Tetrahedral intermediate complex

Hangauer et al. (220) used computer modeling techniques to investigate the mechanism of peptide hydrolysis by thermolysin using the crystallographic information on the enzyme, inhibitor, and substrate along with available structure-activity relationships. Using a model substrate, Z-Phe-Phe-Leu-Trp, they modeled the Michaelis complex as well as the tetrahedral intermediate complex. 

Figure 23.8 (a) Catalytic machinery of CatA, revealed by the tetrahedral intermediate complex with compound 6. (b) Cut through the CatA surface with the covalently bound... 

The reaction is proposed to proceed from the anion (9) of A/-aminocatbonylaspattic acid [923-37-5] to dehydrooranate (11) via the tetrahedral activated complex (10), which is a highly charged, unstable sp carbon species. In order to design a stable transition-state analogue, the carboxylic acid in dihydrooronate (hexahydro-2,6-dioxo-4-pyrimidinecarboxylic acid) [6202-10-4] was substituted with boronic acid the result is a competitive inhibitor of dibydroorotase witb a iC value of 5 ]lM. Its inhibitory function is supposedly due to tbe formation of tbe charged, but stable, tetrabedral transition-state intermediate (8) at tbe active site of tbe enzyme. 

R = CH3 and AR = C6H4NO2.) Actually Scheme XXV and Eq. (3-176) both take place, with some of the hydroxamic acid being formed directly and some via the intermediate. (Note that each of these reactions is itself complex, presumably occurring via a tetrahedral intermediate as shown in Scheme XXII for ester hydrolysis.)... 

The reaction is known to be complex, proceeding through a tetrahedral intermediate called a carbinolamine. Generalizing to the reactions of amines with carbonyls, the two-step reaction sequence is... 

If the reaction is complex, a change in the rate-determining step may take place along the pK scale. Most acyl transfers are thought to take place via a tetrahedral intermediate, as in Scheme II. 

Only the hydrophobic and steric terms were involved in these equations. There are a few differences between these equations and the corresponding equations for cyclo-dextrin-substituted phenol systems. However, it is not necessarily required that the mechanism for complexation between cyclodextrin and phenyl acetates be the same as that for cyclodextrin-phenol systems. The kinetically determined Kj values are concerned only with productive forms of inclusion complexes. The productive forms may be similar in structure to the tetrahedral intermediates of the reactions. To attain such geometry, the penetration of substituents of phenyl acetates into the cyclodextrin cavity must be shallow, compared with the cases of the corresponding phenol systems, so that the hydrogen bonding between the substituents of phenyl acetates and the C-6 hydroxyl groups of cyclodextrin may be impossible. 

The rates of reaction of both enantiomers of amino-acid esters in the presence of (S)-[324] are the same, but with (S)-[323] they are in most cases different. The reactions of L-amino acid esters in the presence of (S)-[323] are faster than those in the presence of (R)-[323] by factors of 9.2 (R = i-Pr), 8.2 (R = C6H5CH2) and 6.0 (R = i-Bu). No difference in rates is observed for L-alanine p-nitrophenyl ester. The results were explained in terms of the formation of diastereomeric tetrahedral intermediates [325] and [326]. The bulk of the group R will determine how much the complex stability of the (D)-complex decreases relative to that of the (L)-complex, which difference is reflected in the activation energy of the rate-determining step. 

Transition metal ions cause a dramatic increase in the rate of hydrolysis of /Madam antibiotics [75][133][134], For example, copper(II) and zinc(II) ions increase the rate of alkaline hydrolysis ca. 108-fold and 104-fold, respectively [76], It has been suggested that the metal ion coordinates with both the carboxylate group and the /3-lactam N-atom of penicillins (A, Fig. 5.20). This complex stabilizes the tetrahedral intermediate and, thus, facilitates cleavage of the C-N bond catalyzed by the HO ion [74] [75], Such a model appears applicable also to clavulanic acid, imipenem, and monobactams, but it re-... 

Fig. 5.20. Modes of coordination of transition metal ions with /3-lactam antibiotics. Complex A In penicillins, the metal ion coordinates with the carboxylate group and the /3-lactam N-atom. This complex stabilizes the tetrahedral intermediate and facilitates the attack of HO-ions from the bulk solution. Complex B In benzylpenicillin Cu11 binds to the deprotonated N-atom of the amide side chain. The hydrolysis involves an intramolecular attack by a Cu-coordinated HO- species on the carbonyl group. Complex C In cephalosporins, coordination of the metal ion is by the carbonyl O-atom and the carboxylate group. Because the transition state is less stabilized than in A, the acceleration factor of metal ions for the hydrolysis of cephalosporins is lower than for penicillins. Complex D /3-Lactams with a basic side chain bind the metal ion to the carbonyl and the amino group in their side chain. This binding mode does not stabilize the tetrahedral transition complex and, therefore, does not affect the rate of... 

Fig. 2. The generally accepted mechanism for the hydrolysis of peptide substrates by the serine proteases. The precise locations of the protons are still moot their positions here are taken from Steitz and Shullman (1982). I, Michaelis complex II and V, tetrahedral intermediates III and IV, acyl-enzyme VI, product complex.

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. 

A bigger effect for H2O than OH is very unusual and is a behavior certainly not shown by the uncoordinated amide. The effect is ascribed to a benefit from cyclization and concerted loss of protonated amide, without formation of the tetrahedral intermediate. Although the coordinated OH is some 10 times less effective than coordinated HjO (Table 6.4), it is still about 10 times faster with 15 than via external attack by OH at pH 7 on the chelated amide 13. Early studies showed that complexes of the type CoN4(H20)OH can promote the hydrolysis of esters, amides and dipeptides and that this probably arises via formation of ester, amide or peptide chelates. These then hydrolyze in the manner above. 

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