Enzymes, inhibition, substrate kinetics

Kreuzman AJ, Turner JR, Yeh WK (1988) Two distinctive O-methyltransferases catalyzing penultimate and terminal reactions of macrolide antibiotic (tylosin) biosynthesis. Substrate specificity, enzyme inhibition, and kinetic mechanism. J Biol Chem 263 15626-15633... 

The three reversible mechanisms for enzyme inhibition are distinguished by observing how changing the inhibitor s concentration affects the relationship between the rate of reaction and the concentration of substrate. As shown in figure 13.13, when kinetic data are displayed as a Lineweaver-Burk plot, it is possible to determine which mechanism is in effect. 

Enzyme reaction kinetics were modelled on the basis of rapid equilibrium assumption. Rapid equilibrium condition (also known as quasi-equilibrium) assumes that only the early components of the reaction are at equilibrium.8-10 In rapid equilibrium conditions, the enzyme (E), substrate (S) and enzyme-substrate (ES), the central complex equilibrate rapidly compared with the dissociation rate of ES into E and product (P ). The combined inhibition effects by 2-ethoxyethanol as a non-competitive inhibitor and (S)-ibuprofen ester as an uncompetitive inhibition resulted in an overall mechanism, shown in Figure 5.20. 

To refer to the kinetics of allosteric inhibition as competitive or noncompetitive with substrate carries misleading mechanistic implications. We refer instead to two classes of regulated enzymes K-series and V-se-ries enzymes. For K-series allosteric enzymes, the substrate saturation kinetics are competitive in the sense that is raised without an effect on V. For V-series allosteric enzymes, the allosteric inhibitor lowers... 

Substrates may affect enzyme kinetics either by activation or by inhibition. Substrate activation may be observed if the enzyme has two (or more) binding sites, and substrate binding at one site enhances the alfinity of the substrate for the other site(s). The result is a highly active ternary complex, consisting of the enzyme and two substrate molecules, which subsequently dissociates to generate the product. Substrate inhibition may occur in a similar way, except that the ternary complex is nonreactive. We consider first, by means of an example, inhibition by a single substrate, and second, inhibition by multiple substrates. 

Another type of inhibitor combines with the enzyme at a site which is often different from the substrate-binding site and as a result will inhibit the formation of the product by the breakdown of the normal enzyme-substrate complex. Such non-competitive inhibition is not reversed by the addition of excess substrate and generally the inhibitor shows no structural similarity to the substrate. Kinetic studies reveal a reduced value for the maximum activity of the enzyme but an unaltered value for the Michaelis constant (Figure 8.7). There are many examples of non-competitive inhibitors, many of which are regarded as poisons because of the crucial role of the inhibited enzyme. Cyanide ions, for instance, inhibit any enzyme in which either an iron or copper ion is part of the active site or prosthetic group, e.g. cytochrome c oxidase (EC 1.9.3.1). 

In general, this first generation of abzymes obtained from TSAs behave like enzymes, present saturation kinetics, substrate specificity, a stereoselectivity and competitive inhibition phenomena. However the acceleration factors obtained, cat/ ncat> remain weak and are limited in theory by the ratio of the constant of... 

MULTISUBSTRATE SYSTEMS. Wong and Hanes were probably among the first to suggest that alternative substrates may be useful in mechanistic studies. Fromm s laboratory was the first to use and extend the theory of alternative substrate inhibition to address specific questions about multisubstrate enzyme kinetic mechanisms. Huang demonstrated the advantages of a constant ratio approach when dealing with alternative substrate kinetics. 

Enzyme inhibition by an extremely tight-binding inhibi-tor When the substrate(s), regardless of the detailed mode of inhibition, has (have) a negligible effect on the formation of enzyme-inhibitor (E-I) complex, the net result is depletion i.e., the removal of enzyme by the inhibitor from the reaction). The observed kinetic pattern is identical to the simple noncompetitive inhibition case the substrate and the inhibitor do not affect each other s binding, because only V sk is changed due to reduced enzyme concentration, while remains unaltered. 

The initial-rate phase may quickly end if one or more products accumulate to concentrations approaching the respective inhibition constants. In these cases, one may seek to minimize this problem by including an auxiliary enzyme (a) to remove product(s) or (b) to regenerate the substrate concentration. Ideally, the auxiliary enzyme should have a lower value for the product of the primary reaction than the corresponding value for the primary enzyme. See Chemical Kinetics ATP/GTP regeneration... 

The enzyme has been partially purified (70-fold) from 38,000 X 9 supernatant fluid from sheep brain homogenates by Ipata (55-58). Thq enzyme (MW 140,000) is reported to be specific for 5 -AMP and 5 -IMP although the substrate specificity does not appear to have been examined closely. 2 - and 3 -AMP are not hydrolyzed (56). Unlike the enzyme from many sources the brain enzyme does not require divalent cations and indeed Co2+, which stimulates several other 5 -nucleotidases, was inhibitory at 5 mM. The enzyme is strongly inhibited by very low concentrations of ATP, UTP, and CTP (50% inhibition by 0.3 pM ATP) but not by GTP. 2 -AMP, 3 -AMP, and a variety of other nucleoside monophosphates, nucleosides, and sugar phosphates do not inhibit. A kinetic examination of ATP, UTP, and CTP inhibition (56-58) revealed that inhibition curves were sigmoidal, indicating cooperativity between inhibitor molecules and an allosteric type of interaction between inhibitor and protein. The metabolic significance of ATP inhibition is... 

For transporters, relatively low protein expression level and limited transport capacity makes for nonlinear, enzyme-like transport kinetics that is, the transport rate saturates with increasing substrate concentration. This phenomenon is the basis for the competitive interactions generally found for chemicals that are handled by one or more common transporters this is usually manifest as inhibition of the transport of one chemical by a structural analog. The extent to which these competitive interactions are important depends on the concentrations of the chemicals involved, their relative affinities for the common transporter, and their phar-macological/toxicological profiles (effects, effective concentrations, therapeutic index). Competition for transport is discussed below in the context of drug-drug interactions. 

The various kinds of reversible inhibition that have been identified all depend on non-covalent binding, but inhibitors differ in how they act, with consequent differences in their kinetic effects. Figure 8-6 depicts a general scheme for enzyme inhibition of a simple single substrate-single product reaction. 

A different form of inhibition arises when the inhibitor binds to a second site on the enzyme, separate from the active site, and in doing so it modifies the enzyme, inhibiting its activity. This mode of inhibition is termed non-competitive inhibition (Figure 8-8), and unlike in competitive inhibition, there is often no structural similarity between the substrate and inhibitor. The simplest case of non-competitive inhibition, which is illustrated in Figure 8-8, is that the inhibitor binds with equal affinity to the free and substrate-bound forms of the enzyme, and that the inhibitor completely abolishes catalytic activity (fc at = 0). With these assumptions, the kinetic equation takes the form ... 

MichaeUs-Menten kinetics predict that as the concentration of the substrate increases, the rate increases hyperbolically. However, some enzymes exist in which a maximum velocity is obtained at low substrate concentration, but further increases in the substrate concentration lead to a decrease in velocity. This effect is known as substrate inhibition and can eventually lead to complete enzyme inhibition or partial enzyme inhibition. It is thought that substrate inhibition occurs if two substrate molecules bind to the enzyme simultaneously in an incorrect orientation and produce an inactive E S S complex, analogous to that discussed for uncompetitive inhibition. The rate of the enzyme reaction that undergoes substrate inhibition is given by Equation 17, where K represents the... 

The barley leaf ADP-Glc PPase has been purihed to homogeneity (69.3 U/mg), and it shows high sensitivity toward activation by 3-PGA and inhibition by phosphate (78). Substrate kinetics and product inhibition studies in the synthesis direction suggested a sequential Iso Ordered Bi Bi kinetic mechanism (78). ATP or ADP-Glc bind hrst to the enzyme in the synthesis or pyrophosphorolysis direction, respectively, which is similar to the E. coli enzyme (58). 

Competitive inhibitors. A competitive inhibitor often has structural features similar to those of the substrates whose reactions they inhibit. This means that a competitive inhibitor and enzyme s substrate are in direct competition for the same binding site on the enzyme. Consequently, binding of the substrate and the inhibitor are mutually exclusive. A kinetic scheme for competitive inhibition is shown in Equation 17.15. 

Mode of inhibition. The kinetics of an enzyme are measured as a function of substrate concentration in the presence and in the absence of 2 mM inhibitor (I). 

Measurement of the in vitro efficacy of compounds as substrates is usually deduced by comparison of their k JK ratios where is the first-order rate constant for product formation and is the Michaelis equilibrium constant [38]. For those compounds which are classical, reversible inhibitors, K, the dissociation (or inhibition) equilibrium constant, and (kassoc) the rate constant for enzyme inhibition, are the most commonly reported kinetic values. These values may be measured while using either a high-molecular-weight natural substrate or a low-molecular-weight synthetic substrate. For alternate-substrate inhibitors, that is, compounds which form a stable complex (an acyl-enzyme ) that dissociates to enzyme and intact inhibitor or to enzyme and an altered form of the inhibitor, the usually reported value is K, the apparent K. For compounds which irreversibly inactivate the enzyme, the kinetics are usually measured under conditions such that the initial enzyme concentration [E] is much lower than the inhibitor concentration [I] which in turn is much lower than the Ky Under these conditions the commonly reported value is obs/[I]> the apparent... 

Enzyme-substrate complexes have been studied by kinetic analysis, chemical modification, inhibition of enzymes by specific compounds that interact with active sites, detection of characteristic spectral absorption bands during reaction of enzymes with substrates, and X-ray crystallographic analysis of enzymes combined with compounds which are in similar structure to the natural substrates. The interaction between enzymes and substrates has been analyzed by the concepts of lock-and-key" and "induced fit". The former presumes that the substrate surface must fit the enzyme surface like a key in a lock, while the latter refined theory assumes that binding of the substrate induces ( informational changes in the enzyme to provide a better fit. 

Enzyme inhibition data are often presented as IC50, the concentration of the inhibitor to cause 50 percent inhibition at one chosen substrate concentration Kt, the inhibition constant (dissociation constant from the inhibitor-enzyme complex) determined by enzyme kinetic analysis (e.g., Dixon plot) and /Cin lcl, the time-dependent inhibition constant for mechanism-based inhibitors. IC50 values can be estimated from the study described earlier. A positive inhibition, defined as dose-dependent inhibition, with the inhibited activity lower than 50 percent of that of the negative control, will require further experimentation to define Ki for a better evaluation of in vivo inhibitory potential. Further, a study to determine Klwul may be performed to evaluate if the inhibitor acts via covalent binding to the active site of the enzyme, leading to time-dependent irreversible inhibition. 

All ingredients are present in the reaction mixture, which is added to a lipid film, and liposomes are prepared containing all macromolecules (enzymes and DNA or RNA templates) as well as all substrate molecules (nucleotides, for example). Consequently, this procedure has to be performed very quickly otherwise, the enzymatic reaction would mainly occur outside the liposomes and a distinction between product molecules synthesized inside from those produced outside and entrapped later would be difficult to draw. After the formation of liposomes, the enzymes outside the liposomes have to be inhibited by potent inhibitors (inhibitors that do their job even in the presence of substantial amounts of phospholipids) or the liposomal dispersion has to be treated by digestive enzymes. This strategy has basically been applied in the case of the RNA replication by QP replicase inside oleic acid/oleate liposomes" and in the case of the polymerase chain reaction (PCR) inside POPC or POPC/PS liposomes." In the former case, EDTA was added after the formation of the liposomes to inhibit the non-entrapped enzymes (and the kinetics was followed after addition of the EDTA molecules), in the latter case, the non-entrapped DNA template molecules were digested by DNase I before the temperature was raised to 95°C and the polymerization started. 

Also some basic kinetic data of the enzyme should be known, especially Michaelis and inhibition constants. For example, an enzyme suffering substrate inhibition, when used at a high substrate concentration, will exhibit only a little activity, whereas at low concentrations the reaction will run quite well. 

---