Combinatorial biocatalysis

Draft genome of the blister beetle, Epicauta chinensis

Existence of cantharidin (CTD) in blister beetles is a significant ecological adaptive mechanism that defends against predators and regulates courtship and mating behaviors. To better understand CTD biosynthetic information as well as its biology and pharmacology, we assembled a genome of 151.88 Mb for Epicauta chinensis using PacBio sequencing technology. Gene annotation yielded 249,238 repeats, 527 non-coding RNAs and 12,520 protein-coding genes. Compared to other 11 insects, expansions of gene families in E. chinensis for most core gene families likely associated with environmental adaptation, such as chemoreception, immunity, and detoxification. We further annotated P450s and immune-related genes, a total of 117 putative P450s comprising 7 CYP2, 67 CYP3, 36 CYP4, and 7 mitochondrial P450s and 281 immune-related genes were identified. Comparative analysis of the insect immune repertoires indicated presence of immune genes detected only from Coleopteran insects such as MD2-like. This suggested a lineage-specific gene evolution for Coleopteran insects. Based on the gene family evolution analysis, we identified two probable candidate genes including CYP4TT1 and phytanoyl-CoA dioxygenase for CTD biosynthesis. The high-quality reference genome of E. chinensis provides the genetic basis for further investigation of CTD biosynthesis and in-depth studies of the development and evolution of blister beetles.

State-of-the-Art Biocatalysis

The use of enzyme-mediated reactions has transcended ancient food production to the laboratory synthesis of complex molecules. This evolution has been accelerated by developments in sequencing and DNA synthesis technology, bioinformatic and protein engineering tools, and the increasingly interdisciplinary nature of scientific research. Biocatalysis has become an indispensable tool applied in academic and industrial spheres, enabling synthetic strategies that leverage the exquisite selectivity of enzymes to access target molecules. In this Outlook, we outline the technological advances that have led to the field's current state. Integration of biocatalysis into mainstream synthetic chemistry hinges on increased access to well-characterized enzymes and the permeation of biocatalysis into retrosynthetic logic. Ultimately, we anticipate that biocatalysis is poised to enable the synthesis of increasingly complex molecules at new levels of efficiency and throughput.

Progress in biocatalysis with immobilized viable whole cells: systems development, reaction engineering and applications

Viable microbial cells are important biocatalysts in the production of fine chemicals and biofuels, in environmental applications and also in emerging applications such as biosensors or medicine. Their increasing significance is driven mainly by the intensive development of high performance recombinant strains supplying multienzyme cascade reaction pathways, and by advances in preservation of the native state and stability of whole-cell biocatalysts throughout their application. In many cases, the stability and performance of whole-cell biocatalysts can be highly improved by controlled immobilization techniques. This review summarizes the current progress in the development of immobilized whole-cell biocatalysts, the immobilization methods as well as in the bioreaction engineering aspects and economical aspects of their biocatalytic applications.

A novel indigoid anti-tuberculosis agent

The structure of a novel indigoid component was characterized by X-ray crystallography. This compound exhibited excellent anti-tuberculosis activity against Mycobacterium tuberculosis H37Rv in whole cell culture showing a submicromolar minimum inhibitory concentration (MIC). A synthesis of this molecule was designed and carried out to produce sufficient material for further testing. The in vitro profile, structure, and first synthesis of this indigoid component is reported.

Application of combinatorial biocatalysis for a unique ring expansion of dihydroxymethylzearalenone

Combinatorial biocatalysis was applied to generate a diverse set of dihydroxymethylzearalenone analogs with modified ring structure. In one representative chemoenzymatic reaction sequence, dihydroxymethylzearalenone was first subjected to a unique enzyme-catalyzed oxidative ring opening reaction that creates two new carboxylic groups on the molecule. These groups served as reaction sites for further derivatization involving biocatalytic ring closure reactions with structurally diverse bifunctional reagents, including different diols and diamines. As a result, a library of cyclic bislactones and bislactams was created, with modified ring structures covering chemical space and structure activity relationships unattainable by conventional synthetic means.

Assembly of a three-dimensional array of glycoconjugates by combinatorial biocatalysis in nonaqueous media

Glycoconjugates can be artificially synthesized by combinatorial biocatalysis. An example is given in this paper describing the construction of glycoconjugates array by using glycosidase and lipase in nonaqueous media. This array was started from glucose, with three aryl alcohols as the aglycone moiety of glycosides and five acids or esters as acyl donors for combinatorial acylation of glycosides, affording a three-dimensional array containing about 30 members with diverse structures. The array would be more abundant if more aglycones and acyl donors with other structures were filled in. Indeed, diverse classes of carbohydrates besides glucose can also be employed for generating diverse glycoconjugates due to their different roles in numerous physiological responses. The composition and distribution of the demonstration glycoconjugates array was detected and evaluated by HPLC-MS with electrospray ionization. And also, the distribution of the artificial array can be adjusted by changing the molar ratio of the auxiliary materials.

Microbial transformation of three bufadienolides by Nocardia sp. and some insight for the cytotoxic structure–activity relationship (SAR)

Resibufogenin, cinobufagin, and bufalin are cytotoxic steroids isolated from the Chinese drug Chan'su. Biotransformation of these three bufadienolides by Nocardia sp. NRRL 5646 was investigated. Notably, resibufogenin was converted to 3-acetyl 15beta-hydroxyl bufotalin, via an unprecedented 14beta,15beta-epoxy ring cleavage and a regio-selective acetoxylation. This product showed significantly increased cytotoxic activity. The regio-selective acetylation of the 3-OH was also involved in the other reactions. The structures of metabolites were established by ESI-LC/MS and 2D NMR techniques. The in vitro cytotoxic activities against human cancer cell lines of the substrates and the transformed products were determined by the MTT method and their structure-activity relationship (SAR) was discussed. This investigation provided a useful approach to prepare new bufadienolides and the SAR research.

On oxygen limitation in a whole cell biocatalytic Baeyer–Villiger oxidation process

In this article, a recombinant cyclohexanone monooxygenase (CHMO), overexpressed in Escherichia coli has been used to study the oxidation of bicyclo[3.2.0]hept-2-en-6-one to its two corresponding lactones at very high enantiomeric excess. The reaction is a useful model for the study of biocatalytic oxidations to create optically pure molecules. The major limitations to a highly productive biocatalytic oxidation in this case are oxygen supply, product inhibition, and biocatalyst stability. In this article, we investigate the effects of whole cell biocatalyst concentration on the rate of reaction at a range of scales from shake flasks to 75 L bioreactors. At low cell concentrations (<2 g(dcw)/L) the maximum specific rate (0.65 g/g(dcw).h) is observed. However, at higher cell concentrations (> 2 g(dcw)/L), the reaction becomes oxygen limited and both the specific rate and absolute rate decrease with further increases in cell concentration. The role of oxygen limitation in reducing the rate of reaction with scale was investigated by increasing the maximum oxygen transfer rate in the reactor at a high cell concentration and observing the increase in product formation rate. We propose a qualitative model demonstrating the relationship between oxygen limitation, biocatalyst concentration, and the rate of reaction. This conceptual model will be a useful guide in the industrial scale-up of whole cell mediated Baeyer-Villiger biocatalysis.

Enzymes in the synthesis of bioactive compounds: the prodigious decades

The growing demand for enantiomerically pure pharmaceuticals has impelled research on enzymes as catalysts for asymmetric synthetic transformations. However, the use of enzymes for this purpose was rather limited until the discovery that enzymes can work in organic solvents. Since the advent of the PCR the number of available enzymes has been growing rapidly and the tailor-made biocatalysts are becoming a reality. Thus, it has been possible the use of enzymes for the synthesis of new innovative medicines such as carbohydrates and their incorporation to modern methods for drug development, such as combinatorial chemistry. Finally, the genomic research is allowing the manipulation of whole genomes opening the door to the combinatorial biosynthesis of compounds. In this review, our intention is to highlight the main landmarks that have led to transfer the chemical efficiency shown by the enzymes in the cell to the synthesis of bioactive molecules in the lab during the last 20 years.

Novel cytotoxic bufadienolides derived from bufalin by microbial hydroxylation and their structure-activity relationships

Microbial transformation was used to prepare novel cytotoxic bufadienolides. Twelve products (3-14) were obtained from bufalin (1) by the fungus Mucor spinosus. Their structures were elucidated by high-resolution mass spectroscopy (HR-MS) and extensive NMR techniques, including 1H NMR, 13C NMR, DEPT, 1H-1H correlation spectroscopy (COSY), two dimensional nuclear Overhauser effect correlation spectroscopy (NOESY), heteronuclear multiple quantum coherence (HMQC), and heteronuclear multiple bond coherence (HMBC). Compounds 3, 4, 9 and 11-14 are new mono- or dihydroxylated derivatives of bufalin with novel oxyfunctionalities at C-1beta, C-7beta, C-11beta, C-12beta and C-16alpha positions. The in vitro cytotoxic activities against human cancer cell lines of 3-14, together with 16 biotransformed products derived from cinobufagin (15-30) were determined by the MTT method, and their structure-activity relationships (SAR) were discussed.

Enzymes in organic media

Enzyme catalysis in low water containing organic solvents is finding an increasing number of applications in diverse areas. This review focuses on some aspects which have not been reviewed elsewhere. Different strategies for obtaining higher activity and stability in such media are described. In this context, the damaging role of lyophilization and the means of overcoming such effects are discussed. Ultrasonication and microwave assistance are two emerging approaches for enhancing reaction rates in low water media. Control of water activity and medium engineering are two crucial approaches in optimization of catalytic behaviour in nonaqueous enzymology. Organometallics and synthesis/modification of polymers are two areas where nonaqueous enzymology can play a greater role in the coming years. The greater understanding of enzyme behaviour in nonaqueous media is expected to lead to larger and even more diverse kinds of applications.

Simple and efficient solid support scavenging of excess acyl donors after enzymatic acylations in organic solvents

A simple and efficient method for removing excess acyl donors following enzymatic acylations in organic solvents was developed. This method is based on selective chemical scavenging of acyl donors using an amino-functionalized solid support, and does not affect the desired acylated product. A wide variety of different acyl donors, including vinyl and trifluoroethyl esters and vinyl carbonates, can be quantitatively removed by this method, thus providing a simple and highly efficient tool for purification of reaction products after enzymatic acylation.

A combinatorial biocatalysis approach to an array of cholic acid derivatives

A 39-member library of bile acid derivatives was prepared starting from 3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-oic acid methyl ester using a combinatorial biocatalytic approach. A regioselective oxidation step, catalyzed by hydroxysteroid dehydrogenases, followed by an acylation step with a series of different acyl donors catalyzed by Candida antarctica lipase B, led to the modification of the bile acid scaffold. Each member of the library was obtained in high purity and good yield.

Accelerated design of bioconversion processes using automated microscale processing techniques

Microscale processing techniques are rapidly emerging as a means to increase the speed of bioprocess design and reduce material requirements. Automation of these techniques can reduce labour intensity and enable a wider range of process variables to be examined. This article examines recent research on various individual microscale unit operations including microbial fermentation, bioconversion and product recovery techniques. It also explores the potential of automated whole process sequences operated in microwell formats. The power of the whole process approach is illustrated by reference to a particular bioconversion, namely the Baeyer-Villiger oxidation of bicyclo[3.2.0]hept-2-en-6-one for the production of optically pure lactones.

Developments and trends in enzyme catalysis in nonconventional media

The conventional notion that enzymes are only active in aqueous media has long been discarded, thanks to the numerous studies documenting enzyme activities in nonaqueous media, including pure organic solvents and supercritical fluids. Enzymatic reactions in nonaqueous solvents offer new possibilities for producing useful chemicals (emulsifiers, surfactants, wax esters, chiral drug molecules, biopolymers, peptides and proteins, modified fats and oils, structured lipids and flavor esters). The use of enzymes in both macro- and microaqueous systems has been investigated especially intensively in the last two decades. Although enzymes exhibit considerable activity in nonaqueous media, the activity is low compared to that in water. This observation has led to numerous studies to modify enzymes for specific purposes by various means including protein engineering. This review covers the historical developments, major technological advances and recent trends of enzyme catalysis in nonconventional media. A brief description of different classes of enzymes and their use in industry is provided with representative examples. Recent trends including use of novel solvent systems, role of water activity, stability issues, medium and biocatalyst engineering aspects have been discussed with examples. Special attention is given to protein engineering and directed evolution.

Enzyme technology: an overview

Enzymes are being used in numerous new applications in the food, feed, agriculture, paper, leather, and textiles industries, resulting in significant cost reductions. At the same time, rapid technological developments are now stimulating the chemistry and pharma industries to embrace enzyme technology, a trend strengthened by concerns regarding health, energy, raw materials, and the environment.

Enzyme activation for nonaqueous media

Highly active enzyme formulations can be prepared for use in nonaqueous media. Considerable progress has been made in the past two years on gaining an improved mechanistic understanding of enzyme function and activation in dehydrated environments. This increased fundamental understanding has led to the development of a broad array of techniques for generating active, stable, and enantioselective and regioselective tailored enzymes for synthetically relevant transformations. This, in turn, is resulting in an exponential increase in the opportunities for enzymatic processes to be developed on a commercial scale.