The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems

Chemical reactions that are named in honor of their true, or at least perceived, discoverers are known as "name reactions". This Review is a collection of biological representatives of named chemical reactions. Emphasis is placed on reaction types and catalytic mechanisms that showcase both the chemical diversity in natural product biosynthesis as well as the parallels with synthetic organic chemistry. An attempt has been made, whenever possible, to describe the enzymatic mechanisms of catalysis within the context of their synthetic counterparts and to discuss the mechanistic hypotheses for those reactions that are currently active areas of investigation. This Review has been categorized by reaction type, for example condensation, nucleophilic addition, reduction and oxidation, substitution, carboxylation, radical-mediated, and rearrangements, which are subdivided by name reactions.

New generation of biocatalysts for organic synthesis

The use of enzymes as catalysts for the preparation of novel compounds has received steadily increasing attention over the past few years. High demands are placed on the identification of new biocatalysts for organic synthesis. The catalysis of more ambitious reactions reflects the high expectations of this field of research. Enzymes play an increasingly important role as biocatalysts in the synthesis of key intermediates for the pharmaceutical and chemical industry, and new enzymatic technologies and processes have been established. Enzymes are an important part of the spectrum of catalysts available for synthetic chemistry. The advantages and applications of the most recent and attractive biocatalysts--reductases, transaminases, ammonia lyases, epoxide hydrolases, and dehalogenases--will be discussed herein and exemplified by the syntheses of interesting compounds.

A single residue influences the reaction mechanism of ammonia lyases and mutases

All ways lead to Rome? Computer modeling and kinetic measurements identified a distinct residue in Phe/Tyr ammonia lyases (PAL/TAL) which controls whether the Friedel-Crafts or an E(1)cB reaction mechanism takes place. Hence, Glu484 in pcPAL favors the Friedel-Crafts reaction (see picture, MIO = 4-methylidene imidazol-5-one) whereas an Asn in TAL gives an elimination reaction. These mechanistic investigations also reveal activity of a PAL mutant and a TAL towards an amino alcohol.

Inhibition of histidine ammonia lyase by heteroaryl-alanines and acrylates

Histidine ammonia lyase (HAL) catalyzes the elimination of ammonia from the substrate to form (E)-urocanate. The interaction between HAL and acrylic acids or alanines substituted with heteroaryl groups in the beta-position was investigated. These proved to be strong competitive inhibitors when the heteroaryl groups were furanyl, thiophenyl, benzofuranyl, and benzothiophenyl, carrying the alanyl or acrylic side chains either in 2 or 3 positions, with K(i) values between 18 and 139 microM. The exception was (furan-3-yl)alanine which was found to be inert. Tryptophan and 1-methyltryptophan, as well as the corresponding acrylates (=prop-2-enoates), are strong mixed inhibitors of HAL. Theoretically, L-histidine can be dissected into 4-methyl-1H-imidazole and glycine. Whereas these two compounds separately are only very weak inhibitors of HAL, equimolar amounts of both show a K(i) value of 1.7+/-0.09 mM which is to be compared with the K(m) value of 15.6 mM for the normal reaction. We conclude that 5-methyl-1H-imidazole and glycine mimic the substrate and occupy the active site of HAL in a similar orientation.

Friedel-Crafts-type mechanism for the enzymatic elimination of ammonia from histidine and phenylalanine

The surprisingly high catalytic activity and selectivity of enzymes stem from their ability to both accelerate the target reaction and suppress competitive reaction pathways that may even be dominant in the absence of enzymes. For example, histidine and phenylalanine ammonia-lyases (HAL and PAL) trigger the abstraction of the nonacidic beta protons of these amino acids while leaving the much more acidic ammonium hydrogen atoms untouched. Both ammonia-lyases have a catalytically important electrophilic group, which was believed to be dehydroalanine for 30 years but has now been revealed by X-ray crystallography and UV spectroscopy to be a highly electrophilic 5-methylene-3,5-dihydroimidazol-4-one (MIO) group. Experiments suggest that the reaction is initiated by the electrophilic attack of MIO on the aromatic ring of the substrate. This incomplete Friedel-Crafts-type reaction leads to the activation of a beta proton and its stereospecific abstraction, followed by the elimination of ammonia and regeneration of the MIO group. The plausibility of such a mechanism is supported by a synthetic model. The application of the PAL reaction in the biocatalytic synthesis of enantiomerically pure alpha-amino beta-aryl propionates from aryl acrylates is also discussed.

Novel amino acid derived natural products from the ascidian Atriolum robustum: identification and pharmacological characterization of a unique adenosine derivative

Investigation of the methanolic extract of the Australian ascidian Atriolum robustum led to the isolation and characterization of five new amino acid derived structures (1-5). The structures were elucidated employing spectroscopic techniques (NMR, MS, UV, and IR). The absolute stereochemistry of 1 and 2 was established by chemical degradation, derivatization, and chiral GC-MS analysis. Structures 4 and 5 are complex nucleosides containing rare methylthioadenosine and methylsulfinyladenosine moieties, respectively. In radioligand binding studies the 5'-deoxy-5'-methylthioadenosine-2',3'-diester 4 exhibited affinity for A(1) and A(3) adenosine receptors with K(i) values below 10 microM. Its affinity was somewhat lower for A(2A) (K(i) = 17 microM) and much lower for A(2B) adenosine receptors. Analytical experiments using capillary electrophoresis showed that compound 4 was stable under the conditions of radioligand binding studies. Incubation with carboxylesterase resulted in slow hydrolysis of the adenosine derivative to 5'-deoxy-5'-methylthioadenosine (MTA), which was about 10-fold more potent at adenosine receptors than compound 4. Thus, the 2',3'-diester derivative 4 may act as a lipophilic prodrug of MTA in addition to its own adenosine receptor activity. GTP shift experiments indicated that the adenosine derivative was a partial agonist at A(1) adenosine receptors of rat brain cortical membranes. Compound 4 inhibited cAMP accumulation in Chinese hamster ovary (CHO) cell membranes recombinantly expressing the human A(3) adenosine receptor, thus indicating that the adenosine derivative also acted as a partial agonist at A(3)ARs. Homology models of the A(1) and the A(3) adenosine receptors in their putative active and inactive conformations were built and used for docking of the sterically demanding compound 4. It was found that this ligand fit well into the binding pockets of both receptor subtypes because of its highly flexible structure, although in somewhat different binding modes.

An active site homology model of phenylalanine ammonia-lyase from Petroselinum crispum

The plant enzyme phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) shows homology to histidine ammonia-lyase (HAL) whose structure has been solved by X-ray crystallography. Based on amino-acid sequence alignment of the two enzymes, mutagenesis was performed on amino-acid residues that were identical or similar to the active site residues in HAL to gain insight into the importance of this residues in PAL for substrate binding or catalysis. We mutated the following amino-acid residues: S203, R354, Y110, Y351, N260, Q348, F400, Q488 and L138. Determination of the kinetic constants of the overexpressed and purified enzymes revealed that mutagenesis led in each case to diminished activity. Mutants S203A, R354A and Y351F showed a decrease in kcat by factors of 435, 130 and 235, respectively. Mutants F400A, Q488A and L138H showed a 345-, 615- and 14-fold lower kcat, respectively. The greatest loss of activity occurred in the PAL mutants N260A, Q348A and Y110F, which were 2700, 2370 and 75 000 times less active than wild-type PAL. To elucidate the possible function of the mutated amino-acid residues in PAL we built a homology model of PAL based on structural data of HAL and mutagenesis experiments with PAL. The homology model of PAL showed that the active site of PAL resembles the active site of HAL. This allowed us to propose possible roles for the corresponding residues in PAL catalysis.

Enzymatic catalysis by Friedel-Crafts-type reactions

Although most enzymes work in aqueous medium, at their active sites they can adjust the polarity to meet the requirements of the reactions they catalyse. Thus, a Friedel-Crafts-type electrophilic substitution which is normally conducted in water-free media, can be used to activate the substrate for chemically difficult transformations. It is shown that histidine and phenylalanine ammonia lyases which contain the rare prosthetic group dehydroalanine, make use of a Friedel-Crafts-type reaction which was formerly thought to occur only in rather abiotic conditions. While histidine ammonia-lyase catalyses the first step of histidine degradation in most cells, phenylalanine ammonia-lyase is an important plant enzyme, producing cinnamic acid which is the precursor of lignins, coumarins and flavonoids responsible for the marvelous colours of many flowers.

On the nature of the irreversible inhibition of histidine ammonia lyase by cysteine and dioxygen

The irreversible inhibition of histidine ammonia lyase by L-cysteine and dioxygen has been reexamined. After denaturation and consecutive digestion of the inhibited enzyme by trypsin and endoproteinase Glu-C, the generated chromophoric system (lambda max = 340 nm) remained intact and was isolated in an octapeptide containing amino acids 138-145, as previously described (Hernandez, D.; Stroh, J.G.; Phillips, A. T. Arch. Biochem. Biophys. 1993, 307, 126). Conducting the inhibition in the presence of 18O2 did not result in the incorporation of the heavy isotope into the isolated octapeptide. Total hydrolysis followed by amino acid analysis of the octapeptide revealed the presence of one arginine in addition to those expected from the deduced sequence (G3SVAD). 1H NMR spectroscopy of the octapeptide confirmed the presence of the amino acids GSVAD and showed no signals for olefinic or aromatic protons. To account for the excess mass of the octapeptide, we propose an oxidative degradation of the dehydroalanine prosthetic group, followed by reaction of the resulting dicarbonyl system with a nearby arginine residue.