Current Organic Chemistry - Volume 14, Issue 17, 2010

Biocatalysis focuses on solving chemical problems using natural catalysts derived from living systems, namely enzymes which were originally evolved for the regulation of the chemistry of life. It has obtained tremendous success in the last three decades for various reasons. These include the systematic use of non natural substances as substrates to perturb enzymes, expanding their range of utility in biocatalysis, breakthroughs in genetic engineering allowing the optimization of an enzyme's property through mutagenesis of its genes, and lastly the increased demand for efficient, selective and environmentally friendly processes for the preparation of precious chemicals with highly defined stereochemistry. Biocatalysis is now a powerful tool and a vital part of organic and green chemistry. It has been broadly applied to a wide range of fields, such as pharmaceuticals, agrochemicals, biofuels, etc. Yet it is also a fast moving field. A full coverage of all of its advances in a single review is in fact a ‘mission impossible’. However, careful readers can easily get the inspiration and essence of the field and find useful information by reading the reviews in this issue written by highly regarded figures in the field. For this purpose, Hailes et al. present their work in “Synthetic strategies of α,α'-dihydroxy ketone and 2-amino-1,3-diols via the use of transketolase”. Kim et al. “Design and Evolution of Biocatalysts” and Zhao et al. “Engineering of Enzymes for Selective Catalysis” both discuss directed evolution (DE) in detail. Lin et al. share their views on the promiscuous activity of enzymes. And Wohlgemuth et al. shed light on Organic Synthesis in “Applications of Baeyer-Villiger Monooxygenases in Organic Synthesis” and “High-Yield Biocatalytic Amination Reactions in Organic Synthesis”. From the dawn of the genomic era in the 20th century to today, scientific frontiers have moved to a new horizon with the ultimate goal of understanding entire biological systems on the basis of genomic information. Zhang et al. share this vision and have made the first steps. Among the various disciplines that have sprung up, Genochemistry, with the powerful technological platform of Biocatalysis as its foundation, has this goal as its central purpose. As complementary technologies in related fields improve, Biocatalysis, for all of its accomplishments, is still a budding field full of potential. With an already glorious history, Biocatalysis may yet have an even brighter future.

Naturally occurring enzymes are truly remarkable catalysts. However, many are not suitable for practical synthetic chemistry because of poor substrate or product selectivity. This review highlights recent advances in engineering enzymes for selective catalysis. Selected topics include altering substrate specificity, altering substrate and product selectivity, engineering enzymes that catalyze carboncarbon bond formation or carbon-oxygen bond cleavage and formation, and engineering multi-function enzymes such as polyketide synthases.

There is increasing interest in the use of biocatalysts in synthetic applications due to their ability to achieve highly stereoselective and atom efficient conversions. Recent developments in molecular biology techniques and synthetic biology have also enhanced potential applications using non-natural substrates. Here we review strategies to α, α '-dihydroxy ketones and 2-amino-1,3-diols via the use of transketolase, a carbon-carbon bond forming biocatalyst, and the enzyme transaminase which converts aldehydes and ketones to amines. Using an integrated strategy we have investigated new chemistries and assays, identified novel biocatalysts and used directed evolution strategies, together with miniaturization studies and modelling to achieve rapid and predictive process scale-up.

Enzymes as biocatalysts offer several advantages over their chemical counterparts, and as such have attracted much attention for use in the synthesis of various organic compounds. However, despite many successes in the practical application of enzymes, the extensive use of enzymes in the synthesis of organic compounds is still hindered by inadequacy in substrate specificity, catalytic activity, enantio-selectivity and stability. Enzymes with desired functions targeted for practical applications have long been a goal in protein/ enzyme engineering. Many approaches have been developed and employed for redesigning enzymes with desired properties, including the structure-guided rational method, directed evolution, computational methods, and combinatorial methods. This review will cover recent advances in the design and evolution of enzymes targeted for specific properties, focusing on the strategy and the applicability of each approach.

The annotation of the sequences that encode enzymes to their functions is a significant step towards better understanding of the world's biological systems. This is precisely the body of knowledge that Biocatalysis has been building throughout the 20th century on a case-by-case basis. Candidate technologies and methodologies to accomplish this goal are largely available, yet they have not been brought into practice for this purpose. Combining the knowledge, technologies, and methodologies for this renewed purpose constitutes in fact, a new distinctive science which rests on the foundation of biocatalysis. We henceforth shall refer to it as Genomic Chemistry, or Genochemistry in short, the study of chemistry based on genomic information, resulting from numerous emerging disciplines in the ‘omics’ cascade. Genochemistry is expected to supply more detailed and descriptive information in order to reveal the relationships of enzymes and their catalytic function and annotation of the genomic sequences. Unlike other ‘omics’ investigations, Genochemistry cannot be conducted by any single technology platform. It requires the building of databases on the basis of experimental data and the use of computational methods as well as bioinformatics tools. In this article, we provide a discussion of a framework, a guideline, and the problems that Genochemistry can tackle from distilled information and amassed literatures, with emphasis on the potentially useful technologies.

The amino functionality gives important biological activity in pharmaceutical compounds. The formation of chiral amines and amino acids can be accomplished by several chemical routes but enzymatic formation of amines offers many advantages in preparing chiral amino compounds or amination of fragile compounds compared to stoichiometric or catalytic chemical transformations. Biocatalytic routes to amines primarily use enzymes of the transaminase class (also known as aminotransferases) which transfer the amino function from a donor organic compound to a ketone or aldehyde acceptor. Although known since 1937, the transamination reaction experiences renewed interest due to the advances in biochemistry and molecular biology and the excellent selectivity of biocatalysts. Other enzymes that have been used to synthesize chiral amines are from the phenylalanine ammonia lyase class that use ammonia as the amino source. The use of recombinant enzymes for the biocatalytic preparation of amines is expanding at a great rate and the range of enzymes revealed in DNA sequence databases is of the order of tens of thousands. Since a large number of substrates like ketones, hydroxyketones and ketoacids can be made by chemical synthesis, the growing toolbox of α- , β-, γ-, δ-, ε- and ω-transaminases enable the synthesis of various new chemical entities by biocatalytic amination reactions. In order to simplify the isolation and purification of the product, it is useful to drive the amination reaction to completion. The biocatalytic processes that have been developed show different strategies of overcoming the kinetic limitations of the transaminase reactions and show how some enzymes have been used in processes to make large quantities of chiral compounds with amino functionalities.

The knowledge about these Baeyer-Villiger monooxygenases has grown tremendously since the first discovery and fundamental progress in the understanding of structure, function, substrate specificities and other enzyme properties has been facilitated by the development of recombinant biocatalysts. Nature uses these biocatalysts in aerobic biodegradation pathways of cyclic and acyclic ketones and in the biosynthetic pathways of natural products. The excellent performance of Baeyer-Villiger monooxygenases in nature for the catalysis of Baeyer-Villiger oxidations with high chemo-, regio- and enantioselectivity is a role model for sustainable catalytic Baeyer- Villiger oxidations in organic synthesis. A broad range of biocatalytic conversions of cyclic ketones to lactones, linear ketones to esters, sulfoxidations and other oxidations is described. Applications in dynamic kinetic resolution as well as process and scale-up issues have been important in making this reaction platform attractive to industrial scale Baeyer-Villiger oxidations. New discoveries of Baeyer- Villiger monooxygenases in biosynthesis are promising for highly selective oxidations.

Enzymatic promiscuity, namely the possibility that one active site of an enzyme can catalyze several different chemical transformations, has been an important research field and valuable synthesis tool for protein engineering and synthetic chemistry. This review will focus on promiscuous enzyme-mediated reactions that are useful in organic synthesis. Examples include promiscuous hydrolysis reactions, Michael addition, Markovnikov addition, aldol condensation, Henry reaction, Mannich reaction, Epoxidation reaction, Baeyer-Villiger oxidation, radical polymerization and tandem reactions catalyzed by natural enzymes or engineered enzymes with existing or induced catalytic promiscuity. Among these examples, many enzymes from different family have been verified to be able to catalyze the same type of reaction through distinct mechanism. Many complex compounds or important intermediates can be synthesized using promiscuous enzymes or through novel synthesis pathways. These examples support the enormous potential of enzymatic promiscuity in synthetic chemistry.

Efforts have been made to understand the underlying mechanism and stereochemistry for the observed enantio- and diastereoselectivities in various chiral amine catalyzed Mannich reactions with special reference to proline and its analogous derivatives. Substrate scope in Mannich reaction tunable by structural modification in acceptor and donor components, recent examples, developments, and applications are discussed.

A broad range of free radical transformations such as hydrogen atom transfer, halogen atom transfer, radical cascade, deoxygenations, and additions to olefins and alkynes have been investigated in the presence of InCl3/coreductant (Bu3SnH, TMS3SiH, H3PO2 or NaBH4) as an efficient hydrogen donor system in water. Reactions proceeded smoothly and in excellent yields, with InCl3 playing a dual role as efficient initiator and hydrogen donor. The approach has expanded the kinetic range, stereospecificity as well as broadened the applicability of the free radical transformations in aqueous media. Mechanistic aspects of described transformations are also addressed.

Reaction of N-methyl/isopropylacetonitrilium hexachloroantimonate 1a, b with N-formylbenzotriazole 2 afforded the corresponding iminium salts 4a, b; of which 4a reacts with the oxime derivatives 5a-d to give the corresponding N-oxyiminium salts 6a-d in a good yield (60-92 %). Reaction of N-methylacetonitrilium hexachloroantimonate 1a with norbornene (7) furnished the new ring system 1,4,4a,5,6,7,8,8a-octahydro-5,8-methano-4(2-norbornyl)-naphthridinium hexachloroantimonate 10 in 85 % yield. The Treatment of 10 with DDQ oxidized the two bridged protons and afforded 1,4,5,6,7,8-hexahydro-5,8-methano-4(2-norbornyl)-naphthrdinium hexachloroantimonate 11 in 80% yield.