Kinetic and Mechanistic Studies of a Novel Carbonyl Reductase Isolated from Candida Parapsilosis

Extended Scope and Understanding of Zinc-Dependent Alcohol Dehydrogenases for Reduction of Cyclic α-Diketones

Alcohol dehydrogenases (ADH) are important tools for generating chiral α-hydroxyketones. Previously, only the ADH of Thauera aromatica was known to convert cyclic α-diketones with appropriate preference. Here, we extend the spectrum of suitable enzymes by three alcohol dehydrogenases from Citrifermentans bemidjiense (CibADH), Deferrisoma camini (DecADH), and Thauera phenylacetica (ThpADH). Of these, DecADH is characterized by very high thermostability; CibADH and ThpADH convert α-halogenated cyclohexanones with increased activity. Otherwise, however, the substrate spectrum of all four ADHs is highly conserved. Structural considerations led to the conclusion that conversion of diketones requires not only the expansion of the active site into a large binding pocket, but also the circumferential modification of almost all amino acid residues that form the first shell of the binding pocket. The constellation appears to be overall highly specific for the relative positioning of the carbonyl functions and the size of the C-ring.

Advanced Insights into Catalytic and Structural Features of the Zinc-Dependent Alcohol Dehydrogenase from Thauera aromatica

The asymmetric reduction of ketones to chiral hydroxyl compounds by alcohol dehydrogenases (ADHs) is an established strategy for the provision of valuable precursors for fine chemicals and pharmaceutics. However, most ADHs favor linear aliphatic and aromatic carbonyl compounds, and suitable biocatalysts with preference for cyclic ketones and diketones are still scarce. Among the few candidates, the alcohol dehydrogenase from Thauera aromatica (ThaADH) stands out with a high activity for the reduction of the cyclic α‐diketone 1,2‐cyclohexanedione to the corresponding α‐hydroxy ketone. This study elucidates catalytic and structural features of the enzyme. ThaADH showed a remarkable thermal and pH stability as well as stability in the presence of polar solvents. A thorough description of the substrate scope combined with the resolution and description of the crystal structure, demonstrated a strong preference of ThaADH for cyclic α‐substituted cyclohexanones, and indicated structural determinants responsible for the unique substrate acceptance.

New insights into the stereospecific reduction by an (S) specific carbonyl reductase from Candida parapsilosis ATCC 7330: experimental and QM/MM studies

The quantum mechanics/molecular mechanics study of an (S) specific carbonyl reductase from C. parapsilosis ATCC 7330 showing a dual kinetic response for the reduction of ketones and α-ketoesters suggests different reaction mechanisms for the same.

Full-time dynamics of batch-wise enzymatic cycling system composed of two kinds of dehydrogenase mediated by NAD(P)H for mass production of chiral hydroxyl compounds

Enzymatic cycling system (coupled dehydrogenase-catalyzed biosystem being composed of two elementary enzymatic reactions mediated by NAD(P)H + NAD(P)⁺) is industrially attractive for reducing prochiral carbonyl compounds to the corresponding chiral hydroxyl compounds. The reaction rate equation of the batch-wise biosystem was generally derived by ordered Bi Bi mechanism of two-substrate enzyme reaction on several reasonable assumptions. The rate equations of the batch-wise biosystem was generalized by transforming them into the dimensionless forms. The dimensionless forms were solved numerically. It was revealed that the batch-wise biosystem was generally made up of unique 3 phases, i.e., phases I, II and III. Phase I was very short transient so that the biosystem entered rapidly phase II. In phase II the consumption rate dynamically balanced with its formation rate so that the concentration of NAD(P)H was invariable with time (and hence NAD(P)⁺ concentration was, too). Phase III was substrate-exhausting phase, and the coenzyme concentration became finally only [NAD(P)⁺] or only [NAD(P)H] depending on the initial molar ratio of the prochiral carbonyl compound to the substrate of the coenzyme regeneration reaction ( [Formula: see text] ) > or <1.0. In phases I and II the numerically calculated values of state variables were very close to the analytical but approximate ones. Preferable initial conditions of the batch-wise enzymatic cycling system, i.e., the initial coenzyme species = NAD(P)⁺ and [Formula: see text] , were proposed. As the main assumption irreversibility of the two elemental enzymatic reactions was discussed. Validity of the proposed rate equations was mentioned.

Discovery of a novel thermostable Zn2+ -dependent alcohol dehydrogenase from Chloroflexus aurantiacus through conserved domains mining

AIMS

The purpose of the study was to demonstrate feasibility of the Conserved Domains Database (CDD) for identification of novel biocatalysts with desirable properties from a class of well-characterized biocatalysts.

METHODS AND RESULTS

The thermostable ADH from Sulfolobus solfataricus with a broad substrate range was applied as a template for the search for novel thermostable ADHs via CDD. From the resulting hits, a putative ADH gene from the thermophilic organism Chloroflexus aurantiacus was cloned and expressed in Escherichia coli. The resulting enzyme was purified and characterized. With a temperature activity optimum of 70°C and a broad substrate spectrum especially for diketones, a versatile new biocatalyst was obtained.

CONCLUSIONS

Database-based mining in CDD is a suitable approach to obtain novel biocatalysts with desirable properties. Thereby, the available diversity of similar but not equal enzymes within this class can be increased.

SIGNIFICANCE AND IMPACT OF THE STUDY

For industrial applications, there is a demand for larger diversity of similar well-characterized enzymes in order to test them for a given process (biodiversity screening). For fundamental science, the comparison of enzymes with similar function but different sequence can provide insight into structure function relationships or the evolution of enzymes. This study gives a good example on how this demand can be efficiently met.

A carbonyl reductase from Candida parapsilosis ATCC 7330: substrate selectivity and enantiospecificity

A purified carbonyl reductase (SRED) asymmetrically reduces ketones and α-ketoesters to (S)-alcohols with a potential application in the synthesis of industrially important chiral molecules.

What's My Substrate? Computational Function Assignment of Candida parapsilosis ADH5 by Genome Database Search, Virtual Screening, and QM/MM Calculations

Zinc-dependent medium chain reductase from Candida parapsilosis can be used in the reduction of carbonyl compounds to pharmacologically important chiral secondary alcohols. To date, the nomenclature of cpADH5 is differing (CPCR2/RCR/SADH) in the literature, and its natural substrate is not known. In this study, we utilized a substrate docking based virtual screening method combined with KEGG, MetaCyc pathway, and Candida genome databases search for the discovery of natural substrates of cpADH5. The virtual screening of 7834 carbonyl compounds from the ZINC database provided 94 aldehydes or methyl/ethyl ketones as putative carbonyl substrates. Out of which, 52 carbonyl substrates of cpADH5 with catalytically active docking pose were identified by employing mechanism based substrate docking protocol. Comparison of the virtual screening results with KEGG, MetaCyc database search, and Candida genome pathway analysis suggest that cpADH5 might be involved in the Ehrlich pathway (reduction of fusel aldehydes in leucine, isoleucine, and valine degradation). Our QM/MM calculations and experimental activity measurements affirmed that butyraldehyde substrates are the potential natural substrates of cpADH5, suggesting a carbonyl reductase role for this enzyme in butyraldehyde reduction in aliphatic amino acid degradation pathways. Phylogenetic tree analysis of known ADHs from Candida albicans shows that cpADH5 is close to caADH5. We therefore propose, according to the experimental substrate identification and sequence similarity, the common name butyraldehyde dehydrogenase cpADH5 for Candida parapsilosis CPCR2/RCR/SADH.

Activity prediction of substrates in NADH-dependent carbonyl reductase by docking requires catalytic constraints and charge parameterization of catalytic zinc environment

Molecular docking of substrates is more challenging compared to inhibitors as the reaction mechanism has to be considered. This becomes more pronounced for zinc-dependent enzymes since the coordination state of the catalytic zinc ion is of greater importance. In order to develop a predictive substrate docking protocol, we have performed molecular docking studies of diketone substrates using the catalytic state of carbonyl reductase 2 from Candida parapsilosis (CPCR2). Different docking protocols using two docking methods (AutoDock Vina and AutoDock4.2) with two different sets of atomic charges (AM1-BCC and HF-RESP) for catalytic zinc environment and substrates as well as two sets of vdW parameters for zinc ion were examined. We have selected the catalytic binding pose of each substrate by applying mechanism based distance criteria. To compare the performance of the docking protocols, the correlation plots for the binding energies of these catalytic poses were obtained against experimental Vmax values of the 11 diketone substrates for CPCR2. The best correlation of 0.73 was achieved with AutoDock4.2 while treating catalytic zinc ion in optimized non-bonded (NBopt) state with +1.01 charge on the zinc ion, compared to 0.36 in non-bonded (+2.00 charge on the zinc ion) state. These results indicate the importance of catalytic constraints and charge parameterization of catalytic zinc environment for the prediction of substrate activity in zinc-dependent enzymes by molecular docking. The developed predictive docking protocol described here is in principle generally applicable for the efficient in silico substrate spectra characterization of zinc-dependent ADH.

Enzyme-catalysed regio- and enantioselective preparative scale synthesis of (S)-2-hydroxy alkanones

The alcohol dehydrogenase CPCR2 was applied for the asymmetric reduction of 2,3-alkanediones to the corresponding (S)-2-hydroxy alkanones with high regio- and stereoselectivity and in preparative scale.

A kinetic study and application of a novel carbonyl reductase isolated from Rhodococcus erythropolis

The newly described carbonyl reductase from Rhodococcus erythropolis (RECR) accepts a broad range of substrates. Based on the kinetic constants of a variety of methyl and ethyl ketones a hypothetical model of the substrate-binding site is proposed. Whether a substrate of interest may be reduced by the RECR can be predicted from this model together with the kinetic data. A study of initial velocities and product inhibition is presented, which shows that the kinetics of the RECR follow a Theorell-Chance mechanism. The pro-R hydride of NADH is transferred by the enzyme to the re face of the carbonyl compounds yielding (S)-alcohols. The reduction of methyl 3-oxobutanoate and ethyl 4-chloro-3-oxobutanoate catalyzed by the oxidoreductase lead to the corresponding hydroxy compounds with high enantiomeric purity [enantiomeric excess (e.e.) > or = 99%]. The synthesis of ethyl (2R,3S)-3-hydroxy-2-methylbutanoate was accomplished with high diastereoselectivity (diastereomeric excess = 95%) and enantioselectivity (e.e. > or = 95%).

A novel NADH-dependent carbonyl reductase with an extremely broad substrate range from Candida parapsilosis: purification and characterization

A novel oxidoreductase catalyzing the NADH-dependent reduction of a variety of carbonyl compounds, especially keto esters, was found in Candida parapsilosis DSM 70125. The enzyme was purified by fractional poly(ethylene glycol) precipitation, anion exchange, and affinity chromatography. The enzyme was enriched about 3100-fold and appeared to be homogeneous as judged by native and sodium dodecyl sulfate gel electrophoresis. The carbonyl reductase from C. parapsilosis is a dimeric enzyme with an apparent molecular mass of about 135 kDa. Important properties concerning the application of the enzyme are the relatively broad pH optimum between pH 6.5 and 9.0, temperature optimum between 36 and 42 degrees C, and good stability. Besides keto esters, the new enzyme reduces other aliphatic, aromatic, and cyclic ketones, as well as aldehydes and ketoacetals with high reaction rates. 4-Halo-3-hydroxybutanoates, which are promising chiral intermediates for the chemical synthesis of L-carnitine, alkaloids and pharmaceuticals, are now accessible by enzymatic reduction, as well as several phenyl-ethanol derivatives, which are important for the synthesis of pharmaceuticals and agrochemicals. The preparative applicability of the enzyme was demonstrated in a coupled enzyme system with regeneration of coenzyme. Methyl 3-oxobutanoate was converted into methyl (S)-(+)-3-hydroxybutanoate (98.5% ee), a versatile chiral building block for the synthesis of pheromones and different antibiotics.