Molecular Modification Strategies of Nitrilase for Its Potential Application in Agriculture

Some feed source plants will produce secondary metabolites such as cyanogenic glycosides during metabolism, which will produce some poisonous nitrile compounds after hydrolysis and remain in plant tissues. The consumption of feed-source plants without proper treatment affect the health of the animals' bodies. Nitrilases can convert nitriles and have been used in industry as green biocatalysts. However, due to their bottleneck problems, their application in agriculture is still facing challenges. Acid-resistant nitrilase preparations, high-temperature resistance, antiprotease activity, strong activity, and strict reaction specificity urgently need to be developed. In this paper, the application potential of nitrilase in agriculture, especially in feed processing industry was explored, the source properties and catalytic mechanism of nitrilase were reviewed, and modification strategies for nitrilase application in agriculture were proposed to provide references for future research and application of nitrilase in agricultural and especially in the biological feed scene.

The mechanistic insights into different aspects of promiscuity in metalloenzymes

Enzymes are nature's ultimate machinery to catalyze complex reactions. Though enzymes are evolved to catalyze specific reactions, they also show significant promiscuity in reactions and substrate selection. Metalloenzymes contain a metal ion or metal cofactor in their active site, which is crucial in their catalytic activity. Depending on the metal and its coordination environment, the metal ion or cofactor may function as a Lewis acid or base and a redox center and thus can catalyze a plethora of natural reactions. In fact, the versatility in the oxidation state of the metal ions provides metalloenzymes with a high level of catalytic adaptability and promiscuity. In this chapter, we discuss different aspects of promiscuity in metalloenzymes by using several recent experimental and theoretical works as case studies. We start our discussion by introducing the concept of promiscuity and then we delve into the mechanistic insight into promiscuity at the molecular level.

Arylacetonitrilases: Potential Biocatalysts for Green Chemistry

Nitrilases are the enzymes that catalyze the hydrolysis of nitriles to corresponding carboxylic acid and ammonia. They are broadly categorized into aromatic, aliphatic, and arylacetonitrilases based on their substrate specificity. Most of the studies pertaining to these enzymes in the literature have focused on aromatic and aliphatic nitrilases. However, arylacetonitrilases have attracted the attention of academia and industry in the last several years due to their aryl specificity and enantioselectivity. They have emerged as interesting biocatalytic tools in green chemistry to synthesize useful aryl acids such as mandelic acid and derivatives of phenylacetic acid. The aim of the present review is to collate information on the arylacetonitrilases and their catalytic properties including enantioselectivity and potential applications in organic synthesis.

A Bibliometric Analysis: Current Perspectives and Potential Trends of Enzyme Thermostability from 1991-2022

Thermostability is considered a crucial parameter to evaluate the viability of enzymes in industrial applications. Over the past 31 years, many studies have been reported on the thermostability of enzymes. However, there is no systematic bibliometric analysis of publications on the thermostability of enzymes. In this study, 16,035 publications related to the thermostability of enzymes were searched and collected, showing an increasing annual trend. China contributed the most publications, while the United States had the highest citation count. International Journal of Biological Macromolecules is the most productive journal in the research field. Moreover, Chinese acad sci and Khosro Khajeh are the most active institutions and prolific authors in the field, respectively. Analysis of references with the strongest citation bursts and keyword co-occurrences, magnetic nanoparticles, metal-organic frameworks, molecular dynamics, and rational design are current hot spots and significant future research directions. This study is the first comprehensive bibliometric analysis summarizing trends and developments in enzyme thermostability research. Our findings could provide scholars with an understanding of the fundamental knowledge framework of the field and identify recent potential hotspots and research trends that could facilitate the discovery of collaboration opportunities.

Designing a novel (R)-ω-transaminase for asymmetric synthesis of sitagliptin intermediate via motif swapping and semi-rational design

The application of (R)-ω-transaminases as biocatalysts for chiral amine synthesis has been hampered by inadequate stereoselectivity and narrow substrate spectrum. Herein, an effective evolution strategy for (R)-ω-transaminase designing for the asymmetric synthesis of sitagliptin intermediate is presented. Since natural transaminases lack activity toward bulky prositagliptin ketone, transaminase scaffolds with catalytic machinery and activity toward the truncated prositagliptin ketone were firstly screened based on substrate walking principle. A transaminase chimera was established synchronously conferring catalytic activity and (R)-selectivity toward prositagliptin ketone through motif swapping, followed by stepwise evolution. The process resulted in a "best" engineered variant MwTAM8, which exhibited 79.2-fold higher activity than the chimeric scaffold MwTAMc. Structural analysis revealed that the heightened activity is mainly due to the enlarged and adaptive substrate pocket and tunnel. The novel (R)-transaminase exhibited unsatisfied industrial operation stability, which is expected to further modify the protein to enhance its tolerance to temperature, pH, and organic solvents to meet sustainable industrial demands. This study underscores a useful evolution strategy of engineering biocatalysts to confer new properties and functions on enzymes for synthesizing high-value drug intermediates.

Biochemical and structural characterization of a glucan synthase GFGLS2 from edible fungus Grifola frondosa to synthesize β-1, 3-glucan

BACKGROUND

Grifola frondosa is a Basidiomycete fungus belonging to the family of Grifolaceae and the order of Polyporales. β-Glucans are the main polymers in G. frondosa, playing a crucial role in the physiology and representing the healthy benefits for humans. The membrane-integrated β-1, 3-glucan synthase (GLS) is responsible for glucan synthesis, cell wall assembly, differentiation and growth of the edible fungi. However, the structural/catalytic characteristics and mechanisms of β-1, 3-glucan synthases in G. frondosa are still unknown due to their extremely complex structures with multi-transmembranes and large molecular masses.

RESULTS

Herein, a β-1, 3-glucan synthase (GFGLS2) was purified and identified from the cultured mycelia with a specific activity of 60.01 pmol min-1 μg-1 for the first time. The GFGLS2 showed a strict specificity to UDP-glucose with a Vmax value of 1.29 ± 0.04 µM min-1 at pH 7.0 and synthesized β-1, 3-glucan with a maximum degree of polymerization (DP) of 62. Sequence Similarity Network (SSN) analysis revealed that GFGLS2 has a close relationship with others in Ganoderma sinense, Trametes coccinea, Polyporus brumalis, and Trametes pubescens. With the assistance of 3D structure modelling by AlphaFold 2, molecular docking and molecular dynamics simulations, the central hydrophilic domain (Class III) in GFGLS2 was the main active sites through binding the substrate UDP-glucose to 11 amino acid residues via hydrogen bonds, π-stacking and salt bridges.

CONCLUSIONS

The biochemical, 3D structural characterization and potential catalytic mechanism of a membrane-bound β-1, 3-glucan synthase GFGLS2 from cultured mycelia of G. frondosa were well investigated and would provide a reasonable full picture of β-1, 3-glucan synthesis in fungi.

Recent Progress in the Production of Cyanide-Converting Nitrilases—Comparison with Nitrile-Hydrolyzing Enzymes

Nitrilases have a high potential for application in organic chemistry, environmental technology, and analytics. However, their industrial uses require that they are produced in highly active and robust forms at a reasonable cost. Some organic syntheses catalyzed by nitrilases have already reached a high level of technological readiness. This has been enabled by the large-scale production of recombinant catalysts. Despite some promising small-scale methods being proposed, the production of cyanide-converting nitrilases (cyanide hydratase and cyanide dihydratase) is lagging in this regard. This review focuses on the prospects of cyanide(di)hydratase-based catalysts. The current knowledge of these enzymes is summarized and discussed in terms of the origin and distribution of their sequences, gene expression, structure, assays, purification, immobilization, and uses. Progresses in the production of other nitrilase catalysts are also tackled, as it may inspire the development of the preparation processes of cyanide(di)hydratases.

Improvement of multi-catalytic properties of nitrilase from Paraburkholderia graminis for efficient biosynthesis of 2-chloronicotinic acid

Nitrilase-catalyzed hydrolysis of nitriles is the promising approach for green and efficient biosynthesis of high value-added carboxylic acids. However, undesirable catalytic efficiency toward non-natural substrates restricts their wide-spread applications. Until now, very few robust nitrilases have been reported for 2-chloronicotinic acid (2-CA) production since the enzymes always show low activity and sometimes with poor reaction specificity. Herein, a nitrilase from Paraburkholderia graminis (PgNIT) was engineered to improve its catalytic properties. We identified the beneficial residues via computational analysis and constructed the mutant library. A series positive mutants were obtained and the "best" mutant F164G/I130L/N167Y/A55S exhibited 6000-folds higher catalytic efficiency to 2-chloronicotinonitrile (2-CN). Its reaction specificity was improved with elimination of hydration activity and meanwhile, the half-lives (t_1/2 ) against different temperatures were increased. Molecular docking and molecular dynamics simulation revealed that the steric hindrance, conformational flexibility, as well as nucleophilic attack distance between the enzyme and substrate were the main reason alternating the catalytic properties of PgNIT. With the mutant as biocatalyst, a product yield of 130 g/L 2-CA was produced from 2-CN after 60 h, laying the foundation for constructing the nitrilase-catalyzed route of 2-CA. This article is protected by copyright. All rights reserved.

Engineering of reaction specificity, enantioselectivity and catalytic activity of nitrilase for highly efficient synthesis of pregabalin precursor

Simultaneous evolution of multiple enzyme properties remains challenging in protein engineering. A chimeric nitrilase (BaNIT_M0 ) with high activity towards isobutylsuccinonitrile (IBSN) was previously constructed for biosynthesis of pregabalin precursor (S)-3-cyano-5-methylhexanoic acid ((S)-CMHA). However, BaNIT_M0 also catalyzed the hydration of IBSN to produce by-product (S)-3-cyano-5-methylhexanoic amide. In order to obtain industrial nitrilase with vintage performance, we carried out engineering of BaNIT_M0 for simultaneous evolution of reaction specificity, enantioselectivity and catalytic activity. The best variant V82L/M127I/C237S (BaNIT_M2 ) displayed higher enantioselectivity (E=515), increased enzyme activity (5.4-fold) and reduced amide formation (from 15.8% to 1.9 %) compared with BaNIT_M0 . Structure analysis and molecular dynamics simulations indicated that mutation M127I and C237S restricted the movement of E66 in the catalytic triad, resulting in decreased amide formation. Mutation V82L was incorporated to induce the reconstruction of the substrate binding region in the enzyme catalytic pocket, engendering the improvement of stereoselectivity. Enantio- and regio-selective hydrolysis of 150 g/L IBSN using 1.5 g/L E. coli cells harboring BaNIT_M2 as biocatalyst afforded (S)-CMHA with >99.0% ee and 45.9% conversion, which highlighted the robustness of BaNIT_M2 for efficient manufacturing of pregabalin. This article is protected by copyright. All rights reserved.

Constitutive expression of nitrilase from Rhodococcus zopfii for efficient biosynthesis of 2-chloronicotinic acid

2-chloronicotinic acid (2-CA) is a key precursor for the synthesis of a series of pesticides and pharmaceuticals. Nitrilase-catalyzed bioprocess is a promising method for 2-CA production from 2-chloronicotinonitrile (2-CN). In this study, a mutant of nitrilase from Rhodococcus zopfii (RzNIT/W167G) was constitutively overexpressed with Escherichia coli as host, which exhibited a onefold increase in enzymatic activity compared with inducible expression. Biosynthesis of 2-CA using whole cells harboring nitrilase as biocatalysts were investigated and 318.5 mM 2-CA was produced, which was the highest level for 2-CA production catalyzed by nitrilase to date. 2-CA was recovered from the reaction mixture through a simple acidification step with a recovery yield of 90%. This study developed an efficient bioprocess for 2-CA with great potential for industrial application.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-022-03119-0.

Rational regulation of reaction specificity of nitrilase for efficient biosynthesis of 2-chloronicotinic acid through a single site mutation

Nitrilase-catalyzed hydrolysis of 2-chloronicotinonitrile (2-CN) is a promising approach for efficient synthesis of 2-chloronicotinic acid (2-CA). Development of nitrilase with ideal catalytic properties is crucial for the biosynthetic route with industrial potentail. Herein, a nitrilase from Rhodococcus zopfii (RzNIT), which showed much higher hydration activity than hydrolysis activity, was designed for efficient hydrolysis of 2-CN. Two residues (N165 and W167) significantly affecting the reaction specificity were precisely identified. By tuning these two residues, a single mutation of W167G with abolished hydration activity and 20-fold improved hydrolysis activity was obtained. Molecular dynamics simulation and molecular docking revealed that the mutation generated a larger binding pocket, causing the substrate 2-CN bound more deeply in the pocket and the formation of delocalized π bond between the residues W190 and Y196, which reduced the negative influence of steric hindrance and electron effect caused by chlorine substituent. With mutant W167G as biocatalyst, 100 mM 2-CN was exclusively converted into 2-CA within 16 h. The study provides useful guidance in nitrilase engineering for simultaneous improvement of reaction specificity and catalytic activity, which are highly desirable in value-added carboxylic acids production from nitriles hydrolysis. Importance 2-CA is an important building block for agrochemicals and pharmaceuticals with rapid increase in demand in recent years. It is currently manufactured from 3-cyanopyridine by chemical methods. However, during the final step of 2-CN hydrolysis under high temperature and strong alkaline conditions, by-product 2-CM was generated except for the target product, leading to low yield and tedious separation steps. Nitrilase-mediated hydrolysis is regarded as a promising alternative for 2-CA production, which proceeds under mild conditions. Nevertheless, nitrilase capable of efficient hydrolysis of 2-CN was not reported till now, since the enzymes showed either extremely low activity or surprisingly high hydration activity towards 2-CN. Herein, the reaction specificity of RzNIT was precisely tuned through a single site mutation. The mutant exhibited remarkably enhanced hydrolysis activity without formation of by-products, providing a robust biocatalyst for 2-CA biosynthesis with industrial potential.

Purification and Characterization of Nit phym , a Robust Thermostable Nitrilase From Paraburkholderia phymatum

Despite the success of some nitrilases in industrial applications, there is a constant demand to broaden the catalog of these hydrolases, especially robust ones with high operational stability. By using the criteria of thermoresistance to screen a collection of candidate enzymes heterologously expressed in Escherichia coli, the enzyme Nit _phym from the mesophilic organism Paraburkholderia phymatum was selected and further characterized. Its quick and efficient purification by heat treatment is of major interest for large-scale applications. The purified nitrilase displayed a high thermostability with 90% of remaining activity after 2 days at 30°C and a half-life of 18 h at 60°C, together with a broad pH range of 5.5-8.5. Its high resistance to various miscible cosolvents and tolerance to high substrate loadings enabled the quantitative conversion of 65.5 g⋅L^-1 of 3-phenylpropionitrile into 3-phenylpropionic acid at 50°C in 8 h at low enzyme loadings of 0.5 g⋅L^-1, with an isolated yield of 90%. This study highlights that thermophilic organisms are not the only source of industrially relevant thermostable enzymes and extends the scope of efficient nitrilases for the hydrolysis of a wide range of nitriles, especially trans-cinnamonitrile, terephthalonitrile, cyanopyridines, and 3-phenylpropionitrile.

Improving the activity and thermostability of GH2 β-glucuronidases via domain reassembly

Glycoside hydrolase family 2 (GH2) enzymes are generally composed of three domains: TIM-barrel domain (TIM), immunoglobulin-like β-sandwich domain (ISD), and sugar-binding domain (SBD). The combination of these three domains yields multiple structural combinations with different properties. Theoretically, the drawbacks of a given GH2 fold may be circumvented by efficiently reassembling the three domains. However, very few successful cases have been reported. In this study, we used six GH2 β-glucuronidases (GUSs) from bacteria, fungi, or humans as model enzymes and constructed a series of mutants by reassembling the domains from different GUSs. The mutants PGUS-At, GUS-PAA, and GUS-PAP, with reassembled domains from fungal GUSs, showed improved expression levels, activity, and thermostability, respectively. Specifically, compared to the parental enzyme, the mutant PGUS-At displayed 3.8 times higher expression, the mutant GUS-PAA displayed 1.0 time higher catalytic efficiency (k_cat /K_m ), and the mutant GUS-PAP displayed 7.5 times higher thermostability at 65°C. Furthermore, two-hybrid mutants, GUS-AEA and GUS-PEP, were constructed with the ISD from a bacterial GUS and SBD and TIM domain from fungal GUSs. GUS-AEA and GUS-PEP showed 30.4% and 23.0% higher thermostability than GUS-PAP, respectively. Finally, molecular dynamics simulations were conducted to uncover the molecular reasons for the increased thermostability of the mutant.

Significantly enhancing the stereoselectivity of a regioselective nitrilase for the production of (S)-3-cyano-5-methylhexanoic acid using an MM/PBSA method

The present investigation describes the successful molecular modification of a regio- and stereo-specific nitrilase toward rac-ISBN to (S)-CMHA, a critical intermediate in the preparation of optically pure pregabalin. Two hotspots of Trp57 and Val134 were identified based on the classical binding free energy molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) calculation method. Mutants W57F/V134M and W57Y/V134M were successfully obtained with high enantioselectivity (E >300). Furthermore, these two mutants were efficiently capable of kinetic resolution of rac-ISBN to (S)-CMHA, with both exhibiting a high e.e. (>99.9%), as well as conversion ratios of 43.8% and 40.9%, respectively. Docking and molecular dynamics simulation analysis clarified that the underlying mechanisms were related to a DC-S switch and the formation of a hydrogen bond in the active center of nitrilase. The successful utilization of the MM/PBSA method for identifying hotspots that modulate the stereoselectivity in our study could provide guidelines for the molecular modification of nitrilases, and the mutants obtained could be potentially utilized for the industrial preparation of optically pure pregabalin.

Biocatalysis: Enzymatic Synthesis for Industrial Applications

Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.

A integrated process for nitrilase-catalyzed asymmetric hydrolysis and easy biocatalyst recycling by introducing biocompatible biphasic system

The whole-cell nitrilase-catalyzed asymmetric hydrolysis of nitriles is a green and efficient preparation approach for chiral carboxylic acids, but often suffers from toxicity and cell lysis from organic substrates. In this work, a novel integrated process for whole-cell nitrilase-catalyzed asymmetric hydrolysis was developed for the first time by introducing a biocompatible ionic liquid (IL)-based biphasic system. The whole-cell nitrilases displayed an outstanding stability and recyclability in the biphasic system and still retained > 85% activity even after 7 cycles reaction. A preparative-scale fed-batch hydrolysis of o-chloromandelonitrile to (R)-o-chloromandelic acid (R-CMA) was performed using the integrated process. The results revealed a yield of 91.3% and a space-time yield of 746.4 g·L^-1·d^-1, which are currently the highest reported values for R-CMA biosynthesis. The proposed integrated process avoids substrate inhibition, facilitates the reusability of whole-cell nitrilases, and thus shows great potential for the sustainable production of chiral carboxylic acids.