Tetrahedral transition state

Serine proteinases cleave peptide bonds by forming tetrahedral transition states... 

Figure 11.6 A schematic view of the presumed binding mode of the tetrahedral transition state intermediate for the deacylation step. The four essential features of the serine proteinases are highlighted in yellow the catalytic triad, the oxyanion hole, the specificity pocket, and the unspecific main-chain substrate binding.

The enzyme provides a general base, a His residue, that can accept the proton from the hydroxyl group of the reactive Ser thus facilitating formation of the covalent tetrahedral transition state. This His residue is part of a catalytic triad consisting of three side chains from Asp, His, and Ser, tvhich are close to each other in the active site, although they are far apart in the amino acid sequence of the polypeptide chain (Figure 11.6). 

The active site of subtilisin is outside the carboxy ends of the central p strands analogous to the position of the binding sites in other a/p proteins as discussed in Chapter 4. Details of this active site are surprisingly similar to those of chymotrypsin, in spite of the completely different folds of the two enzymes (Figures 11.14 and 11.9). A catalytic triad is present that comprises residues Asp 32, His 64 and the reactive Ser 221. The negatively charged oxygen atom of the tetrahedral transition state binds in an oxyanion hole,... 

Reaction of 2a with Cl2BCH2SiMe3 yields the compound 3a [18]. When the symmetrically substituted 3a is reacted with lithium in diethyl ether, the unsymmetri-cally substituted folded 4b [18] is obtained (Scheme 3.2-3). Formation of 4b can be explained by a rapid isomerization of the first formed 4a via the distorted tetrahedral transition state 5a. 

Another chelate structure exists for fi-lactams bearing a basic side chain. In ampicillin and cephalexin, e.g., the metal ion is bound by the carbonyl and amino groups (D, Fig. 5.20) [137]. When so attached, the metal ion does not appear to stabilize the tetrahedral transition-state complex, and, indeed, Cu11 ions did not significantly affect the hydrolysis of cefaclor [125]. 

Fig. 8.5. Mechanism postulated for competitive, specific base catalyzed hydrolysis and acyl migration of catechol monoesters, as seen with 4-pivaloyl-L-dopa (8.81) [114a]. Deprotonation (Reactions a and b) accelerates intramolecular nucleophilic attack (Reactions c and d) to form a tetrahedral transition state. The latter is postulated to be the intermediate common to hydrolysis (Reaction e) and acyl migration. 

Fig. 10.6. Simplified representation of the postulated catalytic cycle of microsomal and cytosolic epoxide hydrolases, showing the roles played by the catalytic triad (i.e., nucleophile, general base, and charge relay acid) and some other residues, a) Nucleophilic attack of the substrate to form a /3-hydroxyalkyl ester intermediate, b) Nucleophilic attack of the /Thydroxyal-kyl ester by an activated H20 molecule, c) Tetrahedral transition state in the hydrolysis of the /f-hydroxyalkyl ester, d) Product liberation, with the enzyme poised for a further catalytic... 

Figure 2 Ester hydrolysis. Design of a stable analogue of the tetrahedral transition state to be used as a hapten to generate catalytic antibodies with an esterase activity.

These hemiketalic adducts are very good mimics of the tetrahedral transition state involved in the enzymatic hydrolysis of an ester bond or a peptidic bond [71,72], The nucleophilic entity of the enzyme active site (e.g. the hydroxyl of hydrolytic serine enzymes) can easily add onto the activated carbonyl of a fluor-oketone leading to a very stable tetrahedral intermediate. The enzyme is not regenerated and is thus inhibited (Fig. 21) [73],... 

A. Tulinsky, R.A. Belvins, Structure of a tetrahedral transition state complex of alpha-chymotrypsin dimer at 1.8-A resolution, J. Biol. Chem. 262(16) (1987) 7737-7743. 

The structural analysis of the trypsin inhibitor from bovine pancreas (BPTI) in complex with trypsin shows that the inhibitor occupies and blocks the substrate binding pocket in a highly complementary maimer (fig. 2.9). In the trypsin-BPTI complex, the catalytically essential Ser-OH of trypsin contacts a CO group of the inhibitor in a manner very similar to the tetrahedral transition state of amide or ester bond hydrolysis (see fig. 2.9b). The inhibitor can be likened to a pseudo-substrate and, as such, is bound with high affinity. The cleavage of the peptide bond is, however, not possible due to other circumstances, such as the fact that water is prevented from reaching the active site with the inhibitor boimd. 

Phosphonates have been widely used as analogues of carboxylic acids. They have been particularly effective as analogues of tetrahedral transition states that occur in the course of enzyme-catalyzed reactions such as hydrolysis of the amide (peptide) bond. As such, they may be used as inhibitors of enzymes (e.g., 82, 83) or as haptens for producing antibodies that are catalytic (e.g., 84). A notable example is H203P— CH2—CH2—CH(—NH2)—COOH, which has effects that are likely to be due to its interference with glutamate as a neurotransmitter (85). 

Mclver and Stanton used group theory to derive selection rules for the symmetry of transition states. For example, they proved that the exchange reaction H2 + D2- 2HD cannot have a tetrahedral transition state. See J. W. Mclver and R. E. Stanton, J. Am. Chem. Soc., 94, 8618 (1972) J. W. Mclver, Accounts Chem. Res., 7, 72 (1974). 

Furthermore, the sulfonamide bond is expected to possess enhanced metabolic stability with structural similarities to the tetrahedral transition state involved in amide bond enzymatic hydrolysis, thus making sulfonamide peptides interesting candidates in the development of protease inhibitors and new drugs. The oligomers and polymers should also be interesting molecular scaffolds, with specific secondary structures enforced by hydrogen bonding)100,101 ... 

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