Engineering the third wave of biocatalysis

Construction of Macroporous β-Glucosidase@MOFs by a Metal Competitive Coordination and Oxidation Strategy for Efficient Cellulose Conversion at 120 °C

Metal-organic frameworks (MOFs) have become promising accommodation for enzyme immobilization in recent years. However, the microporous nature of MOFs affects the accessibility of large molecules, resulting in a significant decline in biocatalysis efficiency. Herein, a novel strategy is reported to construct macroporous MOFs by metal competitive coordination and oxidation with induced defect structure using a transition metal (Fe²⁺) as a functional site. The feasibility of in situ encapsulating β-glucosidase (β-G) within the developed macroporous MOFs endows an enzyme complex (β-G@MOF-Fe) with remarkably enhanced synergistic catalysis ability. The 24 h hydrolysis rate of β-G@MOF-Fe (with respect to cellobiose) is as high as approximately 99.8%, almost 32.2 times that of free β-G (3.1%). Especially, the macromolecular cellulose conversion rate of β-G@MOF-Fe reached 90% at 64 h, while that of β-G@MOFs (most micropores) was only 50%. This improvement resulting from the expansion of pores (significantly increased at 50-100 nm) can provide enough space for the hosted biomacromolecules and accelerate the diffusion rate of reactants. Furthermore, unexpectedly, the constructed β-G@MOF-Fe showed a superior heat resistance of up to 120 °C, attributing to the new strong coordination bond (Fe²⁺-N) formation through the metal competitive coordination. Therefore, this study offers new insights to solve the problem of the high-temperature macromolecular substrate encountered in the actual reaction.

Possibilities of Using De Novo Design for Generating Diverse Functional Food Enzymes

Food enzymes have an important role in the improvement of certain food characteristics, such as texture improvement, elimination of toxins and allergens, production of carbohydrates, enhancing flavor/appearance characteristics. Recently, along with the development of artificial meats, food enzymes have been employed to achieve more diverse functions, especially in converting non-edible biomass to delicious foods. Reported food enzyme modifications for specific applications have highlighted the significance of enzyme engineering. However, using direct evolution or rational design showed inherent limitations due to the mutation rates, which made it difficult to satisfy the stability or specific activity needs for certain applications. Generating functional enzymes using de novo design, which highly assembles naturally existing enzymes, provides potential solutions for screening desired enzymes. Here, we describe the functions and applications of food enzymes to introduce the need for food enzymes engineering. To illustrate the possibilities of using de novo design for generating diverse functional proteins, we reviewed protein modelling and de novo design methods and their implementations. The future directions for adding structural data for de novo design model training, acquiring diversified training data, and investigating the relationship between enzyme-substrate binding and activity were highlighted as challenges to overcome for the de novo design of food enzymes.

Using Defect Control To Break the Stability-Activity Trade-Off in Enzyme Immobilization via Competitive Coordination

Immobilization of enzymes within metal-organic frameworks is a powerful strategy to enhance the long-term usability of labile enzymes. However, the thus-confined enzymes suffer from the trade-off between enhanced stability and reduced activity because of the contradiction between the high crystallinity and the low accessibility. Here, by taking laccase and zeolitic imidazolate framework-8 (ZIF-8) as prototypes, we disclosed an observation that the stability-activity trade-off could be solved by controlling the defects via competitive coordination. Owing to the presence of competitive coordination between laccase and the ligand precursor of ZIF-8, there existed a three-stage process in the de novo encapsulation: nucleation-crystallization-recrystallization. Our results show that the biocomposites collected before the occurrence of recrystallization possessed both increased activity and enhanced stability. The findings here shed new light on the control of defects through the subtle use of competitive coordination, which is of great significance for the engineering application of biomacromolecules.

Tuning Local Coordination Environments of Manganese Single-Atom Nanozymes with Multi-Enzyme Properties for Selective Colorimetric Biosensing

Single-atom nanozymes (SAzymes) are promising in next-generation nanozymes, nevertheless, how to rationally modulate the microenvironment of SAzymes with controllable multi-enzyme properties is still challenging. Herein, we systematically investigate the relationship between atomic configuration and multi-enzymatic performances. The constructed Mn_SA -N₃ -coordinated SAzymes (Mn_SA -N₃ -C) exhibits much more remarkable oxidase-, peroxidase-, and glutathione oxidase-like activities than that of Mn_SA -N₄ -C. Based on experimental and theoretical results, these multi-enzyme-like behaviors are highly dependent on the coordination number of single atomic Mn sites by local charge polarization. As a consequence, a series of colorimetric biosensing platforms based on Mn_SA -N₃ -C SAzymes is successfully built for specific recognition of biological molecules. These findings provide atomic-level insight into the microenvironment of nanozymes, promoting rational design of other demanding biocatalysts.

Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity

Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable.

Construction nanoenzymes with elaborately regulated multi-enzymatic activities for photothermal-enhanced catalytic therapy of tumor

In order to solve the limitation of tumor microenvironment on the anticancer effect of nanozymes, a multifunctional nanoenzyme Co/La-PB@MOF-199/GOx was designed in this work. By doping Co²⁺ and La³⁺ in different proportions, Co/La-PB with the optimal photothermal-enhanced catalytic performance was screened, which can catalyze H₂O₂ to generate more hydroxyl radicals (•OH) and oxygen, showing peroxidase (POD)-like and catalase(CAT)-like property. Through MOF-199 coating and loading glucose oxidase (GOx), a multifunctional nanoenzyme Co/La-PB@MOF-199/GOx was achieved. Due to the pH response of MOF-199, GOx can be accurately released into tumors to catalyze the reaction of glucose and oxygen to produce H₂O₂. In this process, the oxygen consumption can be compensated by the CAT-like property to realize continuous consumption of glucose and self-supply of H₂O₂ to continuously produce •OH. In the presence of high oxidation state metal ions (Co³⁺ and Fe³⁺), GSH consumption is accelerated to avoid weakening of •OH, showing the glutathione oxidase (GPx-like) activity. Besides, magnetic resonance imaging (MRI) experiments showed the potential application in imaging guided therapy. In vivo anti-tumor experiments showed a satisfactory anti-cancer effect through multi-enzymatic activities.

Asymmetric Ene-Reduction by F420 -Dependent Oxidoreductases B (FDOR-B) from Mycobacterium smegmatis

Asymmetric reduction by ene-reductases has received considerable attention in recent decades. While several enzyme families possess ene-reductase activity, the Old Yellow Enzyme (OYE) family has received the most scientific and industrial attention. However, there is a limited substrate range and few stereocomplementary pairs of current ene-reductases, necessitating the development of a complementary class. Flavin/deazaflavin oxidoreductases (FDORs) that use the uncommon cofactor F₄₂₀ have recently gained attention as ene-reductases for use in biocatalysis due to their stereocomplementarity with OYEs. Although the enzymes of the FDOR-As sub-group have been characterized in this context and reported to catalyse ene-reductions enantioselectively, enzymes from the similarly large, but more diverse, FDOR-B sub-group have not been investigated in this context. In this study, we investigated the activity of eight FDOR-B enzymes distributed across this sub-group, evaluating their specific activity, kinetic properties, and stereoselectivity against α,β-unsaturated compounds. The stereochemical outcomes of the FDOR-Bs are compared with enzymes of the FDOR-A sub-group and OYE family. Computational modelling and induced-fit docking are used to rationalize the observed catalytic behaviour and proposed a catalytic mechanism.

A Photoenzymatic Strategy for Radical-Mediated Stereoselective Hydroalkylation with Diazo Compounds

Carbene insertion reactions initiated with diazo compounds have been widely used to develop unnatural enzymatic reactions. However, alternative functionalization of diazo compounds in enzymatic processes has been unexploited. Herein, we describe a photoenzymatic strategy for radical-mediated stereoselective hydroalkylation with diazo compounds. This method generates carbon-centered radicals through an ene reductase catalyzed photoinduced electron transfer process from diazo compounds, enabling the synthesis of γ-stereogenic carbonyl compounds in good yields and stereoselectivities. This study further expands the possible reaction patterns in photo-biocatalysis and offers a new approach to solving the selectivity challenges of radical-mediated reactions.

Biocatalytic Synthesis of Antiviral Nucleosides, Cyclic Dinucleotides, and Oligonucleotide Therapies

Nucleosides, nucleotides, and oligonucleotides modulate diverse cellular processes ranging from protein production to cell signaling. It is therefore unsurprising that synthetic analogues of nucleosides and their derivatives have emerged as a versatile class of drug molecules for the treatment of a wide range of disease areas. Despite their great therapeutic potential, the dense arrangements of functional groups and stereogenic centers present in nucleic acid analogues pose a considerable synthetic challenge, especially in the context of large-scale manufacturing. Commonly employed synthetic methods rely on extensive protecting group manipulations, which compromise step-economy and result in high process mass intensities. Biocatalytic approaches have the potential to address these limitations, enabling the development of more streamlined, selective, and sustainable synthetic routes. Here we review recent achievements in the biocatalytic manufacturing of nucleosides and cyclic dinucleotides along with progress in developing enzymatic strategies to produce oligonucleotide therapies. We also highlight opportunities for innovations that are needed to facilitate widespread adoption of these biocatalytic methods across the pharmaceutical industry.

MOF-Immobilized Two-in-One Engineered Enzymes Enhancing Activity of Biocatalytic Cascade for Tumor Therapy

Biocatalytic systems based on enzyme cascade reactions have attracted growing interest in the field of biocatalytic medicine. However, it is a major challenge to reasonably construct enzyme cascade reactions with high stability, selectivity, and catalytic efficiency for the in vivo biocatalytic application. Herein, two-in-one engineered glucose oxidase (GOx-Fe⁰ ) is fabricated by a biomineralization strategy, through which a nanozyme (Fe⁰ NP) is anchored within the inner cavity of GOx. Then, GOx-Fe⁰ is immobilized in a pH-sensitive metal-organic framework (MOF) zeolitic imidazolate framework-8 (ZIF-8) to establish a stable and effective MOF-immobilized two-in-one engineered enzyme, GOx-Fe⁰ @ZIF-8. In vitro studies show that GOx-Fe⁰ @ZIF-8 exhibits excellent stability and high pH/glucose selectivity, and the shorter spacing between cascade enzymes can increase the cascade throughput and effectively improve the reaction efficiency of the enzyme cascade. In vivo experiments exhibit that GOx-Fe⁰ @ZIF-8 solves the instability and systemic toxicity of free enzymes, and achieves deep tumor penetration and significant chemodynamic therapeutic efficacy through a pH/glucose-selective enzyme cascade reaction in tumor site. Taken together, such an orchestrated enzyme engineering strategy can effectively improve enzyme stability, selectivity, and enzyme cascade reaction efficiency via chemical transformations, and also provide a promising strategy for the application of biocatalytic cascade reactions in vivo.

Engineering of a T7 Bacteriophage Endolysin Variant with Enhanced Amidase Activity

The therapeutic use of bacteriophage-encoded endolysins as enzybiotics has increased significantly in recent years due to the emergence of antibiotic resistant bacteria. Phage endolysins lyse the bacteria by targeting their cell wall. Various engineering strategies are commonly used to modulate or enhance the utility of therapeutic enzymes. This study employed a structure-guided mutagenesis approach to engineer a T7 bacteriophage endolysin (T7L) with enhanced amidase activity and lysis potency via replacement of a noncatalytic gating residue (His 37). Two H37 variants (H37A and H37K) were designed and characterized comprehensively using integrated biophysical and biochemical techniques to provide mechanistic insights into their structure-stability-dynamics-activity paradigms. Among the studied proteins, cell lysis data suggested that the obtained H37A variant exhibits amidase activity (∼35%) enhanced compared to that of wild-type T7 endolysin (T7L-WT). In contrast to this, the H37K variant is highly unstable, prone to aggregation, and less active. Comparison of the structure and dynamics of the H37A variant to those of T7L-WT evidenced that the alteration at the site of H37 resulted in long-range structural perturbations, attenuated the conformational heterogeneity, and quenched the microsecond to millisecond time scale motions. Stability analysis confirmed the altered stability of H37A compared to that of its WT counterpart. All of the obtained results established that the H37A variant enhances the lysis activity by regulating the stability-activity trade-off. This study provided deeper atomic level insights into the structure-function relationships of endolysin proteins, thus aiding researchers in the rational design of engineered endolysins with enhanced therapeutic properties.

Tuning Selectivity in CalA Lipase: Beyond Tunnel Engineering

Engineering studies of Candida (Pseudozyma) antarctica lipase A (CalA) have demonstrated the potential of this enzyme in the selective hydrolysis of fatty acid esters of different chain lengths. CalA has been shown to bind substrates preferentially through an acyl-chain binding tunnel accessed via the hydrolytic active site; it has also been shown that selectivity for substrates of longer or shorter chain length can be tuned, for instance by modulating steric hindrance within the tunnel. Here we demonstrate that, whereas the tunnel region is certainly of paramount importance for substrate recognition, residues in distal regions of the enzyme can also modulate substrate selectivity. To this end, we investigate variants that carry one or more substitutions within the substrate tunnel as well as in distal regions. Combining experimental determination of the substrate selectivity using natural and synthetic substrates with computational characterization of protein dynamics and of tunnels, we deconvolute the effect of key substitutions and demonstrate that epistatic interactions contribute to procuring selectivity toward either long-chain or short/medium-chain fatty acid esters. We demonstrate that various mechanisms contribute to the diverse selectivity profiles, ranging from reshaping tunnel morphology and tunnel stabilization to obstructing the main substrate-binding tunnel, highlighting the dynamic nature of the substrate-binding region. This work provides important insights into the versatility of this robust lipase toward diverse applications.

Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw

Over the years, protein engineers have studied nature and borrowed its tricks to accelerate protein evolution in the test tube. While there have been considerable advances, our ability to generate new proteins in the laboratory is seemingly limited. One explanation for these shortcomings may be that insertions and deletions (indels), which frequently arise in nature, are largely overlooked during protein engineering campaigns. The profound effect of indels on protein structures, by way of drastic backbone alterations, could be perceived as "saltation" events that bring about significant phenotypic changes in a single mutational step. Should we leverage these effects to accelerate protein engineering and gain access to unexplored regions of adaptive landscapes? In this Perspective, we describe the role played by indels in the functional diversification of proteins in nature and discuss their untapped potential for protein engineering, despite their often-destabilizing nature. We hope to spark a renewed interest in indels, emphasizing that their wider study and use may prove insightful and shape the future of protein engineering by unlocking unique functional changes that substitutions alone could never achieve.

Expanding the Synthetic Toolbox through Metal-Enzyme Cascade Reactions

The combination of metal-, photo-, enzyme-, and/or organocatalysis provides multiple synthetic solutions, especially when the creation of chiral centers is involved. Historically, enzymes and transition metal species have been exploited simultaneously through dynamic kinetic resolutions of racemates. However, more recently, linear cascades have appeared as elegant solutions for the preparation of valuable organic molecules combining multiple bioprocesses and metal-catalyzed transformations. Many advantages are derived from this symbiosis, although there are still bottlenecks to be addressed including the successful coexistence of both catalyst types, the need for compatible reaction media and mild conditions, or the minimization of cross-reactivities. Therefore, solutions are here also provided by means of catalyst coimmobilization, compartmentalization strategies, flow chemistry, etc. A comprehensive review is presented focusing on the period 2015 to early 2022, which has been divided into two main sections that comprise first the use of metals and enzymes as independent catalysts but working in an orchestral or sequential manner, and later their application as bionanohybrid materials through their coimmobilization in adequate supports. Each part has been classified into different subheadings, the first part based on the reaction catalyzed by the metal catalyst, while the development of nonasymmetric or stereoselective processes was considered for the bionanohybrid section.

Ammonia Production Using Bacteria and Yeast toward a Sustainable Society

Ammonia is an important chemical that is widely used in fertilizer applications as well as in the steel, chemical, textile, and pharmaceutical industries, which has attracted attention as a potential fuel. Thus, approaches to achieve sustainable ammonia production have attracted considerable attention. In particular, biological approaches are important for achieving a sustainable society because they can produce ammonia under mild conditions with minimal environmental impact compared with chemical methods. For example, nitrogen fixation by nitrogenase in heterogeneous hosts and ammonia production from food waste using microorganisms have been developed. In addition, crop production using nitrogen-fixing bacteria has been considered as a potential approach to achieving a sustainable ammonia economy. This review describes previous research on biological ammonia production and provides insights into achieving a sustainable society.

Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes

In vitro biotransformation (ivBT) refers to the use of an artificial biological reaction system that employs purified enzymes for the one-pot conversion of low-cost materials into biocommodities such as ethanol, organic acids, and amino acids. Unshackled from cell growth and metabolism, ivBT exhibits distinct advantages compared with metabolic engineering, including but not limited to high engineering flexibility, ease of operation, fast reaction rate, high product yields, and good scalability. These characteristics position ivBT as a promising next-generation biomanufacturing platform. Nevertheless, challenges persist in the enhancement of bulk enzyme preparation methods, the acquisition of enzymes with superior catalytic properties, and the development of sophisticated approaches for pathway design and system optimization. In alignment with the workflow of ivBT development, this chapter presents a systematic introduction to pathway design, enzyme mining and engineering, system construction, and system optimization. The chapter also proffers perspectives on ivBT development.

Progresses in Cell-Free In Vitro Evolution

Biopolymers, such as proteins and RNA, are integral components of living organisms and have evolved through a process of repeated mutation and selection. The technique of "cell-free in vitro evolution" is a powerful experimental approach for developing biopolymers with desired functions and structural properties. Since Spiegelman's pioneering work over 50 years ago, biopolymers with a wide range of functions have been developed using in vitro evolution in cell-free systems. The use of cell-free systems offers several advantages, including the ability to synthesize a wider range of proteins without the limitations imposed by cytotoxicity, and the capacity for higher throughput and larger library sizes than cell-based evolutionary experiments. In this chapter, we provide a comprehensive overview of the progress made in the field of cell-free in vitro evolution by categorizing evolution into directed and undirected. The biopolymers produced by these methods are valuable assets in medicine and industry, and as a means of exploring the potential of biopolymers.

Fundamentals of chirality, resolution, and enantiopure molecule synthesis methods

The chirality of molecules is a concept that explains the interactions in nature. We may observe the same formula but different organizations revolving around the chiral center. Since Pasteur's meticulous observation of sodium ammonium tartrate crystals' structure, scientists have discovered many features of chiral molecules. The number of newly approved single enantiomeric drugs increases every year and takes place in the market. Thus, separation or resolution methods of racemic mixtures are of continued importance in the efficacy of drugs, installation of affordable production processes, and convenient synthetic chemistry practice. This article presents the asymmetric synthesis approaches and the classification of direct resolution methods of chiral molecules.

A transaminase with β-activity from Variovorax boronicumulans for the production of enantiopure β-amino acids

Enantioselective transamination of amino acids is a great challenge in biotechnology as suitable enzymes with wide substrate spectrum are rare. Here, we present a new transaminase from Variovorax boronicumulans (VboTA, Variovorax boronicumulansω-transaminase) which is specific for β-amino acids. The amino acid sequence of VboTA is similar to an ω-transaminase from Variovorax paradoxus, for which a crystal-structure is available. This similarity is allowing us to classify VboTA as a fold type 1 ω-transaminase (ω-TA). Although both enzymes have a high sequence similarity (86% identities, 92% positives), there are differences in the active center, which allow VboTA to accept a broader substrate spectrum. Both enzymes have also a different temperature stability and temperature optimum. VboTA deaminates the D-form of aromatic β-amino acids, such as β-homophenylalanine and β-phenylalanine as well as aliphatic β-amino acids, such as β-homoalanine and β-leucine. The optimal reaction conditions turned out to be 32 °C and pH 9. Kinetic resolution lead to high enantiomeric excess of 86.6% to >99.9%, depending on the amino donor/acceptor pair. In contrast to many other ω-TAs, VboTA has a broad substrate spectrum and uses both aromatic or aliphatic amino acids. With γ-amino acids as substrates, VboTA showed no activity at all.

Enantioselective Single and Dual α-C-H Bond Functionalization of Cyclic Amines via Enzymatic Carbene Transfer

Cyclic amines are ubiquitous structural motifs found in pharmaceuticals and biologically active natural products, making methods for their elaboration via direct C-H functionalization of considerable synthetic value. Herein, we report the development of an iron-based biocatalytic strategy for enantioselective α-C-H functionalization of pyrrolidines and other saturated N-heterocycles via a carbene transfer reaction with diazoacetone. Currently unreported for organometallic catalysts, this transformation can be accomplished in high yields, high catalytic activity, and high stereoselectivity (up to 99:1 e.r. and 20,350 TON) using engineered variants of cytochrome P450 CYP119 from Sulfolobus solfataricus. This methodology was further extended to enable enantioselective α-C-H functionalization in the presence of ethyl diazoacetate as carbene donor (up to 96:4 e.r. and 18,270 TON), and the two strategies were combined to achieve a one-pot as well as a tandem dual C-H functionalization of a cyclic amine substrate with enzyme-controlled diastereo- and enantiodivergent selectivity. This biocatalytic approach is amenable to gram-scale synthesis and can be applied to drug scaffolds for late-stage C-H functionalization. This work provides an efficient and tunable method for direct asymmetric α-C-H functionalization of saturated N-heterocycles, which should offer new opportunities for the synthesis, discovery, and optimization of bioactive molecules.

Shifting the pH Optima of (R)-Selective Transaminases by Protein Engineering

Amine transaminases (ATAs) are powerful biocatalysts for the stereoselective synthesis of chiral amines. However, wild-type ATAs usually show pH optima at slightly alkaline values and exhibit low catalytic activity under physiological conditions. For efficient asymmetric synthesis ATAs are commonly used in combination with lactate dehydrogenase (LDH, optimal pH: 7.5) and glucose dehydrogenase (GDH, optimal pH: 7.75) to shift the equilibrium towards the synthesis of the target chiral amine and hence their pH optima should fit to each other. Based on a protein structure alignment, variants of (R)-selective transaminases were rationally designed, produced in E. coli, purified and subjected to biochemical characterization. This resulted in the discovery of the variant E49Q of the ATA from Aspergillus fumigatus, for which the pH optimum was successfully shifted from pH 8.5 to 7.5 and this variant furthermore had a two times higher specific activity than the wild-type protein at pH 7.5. A possible mechanism for this shift of the optimal pH is proposed. Asymmetric synthesis of (R)-1-phenylethylamine from acetophenone in combination with LDH and GDH confirmed that the variant E49Q shows superior performance at pH 7.5 compared to the wild-type enzyme.

The Time and Place for Nature in Drug Discovery

The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.

Redox Biocatalysis: Quantitative Comparisons of Nicotinamide Cofactor Regeneration Methods

Enzymatic processes, particularly those capable of performing redox reactions, have recently been of growing research interest. Substrate specificity, optimal activity at mild temperatures, high selectivity, and yield are among the desirable characteristics of these oxidoreductase catalyzed reactions. Nicotinamide adenine dinucleotide (phosphate) or NAD(P)H-dependent oxidoreductases have been extensively studied for their potential applications like biosynthesis of chiral organic compounds, construction of biosensors, and pollutant degradation. One of the main challenges associated with making these processes commercially viable is the regeneration of the expensive cofactors required by the enzymes. Numerous efforts have pursued enzymatic regeneration of NAD(P)H by coupling a substrate reduction with a complementary enzyme catalyzed oxidation of a co-substrate. While offering excellent selectivity and high total turnover numbers, such processes involve complicated downstream product separation of a primary product from the coproducts and impurities. Alternative methods comprising chemical, electrochemical, and photochemical regeneration have been developed with the goal of enhanced efficiency and operational simplicity compared to enzymatic regeneration. Despite the goal, however, the literature rarely offers a meaningful comparison of the total turnover numbers for various regeneration methodologies. This comprehensive Review systematically discusses various methods of NAD(P)H cofactor regeneration and quantitatively compares performance across the numerous methods. Further, fundamental barriers to enhanced cofactor regeneration in the various methods are identified, and future opportunities are highlighted for improving the efficiency and sustainability of commercially viable oxidoreductase processes for practical implementation.

Cofactor and Process Engineering for Nicotinamide Recycling and Retention in Intensified Biocatalysis

There is currently considerable interest in the intensification of biocatalytic processes to reduce the cost of goods for biocatalytically produced chemicals, including pharmaceuticals and advanced pharmaceutical intermediates. Continuous-flow biocatalysis shows considerable promise as a method for process intensification; however, the reliance of some reactions on the use of diffusible cofactors (such as the nicotinamide cofactors) has proven to be a technical barrier for key enzyme classes. This minireview covers attempts to overcome this limitation, including the cofactor recapture and recycling retention of chemically modified cofactors. For the latter, we also consider the state of science for cofactor modification, a field reinvigorated by the current interest in continuous-flow biocatalysis.

Engineering enzyme activity using an expanded amino acid alphabet

Enzyme design and engineering strategies are typically constrained by the limited size of nature's genetic alphabet, comprised of only 20 canonical amino acids. In recent years, site-selective incorporation of non-canonical amino acids (ncAAs) via an expanded genetic code has emerged as a powerful means of inserting new functional components into proteins, with hundreds of structurally diverse ncAAs now available. Here, we highlight how the emergence of an expanded repertoire of amino acids has opened new avenues in enzyme design and engineering. ncAAs have been used to probe complex biological mechanisms, augment enzyme function and, most ambitiously, embed new catalytic mechanisms into protein active sites that would be challenging to access within the constraints of nature's genetic code. We predict that the studies reviewed in this article, along with further advances in genetic code expansion technology, will establish ncAA incorporation as an increasingly important tool for biocatalysis in the coming years.

Directed reconstruction of a novel ancestral alcohol dehydrogenase featuring shifted pH-profile, enhanced thermostability and expanded substrate spectrum

Ancestral enzymes are promising for industrial biotechnology due to high stability and catalytic promiscuity. An effective protocol was developed for the directed resurrection of ancestral enzymes. Employing genome mining with diaryl alcohol dehydrogenase KpADH as the probe, descendant enzymes D10 and D11 were firstly identified. Then through ancestral sequence reconstruction, A64 was resurrected with a specific activity of 4.3 U·mg^-1. The optimum pH of A64 was 7.5, distinct from 5.5 of D10. The T15 50 and T_m values of A64 were 57.5 °C and 61.7 °C, significantly higher than those of the descendant counterpart. Substrate spectrum of A64 was quantitively characterized with a Shannon-Wiener index of 2.38, more expanded than D10, especially, towards bulky ketones in Group A and B. A64 also exhibited higher enantioselectivity. This study provides an effective protocol for constructing of ancestral enzymes and an efficient ancestral enzyme of industrial relevance for asymmetric synthesis of chiral alcohols.

Recombinant acetylxylan esterase of Halalkalibacterium halodurans NAH-Egypt: molecular and biochemical study

Acetylxylan esterase plays a crucial role in xylan hydrolysis as the acetyl side-groups restrict endoxylanase action by stearic hindrance. In this study, an acetylxylan esterase (AXE-HAS10: 960 bp & 319 a.a) putative ORF from Halalkalibacterium halodurans NAH-Egypt was extensively studied through heterologous overexpression in Escherichia coli, biochemical characterization, and structural modeling. The AXE-HAS10 tertiary structure was predicted by the Local Meta Threading Server. AXE-HAS10 belongs to the carbohydrate esterase Family 7. Purified to homogeneity AXE-HAS10 showed specific activity (36.99 U/mg), fold purification (11.42), and molecular mass (41.39 kDa). AXE-HAS10 showed optimal pH (8.5) and temperature (40 oC). After 15 h of incubation at pH 7.0–9.0, AXE-HAS10 maintained 100% activity. After 120 min at 35 and 40 oC, the retained activity was 80 and 50%, respectively. At 10 mM Mn2+, Fe3+, K+, and Ca2+ after 30 min, retained activity was 329 ± 15, 212 ± 5.2, 123 ± 1.4, and 120 ± 3.0%, respectively. After 30 min of preincubation with triton x-100, SDS, and CTAB at 0.1% (v/v), the retained activity was 150 ± 19, 88 ± 4, and 82 ± 7%, respectively. At 6.0 M NaCl after 30 min, retained activity was 58%. A 1.44-fold enhancement of beechwood xylan hydrolysis was achieved by AXE-HAS10 and Penicillium chrysogenum DSM105774 β-xylanase concurrently. Present data underpins AXE-HAS10 as a promising AXE for industrial exploitation.

Lipase and Its Unique Selectivity: A Mini-Review

Contrary to other solid catalysts, enzymes facilitate more sophisticated chemical reactions because most enzymes specifically interact with substrates and release selective products. Lipases (triacylglycerol hydrolase, EC 3.1.1.3), which can catalyze the cleavage and formation of various acyl compounds, are one of the best examples of enzymes with a unique substrate selectivity. There are already several commercialized lipases that have become important tools for various lipid-related studies, although there is still a need to discover novel lipases with unique substrate selectivity to facilitate more innovative reactions in human applications such as household care, cosmetics, foods, and pharmaceuticals. In this mini-review, we focus on concisely demonstrating not only the general information of lipases but also their substate selectivities: typoselectivity, regioselectivity, and stereoselectivity. We highlight the essential studies on selective lipases in terms of enzymology. Furthermore, we introduce several examples of analysis methodology and experimental requirements to determine each selectivity of lipases. This work would stress the importance of integrating our understanding of lipase chemistry to make further advances in the relevant fields.

Bioinspired Photocatalytic NADH Regeneration by Covalently Metalated Carbon Nitride for Enhanced CO2 Reduction

Natural photosynthesis is a highly unified biocatalytic system, which coupled cofactor (NAD(P)H) regeneration and enzymatic CO₂ reduction efficiently for solar energy conversion. Mimicking nature, a novel system with Rh complex covalently grafted onto NH₂ -functionalized polymeric carbon nitride (NH₂ -PCN) was constructed. The integrated connection of the light-harvesting and electron mediation modules as Rh_m3 -N-PCN could promote the efficient NAD⁺ reduction to NADH. As a result, the integrated system exhibited a conversion of ∼66 % within 20 minutes. By further coupling in situ generated NADH with formate dehydrogenase (FDH), a photoenzymatic production of formic acid (HCOOH) from CO₂ was accomplished. Moreover, by immobilizing FDH onto a hydrophobic membrane, an enhanced HCOOH production of ∼5.0 mM can be obtained due to the concentrated CO₂ on the gas-liquid-solid three-phase interface. Our work herein provides an integrated strategy for coupling the anchored electron mediator with immobilized enzyme for enhanced artificial photosynthesis.

NMR-guided directed evolution

Directed evolution is a powerful tool for improving existing properties and imparting completely new functionalities to proteins1-4. Nonetheless, its potential in even small proteins is inherently limited by the astronomical number of possible amino acid sequences. Sampling the complete sequence space of a 100-residue protein would require testing of 20100 combinations, which is beyond any existing experimental approach. In practice, selective modification of relatively few residues is sufficient for efficient improvement, functional enhancement and repurposing of existing proteins5. Moreover, computational methods have been developed to predict the locations and, in certain cases, identities of potentially productive mutations6-9. Importantly, all current approaches for prediction of hot spots and productive mutations rely heavily on structural information and/or bioinformatics, which is not always available for proteins of interest. Moreover, they offer a limited ability to identify beneficial mutations far from the active site, even though such changes may markedly improve the catalytic properties of an enzyme10. Machine learning methods have recently showed promise in predicting productive mutations11, but they frequently require large, high-quality training datasets, which are difficult to obtain in directed evolution experiments. Here we show that mutagenic hot spots in enzymes can be identified using NMR spectroscopy. In a proof-of-concept study, we converted myoglobin, a non-enzymatic oxygen storage protein, into a highly efficient Kemp eliminase using only three mutations. The observed levels of catalytic efficiency exceed those of proteins designed using current approaches and are similar with those of natural enzymes for the reactions that they are evolved to catalyse. Given the simplicity of this experimental approach, which requires no a priori structural or bioinformatic knowledge, we expect it to be widely applicable and to enable the full potential of directed enzyme evolution.

Assessing the Influence of Betaine-Based Natural Deep Eutectic Systems on Horseradish Peroxidase

To validate the use of horseradish peroxidase (HRP) in natural deep eutectic systems (NADES), five different betaine-based NADES were characterized in terms of water content, water activity, density, and viscosity experimentally and by thermodynamic modeling. The results show that the NADES under study have a water activity of about 0.4 at 37 °C for water contents between 14 and 22 wt %. The densities of the studied NADES had values between 1.2 and 1.3 g^.cm^-3 at 20 °C. The density was modeled with a state-of-the-art equation of state; an excellent agreement with the experimental density data was achieved, allowing reasonable predictions for water activities. The system betaine:glycerol (1:2) was found to be the most viscous with a dynamic viscosity of ∼600 mPa^.s at 40 °C, while all the other systems had viscosities <350 mPa^.s at 40 °C. The impact of the NADES on the enzymatic activity, as well as on, conformational and thermal stability was assessed. The system betaine/sorbitol:water (1:1:3) showed the highest benefit for enzymatic activity, increasing it by two-folds. Moreover, upon NADES addition, thermal stability was increased followed by an increment in a-helix secondary structure content.

Probing the Biotransformation Process of Sclareol by Resting Cells of Hyphozyma roseonigra

Sclareol glycol is a key starting material with significant market interest for synthesizing high-value ambroxide, a sustainable substitute for ambergris in high-end fragrances. Sclareol glycol can be obtained by biotransformation of sclareol, a labdane-type diterpene, using Hyphozyma roseonigra. However, the pathway and mechanism of sclareol glycol biosynthesis remain unclear. In this study, the dynamic time course of sclareol biotransformation was explored by resting cell assays and several intermediates produced during biotransformation were detected. The results show that (1) sclareol glycol and sclareolide are not interconverted and are potentially synthesized via different metabolic pathways and (2) several putative intermediates resulting from biotransformation are featured with a labdane carbon backbone, including isomerized and oxidized analogues. A plausible transformation pathway of sclareol in H. roseonigra was proposed based on detected metabolites. This study sheds light on the biosynthetic mechanism of sclareol glycol and paves a way for the future biotechnological production of this promising compound.

Advances in Metal-Organic Framework (MOFs) based biosensors for diagnosis: An update

Metal-organic frameworks (MOFs) have significant advantages over other candidate classes of chemo-sensory materials owing to their extraordinary structural tunability and characteristics. MOF-based biosensing is a simple, and convenient method for identifying various species. Biomarkers are molecular or cellular processes that link environmental exposure to a health outcome. Biomarkers are important in understanding the links between environmental chemical exposure and the development of chronic diseases, as well as in identifying disease-prone subgroups. Until now, several species, including nanoparticles (NPs) and their nanocomposites, small molecules, and unique complex systems, have been used for the chemical sensing of biomarkers. Following the overview of the field, we discussed the various fabrication methods for MOFs development in this review. We provide a thorough overview of the previous five years of progress to broaden the scope of analytes for future research. Several enzymatic and non-enzymatic sensors are offered, together with a mandatory measuring method that includes detection range and dynamic range. In addition, we reviewed the comparison of enzymatic and non-enzymatic biosensors, inventive edges, and the difficulties that need to be solved. This work might open up new possibilities for material production, sensor development, medical diagnostics, and other sensing fields.

Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization

Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.

Chemo-Biocascade Reactions Enabled by Metal–Organic Framework Micro-Nanoreactor

The one-pot combination of biocatalytic and chemocatalytic reactions represents an economically and ecologically attractive concept in the emerging cascade processes for manufacturing. The mutual incompatibility of biocatalysis and chemocatalysis, however, usually causes the deactivation of catalysts, the mismatching of reaction dynamic, and further challenges their integration into concurrent chemo-biocascades. Herein, we have developed a convenient strategy to construct versatile functional metal–organic framework micro-nanoreactors (MOF–MNRs), which can realize not only the encapsulation and protection of biocatalysts but also the controllable transmission of substances and the mutual communication of the incompatible chemo-biosystems. Importantly, the MOFs serving as the shell of MNRs have the capability of enriching the chemocatalysts on the surface and improving the activity of the chemocatalysts to sufficiently match the optimum aqueous reaction system of biocatalysts, which greatly increase the efficiency in the combined concurrent chemo-biocatalysis. Such strategy of constructing MOF–MNRs provides a unique platform for connecting the “two worlds” of chemocatalysis and biocatalysis.

Enzyme-catalyzed allylic oxidation reactions: A mini-review

Chiral allylic oxidized products play an increasingly important role in the pharmaceutical, agrochemical, and pharmaceutical industries. Biocatalytic C–H oxyfunctionalization to synthesize allylic oxidized products has attracted great attention in recent years, with the ability to simplify synthetic approaches toward complex compounds. As a result, scientists have found some new enzymes and mutants through techniques of gene mining and enzyme-directed evolution in recent years. This review summarizes the recent developments in biocatalytic selective oxidation of olefins by different kinds of biocatalysts.

Confining enzymes in porous organic frameworks: from synthetic strategy and characterization to healthcare applications

Enzymes are a class of natural catalysts with high efficiency, specificity, and selectivity unmatched by their synthetic counterparts and dictate a myriad of reactions that constitute various cascades in living cells. The development of suitable supports is significant for the immobilization of structurally flexible enzymes, enabling biomimetic transformation in the extracellular environment. Accordingly, porous organic frameworks, including metal organic frameworks (MOFs), covalent organic frameworks (COFs) and hydrogen-bonded organic frameworks (HOFs), have emerged as ideal supports for the immobilization of enzymes because of their structural features including ultrahigh surface area, tailorable porosity, and versatile framework compositions. Specially, organic framework-encased enzymes have shown significant enhancement in stability and reusability, and their tailorable pore opening provides a gatekeeper-like effect for guest sieving, which is beneficial for mimicking intracellular biocatalysis processes. This immobilization technique brings new insight into the development of next-generation enzyme materials and shows huge potential in healthcare applications, such as biomarker diagnosis, biostorage, and cancer and antibacterial therapies. In this review, we describe the state-of-the-art strategies for the structural immobilization of enzymes using the well-explored MOFs and burgeoning COFs and HOFs as scaffolds, with special emphasis on how these porous framework-confined technologies can provide a favorable microenvironment for mimicking natural biocatalysis. Subsequently, advanced characterization techniques for enzyme conformation, the effect of the confined microenvironment on the activity of enzymes, and the emerging healthcare applications will be surveyed.