Enzyme-Inhibitor Interactions

Matrix metalloproteinase structural studies of the P -side inhibitors to date show a common set of inhibitor-enzyme interactions. This can be attributed primarily to the strong directional zinc-binding forces. Further stabilizing forces from the backbone hydrogen-bonding patterns common to a (3 sheet allow for minor adjustments due to the zinc interactions to be made while maintaining a common pharmacophore. 

SA Biller, MJ Sofia, B DeLange, C Foster, EM Gordon, T Harrity, LC Rich, CP Ciosek. The first potent inhibitor of squalene synthase a profound contribution of an ether oxygen to inhibitor-enzyme interaction. J Am Chem Soc 113 8522-8527, 1991. 

Thirty 5 -thiourea-substituted a-thymidine analogues used to develop receptor-independent 4D-QSARmodels ( 3 = 0.83) for thymidine monophosphate kinase inhibitors. The model was also put into the context of reported crystallographically characterized inhibitor/enzyme interactions... 

A high degree of structural specificity for inhibitor-enzyme interaction was demonstrated in studies where several isoquinoline and pyridine derivatives were tested with the reductase (150—155). The partially competitive relationship between inhibitor and dithiol substrate and the specificity of inhibitor binding are consistent with a model in which an inhibitor-iron complex binds, or free inhibitor coordinates with holo-enzyme, at or adjacent to a site normally occupied by dithiol substrate. Studies of this class of inhibitors have not only served as a probe into the structure of the mammalian reductases but also as a measure of differ-... 

Enzyme inhibitors are classified in several ways. The inhibitor may interact either reversibly or irreversibly with the enzyme. Reversible inhibitors interact with the enzyme through noncovalent association/dissociation reactions. In contrast, irreversible inhibitors usually cause stable, covalent alterations in the enzyme. That is, the consequence of irreversible inhibition is a decrease in the concentration of active enzyme. The kinetics observed are consistent with this interpretation, as we shall see later. 

Hannongbua S (2006) Structural Information and Drug-Enzyme Interaction of the Non-Nucleoside Reverse Transcriptase Inhibitors Based on Computational Chemistry Approaches. 4 55-84... 

It is worth noting here that inhibitors that interact with enzyme active site functionalities in ways that mimic the structure of covalent intermediates of catalysis can bind with very high affinity. This was seen in Chapter 1 with the example of statine-and hydroxyethylene-based inhibitors of aspartic proteases other examples of this inhibitor design strategy will be seen in subsequent chapters of this text. 

Until now our discussions of enzyme inhibition have dealt with compounds that interact with binding pockets on the enzyme molecule through reversible forces. Hence inhibition by these compounds is always reversed by dissociation of the inhibitor from the binary enzyme-inhibitor complex. Even for very tight binding inhibitors, the interactions that stabilize the enzyme-inhibitor complex are mediated by reversible forces, and therefore the El complex has some, nonzero rate of dissociation—even if this rate is too slow to be experimentally measured. In this chapter we turn our attention to compounds that interact with an enzyme molecule in such a way as to permanendy ablate enzyme function. We refer to such compounds as enzyme inactivators to stress the mechanistic distinctions between these molecules and reversible enzyme inhibitors. 

The concentration of inhibitor, causing 50% inhibition of enzyme activity (I50/ M) was calculated. In many cases the enzyme-inhibitor rate interaction constant (k2 M 1 min 1) was calculated according to the formula ... 

In enzyme catalyzed reactions the inhibitor may interact in various ways either reversibly or irreversibly. In irreversible inhibition, the inhibitor associates with enzyme and block the active site of the enzyme or form a unstable complex with enzyme and thus retards the rate of reaction. 

To understand the inhibition of a-amylase by peptide inhibitors it is crucial to first understand the native substrate-enzyme interaction. The active site and the reaction mechanism of a-amylases have been identified from several X-ray structures of human and pig pancreatic amylases in complex with carbohydrate-based inhibitors. The structural aspects of proteinaceous a-amylase inhibition have been reviewed by Payan. The sequence, architecture, and structure of a-amylases from mammals and insects are fairly homologous and mechanistic insights from mammalian enzymes can be used to elucidate inhibitor function with respect to insect enzymes. The architecture of a-amylases comprises three domains. Domain A contains the residues responsible for catalytic activity. It complexes a calcium ion, which is essential to maintain the active structure of the enzyme and the presence of a chloride ion close to the active site is required for activation. 

It was originally assumed that in LADH the zinc existed in an octahedral form with six bonds available for coordination, until in 1967 Vallee and co-workers showed that the enzyme contained two different types of zinc atom.13773 Loss of two zinc atoms from the enzyme resulted in loss of catalytic activity but maintained the tertiary structure. It was postulated from this that one metal ion per subunit played a role maintaining the tertiary structure, while the other zinc functioned in a catalytic role. Only two of the zinc ions in the liver enzyme interact with the inhibitors 1,10-phenanthroline and 2,2 -bipyridyl, thus demonstrating the different chemical reactivities of the zinc ions.1378 It was also shown that one zinc per subunit could be selectively exchanged or removed by dialysis. This modified enzyme containing one zinc per subunit did not bind 1,10-phenanthroline, hence the catalytic zinc is removed first during dialysis.1379 The second zinc atom can be selectively removed in preference to the catalytic zinc, by carboxymethylation followed by dialysis.1377 ... 

Competitive, reversible inhibitors bind the active site of the enzyme and therefore block substrate-enzyme interactions. The inhibitor (I) and substrate may not bind simultaneously (Scheme 4.11). In something of a chemical love triangle, the enzyme s binding ability is split between two molecules, the substrate and inhibitor. Therefore, the effective affinity of the enzyme for the substrate alone drops. Km of the substrate will A... 

Schemes 4.2 and 4.4 are cartoon-type diagrams of inhibitor-enzyme-substrate interactions. Draw a related diagram that describes how indole (4.13) can behave as either a pure or mixed noncompetitive inhibitor for a-chymotrypsin depending on the substrate. 

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