Oxyanion stabilization

An efficient aqueous phase Suzuki-Miyaura reaction of activated aryl chlorides with aryl boronic acids has been reported. The method uses a new D-glucosamine-based dicyclohexylarylphosphine ligand for the palladium catalyst and works well with nitro-and cyano-activated chlorides.32 The aryl fluoride bond has been considered inert to palladium-catalysed substitution reactions. However, a computational study, backed up by experiment, shows that the presence of a carboxylate group ortho to fluorine will allow reaction both with phenylboronic acids in a Suzuki-type reaction and with organotin reagents in a Stille-type reaction the presence of the adjacent oxyanion stabilizes the transition state.33... 

An alternative suggestion is that the coordinated monomer dissociates to give an oxyanion stabilized by the nucleophile s counterion, most commonly, tetrabutylammonium or cesium ions,69 by analogy to the mechanism proposed for activation of tributylstannyl ethers by nucleophiles.57 This proposal is summarized in Fig. 14, which also shows the product mixture obtained for methyl (2S,3R)-2,3-dihydroxybutanoate. For this compound, reaction on the oxygen atom of the inherently less acidic hydroxyl is favored. Both anions, E and F, are in equilibrium with the coordinated monomer, and the less populated (but more reactive) anion E reacts to a greater extent, or in other words, the difference in the rate constants for trapping is greater than the difference in equilibrium constants. 

The single mutation Asp 32-Ala reduces the catalytic reaction rate by a factor of about lO compared with wild type. This rate reduction reflects the role of Asp 32 in stabilizing the positive charge that His 64 acquires in the transition state. A similar reduction of kcat and kcat/ m (2.5 x 10 ) is obtained for the single mutant Asn 155-Thr. Asn 155 provides one of the two hydrogen bonds to the substrate transition state in the oxyanion hole of subtilisin. 

The oxyanion binding site stabilizes the transition state by forming two hydrogen bonds to a negatively charged oxygen atom of the substrate. Mutations that prevent formation of one of these bonds in subtilisin decrease the rate by a factor of about 10. ... 

X-ray crystallographic studies of serine protease complexes with transition-state analogs have shown how chymotrypsin stabilizes the tetrahedral oxyanion transition states (structures (c) and (g) in Figure 16.24) of the protease reaction. The amide nitrogens of Ser and Gly form an oxyanion hole in which the substrate carbonyl oxygen is hydrogen-bonded to the amide N-H groups. 

The oxyanion hole of chymotryp.sin. stabilize.s the tetrahedral oxyanion tran.sition. state.s of die mechani.sm in Figure 16.24. 

For many serine and cysteine peptidases catalysis first involves formation of a complex known as an acyl intermediate. An essential residue is required to stabilize this intermediate by helping to form the oxyanion hole. In cathepsin B a glutamine performs this role and sometimes a catalytic tetrad (Gin, Cys, His, Asn) is referred too. In chymotrypsin, a glycine is essential for stabilizing the oxyanion hole. 

The family of serine proteases has been subjected to intensive studies of site-directed mutagenesis. These experiments provide unique information about the contributions of individual amino acids to kcat and KM. Some of the clearest conclusions have emerged from studies in subtilisin (Ref. 9), where the oxyanion intermediate is stabilized by t>e main-chain hydrogen bond of Ser 221 and an hydrogen bond from Asn 155 (Ref. 2). Replacement of Asn 155 (e.g., the Asn 155— Ala 155 described in Fig. 7.9) allows for a quantitative assessment of the effect of the protein dipoles on Ag. ... 

Tetrhedral intermediate, 172 Thermodynamic cycles, 186 Thermolysin, zinc as cofactor for, 204 Thrombin, 170 Torsional potential, 111 Transition states, 41-42,44, 45,46, 88, 90-92 in amide hydrolysis, 219-221 oxyanion hole and, 181 stabilization of, 181,181 carbonium ion, 154,155,156-161, 167-169 for gas-phase reactions, 43... 

The mechanism for the lipase-catalyzed reaction of an acid derivative with a nucleophile (alcohol, amine, or thiol) is known as a serine hydrolase mechanism (Scheme 7.2). The active site of the enzyme is constituted by a catalytic triad (serine, aspartic, and histidine residues). The serine residue accepts the acyl group of the ester, leading to an acyl-enzyme activated intermediate. This acyl-enzyme intermediate reacts with the nucleophile, an amine or ammonia in this case, to yield the final amide product and leading to the free biocatalyst, which can enter again into the catalytic cycle. A histidine residue, activated by an aspartate side chain, is responsible for the proton transference necessary for the catalysis. Another important factor is that the oxyanion hole, formed by different residues, is able to stabilize the negatively charged oxygen present in both the transition state and the tetrahedral intermediate. 

Clearly, the oxyanion hole is now as significant a feature of the binding site of such acyl transfer abzymes as it is already for esterases and peptidases — and not without good reason. Knossow has analysed the structures of three esterase-like catalytic antibodies, each elicited in response to the same phosphonate TSA hapten (Charbonnier et al., 1997). Catalysis for all three is accounted for by transition state stabilization and in each case there is an... 

Carbothioic O-acid esters (3.1 to be distinguished from carbothioic S-acid esters, R-CO-SR, discussed in Chapt. 7) are not hydrolyzed by serine peptidases. It has been postulated that the thiocarbonyl S-atom, which is larger and less prone to H-bonding than the carbonyl O-atom, cannot interact effectively with the oxyanion hole. The resulting inability to stabilize the transition state considerably reduces the rate of hydrolysis. 

Fig. 5.8. Model for catalytic role of E2 active-site asparagine. The side chain of the asparagine in the conserved HPN" motif (Figure 5.2) stabilizes the oxyanion that forms when the substrate s lysine attacks the E2/ubiquitin thiol ester bond. N79 is numbering for Ubcl (Figure 5.2).

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