Directed evolution of a carbonyl reductase LsCR for the enantioselective synthesis of (1S)-2-chloro-1-(3,4-difluorophenyl) ethanol

Semi-rational engineering of an α-L-fucosidase for regioselective synthesis of fucosyl-N-acetylglucosamine disaccharides

α-L-Fucosidases are attractive biocatalysts for the production of bioactive fucosylated oligosaccharides, however, poor regioselectivity and activity for transglycosylation have significantly limited their applications. We have recently derived an α-L-Fucosidase, BF3242, from Bacteroides fragilis NCTC9343, which could efficiently synthesize a mixture of Fuc-α-1,3/1,6-GlcNAc, but its 1,3/1,6-regioselectivity was observably affected by reaction temperature. Here, we integrated loop-targeted random mutagenesis and site-directed mutagenesis to engineer the regioselectivity and transglycosylation activity of BF3242. Loop-targeted random mutagenesis revealed that L266 in the loop-4 (H242-S267) within the model of BF3242 was a key residue for the regioselectivity for transglycosylation, and the saturation mutagenesis at residue L266 uncovered a mutant L266H with a significantly increased 1,3-regioselectivity of 97 % from 69 % of WT BF3242. Subsequently, five designed single-site mutations at the putative aglycone subsites were performed, resulting in a double-site mutant L266H/M285C that increased the overall yield of Fuc-α-1,3/1,6-GlcNAc to 76 % from 68 % of WT BF3242. The saturation mutagenesis at residue M285 finally generated a double-site mutant L266H/M285T with the maximal overall yield of Fuc-α-1,3/1,6-GlcNAc of 85 % and 1,3-regioselectivity of 98 %. The R T/H of L266H/M285T was approximately 2.7-fold higher than that of the WT BF3242. Molecular dynamics simulations revealed that the structural flexibility of the loop-4 was substantially reduced in mutant L266H, and the hydrogen bond formation and binding affinity between mutant L266H/M285T and Fuc-α-1,3-GlcNAc was significantly enhanced. The semi-rationally engineered enzyme L266H/M285T would be a promising biocatalyst for highly 1,3-regioselective synthesis of fucosyl-N-acetylglucosamine disaccharide.

Multisite synergistic evolution of oleate hydratase via DCCM and the orthogonal location of distal sites

The evolution of enzymes through multisite combinations is often constrained by the dynamic correlations among residues, resulting in the challenge of achieving additive effects when combining single-site positive mutants. Nevertheless, the incorporation of distal-site residue mutants offers a promising avenue to unlock synergistic interactions, particularly in enzymes with channels that mediate substrate and product transport. While combinatorial mutagenesis typically requires exhaustive screening of extensive mutant libraries to identify superior variants. In this study, a multisite combination strategy using dynamic cross-correlation matrices (DCCM) iterative analysis, coupled with location orthogonal filtration (DCCM/OL) was established based on single-site mutants enhancing enzyme performance by engineering distal residues using the "Structure, SCANEER, and Sequence (3S)" approach. Thirteen beneficial single mutants of oleate hydratase from Staphylococcus aureus (SaOhy), which catalyzes the hydration of linoleic acid, were targeted using the "3S" approach. By employing the DCCM/OL strategy, the number of candidates in the combination mutation library for experimental screening were reduced from 60 to 5. And a triple-site mutant, SaOhy_L151V/I411L/V135A, was ultimately identified, which increased the catalytic efficiencies with linoleic acid and oleic acid by a 4- and 2.3-fold, respectively. The philosophy of multisite mutation based on distal residues using the DCCM/OL strategy effectively achieves an amplification of enzymatic activity with distinct substrates simultaneously. This study offers a promising strategy for the construction of a mutant smart library and multisite combinations to efficiently increase enzymatic performance.

Structure-Guided Engineering of Carbonyl Reductase LbCR to Simultaneously Enhance Catalytic Activity and Thermostability toward Bulky Ketones

(S)-2-Chloro-1-(2,4-dichlorophenyl)ethanol ((S)-TCPE) is an important building block for the synthesis of antifungal drug luliconazole. Herein, a carbonyl reductase (CR) from Levilactobacillus brevis (LbCR) was identified for synthesis of (S)-TCPE. Through comprehensive Ala scanning and site-saturated mutagenesis (SSM) targeting the residues surrounding the substrate-binding pocket, the "best" variant LbCRM4 (N96V/E145A/A202L/M206A) was developed, which displays a 26.0-fold increase in catalytic activity, 83.5-fold enhancement in half-life (t1/2) at 40 °C (101.4 h), excellent enantioselectivity (>99.9% e.e.), and broad substrate scope. Compared to the wild-type (WT) LbCR, catalytic efficiency (kcat/KM) of LbCRM4 was increased by 28.0 folds. Furthermore, a high concentration of TCAP (400 g/L) can be transformed (99.9% conversion) within 7 h by using LbCRM4 and an isopropanol/alcohol dehydrogenase/NADPH cofactor regeneration system, giving (S)-TCPE in >99.9% e.e., which is the highest recorded space-time yield (STY, 1288.9 g/L/day) to date. Molecular dynamics (MD) simulations and dynamic cross-correlation matrix analysis elucidated the substantial catalytic performance improvement of LbCRM4. Together, the development of LbCRM4 not only overcomes the trade-offs between catalytic activity and thermostability but also affords an efficient biocatalytic approach for the synthesis of (S)-TCPE featuring a record STY, laying a solid foundation for industrial manufacturing of luliconazole and other active pharmaceutical intermediates.

Design of a Distal Site Saturation Test-Iterative Parallel Mutagenesis for Engineering Hydroxysteroid Dehydrogenase

Distal protein engineering facilitates the efficient identification of novel modification sites and synergistic modulation of enzyme functions to meet the demands of biocatalysts for industrial applications. Using hydroxysteroid dehydrogenase as a target protein, this study presents a distal site saturation test-iterative parallel mutagenesis (DSST-IPM) strategy to design high-performance enzymes. Twelve single-point mutations were identified to improve the stability-activity trade-off in the distal site, targeting 34 residues. S176G and Q245L exhibited a significant melting temperature (Tm) increase of 11.3 and 10.6 °C, respectively. Iterative parallel screening of mutations yielded the mutation7β-HSDH-M6b, which showed a 13.3 °C higher Tm and 5.92-fold higher catalytic activity (kcat/Km) than the wild-type 7β-HSDH. Systematic analysis of molecular dynamics simulations, quantum mechanical calculations, and dynamic cross-correlation matrix (DCCM), the mechanism behind the enhanced catalytic performance of M6b was elucidated. It uncovered that the critical fourth shell could influence conformational dynamics during the enzyme-catalyzed reaction, leading to alterations in the inter-regional force interaction network. This study thus offers an advanced design framework for improving the efficiency of engineering highly active, thermostable biocatalysts for industrial applications.

Construction of highly active and stable recombinant nattokinase by engineered bacteria and computational design

Nattokinase (NK) is an enzyme that has been recognized as a new potential thrombolytic drug due to its strong thrombolytic activity. However, it is difficult to maintain the enzyme activity of NK during high temperature environment of industrial production. In this study, we constructed six NK mutants with potential for higher thermostability using a rational protein engineering strategy integrating free energy-based methods and molecular dynamics (MD) simulation. Then, wild-type NK and NK mutants were expressed in Escherichia coli (E. coli), and their thermostability and thrombolytic activity were tested. The results showed that, compared with wild-type NK, the mutants Y256P, Q206L and E156F all had improved thermostability. The optimal mutant Y256P showed a higher melting temperature (Tm) of 77.4 °C, an increase of 4 °C in maximum heat-resistant temperature and an increase of 51.8 % in activity at 37 °C compared with wild-type NK. Moreover, we also explored the mechanism of the increased thermostability of these mutants by analysing the MD trajectories under different simulation temperatures.

Engineering of a hydroxysteroid dehydrogenase with simultaneous enhancement in activity and thermostability for efficient biosynthesis of ursodeoxycholic acid

Hydroxysteroid dehydrogenases (HSDHs) catalyze the oxidation/reduction of hydroxyl/keto groups of steroids with high regio- or stereoselectivity, playing an essential role in producing optically pure chemicals. In this work, a novel approach was developed to simultaneously improve the stability and activity of 7β-hydroxysteroid dehydrogenase (7β-HSDH) by combining B-factor analysis and computer-aided prediction. Several advantageous mutants were identified, and the most promising variant, S51Y/P202Y, exhibited 2.3-fold improvements in catalytic activity, 3.3-fold in half-life at 40°C, and 4.7-fold in catalytic efficiency (kcat/Km), respectively. Structural modeling analysis showed that the shortened reversible oxidation reaction catalytic distance and the strengthened residue interactions compared to the wild type were attributed to the improved stability and activity of the obtained mutants. To synthesize ursodeoxycholic acid cost-effectively by mutant S51Y/P202Y, a NAD-kinase was employed to facilitate the substitution of nicotinamide adenine dinucleotide phosphate (NADP+) with nicotinamide adenine dinucleotide (NAD+) in the whole-cell catalysis system. The substrate 7-ketolithocholic acid (100 mM) was converted completely in 0.5 h, achieving a space-time yield of 1,887.3 g L-1 d-1. This work provided a general target-oriented strategy for obtaining stable and highly active dehydrogenase for efficient biosynthesis.

IMPORTANCE

Hydroxysteroid dehydrogenases have emerged as indispensable tools in the synthesis of steroids, bile acids, and other steroid derivatives for the pharmaceutical and chemical industries. In this study, a novel approach was developed to simultaneously improve the stability and activity of a hydroxysteroid dehydrogenase by combining B-factor analysis and computer-aided prediction. This semi-rational method was demonstrated to be highly effective for enzyme engineering. In addition, NAD kinase was introduced to convert NAD+ to NADP+ for effective coenzyme regeneration in the whole-cell multienzyme-catalyzed system. This strategy reduces the significant economic costs associated with externally supplemented cofactors in NADP-dependent biosynthetic pathways.

Advances in aldo-keto reductases immobilization for biocatalytic synthesis of chiral alcohols

Chiral alcohols are essential building blocks of numerous pharmaceuticals and fine chemicals. Aldo-keto reductases (AKRs) constitute a superfamily of oxidoreductases that catalyze the reduction of aldehydes and ketones to their corresponding alcohols using NAD(P)H as a coenzyme. Knowledge about the crucial roles of AKRs immobilization in the biocatalytic synthesis of chiral alcohols is expanding. Herein, we reviewed the characteristics of various AKRs immobilization approaches, the applications of different immobilization materials, and the prospects of continuous flow bioreactor construction by employing these immobilized biocatalysts for synthesizing chiral alcohols. Finally, the opportunities and ongoing challenges for AKR immobilization are discussed and the outlook for this emerging area is analyzed.

Stairway to Stereoisomers: Engineering Short- and Medium-Chain Ketoreductases To Produce Chiral Alcohols

The short- and medium-chain dehydrogenase/reductase superfamilies are responsible for most chiral alcohol production in laboratories and industries. In nature, they participate in diverse roles such as detoxification, housekeeping, secondary metabolite production, and catalysis of several chemicals with commercial and environmental significance. As a result, they are used in industries to create biopolymers, active pharmaceutical intermediates (APIs), and are also used as components of modular enzymes like polyketide synthases for fabricating bioactive molecules. Consequently, random, semi-rational and rational engineering have helped transform these enzymes into product-oriented efficient catalysts. The rise of newer synthetic chemicals and their enantiopure counterparts has proved challenging, and engineering them has been the subject of numerous studies. However, they are frequently limited to the synthesis of a single chiral alcohol. The study attempts to defragment and describe hotspots of engineering short- and medium-chain dehydrogenases/reductases for the production of chiral synthons.

Coevolving stability and activity of LsCR by a single point mutation and constructing neat substrate bioreaction system

Carbonyl reductase (CR)-catalyzed bioreduction in the organic phase and the neat substrate reaction system is a lasting challenge, placing higher requirements on the performance of enzymes. Protein engineering is an effective method to enhance the properties of enzymes for industrial applications. In the present work, a single point mutation E145A on our previously constructed CR mutant LsCR_M3 , coevolved thermostability, and activity. Compared with LsCR_M3 , the catalytic efficiency k_cat /K_M of LsCR_M3 -E145A (LsCR_M4 ) was increased from 6.6 to 21.9 s^-1  mM^-1 . Moreover, E145A prolonged the half-life t_1/2 at 40°C from 4.1 to 117 h, T m ${T}_{m}$ was increased by 5°C, T 50 30 ${T}_{50}^{30}$ was increased by 14.6°C, and T_opt was increased by 15°C. Only 1 g/L of lyophilized Escherichia coli cells expressing LsCR_M4 completely reduced up to 600 g/L 2-chloro-1-(3,4-difluorophenyl)ethanone (CFPO) within 13 h at 45°C, yielding the corresponding (1S)-2-chloro-1-(3,4-difluorophenyl)ethanol ((S)-CFPL) in 99.5% ee_P , with a space-time yield of 1.0 kg/L d, the substrate to catalyst ratios (S/C) of 600 g/g. Compared with LsCR_M3 , the substrate loading was increased by 50%, with the S/C increased by 14 times. Compared with LsCR_WT , the substrate loading was increased by 6.5 times. In contrast, LsCR_M4 completely converted 600 g/L CFPO within 12 h in the neat substrate bioreaction system.

Enhancing the Activity of an Alcohol Dehydrogenase by Using "Aromatic Residue Scanning" at Potential Plasticity Sites

An alcohol dehydrogenase LkADH was successfully engineered to exhibit improved activity and substrate tolerance for the production of (S)-2-chloro-1-(3,4-difluorophenyl)ethanol, an important precursor of ticagrelor. Five potential hotspots were identified for enzyme mutagenesis by using natural residue abundance as an indicator to evaluate their potential plasticity. A semi-rational strategy named "aromatic residue scanning" was applied to randomly mutate these five sites simultaneously by using tyrosine, tryptophan, and phenylalanine as "exploratory residues" to introduce steric hindrance or potential π-π interactions. The best variant Lk-S96Y/L199W identified with 17.2-fold improvement in catalytic efficiency could completely reduce up to 600 g/L (3.1 M) 2-chloro-1-(3,4-difluorophenyl)ethenone in 12 h with >99.5 % ee, giving the highest space-time yield ever reported. This study, therefore, offers a strategy for mutating alcohol dehydrogenase to reduce aromatic substrates and provides an efficient variant for the efficient synthesis of (S)-2-chloro-1-(3,4-difluorophenyl)ethanol.