Enzymatic reaction inhibitors

Compounds that reduce the rate of a reaction are called inhibitors (I). Inhibition can be brought about by a wide variety of mechanisms. In enzymatic reactions, inhibitors can be classified as either irreversible or... 

The three most common types of inhibitors in enzymatic reactions are competitive, non-competitive, and uncompetitive. Competitive inliibition occurs when tlie substrate and inhibitor have similar molecules that compete for the identical site on the enzyme. Non-competitive inhibition results in enzymes containing at least two different types of sites. The inhibitor attaches to only one type of site and the substrate only to the other. Uncompetitive inhibition occurs when the inhibitor deactivates the enzyme substrate complex. The effect of an inhibitor is determined by measuring the enzyme velocity at various... 

It is revealing to compare the equation for the uninhibited case. Equation (14.23) (the Michaelis-Menten equation) with Equation (14.43) for the rate of the enzymatic reaction in the presence of a fixed concentration of the competitive inhibitor, [I]... 

Cheng, Y. C., andPrasoff, W. H. (1973). Relationship between the inhibition constant (Ki) and the concentration of inhibitor which causes 50 percent inhibition (150) of an enzymatic reaction. Biochem. Pharmacol. 22 3099—3108. 

There are other substrates for the E. coli Met(0) peptide reductase, one of which is Met(0)-a-l-PI. The native protein is the major serum elastase inhibitor that functions by forming a binary complex with elastase which inhibits its activity. Met(0)-a-l-PI, on the other hand, which can be formed by treatment of the protein with TV-chlorosuccinimide, cannot form a complex with elastase and therefore is not able to inhibit elastase activity117,118. Table 6 shows, however, that when Met(0)-a-l-PI is incubated in the presence of Met(0)-peptide reductase and dithiothreitol the protein regains its ability to form a complex with elastase and inhibit elastase activity119. Similar to results found with Met(0)-L12 reduced thioredoxin could replace the dithiothreitol as reductant in the enzymatic reaction. 

Each of these compounds, 53-56, was shown to be a very effective competitive inhibitor of the enzyme with respect to the fructose 1,6-diphosphate, whereas several other analogs, including acyclic structures, had no effect. These and other results suggest that the furanose form of the sugar diphosphate is the active form in the enzymatic reaction (105). More recent studies using rapid quenching techniques and C-nmr measurements have confirmed this hypothesis and indicate that the enzyme uses the a anomer 52 much more rapidly than the 3 anomer 50 and probably uses the a anomer exclusively (106). 

As we have seen before, the enzymatic reaction begins with the reversible binding of substrate (S) to the free enzyme ( ) to form the ES complex, as quantified by the dissociation constant Ks. The ES complex thus formed goes on to generate the reaction product(s) through a series of chemical steps that are collectively defined by the first-order rate constant kCM. The first mode of inhibitor interaction that can be con-... 

Enzymatic reactions are influenced by a variety of solution conditions that must be well controlled in HTS assays. Buffer components, pH, ionic strength, solvent polarity, viscosity, and temperature can all influence the initial velocity and the interactions of enzymes with substrate and inhibitor molecules. Space does not permit a comprehensive discussion of these factors, but a more detailed presentation can be found in the text by Copeland (2000). Here we simply make the recommendation that all of these solution conditions be optimized in the course of assay development. It is worth noting that there can be differences in optimal conditions for enzyme stability and enzyme activity. For example, the initial velocity may be greatest at 37°C and pH 5.0, but one may find that the enzyme denatures during the course of the assay time under these conditions. In situations like this one must experimentally determine the best compromise between reaction rate and protein stability. Again, a more detailed discussion of this issue, and methods for diagnosing enzyme denaturation during reaction can be found in Copeland (2000). 

In Chapter 3 we saw that inhibitors of different modalities respond differently to the concentration of substrate used in an enzymatic reaction. Recall that the apparent affinity of the free enzyme for substrate was diminished in the presence of a competitive inhibitor, and vice versa, the apparent affinity of a competitive inhibitor could be abrogated at high substrate concentrations. On the other hand, the appar-... 

Figure 5.3 A convenient scheme for performing an inhibitor titration in 96-well format. Four compounds (1-4) are assessed in duplicate at each of 11 inhibitor concentrations. The inhibitor concentrations follow a threefold serial dilution from a maximum concentration of 1000 (molarity units nM, LlM, etc.). The right most column of wells is reserved for control samples. In this illustration four of the wells of column 12 are used for zero inhibitior positive controls, and the other four are used to establish the assay background as negative controls. Negative controls could represent any sample for which one knows that the enzymatic reaction has be abrogated. For example, the negative control wells could contain all of the reaction mixture components except the enzyme. See Chapter 4 for other potential forms of negative controls.

Figure 6.2 Effect of preincubation time with inhibitor on the steady state velocity of an enzymatic reaction for a very slow binding inhibitor. (A) Preincubation time dependence of velocity in the presence of a slow binding inhibitor that conforms to the single-step binding mechanism of scheme B of Figure 6.3. (B) Preincubation time dependence of velocity in the presence of a slow binding inhibitor that conforms to the two-step binding mechanism of scheme C of Figure 6.3. Note that in panel B both the initial velocity (y-intercept values) and steady state velocity are affected by the presence of inhibitor in a concentration-dependent fashion.

Figure 6.19 Fractional velocity for the enzymatic reaction of COX2 as a function of preincubation time with varying concentrations of the slow binding inhibitor DuP697. The lines drawn through the data represent the best fits to Equation (6.4).

If more than one substrate participates in an enzymatic reaction, the kinetic effects of an inhibitor can be quite complex. In this case, rules formulated by Cleland (36) are useful in gaining a qualitative picture of the inhibition patterns to be expected of a given mechanism. 

In this section, we present some recent applications of DFT to the study of enzymatic reactions of pharmaceutical interest. One of the major aims of these studies was to identify TS features that, because the biological targets investigated are involved in the pathogenesis of diseases, could be exploited when designing inhibitors of these enzymes. 

The transesterification of cocaine to cocaethylene is an enzymatic reaction catalyzed by microsomal carboxylesterases and blocked by inhibitors of serine hydrolases [124][125], In Chapt. 3, we have discussed the mechanism of serine hydrolases, showing how a H20 molecule enters the catalytic cycle to hydrolyze the acylated serine residue in the active site of the enzyme. In the case of cocaine, the acyl group is the benzoylecgoninyl moiety (Fig. 7.9,d ), which undergoes esterification with ethanol according to Steps e and/ (Fig. 7.9). 

Enzymatic reactions can be impeded by the addition of exogenous molecules. This is how drugs are used to control biochemical reactions, and most drugs are used for inhibitory functions. Drugs may function as competitive inhibitors or as noncompetitive inhibitors. Competitive inhibitors compete with the substrates for binding to the active sites, whereas noncompetitive inhibitors bind to another location (allosteric site) but affect the active site and its consequential interactions with the substrates. Some drugs used as enzyme inhibitors are the following ... 

Drugs are also used to inhibit the enzymatic reactions of foreign pathogens that enter the human body. An example is the use of reverse transcriptase inhibitor and protease inhibitor for combating the human immunodeficiency virus (HIV), as shown in Exhibit 2.12. Some new inhibitors are used to block HIV from attaching to the human cell, CD4, thus stopping replication and infection of other cells, as presented in Exhibit 2.13. 

---