Transition state inhibition

This article describes various approaches to inhibition of enzyme catalysis. Reversible inhibition includes competitive, uncompetitive, mixed inhibition, noncompetitive inhibition, transition state, and slow tight-binding inhibition. Irreversible inhibition approaches include affinity labeling and mechanism-based enzyme inhibition. The kinetics of the various inhibition approaches are summarized, and examples of each type of Inhibition are presented. 

It follows that the energetic differences as compared with the no-inhibition case are due to the turmeling induced by the inhibited transition states which regulate the delayed times of mixed catalysis. 

Herbicidal Inhibition of Enzymes. The Hst of known en2yme inhibitors contains five principal categories group-specific reagents substrate or ground-state analogues, ie, rapidly reversible inhibitors affinity and photo-affinity labels suicide substrate, or inhibitors and transition-state, or reaction-intermediate, analogues, ie, slowly reversible inhibitors (106). 

Nebularine. Nebularine(44) is a naturaHy occurring purine riboside isolated from S.jokosukanensis (1,3,4). It is phosphorylated, and inhibits purine biosynthesis and RNA synthesis, but is not incorporated into RNA by E. coli RNA polymerase. It has also found appHcation as a transition state analogue for treatment of schistosomiasis and as a substrate for the restriction endonuclease, Hindll (138—141). 

Concerning the reaction rate, a considerable decrease is observed qualitatively when R = C02Et or Ph. The presence of two Bu groups in the 3- and 5-positions (242 r3 = r5 = gyt) completely inhibits the reaction. Structure (248) for the transition state has been established from a kinetic study of the reaction between pyrazole and l-fluoro-2,4-dinitrobenzene <72JCS(P2)1420). 

Pertiaps the most obvious experiment is to compare the rate of a reaction in the presence of a solvent and in the absence of the solvent (i.e., in the gas phase). This has long been possible for reactions proceeding homolytically, in which little charge separation occurs in the transition state for such reactions the rates in the gas phase and in the solution phase are similar. Very recently it has become possible to examine polar reactions in the gas phase, and the outcome is greatly different, with the gas-phase reactivity being as much as 10 greater than the reactivity in polar solvents. This reduced reactivity in solvents is ascribed to inhibition by solvation in such reactions the role of the solvent clearly overwhelms the intrinsic reactivity of the reactants. Gas-phase kinetic studies are a powerful means for interpreting the reaction coordinate at a molecular level. 

Adenylyl Cyclases. Figure 6 Adenylyl cyclase catalytic cycle. Points during the catalytic cycle of adenylyl cyclases at which inhibition by competitive and noncompetitive nucleotides occur E represents the catalytic transition state. 

P-site ligands inhibit adenylyl cyclases by a noncompetitive, dead-end- (post-transition-state) mechanism (cf. Fig. 6). Typically this is observed when reactions are conducted with Mn2+ or Mg2+ on forskolin- or hormone-activated adenylyl cyclases. However, under- some circumstances, uncompetitive inhibition has been noted. This is typically observed with enzyme that has been stably activated with GTPyS, with Mg2+ as cation. That this is the mechanism of P-site inhibition was most clearly demonstrated with expressed chimeric adenylyl cyclase studied by the reverse reaction. Under these conditions, inhibition by 2 -d-3 -AMP was competitive with cAMP. That is, the P-site is not a site per se, but rather an enzyme configuration and these ligands bind to the post-transition-state configuration from which product has left, but before the enzyme cycles to accept new substrate. Consequently, as post-transition-state inhibitors, P-site ligands are remarkably potent and specific inhibitors of adenylyl cyclases and have been used in many studies of tissue and cell function to suppress cAMP formation. 

A quantitative interpretation of aldonolactone inhibition in terms of an adaptation of the active site to a transition state approaching a planar, glycosyl oxocarbonium ion is made difficult for several reasons. Due to the interconversion between the 1,4- and 1,5-lactones, and their hydrolysis to the aldonic acids, their use is limited to kinetic studies with incubation times of 10 min or less. This was not realized by most investigators prior to 1970. In many cases, only the 1,4-lactone can be isolated its (partial) conversion into... 

A case similar to the slow, practically irreversible inhibition of jack bean a-D-mannosidase by swainsonine is represented by the interaction of castanospermine with isomaltase and rat-intestinal sucrase. Whereas the association constants for the formation of the enzyme-inhibitor complex were similar to those of other slow-binding glycosidase inhibitors (6.5 10 and 0.3 10 M s for sucrase and isomaltase, respectively), the dissociation constant of the enzyme-inhibitor complex was extremely low (3.6 10 s for sucrase) or could not be measured at all (isomaltase), resulting in a virtually irreversible inhibition. Danzin and Ehrhard discussed the strong binding of castanospermine in terms of the similarity of the protonated inhibitor to a D-glucosyl oxocarbenium ion transition-state, but were unable to give an explanation for the extremely slow dissociation of the enzyme-inhibitor complex. 

For clarity it is emphasized that the effect occurs because the transition state develops an electric dipole. Neither nitrogen nor methane has a dipole in the gas phase, but when interacting with the metal electrons they develop one. With nitrogen the dipole is opposite that of the alkali adsorbate, while for methane it is in the same direction, leading to promotion and inhibition respectively. 

Zeolites have led to a new phenomenon in heterogeneous catalysis, shape selectivity. It has two aspects (a) formation of an otherwise possible product is blocked because it cannot fit into the pores, and (b) formation of the product is blocked not by (a) but because the transition state in the bimolecular process leading to it cannot fit into the pores. For example, (a) is involved in zeolite catalyzed reactions which favor a para-disubstituted benzene over the ortho and meso. The low rate of deactivation observed in some reactions of hydrocarbons on some zeoUtes has been ascribed to (b) inhibition of bimolecular steps forming coke. 

The first substrate analogue inhibitors of FAAH were reported in 1994. The anandamide analogues prepared represented three elasses of putative transition-state inhibitors a-trifluoromethyl ketones, a-ketoesters and a-ketoamides [62], In the initial sereening studies, it was found that the trifluoromethyl ketone eompounds tested were effeetive inhibitors of AEA hydrolysis. A selected set of a-keto esters also inhibited hydrolysis, while a-keto amides were ineffective. In particular, arachidonyl trifluoromethyl ketone (32), gave almost 100% inhibition of anandamide hydrolysis. A detailed investigation of the structural requirements for FAAH inhibition with a-trifluoromethyl ketones has been carried out by Roger and co-workers [63]. 

On the other hand, the use of a-cyclodextrin decreased the rate of the reaction. This inhibition was explained by the fact that the relatively smaller cavity can only accommodate the binding of cyclopentadiene, leaving no room for the dienophile. Similar results were observed between the reaction of cyclopentadiene and acrylonitrile. The reaction between hydroxymethylanthracene and N-ethylmaleimide in water at 45°C has a second-order rate constant over 200 times larger than in acetonitrile (Eq. 12.2). In this case, the P-cyclodextrin became an inhibitor rather than an activator due to the even larger transition state, which cannot fit into its cavity. A slight deactivation was also observed with a salting-in salt solution (e.g., quanidinium chloride aqueous solution). 

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