Active site-directed enzyme

VI. Conformationally Restricted Active-Site-Directed Enzyme Inhibitors... 

VI. CONFORMATIONALLY RESTRICTED ACTIVE-SITE-DIRECTED ENZYME INHIBITORS... 

W-R Shieh. Part I. Studies on the active site-directed enzyme inhibitors of soybean lipoxygenase. Part n. Purification and studies on the [i-keto ester reductases from baker s yeast. Ph.D thesis. University of Wisconsin, Madison, WI, 1987. 

Affinity Labels. Active site-directed, irreversible inhibitors or affinity labels are usually substrate analogues that contain a reactive electrophilic functional group. In the first step, they bind to the active site of the target enzyme in a reversible fashion. Subsequentiy, an active site nucleophile in close proximity reacts with the electrophilic group on the substrate to form a covalent bond between the enzyme and the inhibitor, typically via S 2 alkylation or acylation. Affinity labels do not require activation by the catalysis of the enzyme, as in the case of a mechanism-based inhibitor. 

The often fast binding step of the inhibitor I to the enzyme E, forming the enzyme inhibitor complex E-I, is followed by a rate-determining inactivation step to form a covalent bond. The evaluation of affinity labels is based on the fulfillment of the following criteria (/) irreversible, active site-directed inactivation of the enzyme upon the formation of a stable covalent linkage with the activated form of the inhibitor, (2) time- and concentration-dependent inactivation showing saturation kinetics, and (3) a binding stoichiometry of 1 1 of inhibitor to the enzyme s active site (34). 

In order to give useful information about an enzyme, a conformationally restricted active-site-directed analog inhibitor need not bind to the enzyme irreversibly. In a study of the enzyme fructose 1,6-diphosphatase from rabbit liver, Benkovic et al, have investigated the question of the reactive form of the fructose 1,6-diphosphate in the enzymatic process (104,105). Three likely forms are shown in structures 50, 51 and 52. 

If k2 > kj, the glycosyl-enzyme intermediate will accumulate, and may be trapped by the rapid denaturation of the enzyme in the presence of (saturating) amounts of substrate. With -glucoside Aj from Asp. wentii and 4-nitrophenyl [ C]-2-deoxy-) -D-irra />jo-hexopyranoside, it was possible to identify the intermediate as a glycosyl ester (acylal) of 2-deoxy-D-arabino-hexose bound to the same aspartate residue that had previously been labeled with the active-site-directed inhibitor conduritol B epoxide and with D-glucal." This constituted an important proof that the carboxylate reacting with the epoxide is directly involved in catalysis. 

Information relevant to the mechanism of an enzyme-catalyzed reaction can, in general, only be obtained from irreversible inhibitors which react specifically at the active site and thereby inactivate the enzyme. As active-site-directed inhibition is treated in detail in Ref. 142 general aspects will be discussed here only briefly. In order to be suitable as an active-site-directed inhibitor, a compound must fulfil the following requirements. 

The power of the pooled GST fusion protein approach will increase as new biochemical reagents and assays become available. The development of chemical probes for biological processes, termed chemical biology, is a rapidly advancing field. For example, the chemical synthesis of an active site directed probe for identification of members of the serine hydrolase enzyme family has recently been described (Liu et al., 1999). The activity of the probe is based on the potent and irreversible inhibition of serine hydrolases by fluorophosphate (FP) derivatives such as diisopropyl fluorophosphate. The probe consists of a biotinylated long-chain fluorophosphonate, called FP-biotin (Liu et al., 1999). The FP-biotin was tested on crude tissue extracts from various organs of the rat. These experiments showed that the reagent can react with numerous serine hydrolases in crude extracts and can detect enzymes at subnanomolar... 

An enzyme consists of a polypeptide chain with a particular spatial configuration specific to that sequence of amino acids. The molecule twists and turns, forming structural features that are catalytically active, these being known as active sites. There may be more than one active site per enzyme molecule. Sometimes an auxiliary catalyst, known as a coenzyme, is also needed. Apparently, only the relevant active site of the enzyme comes into contact with the substrate and is directly involved in the catalysed reaction. The active site consists of only a few amino acid residues. These are not necessarily adjacent to one another in the peptide chain but may be brought into proximity by the characteristic folding of the enzyme structure. The active site may also include the coenzyme. The remainder of the enzyme molecule fulfils the essential function of holding the components of the active site in their appropriate relative positions and orientation. 

Activity-based protein profiling (ABPP) is a chemical proteomic strategy in which active-site-directed covalent probes are used to profile the functional states of enzymes in complex proteomes. Activity-based probes (ABPs) can distinguish active enzymes from their inactive zymogens or inhibitor-bound forms. They contain a reactive group intended to modify enzyme active sites covalently and a reporter group (typically rhodamine or biotin) that assists in detection and identification of protein targets. 

Tapia, O., Paulino, M. and Stamato, F. M. L. G. Computer assisted simulations and molecular graphics methods in molecular design. 1.Theory and applications to enzyme active-site directed drug design,... 

The discussion of Krs values above is an attempt to show how they may be used to gain insights into transition state binding at or near the active sites of enzymes. For other examples of the explicit or implicit application of Kurz s ideas to enzymes, the reader is directed to the references cited at the start of this subsection and in the Introduction, particularly the reviews by Kraut (1988) and by Wolfenden and Kati (1991). 

Boeodovsky, a., Kessler, B. M., Casageande, R., Oveekleeet, H. S., Wilkinson, K. D., and Ploegh, H. L. A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14, EmboJ, 2001, 20, 5187-96. 

In the previous studies using inhibitors and additives, it became clear that AMDase requires no cofactors, such as biotin, coenzyme A and ATP. It is also suggested that at least one of four cysteine residues plays an essential role in asymmetric decarboxylation. One possibility is that the free SH group of a cysteine residue activates the substrate in place of coenzyme A. Aiming at an approach to the mechanism of the new reaction, an active site-directed inhibitor was screened and its mode of interaction was studied. Also, site-directed mutagenesis of the gene coding the enzyme was performed in order to determine which Cys is located in the active site. 

The main purpose of redox mediation is to increase the rate of electron transfer between the active site of enzyme biocatalysts and an electrode by eliminating the need for the enzyme to interact directly with the electrode surface. Depending on the enzyme and... 

B. R. Baker, Design of Active-Site-Directed Irreversible Enzyme Inhibitors-, The Organic Chemistry of the Enzymic Active Site, John Wiley, Inc. New York, 1967... 

Other Proteins The ouabain-binding site on (Na /K -adenosine-5 -triphosphatase, 46, 523 penicillin isocyanates for /3-lactamase, 46, 531 active site-directed addition of a small group to an enzyme the ethylation of ludferin, 46, 537 mandelate racemase, 46, 541 d imethylpyrazole carboxamidine and related derivatives, 46, 548 labeling of catechol O-methyltransferase with N-haloace-tyl derivatives, 46, 554 affinity labeling of binding sites in proteins by sensitized photooxidation, 46, 561 bromocolchicine as a iabei for tubuiin, 46, 567. 

The weight (or more correctly, the mass) of a protein expressed in grams per mole of active sites. Not all oligomeric proteins, even some with identical subunits, have a number of active sites equal to the number of subunits. Enzyme normality (Le., the concentration of enzyme active sites) is typically determined by active site titration with an active-site-directed irreversible inhibitor. This is... 

Having an increased or elevated reactivity. This term has been used in reference to the relative activity of amino acyl residues at the active sites of enzyme. The immediate environment (Le., the microenvironment) may allow simple reagents to react faster with the amino acid than would normally be expected. Thus, in labeling of proteins with active site-directed reagents, an investigator should always consider the basis of increased reactivity Is it due to facilitation of the reaction by increased affinity (Le., affinity labeling), or is it due to increased activity of the amino acyl side chain (e.g., perhaps increased nucleophilicity due to the microenvironment). 

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