Artificial enzymes structure

In the enzyme design approach, as discussed in the first part of this chapter, one attempts to utilize the mechanistic understanding of chemical reactions and enzyme structure to create a new catalyst. This approach represents a largely academic research field aiming at fundamental understanding of biocatalysis. Indeed, the invention of functional artificial enzymes can be considered to be the ultimate test for any theory on enzyme mechanisms. Most artificial enzymes, to date, do not fulfill the conditions of catalytic efficiency and price per unit necessary for industrial applications. 

As we saw in the previous sections, inclusion compounds have many structural properties which relate them to other systems based on the hierarchy of non-bound interactions, like enzymes or enzyme-substrate complexes. As a matter of fact, most of the so-called artificial enzymes are based on well-known host molecules (e.g. P-cyclodextrin) and are designed to act partly on such bases 108>109). Most of these models, however, take advantage of the inclusion (intra-host encapsulation) phenomena. Construction of proper covalently bound model molecules is a formidable task for the synthetic chemistuo>. Therefore, any kind of advance towards such a goal is welcomed. 

Numerous examples of modiflcations to the fundamental cyclodextrin structure have appeared in the literature.The aim of much of this work has been to improve the catalytic properties of the cyclodextrins, and thus to develop so-called artificial enzymes. Cyclodextrins themselves have long been known to be capable of catalyzing such reactions as ester hydrolysis by interaction of the guest with the secondary hydroxyl groups around the rim of the cyclodextrin cavity. The replacement, by synthetic methods, of the hydroxyl groups with other functional groups has been shown, however, to improve remarkably the number of reactions capable of catalysis by the cyclodextrins. For example, Breslow and CO workersreported the attachment of the pyridoxamine-pyridoxal coenzyme group to beta cyclodextrin, and thus found a two hundred-fold acceleration of the conversion of indolepyruvic acid into tryptophan. 

This interesting result strongly suggests that even for the substituted cyclodextrins the capacity of inclusion formation is much the same as for the parent cyclodextrin. Therefore, we may extend the basic concept of the structure of cyclodextrin inclusion to molecular design for the preparation of artificial enzymes having satisfactory substrate specificities and catalytic activities. 

The preparation and characterization of short peptidic molecules that adopt a stable and predictible structure in solution is a prerequisite for the construction of de now-designed artificial enzymes and proteins. In natural polypeptides, the secondary structures are parts of a larger system and their conformational stability is due to several intra- and interchain non-covalent interactions such as van der Waals forces, electrostatic forces, hydrogen bonding, and hydrophobic forces [2], However, these interactions are less important in short... 

Finally, three groups have reported the preparation of artificial enzymes with catalytic activity. Stewart and co-workers [73] incorporated a catalytic triad from the serine proteases into a designed four a-helix protein (80). In their design, they incorporated one of the amino acids involved in the catalytic function at the N-terminal side of the a-helices that are linked together by their C-terminal position (Fig. 29). The authors proposed that the oxyanion hole and the hydrophobic binding pocket are created by the three-dimensional structure formed by the folding of 80. Compared to the spontaneous reaction, impressive... 

Wulff G, Chong BO, Kolb U. Soluble single-molecule nanogels of controlled structure as a matrix for efficient artificial enzymes. Angewandte Chemie, International Edition 2006, 45, 2955-2958. 

The approaches that have been proposed to immobilize artificial mediators include the adsorption of the redox mediator (9), the immobilization in carbon paste (75), the covalent linkage on electroinactive (75) or conducting polymer backbone (10), the covalent attachement to the enzyme structures (3) and... 

I have been pursuing enzyme mimics, artificial enzymes that perform biomimetic chemistry, since starting my independent career in 1956. In the first work [52-59] my co-workers and I studied models for the function of thiamine pyrophosphate 1 as a coenzyme in enzymes such as carboxylase. We discovered the mechanism by which it acts, by forming an anion 2 that we also described as a stabilized carbene, one of its resonance forms. We examined the related anions from imidazolium cations and oxazolium cations, which produce anions 3 and 4 that can also be described as nucleophilic carbenes. We were able to explain the structure-activity relationships in this series, and the reasons why the thiazolium ring is best suited to act as a biological... 

Phosphate ester cleavage can also be achieved with artificial enzymes using both a metal ion and an additional catalytic group, as in the amide and ester hydrolyses described above. In our first example, catalysts 32 and 33 combined a Zn2+ with a thio-phenol and an imidazole group respectively [121]. The rigid structure prevented the... 

Figure 11.21 Structure of the monomer set Mi used for the synthesis of the polyacid amide artificial enzyme library L15 and the library individual 11.35.

Another example of a cyclodextrin-based artificial enzyme is shown in Fig. 2.15. A phosphodiester is hydrolyzed through cooperative interactions with two imidazolyl groups. The relative positions of the imidazolyl groups and the inclusion geometry of the hydrophobic substrate are structurally well-matched. This artificial enzyme can be regarded as a model of ribonucle-ase A. 

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