Stereoselective pocket

One of the most direct questions to ask in the perspective of enzyme design is whether an already existing protein with a binding pocket might be turned into a new catalyst by introducing catalytic residues directly, rather than by the elaborated TSA mimicry approach used for catalytic antibodies, hoping to create a new biocatalyst that could harness both the activity and the selectivity, in particular stereoselectivity, that is possible with enzymes. 

Stereoselective intramolecular conjugate addition reactions (Scheme 4) of dithiane anions tethered to an a,/ -unsaturated nitrile have been developed to advantage for the synthesis of axially substituted indolizidines and quinolizidines.81 The control of axial nitrile orientation by a peg-in-a-pocket template effect has been discussed. 

Kremer et al. [123] observed the hydrophobic pockets as the binding site on AGP protein. However, more than one binding site was reported. Haupt et al. [124] presented a retention model for the chiral resolution of uncharged solutes, felodipine, on AGP and the model has assumed the presence of two different stereoselective sites for different enantiomers. In another study, Waters et al. [125] carried out certain thermodynamic experiments for the determination of the mechanism of chiral resolution on AGP protein. The authors reported the two... 

The stereoselectivity for substrates bearing a small and a large substituent (e.g. a secondary alcohol as shown in fig.6) is explained by assuming that when the secondary alcohol is subjected to resolution by a lipase, the fast reacting enantiomer binds to the active side in the manner shown in fig. 6a, however, when the other enantiomer reacts with the lipase, it is forced to accommodate its large substituent into the smallest pocket (fig. 6b). This rule works well for secondary alcohols. However for primary alcohols, the rule is only applicable if an oxygen atom is attached to the stereocenter. A similar rue was also proposed for the resolution of carboxylic acids. 

There are two possibilities for the origin of the stereoselectivity in the first one, the reactant loosely associates or collides with the proteins in a stereoselective way. In the other one, the reactant stereoselectively diffuses through the protein. Though both possibilities provide reasonable explanation of the stereoselectivity, the authors suggested that the former was plausible because the cationic quencher attacked the positively charged Lys and/or Arg residue(s) in the heme pocket, and the bulky quenchers might not diffuse into the heme pocket in other words, the reaction would occur at the surface of the protein [68]. 

Shin and Kim [39] used the accessible surface area of essential amino acid residues of the amine pyruvate aminotransferase and various amino donors and acceptors to explore the active site structure. Their results suggested a model consisting of two pockets, one large and the other small. The size difference between the binding pockets and the strong repulsion for a carboxylate in the small pocket were key determinants of the substrate specificity and stereoselectivity. 

Despite the advantage of their easy separation, the use of conventional insoluble polymer-supported catalysts often suffered from a reduced catalytic activity and stereoselectivity, due either to diffusion problems or to a change of the preferred conformations within the chiral pocket created by the ligand around the metal center. In order to circumvent these problems, a new class of crosslinked macromolecule-namely dendronized polymers-has been developed and employed as catalyst supports. In general, two types of such solid-supported dendrimer have been reported (i) with the dendrimer as a hnker of the polymer support and (ii) with dendrons attached to the polymer support [12, 113]. 

Summarizing this part of the study since no steric restriction and no stereoselectivity concerning the substituent in position 3 could be found the binding pocket is supposed to be rather large. 

The adduct of diethylzinc to diols is known to exist as a dimer. This reaction, therefore, proceeded through a mechanism proposed in Scheme 3. The results in Table 2 show that in the addition of diethylzinc to benzaldehyde the polymer-supported tartaric acid creates a chiral pocket that facilitates a stereoselective addition. The data also indicate that the presence of electronegative groups such as hydroxyl and chloro decrease the binding ability of the aldehyde to zinc and thereby slow the rate of the reaction. Therefore, relatively lower yields of the product are obtained. On the other hand, a methyl group lowers the selectivity through steric hindrance. 

Although the acyl pocket is critical in determining the fit of OPs into the active site gorge, Ordentlich et al. (2004) documented the importance of the peripheral anionic site, as well as several additional sites, in determining the stereoselectivity of AChE toward enantiomers of methylphosphonates. 

Ordentlich, A., Barak, D., Sod-Moriah, G., Kaplan, D., Mizrahi, D Segall, Y.. Kronman, C, Karton, Y., Lazar, A., Marcus, D, Velan, B.. and Shatferman, A. (2004). Stereoselectivity toward VX is determined by interactions with residues of the acyl pocket as well as of the peripheral anionic site of AChE, Biochemiury A3,11255-11265. 

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