Prephenate, Claisen rearrangement

Woodcock HL, M Hodoscek, P Sherwood, YS Lee, HF Schaefer, BR Brooks (2003) Exploring the quantum mechanical/molecular mechanical replica path method a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase. Theor. Chem. Acc. 109 (3) 140-148... 

Extensive theoretical studies have been reported for the parent Claisen rearrangement and for allyl vinyl ethers related to the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase [16]. There has been, by comparison, much less study of the Ireland-Claisen rearrangement. 

In this contribution, we describe work from our group in the development and application of alternatives that allow the explicit inclusion of environment effects while treating the most relevant part of the system with full quantum mechanics. The first methodology, dubbed MD/QM, was used for the study of the electronic spectrum of prephenate dianion in solution [18] and later coupled to the Effective Fragment Potential (EFP) [19] to the study of the Claisen rearrangement reaction from chorismate to prephenate catalyzed by the chorismate mutase (CM) enzyme [20]. 

The Shikimate pathway is responsible for biosynthesis of aromatic amino acids in bacteria, fungi and plants [28], and the absence of this pathway in mammals makes it an interesting target for designing novel antibiotics, fungicides and herbicides. After the production of chorismate the pathway branches and, via specific internal pathways, the chorismate intermediate is converted to the three aromatic amino acids, in addition to a number of other aromatic compounds [29], The enzyme chorismate mutase (CM) is a key enzyme responsible for the Claisen rearrangement of chorismate to prephenate (Scheme 1-1), the first step in the branch that ultimately leads to production of tyrosine and phenylalanine. 

Chorismate mutase catalyzes the Claisen rearrangement of chorismate to prephenate at a rate 106 times greater than that in solution (Fig. 5.5). This enzyme reaction has attracted the attention of computational (bio)chemists, because it is a rare example of an enzyme-catalyzed pericyclic reaction. Several research groups have studied the mechanism of this enzyme by use of QM/MM methods [76-78], It has also been studied with the effective fragment potential (EFP) method [79, 80]. In this method the chemically active part of an enzyme is treated by use of the ab initio QM method and the rest of the system (protein environment) by effective fragment potentials. These potentials account... 

Claisen rearrangement chorismic acid to prephenic acid... 

The hydrophobic effects between the apolar gronps involved in the Diels-Alder reaction also occnr when the apolar gronps belong to the same molecules, and thus should also be beneficial to the Claisen rearrangement. The nonenzymatic rearrangement of chorismate to prephenate occurs 100 times faster in water than in methanol (Copley and Knowles, 1987 Grieco et al., 1989). 

Claisen rearrangement plays an important part in the biosynthesis of several natural products. For example, the chorismate ion is rearranged to the prephenate ion by the Claisen rearrangement, which is catalysed by the enzyme chorismate mutase. This prephenate ion is a key intermediate in the shikimic acid pathway for the biosynthesis of phenylalanine, tyrosine and many other biologically important natural products. 

A biochemically significant Claisen rearrangement is the transformation of choris-mate into prephenate [232] via a chair transition state. Although it is impossible to settle the question of the direction of electron flow during the reorganization, that shown by the arrows in the formula should be preferred when the influence of the various substituents is considered. 

FIGURE 22-19 Biosynthesis of phenylalanine and tyrosine from chorismate in bacteria and plants. Conversion of chorismate to prephenate is a rare biological example of a Claisen rearrangement. 

Chorismate mutase (CM) catalyzes conversion of chorismate into prephenate in a Claisen rearrangement prephenate is a precursor in the biosynthesis of both i-phenylalanine (i-Phe) and i-tyrosine (i-Ttyr). CM occurs as a dimer for structural studies, the monomer was needed (MacBeath, 1998). The assay for CM activity was based on growth of the colonies in the absence of i-Phe and L-Tyr and thus was based on selection, not screening. One resulting mutant was found to be a monomer and to contain a somewhat polar Ala-Arg-Trp-Pro-Trp-Ala sequence. 

A thoroughly investigated reaction on the biosynthetic pathway to aromatics is the [3+3]-sigmatropic Claisen rearrangement from chorismic acid to prephenic acid (Figure 18.8). 

Figure 18.8 Claisen rearrangement from chorismate to prephenate catalyzed by antibodies.

The Claisen rearrangement has attracted special attention because of the pronounced solvent dependence of the reaction [92] and the biochemically important Claisen rearrangement of chorismate to prephenate in the shikimic add pathway [93] (Fig. 12). Both aspects of the reaction have been studied recently using DFT methods. 

Chorismate mutase catalyses the Claisen rearrangement of chorismate to form prephenate. It is an excellent system for analysing catalysis because the same reaction occurs in solution with the same reaction mechanism no covalent catalysis by the... 

Hur S, TC Bruice (2003a) Comparison of formation of reactive conformers (NACs) for the Claisen rearrangement of chorismate to prephenate in water and in the E-coli mutase The efficiency of the enzyme catalysis. J. Am. Chem. Soc. 125 (19) 5964-5972... 

Before we embark on our journey into the world of six-membered transition states, I would like to speak briefly about one reaction, to illustrate how a transition state is drawn throughout the book. The enzyme-catalyzed transformation of chorsimate (2) to prephenate (3) is a classic example of a [3,3]-sigmatropic Claisen rearrangement6 (Scheme IV). As an old bond is being broken and at the same time a new bond is formed in the transition state, the transition state for the Claisen rearrangement of chorismate to prephenate would look more like transistion state A than like B. Still, for the convenience of following the bond connection event clearly, I prefer to draw the transition state like B. 

Chorismate mutase catalyzes the conversion of chorismate to prephenate (Equation 17.44). This reaction is unusual, in that it is the only pericyclic [3,3] sigmatropic rearrangement (Claisen rearrangement) that is catalyzed by an enzyme. 

Chorismate mutase provides an example of an enzyme where QM/MM calculations have identified an important catalytic principle at work [8], This enzyme catalyses the Claisen rearrangement of chorismate to prephenate. The reaction within the enzyme is not believed to involve chemical catalysis, and this pericylic reaction also occurs readily in solution. Lyne et al. [8] investigated the reaction in chorismate mutase in QM/MM calculations, at the AMI QM level (AMI was found to perform acceptably well for this reaction in comparisons with ab initio results for the reaction in the gas phase [8]). Different sizes of QM system were tested in the QM/MM studies (e.g. including the substrate and no, or up to three, protein side chains), and similar results found in all cases. The reaction was modelled by minimization along an approximate reaction coordinate, defined as the ratio of the forming C-C and breaking C-0 bonds. Values of the reaction coordinate were taken from the AMI intrinsic reaction coordinate for the gas-phase reaction. 

Fig. 10). Internal Claisen rearrangement on chorismic acid yields prephenic acid en route to phenylalanine. During the course of the hydroxylation of phenylalanine to tyrosine, there is a characteristic NIH shift of... 

Figure 1 In a QM/MM calculation, a small region is treated by a quantum mechanical (QM) electronic structure method, and the surroundings treated by simpler, empirical, molecular mechanics. In treating an enzyme-catalysed reaction, the QM region includes the reactive groups, with the bulk of the protein and solvent environment included by molecular mechanics. Here, the approximate transition state for the Claisen rearrangement of chorismate to prephenate (catalysed by the enzyme chorismate mutase) is shown. This was calculated at the RHF(6-31G(d)-CHARMM QM-MM level. The QM region here (the substrate only) is shown by thick tubes, with some important active site residues (treated by MM) also shown. The whole model was based on a 25 A sphere around the active site, and contained 4211 protein atoms, 24 atoms of the substrate and 947 water molecules (including 144 water molecules observed by X-ray crystallography), a total of 7076 atoms. The results showed specific transition state stabilization by the enzyme. Comparison with the same reaction in solution showed that transition state stabilization is important in catalysis by chorismate mutase78.

The Claisen rearrangement of chorismate to prephenate, catalyzed by chorismate mutase, is illustrated below. It... 

Figure 12.29 The concerted thermal rearrangement of chorismate to prephenate is a biochemical example of a Claisen rearrangement that is part of the bacterial biosynthesis of the amino acids phenylalanine and tyrosine.

The enzyme chorismate mutase258-259 catalyzes the Claisen rearrangement of chorismate to prephenate in the shikimic acid pathway2f n,2fil. 

Enzymatic studies with chorismate mutase prephenate dehydrogenase from Escherichia coli show that the chorismate prephenate analog 7 is not a substrate for chorismate mutase65. Both 7 and 8 are moderately competitive inhibitors for chorismate mutase. Ester derivatives 4 and 5, as well as 6, readily undergo Claisen rearrangements in organic solvents. 

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