Microbial and Enzymatic Processes for the Production of Biologically and Chemically Useful Compounds [New Synthetic Methods (69)]

Regioselective asymmetric bioreduction of trans-4-phenylbut-3-en-2-one by whole-cell of Weissella cibaria N9 biocatalyst

There is a considerable interest in the asymmetric production of chiral allylic alcohols, the main building blocks of many functional molecules. The asymmetric reduction of α,β-unsaturated ketones is difficult with traditional chemical protocols in a regioselective and stereoselective manner. In this study, the reductive capacity of whole cell of Leuconostoc mesenteroides N6, Weissella paramesenteroides N7, Weissella cibaria N9, and Leuconostoc pseudomesenteroides N13 was investigated as whole-cell biocatalysts in the enantioselective reduction of (E)-4-phenylbut-3-en-2-one (1). The biocatalytic reduction of 1 to (S,E)-4-phenylbut-3-en-2-ol ((S,E)-2) using the whole cell of W. cibaria N9 isolated from Turkish sourdough was developed in a regioselective fashion, occurring with excellent conversion and recovering the product in good yield. In biocatalytic reduction reactions, the conversion of the substrate and the enantiomeric excess (ee) of the product are significantly affected by optimization parameters such as temperature, agitation rate, pH, and incubation time. Effects of these parameters on ee and conversion were investigated comprehensively. In addition, to our knowledge, this is the first report on production of (S,E)-2 using whole-cell biocatalyst in excellent yield, conversion with enantiopure form and at gram scale. These findings pave the way for the use of whole cell of W. cibaria N9 for challenging higher substrate concentrations of different α,β-unsaturated ketones for regioselective reduction at industrial scale.

Surface-Templated Nanobubbles Protect Proteins from Surface-Mediated Denaturation

In this Letter, we report that surface-bound nanobubbles reduce protein denaturation on methylated glass by irreversible protein shell formation. Single-molecule total internal reflection fluorescence (SM-TIRF) microscopy was combined with intramolecular Förster resonance energy transfer (FRET) to study the conformational dynamics of nitroreductase (NfsB) on nanobubble-laden methylated glass surfaces, using reflection brightfield microscopy to register nanobubble locations with NfsB adsorption. First, NfsB adsorbed irreversibly to nanobubbles with no apparent desorption after 5 h. Moreover, virtually all (96%) of the NfsB molecules that interacted with nanobubbles remained folded, whereas less than 50% of NfsB molecules remained folded in the absence of nanobubbles on unmodified silica or methylated glass surfaces. This trend was confirmed by ensemble-average fluorometer TIRF experiments. We hypothesize that nanobubbles reduce protein damage by passivating strongly denaturing topographical surface defects. Thus, nanobubble stabilization on surfaces may have important implications for antifouling surfaces and improving therapeutic protein storage.

Characterization of an α-amino-ɛ-caprolactam racemase with broad substrate specificity from Citreicella sp. SE45

α-Amino-ε-caprolactam (ACL) racemizing activity was detected in a putative dialkylglycine decarboxylase (EC 4.1.1.64) from Citreicella sp. SE45. The encoding gene of the enzyme was cloned and transformed in Escherichia coli BL21 (DE3). The molecular mass of the enzyme was shown to be 47.4 kDa on SDS-polyacrylamide gel electrophoresis. The enzymatic properties including pH and thermal optimum and stabilities were determined. This enzyme acted on a broad range of amino acid amides, particularly unbranched amino acid amides including L-alanine amide and L-serine amide with a specific activity of 17.5 and 21.6 U/mg, respectively. The K _m and V _max values for D- and L-ACL were 5.3 and 2.17 mM, and 769 and 558 μmol/min.mg protein, respectively. Moreover, the turn over number (K _cat) and catalytic efficiency (K _cat/K _m ) of purified ACL racemase from Citreicella sp. SE45 using L-ACL as a substrate were 465 S^-1 and 214 S^-1mM^-1, respectively. The new ACL racemase from Citreicella sp. SE45 has a potential to be used as the biocatalytic application.

Biocatalytic reduction of racemic 2-arenoxycycloalkanones by yeasts P. glucozyma and C. glabrata: one way of achieving chiral 2-arenoxycycloalcohols

Chiral β-aryloxy alcohols are interesting building blocks that form part of drugs like β adrenergic antagonists. Acquiring cyclic rigid analogs to obtain more selective drugs is interesting. Thus, we used whole cells of yeast strains Pichia glucozyma and Candida glabrata to catalyze the reduction of several 2-arenoxycycloalkanones to produce chiral 2-arenoxycycloalcohols with good/excellent enantioselectivity. In both cases, the alcohol configuration that resulted from the carbonyl group reduction was S. Yeast P. glucozyma allowed the conversion of both enantiomers of the starting material to produce 2-arenoxycycloalcohols with configuration (1S, 2R) and (1S, 2S). The reaction with C. glabrata nearly always allowed the kinetic resolution of the starting ketone, recovering 2-arenoxycycloalkanone with configuration S and (1S, 2R)-2-arenoxycycloalcohol.All the four possible stereoisomers of 2-phenoxycyclohexanol and the two enantiomers of 2-phenoxycyclohexanone were obtained by combining the biocatalyzed reaction with the oxidation/reduction of the chiral compounds with standard reagents. This is a simple approach for the synthesis of the rigid chiral moiety 2-arenoxycycloalcohols contained in putative β-blockers 2-arenoxycycloalkanepropanolamines.

Enzymatic strategies and biocatalysts for amide bond formation: tricks of the trade outside of the ribosome

Amide bond-containing (ABC) biomolecules are some of the most intriguing and functionally significant natural products with unmatched utility in medicine, agriculture and biotechnology. The enzymatic formation of an amide bond is therefore a particularly interesting platform for engineering the synthesis of structurally diverse natural and unnatural ABC molecules for applications in drug discovery and molecular design. As such, efforts to unravel the mechanisms involved in carboxylate activation and substrate selection has led to the characterization of a number of structurally and functionally distinct protein families involved in amide bond synthesis. Unlike ribosomal synthesis and thio-templated synthesis using nonribosomal peptide synthetases, which couple the hydrolysis of phosphoanhydride bond(s) of ATP and proceed via an acyl-adenylate intermediate, here we discuss two mechanistically alternative strategies: ATP-dependent enzymes that generate acylphosphate intermediates and ATP-independent transacylation strategies. Several examples highlighting the function and synthetic utility of these amide bond-forming strategies are provided.

The locks and keys to industrial biotechnology

The sustainable use of resources by Nature to synthesize the required products at the right place, when they are needed, continues to be the role model for total synthesis and production in general. The combination of molecular and engineering science and technology in the biotechnological approach needs no protecting groups at all and has therefore been established for numerous large-scale routes to both natural and synthetic products in industry. The use of biobased raw materials for chemical synthesis, and the economy of molecular transformations like atom economy and step economy are of growing importance. As safety, health and environmental issues are key drivers for process improvements in the chemical industry, the development of biocatalytic reactions or pathways replacing hazardous reagents is a major focus. The integration of the biocatalytic reaction and downstream processing with product isolation has led to a variety of in situ product recovery techniques and has found numerous successful applications. With the growing collection of biocatalytic reactions, the retrosynthetic thinking can be applied to biocatalysis as well. The introduction of biocatalytic reactions is uniquely suited to cost reductions and higher quality products, as well as to more sustainable processes. The transfer of Nature's simple and robust sensing and control principles as well as its reaction and separation organization into useful technical systems can be applied to different fermentations, biotransformations and downstream processes. Biocatalyst and pathway discovery and development is the key towards new synthetic transformations in industrial biotechnology.

Enzymes acting on peptides containing D-amino acid

Mainly microorganisms but only a few higher organisms are presently known to express enzymes that hydrolyze peptides containing D-amino acids. These enzymes can be involved in proceedings at the bacterial cell wall, in either assembly or modification, and thus cause resistance to glycopeptide antibiotics, or mediate resistance against beta-lactam antibiotics. In other cases the in vivo function is still unknown. New enzymes screened from nature, such as D-aminopeptidase, D-amino acid amidase, alkaline D-peptidase or D-aminoacylase, offer potential application in the production of D-amino acids, the synthesis of D-amino acid oligomers by promoting the reversed reaction under appropriate conditions, or in the field of semi-synthetic antibiotics.

An efficient asymmetric synthesis of (S)-atenolol: using hydrolytic kinetic resolution

Enantiomerically pure (S)-atenolol was prepared by using (R,R) salen Co(III) complex for the resolution of terminal epoxide. This process was carried out at room temperature in excellent enantio selectivity. The method can be applied for large-scale preparation of (S)-atenolol without any problem.

Hydratases involved in nitrile conversion: screening, characterization and application

The discovery of new enzymes with greater activity and specificity opens new, simple routes for synthetic processes, and consequently, new methods to solve environmental problems. A number of nitrile-related enzymes have been screened over the past few years for use in developing synthetic applications. Microbial nitrile hydratase (NHase) has great potential as a catalyst in organic chemical processing because the enzyme can convert nitriles to the corresponding higher value amides under mild conditions, and has now been applied to the industrial productions of acrylamide and nicotinamide. Particularly, the former production is the first successful example of a bioconversion process for the manufacture of a commodity chemical. The characterization of the enzyme at the molecular level has provided new insights into how the molecular structure determines the enzyme function, and how the regulatory system controls the expression of the enzyme genes to improve the enzyme and the NHase-dependent process.

Industrial microbial enzymes: their discovery by screening and use in large-scale production of useful chemicals in Japan

The application of microbial enzymes to large-scale organic synthesis is currently attracting much attention, and has been uniquely developed especially in Japan. The discovery of new microbial enzymes through extensive and persistent screening has brought about many new and simple routes for synthetic processes. The application of these enzymes in so-called 'hybrid processes' of enzymatic and chemical reactions, provide one possible way to solve environmental problems.

Synthesis of (R)-1,3-butanediol by enantioselective oxidation using whole recombinant Escherichia coli cells expressing (S)-specific secondary alcohol dehydrogenase

The synthesis of (R)-1,3-butanediol (BDO) from its racemate was studied using whole cells of recombinant Escherichia coli expressing an (S)-specific secondary alcohol dehydrogenase (CpSADH) from Candida parapsilosis by enantioselective oxidation. Under the optimized conditions, the yield of (R)-1,3-BDO reached 72.6 g/l, with a molar recovery yield of 48.4% from a racemate of 15% and an optical purity of 95% ee.

Overview of screening for new microbial catalysts and their uses in organic synthesis--selection and optimization of biocatalysts

As a typical example of screening for a microbial biocatalyst from nature, isolation of aldoxime-degrading microorganisms, characterization of a new enzyme phenylacetaldoxime dehydratase, and application of this enzyme to nitrile synthesis are described. The pathway in which aldoximes are successively degraded via nitrile in microorganisms could be named as 'aldoxime-nitrile pathway'. As an example of a post-screening procedure, a directed molecular evolution technique was successfully used to change the properties of nucleoside pyrophosphate phosphotransferase to make it suitable for synthesis of inosine-5'-monophosphate (5'-IMP). With the mutant enzyme, the efficiency of the production of 5'-IMP, a food additive, was much improved.

Effects of charged water-soluble polymers on the stability and activity of yeast alcohol dehydrogenase and subtilisin Carlsberg

Remarkable increases in enzyme catalytic stability resulting from addition of charged water-soluble polymers have recently been reported, suggesting that use of these polymers may be an attractive general strategy for enzyme stabilization. To test the proposed hypothesis that coulombic forces between water-soluble polymers and enzymes are primarily responsible for enzyme stabilization, we examined the catalytic stability and activity of two enzymes in the presence of polymers differing in net charge. All polymers tested increased enzyme lifetimes, regardless of their net charge, suggesting that stabilization of these enzymes by water-soluble polymers is not solely dependent on simple electrostatic interactions between the polymers and enzymes.

Microbial and reducing agents catalyze the rearrangement of taxanes

5alpha, 7beta, 9alpha, 10beta, 13alpha-Pentahydroxy-4(20),11(12)-taxadiene derivative 1 was converted to two unprecedented 1(15-->11)abeo-taxanes and a taxane derivative with a C10-C11 double bond by Absidia coerula ATCC 10738a. A similar compound was obtained from treatment with zinc of a triacetoxy-4(20),11(12)-taxadiene derivative.

Functional expression and characterization of the two cyclic amidohydrolase enzymes, allantoinase and a novel phenylhydantoinase, from Escherichia coli

A superfamily of cyclic amidohydrolases, including dihydropyrimidinase, allantoinase, hydantoinase, and dihydroorotase, all of which are involved in the metabolism of purine and pyrimidine rings, was recently proposed based on the rigidly conserved structural domains in identical positions of the related enzymes. With these conserved domains, two putative cyclic amidohydrolase genes from Escherichia coli, flanked by related genes, were identified and characterized. From the genome sequence of E. coli, the allB gene and a putative open reading frame, tentatively designated as a hyuA (for hydantoin-utilizing enzyme) gene, were predicted to express hydrolases. In contrast to allB, high-level expression of hyuA in E. coli of a single protein was unsuccessful even under various induction conditions. We expressed HyuA as a maltose binding protein fusion protein and AllB in its native form and then purified each of them by conventional procedures. allB was found to encode a tetrameric allantoinase (453 amino acids) which specifically hydrolyzes the purine metabolite allantoin to allantoic acid. Another open reading frame, hyuA, located near 64.4 min on the physical map and known as a UUG start, coded for D-stereospecific phenylhydantoinase (465 amino acids) which is a homotetramer. As a novel enzyme belonging to a cyclic amidohydrolase superfamily, E. coli phenylhydantoinase exhibited a distinct activity toward the hydantoin derivative with an aromatic side chain at the 5' position but did not readily hydrolyze the simple cyclic ureides. The deduced amino acid sequence of the novel phenylhydantoinase shared a significant homology (>45%) with those of allantoinase and dihydropyrimidinase, but its functional role still remains to be elucidated. Despite the unclear physiological function of HyuA, its presence, along with the allantoin-utilizing AllB, strongly suggested that the cyclic ureides might be utilized as nutrient sources in E. coli.

Construction and evaluation of a novel bifunctional N-carbamylase-D-hydantoinase fusion enzyme

A fully enzymatic process employing two sequential enzymes, D-hydantoinase and N-carbamylase, is a typical case requiring combined enzyme activity for the production of D-amino acids. To test the possibility of generating a bifunctional fusion enzyme, we constructed a fusion protein via end-to-end fusion of a whole gene that encodes an intact protein at the N terminus of the D-hydantoinase. Firstly, maltose-binding protein (MBP) gene of E. coli was fused with D-hydantoinase gene from Bacillus stearothermophilus SD1, and the properties of the resulting fusion protein (MBP-HYD) were compared with those of native D-hydantoinase. Gel filtration and kinetic analyses clearly demonstrated that the typical characteristics of D-hydantoinase are maintained even in a fusion state. Based on this result, we constructed an artificial fusion enzyme composed of the whole length of N-carbamylase (304 amino acids [aa]) from Agrobacterim radiobacter NRRL B11291 and D-hydantoinase (471 aa). The fusion enzyme (CAB-HYD) was functionally expressed with an expected molecular mass of 86 kDa and efficiently converted exogenous hydantoin derivatives to the D-amino acids. A related D-hydantoinase (HYD1) gene from Bacillus thermocatenulatus GH2 was also fused with the N-carbamylase gene at its N terminus. The resulting enzyme (CAB-HYD1) was bifunctional as expected and showed better performance than the CAB-HYD fusion enzyme. The conversion of hydantoin derivatives to corresponding amino acids by the fusion enzymes was much higher than that by the separately expressed enzymes, and comparable to that by the coexpressed enzymes. Thus, the fusion enzyme might be useful as a potential biocatalyst for the production of nonnatural amino acids.

Resolution and synthesis of (S)-1-(2-naphthyl)ethanol with immobilized pea protein: as a new biocatalyst

(S)-1-(2-Naphthyl)ethanol was yielded by immobilized pea (Pisum sativum L.) protein (IPP) from (R, S) 2-naphthyl ethanol (> 99% ee, yield; about 50%), in which the (R)-enantiomer was selectively oxidized to 2-acetonaphthone. IPP could be reused consecutively at least three times without any decrease of yield and optical purity.

Microbial models for drug metabolism

This review describes microbial transformation studies of drugs, comparing them with the corresponding metabolism in animal systems, and providing technical methods for developing microbial models. Emphasis is laid on the potential for selected microorganisms to mimic all patterns of mammalian biotransformations and to provide preparative methods for structural identification and toxicological and pharmacological studies of drug metabolites.

C-terminal regions of D-hydantoinases are nonessential for catalysis, but affect the oligomeric structure

Most microbial D-hydantoinases have been reported to have catalytic properties similar to those of mammalian dihydropyrimidinases. Comparison of the primary structures of microbial D-hydantoinases with mammalian dihydropyrimidinases revealed that the amino acid homology is about 37% and functionally important residues are rigidly conserved at identical positions. Interestingly, however, the C-terminal regions were found to be completely mismatched with each other. In order to investigate the possible role of the C-terminal regions, we deleted the C-terminal regions of the D-hydantoinases from two thermophilic Bacilli and compared the catalytic and structural properties of the mutant enzymes with those of wild-type enzymes. As a result, the C-terminal region was found not to be essential for catalysis, but it does affect the oligomeric structure of the enzyme.