Candida antarctica Lipase B: An Ideal Biocatalyst for the Preparation of Nitrogenated Organic Compounds

Engineering of Candida antarctica lipase B for hydrolysis of bulky carboxylic acid esters

Candida antarctica lipase B (CALB) is a widely used biocatalyst with high activity and specificity for a wide range of primary and secondary alcohols. However, the range of converted carboxylic acids is more narrow and mainly limited to unbranched fatty acids. To further broaden the biotechnological applications of CALB it is of interest to expand the range of converted carboxylic acid and extend it to carboxylic acids that are branched or substituted in close proximity of the carboxyl group. An in silico library of 2400 CALB variants was built and screened in silico by substrate-imprinted docking, a four step docking procedure. First, reaction intermediates of putative substrates are covalently docked into enzyme active sites. Second, the geometry of the resulting enzyme-substrate complex is optimized. Third, the substrate is removed from the complex and then docked again into the optimized structure. Fourth, the resulting substrate poses are rated by geometric filter criteria as productive or non-productive poses. Eleven enzyme variants resulting from the in silico screening were expressed in Escherichia coli BL21 and measured in the hydrolysis of two branched fatty acid esters, isononanoic acid ethyl ester and 2-ethyl hexanoic acid ethyl esters. Five variants showed an initial increase in activity. The variant with the highest wet mass activity (T138S) was purified and further characterized. It showed a 5-fold increase in hydrolysis of isononanoic acid ethyl ester, but not toward sterically more demanding 2-ethyl hexanoic acid ethyl ester.

Selection of CalB immobilization method to be used in continuous oil transesterification: analysis of the economical impact

Enzymatic transesterification of triglycerides in a continuous way is always a great challenge with a large field of applications for biodiesel, bio-lubricant, bio-surfactant, etc. productions. The lipase B from Candida antarctica (CalB) is the most appreciated enzyme because of its high activity and its non-regio-selectivity toward positions of fatty acid residues on glycerol backbone of triglycerides. Nevertheless, in the field of heterogeneous catalysis, we demonstrated that the medium hydrophilic nature of the support used for its commercial form (Lewatit VPOC1600) is a limitation. Glycerol is adsorbed onto support inducing drastic decrease in enzyme activity. Glycerol would form a hydrophilic layer around the enzyme resulting in diffusional limitations during triglyceride transfer to the enzyme. Accurel MP, a very hydrophobic macroporous polymer of propylene, was found not to adsorb glycerol. Immobilization conditions using this support were optimized. The best support was Accurel MP1001 (particle size<1000 μm) and a pre-treatment of the support with acetone instead of ethanol enables the adsorption rate and the immobilized enzyme quantity to be maximized. An economical approach (maximization of the process net present value) was expanded in order to explore the impact of immobilization on development of an industrial packed bed reactor. The crucial ratio between the quantity of lipase and the quantity of support, taking into account enzyme, support and equipped packed bed reactor costs was optimized in this sense. The biocatalyst cost was found as largely the main cost centre (2-10 times higher than the investments for the reactor vessel). In consequence, optimal conditions for immobilization were a compromise between this immobilization yield (90% of lipase immobilized), biocatalyst activity, reactor volume and total investments.

Enzymatic reactions and synthesis of n-butyl caproate: esterification, transesterification and aminolysis using a recombinant lipase from Geobacillus thermoleovorans CCR11

The recombinant lipase LipMatCCR11 from the thermophilic strain Geobacillus thermoleovorans CCR11 was applied in the synthesis of n-butyl caproate via transesterification in hexane and xylene. The short chain flavour ester was obtained by alcoholysis from ethyl caproate and n-butyl alcohol and acidolysis from n-butyl butyrate and caproic acid. This enzyme was also used in the condensation reaction from caproic acid and n-butanol. The conversion percentages at equilibrium (Xe) were similar to those obtained with Candida antarctica lipase fraction B (CAL-B) in the same reaction conditions, while lower conversion velocities (k) were attained. LipMatCCR11 reached high conversion percentages in either hexane or xylene as organic media (> 63%); the enzyme was also able to catalyze the aminolysis reaction of ethyl caproate with benzyl amine in hexane obtaining a conversion percentage > 62%.

Using hydrogel microparticles to transfer hydrophilic nanoparticles and enzymes to organic media via stepwise solvent exchange

We present a simple and versatile approach of using hydrogel microparticles to transfer both inorganic hydrophilic nanoparticles (NPs) such as CdTe quantum dots and enzymes such as lipase B from Candida antarctica (CalB) to organic media and eventually encapsulate them in the gel microparticles by consecutive exchange of the water swollen in the hydrogel microparticles with water-miscible organic solvents and water-immiscible solvents. The entrapment of hydrophilic nanoparticles is due to their incompatibility with water-immiscible organic solvents soaked in the gel matrices and in the surrounding environment, so the present approach obviates the need for any chemical modification to the NP surface or to the hydrogel and furthermore does not require any size matching or chemical affinity of the NPs for the hydrogel networks. The solvent exchange process causes little change of the intrinsic properties of hydrophilic nanoparticles; CdTe quantum dots encapsulated in hydrogel microparticles, dispersed in water-immiscible organic solvents, remain strongly fluorescent, and CalB retains high catalytic activity. Of importance is that the hydrophilic nanoparticles encapsulated in the gel microparticles in organic media can be completely recovered in aqueous media via reversed solvent exchange. As a consequence, the present approach should hold immense promise for technical applications, especially in catalysis.

Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A

Background

The Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the α/β hydrolase fold. A new superfamily for Candida antarctica lipase A (CALA) was introduced including the recently published crystal structure of CALA. Since CALA has a highly divergent sequence in comparison to other α/β hydrolases, the Lipase Engineering Database was used to classify CALA in the frame of the already established classification system. This involved the comparison of CALA to similar structures as well as sequence-based comparisons against the content of the LED.

Results

The new release 3.0 (December 2009) of the Lipase Engineering Database contains 24783 sequence entries for 18585 proteins as well as 656 experimentally determined protein structures, including the structure of CALA. In comparison to the previous release [1] with 4322 protein and 167 structure entries this update represents a significant increase in data volume. By comparing CALA to representative structures from all superfamilies, a structure from the deacetylase superfamily was found to be most similar to the structure of CALA. While the α/β hydrolase fold is conserved in both proteins, the major difference is found in the cap region. Sequence alignments between both proteins show a sequence similarity of only 15%. A multisequence alignment of both protein families was used to create hidden Markov models for the cap region of CALA and showed that the cap region of CALA is unique among all other proteins of the α/β hydrolase fold. By specifically comparing the substrate binding pocket of CALA to other binding pockets of α/β hydrolases, the binding pocket of Candida rugosa lipase was identified as being highly similar. This similarity also applied to the lid of Candida rugosa lipase in comparison to the potential lid of CALA.

Conclusion

The LED serves as a valuable tool for the systematic analysis of single proteins or protein families. The updated release 3.0 was used for the evaluation of α/β hydrolases. The HTML version of the database with new features is available at http://www.led.uni-stuttgart.de and provides sequences, structures and a set of analysis tools including phylogenetic trees and HMM profiles

Lipase-catalyzed polyester synthesis--a green polymer chemistry

This article is a short comprehensive review describing in vitro polyester synthesis catalyzed by a hydrolysis enzyme of lipase, most of which has been developed for these two decades. Polyesters are prepared by repeated ester bond-formation reactions; they include two major modes, ring-opening polymerization (ROP) of cyclic monomers such as cyclic esters (lactones) and condensation polymerization via the reaction between a carboxylic acid or its ester group and an alcohol group. Polyester synthesis is, therefore, a reaction in reverse way of in vivo lipase catalysis of ester bond-cleavage with hydrolysis. The lipase-catalyzed polymerizations show very high chemo-, regio-, and enantio-selectivities and involve various advantageous characteristics. Lipase is robust and compatible with other chemical catalysts, which allows novel chemoenzymatic processes. New syntheses of a variety of functional polyesters and a plausible reaction mechanism of lipase catalysis are mentioned. The polymerization characteristics are of green nature currently demanded for sustainable society, and hence, desirable for conducting 'green polymer chemistry'.

Dynamic asymmetric multicomponent resolution: lipase-mediated amidation of a double dynamic covalent system

The Strecker reaction is one of the most important multicomponent reactions developed, leading to alpha-aminonitriles that are versatile substrates for many synthetic applications. In the present study, this reaction type has been applied to a double dynamic covalent resolution protocol, leading to efficient C-C- and C-N-bond generation as well as chiral discrimination. The combination of transimination with imine-cyanation enabled the dynamic exchange in more than one direction around a single stereogenic center of restricted structure. This multiple exchange process could generate a vast range of compounds from a low number of starting materials in very short time. The resulting double dynamic covalent systems, created under thermodynamic control, were subsequently coupled in a one-pot process with kinetically controlled lipase-mediated transacylation. This resulted in complete resolution of the dynamic systems, yielding the optimal N-acyl-alpha-aminonitriles for the enzyme, where the individual chemoenzymatic reactions could produce enantiomerically pure acylated N-substituted alpha-aminonitriles in good yields.

Structure-based substrate screening for an enzyme

Background

Nowadays, more and more novel enzymes can be easily found in the whole enzyme pool with the rapid development of genetic operation. However, experimental work for substrate screening of a new enzyme is laborious, time consuming and costly. On the other hand, many computational methods have been widely used in lead screening of drug design. Seeing that the ligand-target protein system in drug design and the substrate-enzyme system in enzyme applications share the similar molecular recognition mechanism, we aim to fulfill the goal of substrate screening by in silico means in the present study.

Results

A computer-aided substrate screening (CASS) system which was based on the enzyme structure was designed and employed successfully to help screen substrates of Candida antarctica lipase B (CALB). In this system, restricted molecular docking which was derived from the mechanism of the enzyme was applied to predict the energetically favorable poses of substrate-enzyme complexes. Thereafter, substrate conformation, distance between the oxygen atom of the alcohol part of the ester (in some compounds, this oxygen atom was replaced by nitrogen atom of the amine part of acid amine or sulfur atom of the thioester) and the hydrogen atom of imidazole of His224, distance between the carbon atom of the carbonyl group of the compound and the oxygen atom of hydroxyl group of Ser105 were used sequentially as the criteria to screen the binding poses. 223 out of 233 compounds were identified correctly for the enzyme by this screening system. Such high accuracy guaranteed the feasibility and reliability of the CASS system.

Conclusion

The idea of computer-aided substrate screening is a creative combination of computational skills and enzymology. Although the case studied in this paper is tentative, high accuracy of the CASS system sheds light on the field of computer-aided substrate screening.

Lipase-catalyzed highly enantioselective kinetic resolution of boron-containing chiral alcohols

The first application of enzymes as catalysts to obtain optically pure boron compounds is described. The kinetic resolution of boron-containing chiral alcohols via enantioselective transesterification catalyzed by lipases was studied. Aromatic, allylic, and aliphatic secondary alcohols containing a boronate ester or boronic acid group were resolved by lipase from Candida antartica (CALB), and excellent E values (E > 200) and high enantiomeric excesses (up to >99%) of both remaining substrates and acetylated product were obtained.