Inhibitor binding kinetic studies

Kinetics is the branch of science concerned with the rates of chemical reactions. The study of enzyme kinetics addresses the biological roles of enzymatic catalysts and how they accomplish their remarkable feats. In enzyme kinetics, we seek to determine the maximum reaction velocity that the enzyme can attain and its binding affinities for substrates and inhibitors. Coupled with studies on the structure and chemistry of the enzyme, analysis of the enzymatic rate under different reaction conditions yields insights regarding the enzyme s mechanism of catalytic action. Such information is essential to an overall understanding of metabolism. 

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). 

Crystallographic analysis of a number of PNP inhibitor complexes revealed significant displacement of the inhibitors. These displacements appear to be the result of close contacts between the inhibitor and the ion in the phosphate binding site. Sulfate ions occupy the phosphate site in PNP crystals as they are grown from ammonium sulfate solution. These inhibitors were more potent when the binding was measured in 1 mMphosphate solution rather than in 50 mMphosphate. Kinetic studies showed that these inhibitors were competitive not only with inosine but also with phosphate, in keeping with the above observation. 

Inhibition studies involving ALR2 have indicated noncompetitive inhibition for virtually all compounds examined to date when the forward (reduction) reaction is monitored. This mode of inhibition is often interpreted as meaning that the inhibitor binds to a site on the enzyme that is independent of the catalytic site. Kinetic and competition studies have both led to this conclusion in the case of ALR2 [24,25]. The crystal structure of the enzyme complexed with both the NADPH cofactor and zopolrestat, however, clearly shows the inhibitor occupying the region directly above the nicotinamide of the NADPH and, therefore, the active site (Figures 5, 6, and 7). 

Additional information <1, 7-9, 12-17, 21> (<7> inhibitory effect of phosphonate analogues of 1,3-diphosphoglycerate, overview [49] <21> no effect by glucose 6-phosphate, fructose 6-phosphate, fructose 1,6-phosphate, pyruvate, phosphoenolpyruvate and lactate [70] <13> double-inhibition studies, kinetics, modeling of inhibitor binding, e.g. phosphate [55] <13> enzyme is regulated by multivalent anions, overview [55] <8> no inhibition by Hg [25] <1,7,9,12-17> yeast enzyme is insensitive to thiol reagents [17]) [17, 25, 49, 55, 70]... 

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. 

The enzyme from B. stearothermophilus is an a4 tetramer of subunit Mr 33 900. Early kinetic studies indicated that the enzyme acts in a manner that is qualitatively consistent with an MWC two-state model. The enzyme acts as a A system i.e., both states have the same value of kcal but different affinities for the principle substrate. In the absence of ligands, the enzyme exists in the T state that binds fructose 6-phosphate more poorly than does the R state. In the absence of ADP, the binding of fructose 6-phosphate is highly cooperative, and h = 3.8. The positive homotropic interactions are lowered on the addition of the allosteric effector ADP, with h dropping to 1.4 at 0.8-mM ADP.52 ADP thus binds preferentially to the R state. The allosteric inhibitor phosphoenolpyruvate binds preferentially to the T... 

These were differently affected by different procedures. For example, when the enzyme was activated at 55°, the increment in ki was slight, but k2 increased 3.5-fold. Similarly, in the presence of EDTA, fc, and k2 values decreased independently, suggesting that the sites for both activities were different. Center and Behai (5) found that with the P. mirabilis enzyme, cyclic 2, 3 -UMP competitively inhibited the hydrolysis of bis(p-nitrophenyl) phosphate. The Ki was 40 pAf very close to the Km for the cyclic nucleotide (Km, 75 yM) which indicated that the two compounds could serve as alternate substrates being hydrolyzed at the same active site. In contrast, 3 -AMP was a mixed inhibitor of cyclic 2, 3 -UMP and bis(p-nitrophenyl) phosphate hydrolysis. Adenosine was a mixed inhibitor of bis(p-nitrophenyl) phosphate hydrolysis but a competitive inhibitor of 3 -AMP hydrolysis. From such kinetic studies Center and Behai (5) suggested that two separate and adjacent sites A and B are involved in the hydrolysis of the diester and phos-phomonoester substrates. Site A serves as a binding site for hydrolysis of ribonucleoside 2, 3 -cyclic phosphates and together with site B catalyzes the hydrolysis of the diester bond. During this reaction 3 -... 

Reversible inhibition occurs rapidly in a system which is near its equilibrium point and its extent is dependent on the concentration of enzyme, inhibitor and substrate. It remains constant over the period when the initial reaction velocity studies are performed. In contrast, irreversible inhibition may increase with time. In simple single-substrate enzyme-catalysed reactions there are three main types of inhibition patterns involving reactions following the Michaelis-Menten equation competitive, uncompetitive and non-competitive inhibition. Competitive inhibition occurs when the inhibitor directly competes with the substrate in forming the enzyme complex. Uncompetitive inhibition involves the interaction of the inhibitor with only the enzyme-substrate complex, while non-competitive inhibition occurs when the inhibitor binds to either the enzyme or the enzyme-substrate complex without affecting the binding of the substrate. The kinetic modifications of the Michaelis-Menten equation associated with the various types of inhibition are shown below. The derivation of these equations is shown in Appendix S.S. 

This mechanism is consistent with a number of observations. Kinetic studies on prolyl 4-hydroxylase [223] and thymine hydroxylase (EC 1.14.11.6) [224] suggest that cofactor binds first, followed by 02. The bound 02 appears to have superoxide character, as superoxide scavengers are competitive inhibitors of 02 consumption [225,226], It is also clear that the oxidative decarboxylation of the keto acid is a distinct phase of the mechanism from the alkane functionalization step, as these two phases can be uncoupled, particularly when poor substrate analogs are employed [227-229], Evidence for an Fe(IV) = 0 intermediate derives from studies with substrate analogs. Besides the hydroxylation of the 5-methyl group of thymine, thymine hydroxylase can also catalyze ally lie hydrox-ylations, epoxidation of olefins, oxidation of sulfides to sulfoxides, and N-de-... 

The compounds potently inhibit factor Xa in vitro with reversible binding kinetics and are able to inhibit not only free but also prothrombinase-bound factor Xa (Ki 41 nM, 0.1 I nM, and 0,5 nM, respectively) (58-60), In contrast, no direct effect on platelet aggregation has been described (60-62), Antithrombotic activity in arterial and venous thrombosis models has been demonstrated and it has a reduced effect on hemorrhage in comparison to standard therapy (58,60,63). Factor Xa inhibitors are able to reduce the endogenous thrombin potential in platelet-poor as well as in platelet-rich plasma (64,65). Thus, thrombin generation seems to be a suitable biomarker for clinical evaluation and has been evaluated in phase I studies (66,67). 

Very early kinetic studies by Hehre30 showed that sucrose became a substrate inhibitor above 200 mM, and this observation was verified by several other studies.31 103-107 Substrate inhibition at relatively high sucrose concentrations has been interpreted to be due to the binding of sucrose at an allosteric site to effect a... 

The C-cluster of carbon monoxide dehydrogenase is the active site for the oxidation of CO to CO 2. This conclusion is based on rapid kinetic studies in which changes in the spectra of Cluster C undergo changes at rates commensurate with the rate of CO oxidation (Kumar et al., 1993). In addition, cyanide, which is a relatively specific inhibitor of CO oxidation, binds specifically to Cluster C (Anderson et al., 1993). 

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