Enzyme Stereospecificity

8 Key excerpts on "Enzyme Stereospecificity"

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  Secondary Plant Products

  A Comprehensive Treatise

  • E. E. Conn(Author)
  • 2013(Publication Date)
  • Academic Press

    (Publisher)

  The importance of stereochemistry in biological systems is impressively documented by two monographs published a few years ago (Bentley, 1969, 1970; Alworth, 1972), which summarized the state of knowledge in this field at that time. Many features of Enzyme Stereospecificity are due to chiral recognition, i.e., the fact that an enzyme, being chiral itself, can recognize stereochemi-cal differences between other molecules or within other molecules and use them to discriminate between stereochemically nonequivalent species or be-tween stereochemically nonequivalent groups within a given molecule. For example, the fact that muscle lactate dehydrogenase converts L-lactate, but not the D isomer, into pyruvate is a clear case of chiral recognition. The enzyme in such cases either cannot bind the 4 4 wrong stereoisomer or it binds it in a manner that does not allow reaction to occur. There are other stereochemical features of enzyme reactions that are not due to chiral recog-nition. For example, it is found that in mixed-function oxygenase-catalyzed hydroxylations at saturated carbon atoms the hydrogen is replaced by the hydroxyl group in a retention mode. This steric course is seen regardless of whether the reaction takes place at a (chiral) methine carbon, in which case chiral recognition could be invoked, at a methylene group, in which the two hydrogens may still be distinct, or at a methyl group, in which there is no longer any intrinsic difference between the three hydrogens that could form the basis for chiral recognition. Obviously, the stereospecificity exhibited by enzymes is not limited to the reactions of chiral molecules for which the steric course of the transforma-tion is evident from the configurations of substrate and product. In fact, the majority of biochemical reactions take place at centers that are not chiral; yet these reactions are usually still stereospecific.

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  Topics in Stereochemistry, Volume 19

  • Ernest L. Eliel, Samuel H. Wilen, Norman L. Allinger, Ernest L. Eliel, Samuel H. Wilen, Norman L. Allinger(Authors)
  • 2009(Publication Date)
  • Wiley-Interscience

    (Publisher)

  To others, the fact that stereochemical diversity correlates with mechanistic diversity, and the presumption that mechanistic diversity must be important are sufficient to conclude that such stereochemical diversity must be adaptive. For example, cryptic stereospecificity is often the same in homologous en- zymes. Its subtlety prompts the belief that it is not adaptive. Thus, the dogma in some quarters is that cryptic stereospecificity is more highly conserved than almost any other enzymatic behavior because it is tightly coupled to tertiary structure in a protein (21). Stereospecificity presumably cannot be reversed without altering tertiary structure and, presumably, destroying catalytic ac- tivity or some other selected behavior. There is remarkably little basis in fact for this opinion. First, as a special example of substrate specificity, stereospecificity is expected to diverge at a rate similar to that for the divergence of substrate specificity in general (9). This rate is rapid, although some of the rate can undoubtedly be ascribed to positive selection for new functions. Further, there are several examples where a modest change in substrate structure or enzyme structure changes the stereospecificity of an enzymatic reaction. For example, the cryptic stereospecificity of citrate synthase from STEVEN A. BENNER ET AL. 133 Clostridium midi-urici is reportedly reversed upon exposure of the enzyme to oxidizing conditions (Figure 2) (22). Data are inadequate to rule out other explanations for the observation; in particular, it is possible that this organ- ism has two isozymes of the enzyme with opposite stereospecificity, and that the more abundant enzyme is more sensitive to destruction by oxygen. The clear implication, however, is that enzymatic stereospecificity can be reversed with only small changes in the structure of the protein. Stereospecificity in an enzymatic reaction can certainly be altered by small changes in substrate structure.

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  Chirality in Supramolecular Assemblies

  Causes and Consequences

  • F. Richard Keene(Author)
  • 2017(Publication Date)
  • Wiley

    (Publisher)

  12 Chirality Related to Biocatalysis and Enzymes in Organic Synthesis

  Declan P. Gavin and Anita R. Maguire

  12.1 Introduction

  The production of chiral compounds as single enantiomers in the synthesis of drugs and intermediates is extremely important to the pharmaceutical industry. In 1992 the US Food and Drug Administration (FDA) issued a policy on stereoisomeric drugs encouraging the commercialization of clinical drugs as single enantiomers [1]; thus chirality is now a crucial aspect of the design and discovery of new drugs. As a result, methods to produce these chiral compounds in an enantioselective manner have become proportionally important.

  Due to the stereoselective interactions of a chiral drug with optically active biological macromolecules, two stereoisomeric compounds tend to differ in their pharmacokinetic/pharmacodynamic properties [2]. Indeed, enantiomeric discrimination displayed by metabolizing enzymes often results in a preference for one enantiomer of a chiral drug [2, 3]. Therefore, one stereoisomer may be responsible for the desired activity of the drug, but its paired enantiomer could have a completely different activity, be an antagonist of the active compound, or may even be inactive [2]. Thus the production of optically active drugs as single enantiomers can be economically desirable.

  Amongst the strategies available to the synthetic organic chemist for controlling the stereochemical outcome of a reaction, catalysis has become the option of choice since the mid‐1980s. In this context the enormous potential of microorganisms and enzymes in the field of asymmetric synthesis has been recognized and the use of whole cells and isolated enzymes is an attractive option for the chemical industry [4, 5].

  12.2 Biocatalysis

  Biocatalysis involves the use of enzymes or whole cells that contain the desired enzyme or enzyme system as catalysts for chemical reactions. Biocatalysis is a broad and growing area of asymmetric synthesis and it is now considered an extremely useful tool for the organic chemist [5–9]. In such a dynamic and burgeoning area, it is not possible to include every aspect of the field and it is not the objective of this chapter to cover in detail the intricacies of every reaction type; the objective is to introduce the concept of biocatalysis and acquaint the reader with some of the many elegant transformations that biocatalysts can perform. Several excellent, general reviews and books exist on the topic for those interested in further reading [5–12].

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  Stereochemistry and Stereoselective Synthesis

  An Introduction

  • Mihály Nógrádi, László Poppe, József Nagy, Gábor Hornyánszky, Zoltán Boros(Authors)
  • 2016(Publication Date)
  • Wiley-VCH

    (Publisher)

  Part III General Characteristics of Stereoselective Reactions

  Selectivity is an all-important key feature of chemical reactions. Selectivity enables multistep reactions to take place economically. Moreover, without selectivity it would be impractical to analyze and purify the products of reactions. After defining stereospecificity and stereoselectivity, this part provides the reader with a systematic analysis of the various types of selectivties with special emphasis on selectivities leading to single enantiomeric products.

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  Chapter 7 Types and Classification of Selectivities

  Selectivity in chemistry is interpreted in various ways. The terms chemoselectivity, regioselectivity, and stereoselectivity (including dia- and enantioselectivity) are widely used. However, there is no general agreement on their precise meaning. Therefore, the following chapters are dedicated to this topic and attempt to provide a uniform interpretative framework.

  7.1 Main Types of Selectivity

  In chemistry, two main types of selectivities can be defined; one depends mainly on the properties of the substrate, while the other differs in the products of a reaction [1]. These two main types of selectivities are shown in the following figures.

  7.1.1 Substrate Selectivity

  A reagent or a catalyst is substrate selective (Figure 7.1 ) when it transforms different substrates (S1 , S2 , …) to products (P1 , P2 , …) under identical conditions at different rates (k1 ≠ k2 ).

  Figure 7.1

  Substrate-selective reactions.

  7.1.2 Product Selectivity

  A reagent or catalyst is product selective (Figure 7.2 ) when it permits the formation of more than one product at different rates (k1 ≠ k2 ) from a single substrate (S) whereby the products (P1 , P2 , …) are formed in a ratio differing from the one statistically expected.1

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  Protein Engineering Handbook

  • Stefan Lutz, Uwe Theo Bornscheuer(Authors)
  • 2012(Publication Date)
  • Wiley-VCH

    (Publisher)

  Chapter 13

  Assessing and Exploiting the Persistence of Substrate Ambiguity in Modern Protein Catalysts

  Kevin K. Desai and Brian G. Miller

  13.1 Quantitative Description of Enzyme Specificity

  A widely accepted tenet of biochemistry is that protein catalysts possess a remarkable level of specificity for their physiological substrates. Indeed, enzymes encounter a surfeit of potential substrates during their normal cellular lifespan, many of which possess overlapping functional groups. Common moieties such as phosphoryl groups, carboxylate side chains and hydroxyl substituents have the potential to complicate molecular recognition inside an active site. Despite the structural and electrostatic similarities of the multitude of metabolites found within a cell, enzymes are capable of selecting from this pool a single substrate for chemical transformation. In so doing, protein catalysts often recognize single atom differences between individual substrates. The discriminatory power of enzymes, which is a hallmark of biological catalysis, is rarely observed in the small-molecule catalytic counterparts that synthetic chemists employ on a daily basis. As a result, chemists and engineers have begun to explore the possibility that Nature’s own catalyst of choice could be subverted for the needs of humankind.

  The ability of enzymes to catalyze the chemical transformations of two competing substrates can be represented by the simple reaction schemes and corresponding rate equations shown below:

  (13.1)

  In Equation 13.1 , E is the enzyme, S1 and S2 are competing substrates, and P1 and P2 are the products of the enzymatic transformations of S1 and S2 , respectively. Similarly, and

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  Enzymes in Organic Synthesis

  • Ruth Porter, Sarah Clark, Ruth Porter, Sarah Clark(Authors)
  • 2009(Publication Date)
  • Wiley

    (Publisher)

  Here we describe a strategy for extending the applicability of esterases of low enantioselectivity in asymmetric synthesis. Theory Origin of enantioselection At present we cannot predict the chirality or the extent of asymmetric induction for a given substrate in biochemical asymmetric catalysis. However, the kinetic functions that govern the process of enantioselection merit attention. 128 ESTERASES IN ASYMMETRIC SYNTHESIS 129 A prochiral substrate S, with enantiotopic ester groupings, may bind to the enzyme (Enz, an esterase) in two modes of equal probability (k, = k;) to generate two complexes Enz-S and Enz-S' , held together with different degrees of tightness (k-l # kLJ. These complexes undergo catalysis to yield the two enantiomers P and Q, according to a simplified reaction mechanism. k2 k3 9 H2O k4 k-2.ROH k-3 k-4 Enz-S - 'Enz-S* - 'Enz-P-Enz+P Enz k; k; * H2O kk Enz-S' - ' Enz-S'* - Enz-Q +Enz + Q kL2.ROH kl_3 kL4 This system consists of multi-step reactions but the relevant steps in enantioselection are only those up to and including the first irreversible step (formation of Enz-S* and Enz-S'*). kcat/Km is the rate constant for the reaction of the enzyme and the substrate at an infinitely low concentration (S+ 0) to give products. Thus enantioselectivity, E', for this system depends on the ratio of (kcat/Km)s to (kcat/Km)s,. (a) High enantioselection. When the substrate undergoes rapid and reversible exchange with the enzyme (i.e. k2 < k-, and k; < kL1), equation (1) is reduced to equation (2). Since the second-order rate constants (k,) for substrates of low molecular weight have values close to those for diffusion controlled processes (Hammes 1982) (so the tightness of substrate binding is determined in most cases by the values of k-J, the formation of Enz-S and Enz-S' occurs with the same probability (k, = ki). Enantioselectivity, E' , therefore depends mainly on the ratio of the reverse commitment to catalysis, Cr/C:.

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  Topics in Stereochemistry, Volume 22

  • Scott E. Denmark(Author)
  • 2009(Publication Date)
  • Wiley-Interscience

    (Publisher)

  Thus, like natural enzymes, antibodies apparently exploit binding interactions remote from the reaction center to control enantioselectivity and stabilize the hydrolytic transition state. The remarkable similarities between 17E8 and six other independently-derived esterolytic antibodies3’ suggest that these conclusions are likely to be general. Although high selectivity is the hallmark of biological catalysis, narrow substrate specificity is disadvantageous for general applications in organic synthesis unless the product of interest is of unusually high value or the transformation cannot be accomplished by standard chemical methods. In general, catalysts that couple high enantio- or diastereoselectivity with broad substrate specificity have the greatest utility, since they obviate the need to develop new agents for each new application. Fuji and co-workers have exploited the emerging structural understanding of antibody-antigen interactions to devise a clever strategy for eliciting highly selective antibody catalysts that also exhibit broad substrate ~pecificity.~~, 34 They reasoned that two sufficiently large hydrophobic groups linked to a stereogenic center in the hapten-for example, to the alcohol leaving group and to the amine protecting group common to a diverse panel of a-amino acid esters-would suffice to induce a deep, chiral pocket capable of providing the desired 90 STEREOSELECTIVE REACTIONS WlTH CATALYTIC ANTIBODIES stereochemical control over the target reaction. The nature and point of attachment of the linker through which the hapten is coupled to camer proteins could then be chosen to accommodate broad structural modifications elsewhere in the molecule.

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  Biochemistry

  • Donald Voet, Judith G. Voet(Authors)
  • 2011(Publication Date)
  • Wiley

    (Publisher)

  We then embark on a detailed examination of the catalytic mechanisms of several of the best characterized enzymes: lysozyme and the serine pro- teases. Their study should lead to an appreciation of the in- tricacies of these remarkably efficient catalysts as well as of the experimental methods used to elucidate their proper- ties. We end with a discussion of how drugs are discovered and tested, a process that depends heavily on the principles of enzymology since many drug targets are enzymes. In do- ing so, we consider how therapeutically effective inhibitors of HIV-1 protease were discovered. 1 CATALYTIC MECHANISMS Catalysis is a process that increases the rate at which a reac- tion approaches equilibrium. Since, as we discussed in Sec- tion 14-1Cb, the rate of a reaction is a function of its free energy of activation (G ‡ ), a catalyst acts by lowering the height of this kinetic barrier; that is, a catalyst stabilizes the transition state with respect to the uncatalyzed reaction. There is, in most cases, nothing unique about enzymatic mechanisms of catalysis in comparison to nonenzymatic mechanisms. What apparently make enzymes such powerful catalysts are two related properties: their specificity of sub- strate binding combined with their optimal arrangement of catalytic groups. An enzyme’s arrangement of binding and catalytic groups is, of course, the product of eons of evolu- tion: Nature has had ample opportunity to fine-tune the performances of most enzymes. The types of catalytic mechanisms that enzymes employ have been classified as: 1. Acid–base catalysis. 2. Covalent catalysis. 3. Metal ion catalysis. 4. Electrostatic catalysis. 5. Proximity and orientation effects. 6. Preferential binding of the transition state complex. In this section, we examine these various phenomena. In doing so we shall frequently refer to the organic model compounds that have been used to characterize these cat- alytic mechanisms.

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