Enzyme/enzymatic transition state analogs

Inhibition of enzymatic reactions by transition state analogs has been an extremely important approach for drug design [20], the principle underlying this is that "nature has developed enzymes for binding efficiently to the transition states of the reactions they catalyse". 

Using the transition-state analog shown on p. 485 a catalytic antibody with chorismate mutase activity was isolated. Many antibodies catalyzing additional reactions have also been found. Although they are usually less active than natural enzymes, in some cases they approach enzymatic rates. Furthermore, they may catalyze reactions for which no known enzymes exist.h... 

Extrapolating from well-characterized enzymatic inhibition in test tubes, numerous mechanistic ideas concerning the in vivo effects of vanadium compounds have been advanced. The effects of vanadium compounds as transition-state analogs of certain enzymes with a phosphoprotein intermediate in their reaction scheme is proposed to account for the action of vanadium [11] in many biological systems. Unfortunately, it is often difficult to determine if the inhibition observed in the test tube occurs in vivo. For example, although vanadate is a potent inhibitor of plasma membrane ion pumps (such as the sodium potassium ATPase) in the test tube, it is difficult to determine if these pumps are actually inhibited in animals exposed to vanadium compounds. Currently, the role of vanadium compounds as protein phosphatase (PTP) inhibitors is believed to be related to the metabolic effects of this... 

Schramm, V.L. (1999) Enzymatic transition state analysis and transition-state analogs, in Schramm, V. L. and Purich, D. L. (eds.), Methods in Enzymology 308, Enzyme kinetics and Mechanism, Part E, Academic Press, San Diego, pp. 301-354. 

Figure 4. Schematic representation of the free energy changes in non-enzymatic and enzymatic reactions and in the reaction of a hypothetical transition state analog (TSA) with the enzyme.

Transition-state inhibitors stably mimic the transition state of the enzymatic reaction, and thereby interact with the substrate-bin-ding and catalytic machinery of the enzyme in a low-energy conformation. Transition-state analogs are competitive, reversible inhibitors, although some have extremely low Kj s and very slow off-rates. All proteases activate a nucleophile to attack a carbonyl, which leads to the formation of a tetrahedral intermediate that then collapses to form the enzyme products—two peptides. Thus, synthetic small molecules that mimic the tetrahedral intermediate of the protease reaction are attractive transition-state analogs. A classic class of protease transition-state inhibitors uses a boronic acid scaffold (4, 10). Boronic acid adopts a stable tetrahedral conformation in the protease active site that is resistant to nucleophilic attack. Boronic acid inhibitors, which are derivatized with different specificity elements, have been developed against every class of protease... 

Enzymes have been successfully enriched from libraries by selecting variants that bind to transition state analogs, or by covalent trapping with surface bound suicide inhibitors,20 but this approach does not usually select the most active enzymatic variants. 

The elucidation of enzyme-substrate interactions has established new paradigms leading to the discovery of biologically active compounds. One such paradigm is the "Transition State Theory as it applies to the mechanism of enzymatic reactions. Based on this theory, series of transition state analog inhibitors known as trifluoromethyl ketones have been synthesized in our laboratory. 

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