should require the presence of the noncognate substrate. 

Almost all enzymes—in contrast to the simplified description given on p. 92—have more than one substrate or product. On the other hand, it is rare for more than two substrates to be bound simultaneously. In bisubstrate reactions of the type A + B C+D, a number of reaction sequences are possible. In addition to the sequential mechanisms (see p.90), in which all substrates are bound in a specific sequence before the product is released, there are also mechanisms in which the first substrate A is bound and immediately cleaved. A part of this substrate remains bound to the enzyme, and is then transferred to the second substrate B after the first product C has been released. This is known as the ping-pong mechanism, and it is used by transaminases, for example (see p.l78). In the Lineweaver— Burk plot (right see p.92), it can be recognized in the parallel shifting of the lines when [B] is varied. 

Depending on the position of the isotopic atom(s) in the labeled substrate or product, various exchanges may be examined. The types of exchanges subject to measurement can be illustrated by considering a bisubstrate reaction ... 

The rates of such bisubstrate reactions can also be analyzed by the Michaelis-Menten approach. Hexokinase has a characteristic Km for each of its substrates (Table 6-6). 

We have introduced kinetics as the primary method for studying the steps in an enzymatic reaction, and we have also outlined the limitations of the most common kinetic parameters in providing such information. The two most important experimental parameters obtained from steady-state kinetics are kcat and kcat/Km. Variation in kcat and kcat/Km with changes in pH or temperature can provide additional information about steps in a reaction pathway. In the case of bisubstrate reactions, steady-state kinetics can help determine whether a ternary complex is formed during the reaction (Fig. 6-14). A more complete picture generally requires more sophisticated kinetic methods that go beyond the scope of an introductory text. Here, we briefly introduce one of the most important kinetic approaches for studying reaction mechanisms, pre-steady state kinetics. 

FIGURE 6-13 Common mechanisms for enzyme-catalyzed bisubstrate reactions, (a) The enzyme and both substrates come together to form a ternary complex. In ordered binding, substrate 1 must bind before substrate 2 can bind productively. In random binding, the substrates can bind in either order. 

FIGURE 6-14 Steady-state kinetic analysis of bisubstrate reactions. 

In practice, uncompetitive and mixed inhibition are observed only for enzymes with two or more substrates—say, Sj and S2—and are very important in the experimental analysis of such enzymes. If an inhibitor binds to the site normally occupied by it may act as a competitive inhibitor in experiments in which [SJ is varied. If an inhibitor binds to the site normally occupied by S2, it may act as a mixed or uncompetitive inhibitor of Si. The actual inhibition patterns observed depend on whether the and S2-binding events are ordered or random, and thus the order in which substrates bind and products leave the active site can be determined. Use of one of the reaction products as an inhibitor is often particularly informative. If only one of two reaction products is present, no reverse reaction can take place. However, a product generally binds to some part of the active site, thus serving as an inhibitor. Enzymologists can use elaborate kinetic studies involving different combinations and amounts of products and inhibitors to develop a detailed picture of the mechanism of a bisubstrate reaction. 

Km and Umax have different meanings for different enzymes. The limiting rate of an enzyme-catalyzed reaction at saturation is described by the constant kcat, the turnover number. The ratio kcat/Km provides a good measure of catalytic efficiency. The Michaelis-Menten equation is also applicable to bisubstrate reactions, which occur by ternary-complex or Ping-Pong (double-displacement) pathways. 

Scheme 12.21 Self-assembling catalysis via a ternary complex involving a bisubstrate reaction template.30...

The general rule for writing the rate equation according to the quasi-equilibrium treatment of enzyme kinetics can be exemplified for the random bisubstrate reaction with substrates A and B forming products P and Q (Figure 7.1), where KaKab = KbKba and KpKpq = KqKqp. 

TABLE 7.2. Cleland Nomenclature for Bisubstrate Reactions Exemplified ... 

Examples of the bisubstrate reactions according to Cleland nomenclature are listed in Table 7.2. 

In the sequential mechanism, all substrates must bind to the enzyme before any product is released. Consequently, in a bisubstrate reaction, a ternary complex of the enzyme and both substrates forms. Sequential mechanisms are of two... 

While almost all synthetically useful catalytic reactions involve two reactants it will be best to first illustrate this graphical approach using a unimolecular process and the way it can be affected by inhibitors. After this some different types of bisubstrate reactions will be discussed. More detailed analyses of the kinetics of multisubstrate systems have been published in texts 13 and... 

Typically, the kinetics of bisubstrate reactions are studied by measuring the initial reaction rates over a range of concentrations of one substrate. A, while holding the concentration of the second substrate, B, constant and doing this for several fixed values of [B]. If specific concentrations of A are used for all of the reaction series, these same rates can also be used to examine changes in reaction rate when [B] is varied at fixed concentrations of A for several values of [A]. 

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