Bioorganometallic chemistry: Co-factor regeneration, enzyme recognition of biomimetic 1,4-NADH analogs, and organic synthesis; tandem catalyzed regioselective formation of N-substituted-1,4-dihydronicotinamide derivatives with [Cp*Rh(bpy)H]+, coupled to chiral S-alcohol formation with HLADH, and engineered cytochrome P450s, for selective C-H oxidation reactions

Design, construction, and application of noncanonical redox cofactor infrastructures

Controlling the flow of carbon and reducing power in biological systems is a central theme in metabolic engineering. Often, trade-offs in pushing carbon flux through targeted pathways while operating in conditions agreeable to the host are required due to the central pools of the shared native redox cofactors NAD(P)/H. Noncanonical redox cofactors (NRCs) have emerged as promising tools to transform how engineers develop biotransformation systems. These new-to-Nature redox cofactors have been demonstrated to function orthogonally to the endogenous cofactors, support pathway thermodynamics optimization, and achieve product scopes previously difficult to reach due to endogenous pathway crosstalk. This review will discuss the development of NRC infrastructures, comprising NRC pools, cofactor reduction sources, and cofactor oxidation sinks, the (pool-source-sink) infrastructure.

Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform

Noncanonical redox cofactors are attractive low-cost alternatives to nicotinamide adenine dinucleotide (phosphate) (NAD(P)+) in biotransformation. However, engineering enzymes to utilize them is challenging. Here, we present a high-throughput directed evolution platform which couples cell growth to the in vivo cycling of a noncanonical cofactor, nicotinamide mononucleotide (NMN+). We achieve this by engineering the life-essential glutathione reductase in Escherichia coli to exclusively rely on the reduced NMN+ (NMNH). Using this system, we develop a phosphite dehydrogenase (PTDH) to cycle NMN+ with ~147-fold improved catalytic efficiency, which translates to an industrially viable total turnover number of ~45,000 in cell-free biotransformation without requiring high cofactor concentrations. Moreover, the PTDH variants also exhibit improved activity with another structurally deviant noncanonical cofactor, 1-benzylnicotinamide (BNA+), showcasing their broad applications. Structural modeling prediction reveals a general design principle where the mutations and the smaller, noncanonical cofactors together mimic the steric interactions of the larger, natural cofactors NAD(P)+.

Use of engineered cytochromes P450 for accelerating drug discovery and development

Numerous steps in drug development, including the generation of authentic metabolites and late-stage functionalization of candidates, necessitate the modification of often complex molecules, such as natural products. While it can be challenging to make the required regio- and stereoselective alterations to a molecule using purely chemical catalysis, enzymes can introduce changes to complex molecules with a high degree of stereo- and regioselectivity. Cytochrome P450 enzymes are biocatalysts of unequalled versatility, capable of regio- and stereoselective functionalization of unactivated CH bonds by monooxygenation. Collectively they catalyze over 60 different biotransformations on structurally and functionally diverse organic molecules, including natural products, drugs, steroids, organic acids and other lipophilic molecules. This catalytic versatility and substrate range makes them likely candidates for application as potential biocatalysts for industrial chemistry. However, several aspects of the P450 catalytic cycle and other characteristics have limited their implementation to date in industry, including: their lability at elevated temperature, in the presence of solvents, and over lengthy incubation times; the typically low efficiency with which they metabolize non-natural substrates; and their lack of specificity for a single metabolic pathway. Protein engineering by rational design or directed evolution provides a way to engineer P450s for industrial use. Here we review the progress made to date toward engineering the properties of P450s, especially eukaryotic forms, for industrial application, and including the recent expansion of their catalytic repertoire to include non-natural reactions.

Artificial photosynthesis systems for solar energy conversion and storage: platforms and their realities

In natural photosynthesis, photosynthetic organisms such as green plants realize efficient solar energy conversion and storage by integrating photosynthetic components on the thylakoid membrane of chloroplasts. Inspired by natural photosynthesis, researchers have developed many artificial photosynthesis systems (APS's) that integrate various photocatalysts and biocatalysts to convert and store solar energy in the fields of resource, environment, food, and energy. To improve the system efficiency and reduce the operation cost, reaction platforms are introduced in APS's since they allow for great stability and continuous processing. A systematic understanding of how a reaction platform affects the performance of artificial photosynthesis is conducive for designing an APS with superb solar energy utilization. In this review, we discuss the recent APS's researches, especially those confined on/in platforms. The importance of different platforms and their influences on APS's performance are emphasized. Generally, confined platforms can enhance the stability and repeatability of both photocatalysts and biocatalysts in APS's as well as improve the photosynthetic performance due to the proximity effect. For functional platforms that can participate in the artificial photosynthesis reactions as active parts, a high integration of APS's components on/in these platforms can lead to efficient electron transfer, enhanced light-harvesting, or synergistic catalysis, resulting in superior photosynthesis performance. Therefore, the integration of APS's components is beneficial for the transfer of substrates and photoexcited electrons in artificial photosynthesis. We finally summarize the current challenges of APS's development and further efforts on the improvement of APS's.

Cell-Free Noncanonical Redox Cofactor Systems

Noncanonical redox cofactor systems utilize nicotinamide adenine dinucleotide (phosphate), NAD(P)H, mimics to perform biotransformation reactions. Compared to systems utilizing native NAD(P)H, these noncanonical redox cofactors can offer decreased cost of cofactor supply, improved system activities, and can even supply reducing power directly to targeted reactions in complex biological environments. When these systems are operated in cell-free settings, the high level of user control afforded by direct access to the reaction system enables specific tuning of cofactor parameters, enzyme activity, and reaction progression to maximize system productivity. In this chapter, we will describe methods for constructing these cell-free noncanonical redox cofactor systems. Specifically, methods, design concepts, and system adaptation will be discussed for applying noncanonical redox cofactors to both purified protein-based and crude lysate-based biotransformation systems.

Design of artificial metalloenzymes for the reduction of nicotinamide cofactors

Artificial metalloenzymes result from the insertion of a catalytically active metal complex into a biological scaffold, generally a protein devoid of other catalytic functionalities. As such, their design requires efforts to engineer substrate binding, in addition to accommodating the artificial catalyst. Here we constructed and characterised artificial metalloenzymes using alcohol dehydrogenase as starting point, an enzyme which has both a cofactor and a substrate binding pocket. A docking approach was used to determine suitable positions for catalyst anchoring to single cysteine mutants, leading to an artificial metalloenzyme capable to reduce both natural cofactors and the hydrophobic 1-benzylnicotinamide mimic. Kinetic studies revealed that the new construct displayed a Michaelis-Menten behaviour with the native nicotinamide cofactors, which were suggested by docking to bind at a surface exposed site, different compared to their native binding position. On the other hand, the kinetic and docking data suggested that a typical enzyme behaviour was not observed with the hydrophobic 1-benzylnicotinamide mimic, with which binding events were plausible both inside and outside the protein. This work demonstrates an extended substrate scope of the artificial metalloenzymes and provides information about the binding sites of the nicotinamide substrates, which can be exploited to further engineer artificial metalloenzymes for cofactor regeneration. SYNOPSIS ABOUT GRAPHICAL ABSTRACT: The manuscript provides information on the design of artificial metalloenzymes based on the bioconjugation of rhodium complexes to alcohol dehydrogenase, to improve their ability to reduce hydrophobic substrates. The graphical abstract presents different binding modes and results observed with native cofactors as substrates, compared to the hydrophobic benzylnicotinamide.

Engineering natural and noncanonical nicotinamide cofactor-dependent enzymes: design principles and technology development

Nicotinamide cofactors enable oxidoreductases to catalyze a myriad of important reactions in biomanufacturing. Decades of research has focused on optimizing enzymes which utilize natural nicotinamide cofactors, namely nicotinamide adenine dinucleotide (phosphate) (NAD(P)+). Recent findings reignite the interest in engineering enzymes to utilize noncanonical cofactors, the mimetics of NAD+ (mNADs), which exhibit superior industrial properties in vitro and enable specific electron delivery in vivo. We compare recent advances in engineering natural versus noncanonical cofactor-utilizing enzymes, discuss design principles discovered, and survey emerging high-throughput platforms beyond the traditional 96-well plate-based methods. Obtaining mNAD-dependent enzymes remains challenging with a limited toolkit. To this end, we highlight design principles and technologies which can potentially be translated from engineering natural to noncanonical cofactor-dependent enzymes.

Recent Progress and Perspectives on Electrochemical Regeneration of Reduced Nicotinamide Adenine Dinucleotide (NADH)

NAD is a cofactor that maintains cellular redox homeostasis and has immense industrial and biological significance. It acts as an enzymatic mediator in several biocatalytic electrochemical reactions and undergoes oxidation/reduction to form NAD⁺ or NADH, respectively. The NAD redox couple (NAD⁺ /NADH) mostly exists in enzyme-assisted metabolic reactions as a coenzyme during which electrons and protons are transferred. NADH shuttles these charges between the enzyme and the substrate. In order to understand such complex metabolic reactions, it is vital to study the bio-electrochemistry of NADH. In addition, the regeneration of NADH in industries has attracted significant attention due to its vast usage and high cost. To make biocatalysis economically viable, primary methods of NADH regeneration including enzymatic, chemical, photochemical and electrochemical methods are widely used. This review is mainly focused on the electrochemical reduction of NAD⁺ to NADH with specific details on the mechanism and kinetics of the reaction. It provides emphasis on the different routes (direct and mediated) to electrochemically regenerate NADH from NAD⁺ highlighting the NAD dimer formation. Also, it describes the electrocatalysts developed until now and the scope for development in this area of research.

1,4-NADH Biomimetic Co-Factors with Horse Liver Alcohol Dehydrogenase (HLADH), Utilizing [Cp*Rh(bpy)H](OTf) for Co-factor Regeneration, Do in Fact, Produce Chiral Alcohols from Reactions with Achiral Ketones

In this Catalysts Comment Article, we will present our latest published results [...]

Synthesis and Biochemical Evaluation of Nicotinamide Derivatives as NADH Analogue Coenzymes in Ene Reductase

Nicotinamide and pyridine-containing conjugates have attracted a lot of attention in research as they have found use in a wide range of applications including as redox flow batteries and calcium channel blockers, in biocatalysis, and in metabolism. The interesting redox character of the compounds' pyridine/dihydropyridine system allows them to possess very similar characteristics to the natural chiral redox agents NAD⁺ /NADH, even mimicking their functions. There has been considerable interest in designing and synthesizing NAD⁺ /NADH mimetics with similar redox properties. In this research, three nicotinamide conjugates were designed, synthesized, and characterized. Molecular structures obtained through X-ray crystallography were obtained for two of the conjugates, thereby providing more detail on the bonding and structure of the compounds. The compounds were then further evaluated for biochemical properties, and it was found that one of the conjugates possessed similar functions and characteristics to the natural NADH. This compound was evaluated in the active enzyme, enoate reductase; like NADH, it was shown to help reduce the C=C double bond of three substrates and even outperformed the natural coenzyme. Kinetic data are reported.

Stereoselective Double Reduction of 3-Methyl-2-cyclohexenone, by Use of Palladium and Platinum Nanoparticles, in Tandem with Alcohol Dehydrogenase

The combination of metal nanoparticles (Pd or Pt NPs) with NAD-dependent thermostable alcohol dehydrogenase (TADH) resulted in the one-flask catalytic double reduction of 3-methyl-2-cyclohexenone to 3-(1S,3S)-methylcyclohexanol. In this article, some assumptions about the interactions between a chemocatalyst and a biocatalyst have been proposed. It was demonstrated that the size of the NPs was the critical parameter for the mutual inhibition: the bigger the NPs, the more harmful for the enzyme they were, even if the NPs themselves were only moderately inactivated. Conversely, the smaller the NPs, the more minimal the TADH denaturation, although they were dramatically inhibited. Resuming, the chemocatalysts were very sensitive to deactivation, which was not related to the amount of enzyme used, while the inhibition of the biocatalyst can be strongly reduced by minimizing the NPs/TADH ratio used to catalyze the reaction. Among some methods to avoid direct binding of NPs with TADH, we found that using large Pd NPs and protecting their surfaces with a silica shell, the overall yield of 3-(1S,3S)-methylcyclohexanol was maximized (36%).

Biocatalyst-artificial metalloenzyme cascade based on alcohol dehydrogenase

Chemo-enzymatic cascades of enzymes with transition metal catalysts can offer efficient synthetic strategies, but their development is challenging due to the incompatibility between proteins and transition metal complexes. Rhodium catalysts can be combined with alcohol dehydrogenases to regenerate nicotinamide cofactors using formate as the hydride donor. However, their use is limited, due to binding of the metals to residues on the enzyme surface, leading to mutual enzyme and catalyst inactivation. In this work, we replaced the zinc from Thermoanaerobacter brockii alcohol dehydrogenase (TbADH) with Rh(iii) catalysts possessing nitrogen donor ligands, by covalent conjugation to the active site cysteine, to create artificial metalloenzymes for NADP+ reduction. TbADH was used as protein scaffold for both alcohol synthesis and the recycling of the cofactor, by combination of the chemically modified species with the non-modified recombinant enzyme. Stability studies revealed that the incorporation of the catalysts into the TbADH pocket provided a shielding environment for the metal catalyst, resulting in increased stability of both the recycling catalyst and the ADH. The reduction of a representative ketone using this novel alcohol dehydrogenase-artificial formate dehydrogenase cascade yielded better conversions than in the presence of free metal catalyst.