Covalent Intermediates

FIGURE 16.10 Formation of a covalent intermediate in the glyceraldehyde-3-phos-phate dehydrogenase reaction. Nucleophilic attack by a cysteine —SH group forms a covalent acylcysteine intermediate. Following hydride transfer to NAD, nucleophilic attack by phosphate yields the product, 1,3-bisphosphoglycerate. 

Thomas A, Jourand D, Bret C, Amara P, Field MJ (1999) Is there a covalent intermediate in the viral neuraminidase reaction A hybrid potential free-energy study. 1 Am Chem Soc 121 9693-9702... 

The cyclic phosphonate (115) is hydrolysed in acid with loss of MeOH whereas in basic solutions ring-opening occurs almost exclusively - a result in accord with the greater restriction on pseudorotation in a penta-covalent intermediate under basic conditions. 

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. 

As a simple model for the enzyme penicillinase, Tutt and Schwartz (1970, 1971) investigated the effect of cycloheptaamylose on the hydrolysis of a series of penicillins. As illustrated in Scheme III, the alkaline hydrolysis of penicillins is first-order in both substrate and hydroxide ion and proceeds with cleavage of the /3-lactam ring to produce penicilloic acid. In the presence of an excess of cycloheptaamylose, the rate of disappearance of penicillin follows saturation kinetics as the cycloheptaamylose concentration is varied. By analogy to the hydrolysis of the phenyl acetates, this saturation behavior may be explained by inclusion of the penicillin side chain (the R group) within the cycloheptaamylose cavity prior to nucleophilic attack by a cycloheptaamylose alkoxide ion at the /3-lactam carbonyl. The presence of a covalent intermediate on the reaction pathway, although not isolated, was implicated by the observation that the rate of disappearance of penicillin is always greater than the rate of appearance of free penicilloic acid. 

More recently, Kaiser and coworkers reported enantiomeric specificity in the reaction of cyclohexaamylose with 3-carboxy-2,2,5,5-tetramethyl-pyrrolidin-l-oxy m-nitrophenyl ester (1), a spin label useful for identifying enzyme-substrate interactions (Flohr et al., 1971). In this case, the catalytic mechanism is identical to the scheme derived for the reactions of the cycloamyloses with phenyl acetates. In fact, the covalent intermediate, an acyl-cyclohexaamylose, was isolated. Maximal rate constants for appearance of m-nitrophenol at pH 8.62 (fc2), rate constants for hydrolysis of the covalent intermediate (fc3), and substrate binding constants (Kd) for the two enantiomers are presented in Table VIII. Significantly, specificity appears in the rates of acylation (fc2) rather than in either the strength of binding or the rate of deacylation. 

The observed first-order appearance of two moles of phenol in the reactions of cycloheptaamylose with the methylphosphonates is of particular interest. This may be explained, as illustrated in Scheme VI, by an intramolecular displacement, within the covalent intermediate, of the second mole of phenol by an adjacent cycloamylose hydroxyl group. Presumably, both the methylphosphonates and the carbonates proceed by this pathway which is similar to the mechanism proposed by Hennrich and Cramer (1965) for the reactions of the cycloamyloses with diaryl pyrophosphates. 

An estimate of the rate enhancement associated with the intramolecular phosphorylation can be made by using isopropyl p-nitrophenyl methyl-phosphonate as a model for the covalent intermediate formed in the initial step of the reaction of cycloheptaamylose with bis (p-nitrophenyl) me thy 1-phosphonate. The first-order rate constant for the alkaline hydrolysis of isopropyl p-nitrophenyl methylphosphonate at pH 9.86 can be obtained from the data of van Hooidonk and Groos (1970) kun = 1.4 X 10-5 sec-1. This value may be compared with the maximal rate constant for the reaction of cycloheptaamylose with bis(p-nitrophenyl) methylphosphonate— k2 = 1.59 X 10-1 sec-1 at pH 9.86—which must be a minimal value for the rate of the intramolecular phosphorylation. This comparison implies a kinetic acceleration of at least 104 which is similar to rate enhancements associated with the formation of cyclic phosphates from nucleoside phosphate diesters. 

As noted in an earlier section of this article, the utility of the cycloamyloses as covalent catalysts is limited by the low reactivity of the catalytically active hydroxyl groups at neutral pH s and by the relatively slow rates of deacylation of the covalent intermediates. In an effort to achieve effective catalysis, several investigators have attempted to selectively modify the cycloamyloses by either (1) introducing an internal catalyst to facilitate deacylation or (2) introducing a more reactive nucleophile to speed acylation and/or deacylation. 

As recently as 1965, Thoma and Stewart predicted that alterations in reaction rates [in the presence of the cycloamyloses] should be anticipated whose magnitude and sign will fluctuate with the reaction type, and added that at the present juncture, it is impossible to sort out confidently. . . which factors may contribute importantly to raising or lowering the activation energy of the reaction. In the short interval between 1965 and the present, a wide variety of cycloamylose-induced rate accelerations and decelerations have, indeed, been revealed. More importantly, rate alterations imposed by the cycloamyloses can now be explained with substantially more confidence. The reactions of derivatives of carboxylic acids and organo-phosphorus compounds with the cycloamyloses, for example, proceed to form covalent intermediates. Other types of reactions appear to be influenced by the dielectric properties of the microscopic cycloamylose cavity. Still other reactions may be affected by the geometrical requirements of the inclusion process. 

Organophosphate and carbamate pesticides are potent inhibitors of the enzyme cholinesterase. The inhibition of cholinesterase activity by the pesticide leads to the formation of stable covalent intermediates such as phosphoryl-enzyme complexes, which makes the hydrolysis of the substrate very slow. Both organophosphorus and carbamate pesticides can react with AChE in the same manner because the acetylation of the serine residue at the catalytic center is analogous to phosphorylation and carbamylation. Carbamated enzyme can restore its catalytic activity more rapidly than phosphorylated enzyme [17,42], Kok and Hasirci [43] reported that the total anti-cholinesterase activity of binary pesticide mixtures was lower than the sum of the individual inhibition values. 

The calculations found there was no covalent intermediate in the viral neuraminidase reaction and the intermediate was more likely to be hydroxylated directly. Because there is only a small energy difference between the two options (formation of a covalent bond or direct hydroxylation) Thomas et al. proposed it might be possible to design inhibitors covalently bound to the enzyme. 

An interesting dinically useful prodrug is 5-fluorouracil, which is converted in vivo to 5-fluoro-2 -deoxyuridine 5 -monophosphate, a potent irreversible inactivator of thymidylate synthase It is sometimes charaderized as a dead end inactivator rather than a suicide substrate since no electrophile is unmasked during attempted catalytic turnover. Rathei since a fluorine atom replaces the proton found on the normal substrate enzyme-catalyzed deprotonation at the 5 -position of uracil cannot occur. The enzyme-inactivator covalent addud (analogous to the normal enzyme-substrate covalent intermediate) therefore cannot break down and has reached a dead end (R. R. Rando, Mechanism-Based Enzyme Inadivators , Pharm. Rev. 1984,36,111-142). 

Zeolites are the main catalyst in the petrochemical industry. The importance of these aluminosilicates is due to their capacity to promote many important reactions. By analogy with superacid media (1), carbocations are believed to be key intermediates in these reactions. However, simple carbocationic species are seldom observed on the zeolite surface as persistent intermediates within the time-scale of spectroscopic techniques. Indeed, only some conjugated cyclic carbocations were observed as long living species, but covalent intermediates, namely alkyl-aluminumsilyl oxonium ions (2) (scheme 1), where the organic moiety is bonded to the zeolite structure, are usually thermodynamically more stable than the free carbocations (3,4). 

The serine hydrolases, threonine hydrolases, and cysteine hydrolases, the attacking nucleophile of which is a serine or threonine OH group or a cysteine thiolate group, respectively, and which form an intermediate covalent complex (i. e., the acylated enzyme). Here, an activated H20 molecule enters the catalytic cycle in the second step, i.e., hydrolysis of the covalent intermediate to regenerate the enzyme. 

Like aspartic peptidases, metallopeptidases act by activating a H20 molecule, and they do not form a covalent intermediate with the substrate. Here, the activation of a H20 molecule is mediated by a residue that acts as general base (e.g., Glu, His, Lys, Arg, or Tyr), with a divalent cation (usually Zn2+ but sometimes Co2+ or Mn2+) perhaps also contributing. The major role of the metal cation, however, is to act as an electrophilic catalyst by coordinating the carbonyl (or phosphoryl) O-atom in the substrate and orienting the latter for nucleophilic attack by the HO ion generated from H20 by the general base. 

E. E. Blatter, D. P. Abriola, R. Pietruszko, Aldehyde Dehydrogenase. Covalent Intermediate in Aldehyde Dehydrogenation and Ester Hydrolysis , Biochem. J. 1992, 282, 353-360. 

F. Muller, M. Arand, H. Frank, A. Seidel, W. Hinz, L. Winkler, K. Hanel, E. Blee, J. K. Beetham, B. D. Hammock, F. Oesch, Visualization of a Covalent Intermediate Between Microsomal Epoxide Hydrolase, but not Cholesterol Epoxide Hydrolase, and Their Substrates , Eur. J. Biochem. 1997, 245, 490 - 496. 

To prove that any complex which formed at the low temperature was both productive and covalent, two additional experiments were carried out. First, an attempt was made to wash the substrate out of the enzyme at low temperature. The crystal was held at -55 C and substrate-free 70% methanol was flowed over it for 4 days. There was no change in the substrate-sensitive reflections, which were monitored every 8 hours during this period, and when another data set was collected at the end of the wash, it revealed the substrate still bound in the active site. However, when the crystal was allowed to warm up to - 10°C, the monitor reflections immediately began to change in intensity, back to the values they had for the native enzyme. In less than 20 hours all of them had returned to these values, and a final set of data was collected as expected, on processing it showed an empty active site and a native elastase structure. These two control experiments indicated that the structure that formed when elastase was exposed to the ester substrate was covalent, and that the covalent intermediate would undergo hydrolysis (presum-... 

Unfortunately, the size of the crystallographic problem presented by elastase coupled with the relatively short lifedme of the acyl-enzyme indicated that higher resolution X-ray data would be difficult to obtain without use of much lower temperatures or multidetector techniques to increase the rate of data acquisition. However, it was observed that the acyl-enzyme stability was a consequence of the known kinetic parameters for elastase action on ester substrates. Hydrolysis of esters by the enzyme involves both the formation and breakdown of the covalent intermediate, and even in alcohol-water mixtures at subzero temperatures the rate-limidng step is deacylation. It is this step which is most seriously affected by temperature, allowing the acyl-enzyme to accumulate relatively rapidly at — 55°C but to break down very slowly. Amide substrates display different kinetic behavior the slow step is acylation itself. It was predicted that use of a />-nitrophenyl amid substrate would give the structure of the pre-acyl-enzyme Michaelis complex or even the putadve tetrahedral intermediate (Alber et ai, 1976), but this experiment has not yet been carried out. Instead, over the following 7 years, attention shifted to the smaller enzyme bovine pancreatic ribonuclease A. 

Much interesting work has been done on catalysis by cycloamyloses in cases where no covalent intermediate is formed. Catalysis in these cases is... 

As discussed above, proteases are peptide bond hydrolases and act as catalysts in this reaction. Consequently, as catalysts they also have the potential to catalyze the reverse reaction, the formation of a peptide bond. Peptide synthesis with proteases can occur via one of two routes either in an equilibrium controlled or a kinetically controlled manner 60). In the kinetically controlled process, the enzyme acts as a transferase. The protease catalyzes the transfer of an acyl group to a nucleophile. This requires an activated substrate preferably in the form of an ester and a protected P carboxyl group. This process occurs through an acyl covalent intermediate. Hence, for kineticmly controlled reactions the eii me must go through an acyl intermediate in its mechanism and thus only serine and cysteine proteases are of use. In equilibrium controlled synthesis, the enzyme serves omy to expedite the rate at which the equilibrium is reached, however, the position of the equilibrium is unaffected by the protease. 

The formation of a ternary complex is entropically disfavoured relative to binary ones. However, kinetic and spectroscopic investigations [39] gave no indication of, e.g., a ping-pong mechanism, and/or the involvement of covalent intermediates... 

Figure 8.9 Covalent intermediates in the DNMT inhibition by zebularine (Ib) and 2 -deoxy-5-fluorocytidine (lllb).

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