Synthetic enzyme mimics

As explained in a later section (Section VII) cyclodipeptides, especially those containing histidine residues, have been used as synthetic enzyme mimics. Three different aspects of the cyclodipeptide molecular architecture have been made use of in achieving those results (a) H-bond formation with one of the NH groups of the piperazinedione (b) stacking of the aromatic ring over the hetero ring due to weak attractive forces, and (c) hydrophobic interactions with aliphatic side chains. 

The secondary structure of the polypeptide chain in hydrolytic enzymes ensures the spatial proximity of the necessary functional groups, which are responsible for the observed catalytic effect. In synthetic enzyme mimics, it is possible to bring the requisite functionalities into close juxtaposition only if there is a rigid framework to which these groups are attached. It was thus logical to examine cyclic peptides, especially cyclodipeptides, which bear the necessary functional groups for their catalytic activity in ester hydrolysis. 

Table 18.2 Reactivity and binding data for synthetic enzyme mimics (Kirby, 1996).

Although the fundamentals of enzymes, mainly formulated in the first half of the twentieth century still explain most of the properties of enzymes, multidisciplinary efforts have furnished a realm of new biocatalysts and synthetic enzyme mimics that expand the traditional biocatalytic world toward a new scenario of still nascent technology. The following overview covers all these aspects setting up the fundamentals for the use of enzymes in analytical science. 

The field of synthetic enzyme models encompasses attempts to prepare enzymelike functional macromolecules by chemical synthesis [30]. One particularly relevant approach to such enzyme mimics concerns dendrimers, which are treelike synthetic macromolecules with a globular shape similar to a folded protein, and useful in a range of applications including catalysis [31]. Peptide dendrimers, which, like proteins, are composed of amino acids, are particularly well suited as mimics for proteins and enzymes [32]. These dendrimers can be prepared using combinatorial chemistry methods on solid support [33], similar to those used in the context of catalyst and ligand discovery programs in chemistry [34]. Peptide dendrimers used multivalency effects at the dendrimer surface to trigger cooperativity between amino acids, as has been observed in various esterase enzyme models [35]. 

Abstract This chapter updates but mostly supplements the author s Ange-wandte Review,111 setting in context recent advances based on protein and nucleic acid engineering. Systems qualify as a true enzyme mimics if there is experimental evidence for both the initial binding interaction and catalysis with turnover, generally in the shape of saturation kinetics. They are discussed under five broad headings mimics based on natural enzymes, on other proteins, on other biopolymers, on synthetic macromolecules and on small-molecule host-guest interactions. 

Mimics based on natural enzymes Mimics based on other proteins Mimics based on other biopolymers Mimics based on synthetic macromolecules Mimics based on small-molecule host-guest interactions... 

Finally, the most complex synthetic reaction clearly catalysed by RNA molecules generated by in vitro selection is the formation of the C-N bond of a nucleoside (Scheme 7), from 4-thiouracil and most of the natural substrate for the natural (uracil phos-phoribotransferase) reaction.1461. (Thiouracil was used because it is easily tagged by alkylation on sulfur.) The catalytic RNAs produced by 11 rounds of selection required Mg++ cations and had kcat as high as 0.13 min-1,with kcaJKM at least 107 times greater than the (undetectable) uncatalyzed reaction. Once again these systems are convincing, rather efficient enzyme mimics. 

Riley, D.P. Rational design of synthetic enzymes and their potential utility as human pharmaceuticals development of manganese(II)-based superoxide dismutase mimics. Adv. Supramol. Chem. 2000, 6, 217-244. 

Some caution should be exercised however when working with synthetic enzymes. A similarly designed and expressed de novo enzyme to mimic the naturally occurring triose phosphate isomerase was reported in 2004 only for the papers to be retracted when it appeared that contamination by unmodified Escherichia coli had been responsible for the observed enzymic activity. For this reason it seems preferential to target reactions that have no known natural catalysts. 

Chemists now use water as a solvent for synthetic reactions, which takes advantage of the selectivities that the hydrophobic effect can induce (4). Many enzyme mimics (vide infra) also use water as the medium to promote substrate binding into the catalyst. Of course, water as a solvent also has important environmental advantages over volatile organic solvents. It remains to be seen how much impact the special properties of water as a solvent wiU have within chemical synthesis and manufacturing. 

The observed stability of this complex was thus adequate to assess this synthetic SOD mimic in a variety of in vitro and in vivo models of superoxide-mediated injury. Most notably this complex exhibits efficacy in in vitro and in vivo models of inflammation, myocardial ischemia-reperfusion injury, " and vascular relaxation and restenosis. In addition, this and other complexes of this class of SOD mimetics derived from I have superior properties to the SOD enzymes in regard to their normal dose-response curve (no deleterious effects observed at high doses in animal models), cellular permeability (dependent on the nature of the R groups), extended in vivo stability, nonimmunogenicity, and projected lower cost. 

RATIONAL DESIGN OF SYNTHETIC ENZYMES AND THEIR POTENTIAL UTILITY AS HUMAN PHARMACEUTICALS DEVELOPMENT OF MANGANESEdD-BASED SUPEROXIDE DISMUTASE MIMICS Dennis P. Riley... 

The possibility to tailor-make MIPs towards a desired selectivity in combination with the high stability of the materials under a broad range of conditions has rendered MIPs attractive for the development of synthetic enzymes [243, 244]. A popular strategy has been to imprint a transition state analog to obtain a polymer that reduces the activation energy of the reaction. Catalytically active groups are often included in the polymer network. This approach has been applied towards ester and amide hydrolysis reactions [245, 246]. Examples of other reactions where MIPs have been utilized as enzyme mimics are isomerization [247], transamination [248], Diels-Alder reaction [249], 3-elimination [250] and regioselective cycloaddition [251]. 

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