Artificial Metalloenzymes on the Verge of New-to-Nature Metabolism

Engineering status of protein for improving microbial cell factories

With the development of metabolic engineering and synthetic biology, microbial cell factories (MCFs) have provided an efficient and sustainable method to synthesize a series of chemicals from renewable feedstocks. However, the efficiency of MCFs is usually limited by the inappropriate status of protein. Thus, engineering status of protein is essential to achieve efficient bioproduction with high titer, yield and productivity. In this review, we summarize the engineering strategies for metabolic protein status, including protein engineering for boosting microbial catalytic efficiency, protein modification for regulating microbial metabolic capacity, and protein assembly for enhancing microbial synthetic capacity. Finally, we highlight future challenges and prospects of improving microbial cell factories by engineering status of protein.

Anchoring a Structurally Editable Proximal Cofactor-like Module to Construct an Artificial Dual-center Peroxygenase

A recent novel strategy for constructing artificial metalloenzymes (ArMs) that target new-to-nature functions uses dual-functional small molecules (DFSMs) with catalytic and anchoring groups for converting P450BM3 monooxygenase into a peroxygenase. However, this process requires excess DFSMs (1000 equivalent of P450) owing to their low binding affinity for P450, thus severely limiting its practical application. Herein, structural optimization of the DFSM-anchoring group considerably enhanced their binding affinity by three orders of magnitude (Kd ≈10-8  M), thus approximating native cofactors, such as FMN or FAD in flavoenzymes. An artificial cofactor-driven peroxygenase was thus constructed. The co-crystal structure of P450BM3 bound to a DFSM clearly revealed a precatalytic state in which the DFSM participates in H2 O2 activation, thus facilitating peroxygenase activity. Moreover, the increased binding affinity substantially decreases the DFSM load to as low as 2 equivalents of P450, while maintaining increased activity. Furthermore, replacement of catalytic groups showed disparate selectivity and activity for various substrates. This study provides an unprecedented approach for assembling ArMs by binding editable organic cofactors as a co-catalytic center, thereby increasing the catalytic promiscuity of P450 enzymes.

Recent Synthetic Advances on the Use of Diazo Compounds Catalyzed by Metalloporphyrins

Diazo compounds are organic substances that are often used as precursors in organic synthesis like cyclization reactions, olefinations, cyclopropanations, cyclopropenations, rearrangements, and carbene or metallocarbene insertions into C-H, N-H, O-H, S-H, and Si-H bonds. Typically, reactions from diazo compounds are catalyzed by transition metals with various ligands that modulate the capacity and selectivity of the catalyst. These ligands can modify and enhance chemoselectivity in the substrate, regioselectivity and enantioselectivity by reflecting these preferences in the products. Porphyrins have been used as catalysts in several important reactions for organic synthesis and also in several medicinal applications. In the chemistry of diazo compounds, porphyrins are very efficient as catalysts when complexed with low-cost metals (e.g., Fe and Co) and, therefore, in recent years, this has been the subject of significant research. This review will summarize the advances in the studies involving the field of diazo compounds catalyzed by metalloporphyrins (M-Porph, M = Fe, Ru, Os, Co, Rh, Ir) in the last five years to provide a clear overview and possible opportunities for future applications. Also, at the end of this review, the properties of artificial metalloenzymes and hemoproteins as biocatalysts for a broad range of applications, namely those concerning carbene-transfer reactions, will be considered.

Artificial Metalloenzyme-Catalyzed Enantioselective Amidation via Nitrene Insertion in Unactivated C(sp3)-H Bonds

Enantioselective C-H amidation offers attractive means to assemble C-N bonds to synthesize high-added value, nitrogen-containing molecules. In recent decades, complementary enzymatic and homogeneous-catalytic strategies for C-H amidation have been reported. Herein, we report on an artificial metalloenzyme (ArM) resulting from anchoring a biotinylated Ir-complex within streptavidin (Sav). The resulting ArM catalyzes the enantioselective amidation of unactivated C(sp³)-H bonds. Chemogenetic optimization of the Ir cofactor and Sav led to significant improvement in both the activity and enantioselectivity. Up to >700 TON and 92% ee for the amidation of unactivated C(sp³)-H bonds was achieved. The single crystal X-ray analysis of the artificial nitrene insertase (ANIase) combined with quantum mechanics-molecular mechanics (QM-MM) calculations sheds light on critical second coordination sphere contacts leading to improved catalytic performance.

Progress, Challenges, and Opportunities with Artificial Metalloenzymes in Biosynthesis

In this Perspective, we present progress, outstanding challenges, and opportunities for the incorporation of artificial metalloenzymes (ArMs) into biosynthetic pathways. We first explain discoveries within the field of ArMs that led to the potential inclusion of these enzymes in biosynthesis. We then describe the specific barriers that our laboratory, in collaboration with the laboratories of Keasling and Mukhopadhyay, addressed to establish a biosynthetic pathway containing an ArM. This biosynthesis produced an unnatural cyclopropyl terpenoid by combining heterologous production of the terpene with modification of its terminal alkene by an ArM built from a cytochrome P450. Finally, we describe the remaining challenges and opportunities related to the application of ArMs in synthetic biology.

In Vivo Biocatalytic Cascades Featuring an Artificial-Enzyme-Catalysed New-to-Nature Reaction

Artificial enzymes utilizing the genetically encoded non-proteinogenic amino acid p-aminophenylalanine (pAF) as a catalytic residue are able to react with carbonyl compounds through an iminium ion mechanism to promote reactions that have no equivalent in nature. Herein, we report an in vivo biocatalytic cascade that is augmented with such an artificial enzyme-catalysed new-to-nature reaction. The artificial enzyme in this study is a pAF-containing evolved variant of the lactococcal multidrug-resistance regulator, designated LmrR_V15pAF_RMH, which efficiently converts benzaldehyde derivatives produced in vivo into the corresponding hydrazone products inside E. coli cells. These in vivo biocatalytic cascades comprising an artificial-enzyme-catalysed reaction are an important step towards achieving a hybrid metabolism.

Therapeutic in vivo synthetic chemistry using an artificial metalloenzyme with glycosylated human serum albumin

The concept of "therapeutic in vivo synthetic chemistry" refers to chemical synthesis in living systems using new-to-nature reactions for the treatment or diagnosis of diseases. This review summarizes our development of therapeutic in vivo synthetic chemistry using glycan-modified human serum albumin (glycoHSA) and utilizing the selective glycan-targeting and metal protective effects of metal catalysts. The four artificial metalloenzymes with glycoHSA provided good cancer treatment results based on on-site drug synthesis and selective cell-tagging strategies. Thus, we propose that therapeutic in vivo synthetic chemistry using glycoHSA as a new modality of therapy or diagnosis is applicable to a wide range of diseases.

Engineering of enzymes using non-natural amino acids

In enzyme engineering, the main targets for enhancing properties are enzyme activity, stereoselective specificity, stability, substrate range, and the development of unique functions. With the advent of genetic code extension technology, non-natural amino acids (nnAAs) are able to be incorporated into proteins in a site-specific or residue-specific manner, which breaks the limit of 20 natural amino acids for protein engineering. Benefitting from this approach, numerous enzymes have been engineered with nnAAs for improved properties or extended functionality. In this review, we focus on applications and strategies for using nnAAs in enzyme engineering. Notably, approaches to computational modelling of enzymes with nnAAs are also addressed. Finally, we discuss the bottlenecks that currently need to be addressed in order to realise the broader prospects of this genetic code extension technique.

An Artificial Metalloenzyme Based on a Copper Heteroscorpionate Enables sp3 C-H Functionalization via Intramolecular Carbene Insertion

The selective functionalization of sp³ C–H bonds is a versatile tool for the diversification of organic compounds. Combining attractive features of homogeneous and enzymatic catalysts, artificial metalloenzymes offer an ideal means to selectively modify these inert motifs. Herein, we report on a copper(I) heteroscorpionate complex embedded within streptavidin that catalyzes the intramolecular insertion of a carbene into sp³ C–H bonds. Target residues for genetic optimization of the artificial metalloenzyme were identified by quantum mechanics/molecular mechanics simulations. Double-saturation mutagenesis yielded detailed insight on the contribution of individual amino acids on the activity and the selectivity of the artificial metalloenzyme. Mutagenesis at a third position afforded a set of artificial metalloenzymes that catalyze the enantio- and regioselective formation of β- and γ-lactams with high turnovers and promising enantioselectivities.

Organometallic catalysis in aqueous and biological environments: harnessing the power of metal carbenes

Translating the power of transition metal catalysis to the native habitats of enzymes can significantly expand the possibilities of interrogating or manipulating natural biological systems, including living cells and organisms. This is especially relevant for organometallic reactions that have shown great potential in the field of organic synthesis, like the metal-catalyzed transfer of carbenes. While, at first sight, performing metal carbene chemistry in aqueous solvents, and especially in biologically relevant mixtures, does not seem obvious, in recent years there has been a growing number of reports demonstrating the feasibility of the task. Either using small molecule metal catalysts or artificial metalloenzymes, a number of carbene transfer reactions that tolerate aqueous and biorelevant media are being developed. This review intends to summarize the most relevant contributions, and establish the state of the art in this emerging research field.

Assembly and Evolution of Artificial Metalloenzymes within E. coli Nissle 1917 for Enantioselective and Site-Selective Functionalization of C─H and C═C Bonds

The potential applications afforded by the generation and reactivity of artificial metalloenzymes (ArMs) in microorganisms are vast. We show that a non-pathogenic E. coli strain, Nissle 1917 (EcN), is a suitable host for the creation of ArMs from cytochrome P450s and artificial heme cofactors. An outer-membrane receptor in EcN transports an iridium porphyrin into the cell, and the Ir-CYP119 (CYP119 containing iridium porphyrin) assembled in vivo catalyzes carbene insertions into benzylic C-H bonds enantioselectively and site-selectively. The application of EcN as a whole-cell screening platform eliminates the need for laborious processing procedures, drastically increases the ease and throughput of screening, and accelerates the development of Ir-CYP119 with improved catalytic properties. Studies to identify the transport machinery suggest that a transporter different from the previously assumed ChuA receptor serves to usher the iridium porphyrin into the cytoplasm.

Corrole–protein interactions in H-NOX and HasA

Mutagenesis was utilised to reveal corrole–protein interactions in H-NOX and HasA. The key interaction is a hydrogen bond between the PO unit of the corrole and a protonated histidine residue.

Unnatural biosynthesis by an engineered microorganism with heterologously expressed natural enzymes and an artificial metalloenzyme

Synthetic biology enables microbial hosts to produce complex molecules that are otherwise produced by organisms that are rare or difficult to cultivate, but the structures of these molecules are limited to those formed by chemical reactions catalyzed by natural enzymes. The integration of artificial metalloenzymes (ArMs) that catalyze unnatural reactions into metabolic networks could broaden the cache of molecules produced biosynthetically by microorganisms. We report an engineered microbial cell expressing a heterologous biosynthetic pathway, which contains both natural enzymes and ArMs, that produces an unnatural product with high diastereoselectivity. To create this hybrid biosynthetic organism, we engineered Escherichia coli (E. coli) with a heterologous terpene biosynthetic pathway and an ArM containing an iridium-porphyrin complex that was transported into the cell with a heterologous transport system. We improved the diastereoselectivity and product titer of the unnatural product by evolving the ArM and selecting the appropriate gene induction and cultivation conditions. This work shows that synthetic biology and synthetic chemistry can produce, together with natural and artificial enzymes in whole cells, molecules that were previously inaccessible to nature.

Exporting Metal-Carbene Chemistry to Live Mammalian Cells: Copper-Catalyzed Intracellular Synthesis of Quinoxalines Enabled by N-H Carbene Insertions

Implementing catalytic organometallic transformations in living settings can offer unprecedented opportunities in chemical biology and medicine. Unfortunately, the number of biocompatible reactions so far discovered is very limited, and essentially restricted to uncaging processes. Here, we demonstrate the viability of performing metal carbene transfer reactions in live mammalian cells. In particular, we show that copper (II) catalysts can promote the intracellular annulation of alpha-keto diazocarbenes with ortho-amino arylamines, in a process that is initiated by an N-H carbene insertion. The potential of this transformation is underscored by the in cellulo synthesis of a product that alters mitochondrial functions, and by demonstrating cell selective biological responses using targeted copper catalysts. Considering the wide reactivity spectrum of metal carbenes, this work opens the door to significantly expanding the repertoire of life-compatible abiotic reactions.

New-to-nature chemistry from old protein machinery: carbene and nitrene transferases

Hemoprotein-catalyzed carbene and nitrene transformations have emerged as powerful tools for constructing complex molecules; they also nicely illustrate how new protein catalysts can emerge, evolve and diversify. These laboratory-invented enzymes exploit the ability of proteins to tame highly reactive carbene and nitrene species and direct their fates with high selectivity. New-to-nature carbene and nitrene transferases catalyze many useful reactions, including some that have no precedent using chemical methods. Here we cover recent advances in this field, including alkyne cyclopropenation, arene cyclopropanation, carbene CH insertion, intramolecular nitrene CH insertion, alkene aminohydroxylation, and primary amination. For such transformations, biocatalysts have exceeded the performance of reported small-molecule catalysts in terms of selectivity and catalyst turnovers. Finally, we offer our thoughts on using these new enzymatic reactions in chemical synthesis, integrating them into biological pathways and chemo-enzymatic cascades, and on their current limitations.

An integrative approach to improving the biocatalytic reactions of whole cells expressing recombinant enzymes

Biotransformation is a selective, stereospecific, efficient, and environment friendly method, compared to chemical synthesis, and a feasible tool for industrial and pharmaceutical applications. The design of biocatalysts using enzyme engineering and metabolic engineering tools has been widely reviewed. However, less importance has been given to the biocatalytic reaction of whole cells expressing recombinant enzymes. Along with the remarkable development of biotechnology tools, a variety of techniques have been applied to improve the biocatalytic reaction of whole cell biotransformation. In this review, techniques related to the biocatalytic reaction are examined, reorganized, and summarized via an integrative approach. Moreover, equilibrium-shifted biotransformation is reviewed for the first time.

Origin and Control of Chemoselectivity in Cytochrome c Catalyzed Carbene Transfer into Si-H and N-H bonds

A cytochrome c heme protein was recently engineered to catalyze the formation of carbon-silicon bonds via carbene insertion into Si-H bonds, a reaction that was not previously known to be catalyzed by a protein. High chemoselectivity toward C-Si bond formation over competing C-N bond formation was achieved, although this trait was not screened for during directed evolution. Using computational and experimental tools, we now establish that activity and chemoselectivity are modulated by conformational dynamics of a protein loop that covers the substrate access to the iron-carbene active species. Mutagenesis of residues computationally predicted to control the loop conformation altered the protein's chemoselectivity from preferred silylation to preferred amination of a substrate containing both N-H and Si-H functionalities. We demonstrate that information on protein structure and conformational dynamics, combined with knowledge of mechanism, leads to understanding of how non-natural and selective chemical transformations can be introduced into the biological world.

Controlled Ligand Exchange Between Ruthenium Organometallic Cofactor Precursors and a Naïve Protein Scaffold Generates Artificial Metalloenzymes Catalysing Transfer Hydrogenation

Many natural metalloenzymes assemble from proteins and biosynthesised complexes, generating potent catalysts by changing metal coordination. Here we adopt the same strategy to generate artificial metalloenzymes (ArMs) using ligand exchange to unmask catalytic activity. By systematically testing RuII (η6 -arene)(bipyridine) complexes designed to facilitate the displacement of functionalised bipyridines, we develop a fast and robust procedure for generating new enzymes via ligand exchange in a protein that has not evolved to bind such a complex. The resulting metal cofactors form peptidic coordination bonds but also retain a non-biological ligand. Tandem mass spectrometry and 19 F NMR spectroscopy were used to characterise the organometallic cofactors and identify the protein-derived ligands. By introduction of ruthenium cofactors into a 4-helical bundle, transfer hydrogenation catalysts were generated that displayed a 35-fold rate increase when compared to the respective small molecule reaction in solution.

Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet

The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.

In Vivo Assembly of Artificial Metalloenzymes and Application in Whole-Cell Biocatalysis*

We report the supramolecular assembly of artificial metalloenzymes (ArMs), based on the Lactococcal multidrug resistance regulator (LmrR) and an exogeneous copper(II)-phenanthroline complex, in the cytoplasm of E. coli cells. A combination of catalysis, cell-fractionation, and inhibitor experiments, supplemented with in-cell solid-state NMR spectroscopy, confirmed the in-cell assembly. The ArM-containing whole cells were active in the catalysis of the enantioselective Friedel-Crafts alkylation of indoles and the Diels-Alder reaction of azachalcone with cyclopentadiene. Directed evolution resulted in two different improved mutants for both reactions, LmrR_A92E_M8D and LmrR_A92E_V15A, respectively. The whole-cell ArM system required no engineering of the microbial host, the protein scaffold, or the cofactor to achieve ArM assembly and catalysis. We consider this a key step towards integrating abiological catalysis with biosynthesis to generate a hybrid metabolism.

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.

Addicting Escherichia coli to New-to-Nature Reactions

Biocontainment is an essential feature when deploying genetically modified organisms (GMOs) in open system applications, as variants escaping their intended operating environments could negatively impact ecosystems and human health. To avoid breaches resulting from metabolic cross-feeding, horizontal gene transfer, and/or genetic mutations, synthetic auxotrophs have been engineered to become dependent on exogenously supplied xenobiotics, such as noncanonical amino acids (ncAAs). The incorporation of these abiological building blocks into essential proteins constitutes a first step toward constructing xenobiological barriers between GMOs and their environments. To transition synthetic auxotrophs further away from familiar biology, we demonstrate how bacterial growth can be confined by transition-metal complexes that catalyze the formation of an essential ncAA through new-to-nature reactions. Specifically, using a homogeneous ruthenium complex enabled us to localize bacterial growth on solid media, while heterogeneous palladium nanoparticles could be recycled and deployed up to five consecutive times to ensure the survival of synthetic auxotrophs in liquid cultures.

Unlocking the Full Evolutionary Potential of Artificial Metalloenzymes Through Direct Metal-Protein Coordination : A review of recent advances for catalyst development

Generation of artificial metalloenzymes (ArMs) has gained much inspiration from the general understanding of natural metalloenzymes. Over the last decade, a multitude of methods generating transition metal-protein hybrids have been developed and many of these new-to-nature constructs catalyse reactions previously reserved for the realm of synthetic chemistry. This perspective will focus on ArMs incorporating 4d and 5d transition metals. It aims to summarise the significant advances made to date and asks whether there are chemical strategies, used in nature to optimise metal catalysts, that have yet to be fully recognised in the synthetic enzyme world, particularly whether artificial enzymes produced to date fully take advantage of the structural and energetic context provided by the protein. Further, the argument is put forward that, based on precedence, in the majority of naturally evolved metalloenzymes the direct coordination bonding between the metal and the protein scaffold is integral to catalysis. Therefore, the protein can attenuate metal activity by positioning ligand atoms in the form of amino acids, as well as making non-covalent contributions to catalysis, through intermolecular interactions that pre-organise substrates and stabilise transition states. This highlights the often neglected but crucial element of natural systems that is the energetic contribution towards activating metal centres through protein fold energy. Finally, general principles needed for a different approach to the formation of ArMs are set out, utilising direct coordination inspired by the activation of an organometallic cofactor upon protein binding. This methodology, observed in nature, delivers true interdependence between metal and protein. When combined with the ability to efficiently evolve enzymes, new problems in catalysis could be addressed in a faster and more specific manner than with simpler small molecule catalysts.

Intracellular Ruthenium-Promoted (2+2+2) Cycloadditions

Metal-mediated intracellular reactions are becoming invaluable tools in chemical and cell biology, and hold promise for strongly impacting the field of biomedicine. Most of the reactions reported so far involve either uncaging or redox processes. Demonstrated here for the first time is the viability of performing multicomponent alkyne cycloaromatizations inside live mammalian cells using ruthenium catalysts. Both fully intramolecular and intermolecular cycloadditions of diynes with alkynes are feasible, the latter providing an intracellular synthesis of appealing anthraquinones. The power of the approach is further demonstrated by generating anthraquinone AIEgens (AIE=aggregation induced emission) that otherwise do not go inside cells, and by modifying the intracellular distribution of the products by simply varying the type of ruthenium complex.

Artificial Glycoproteins as a Scaffold for Targeted Drug Therapy

Akin to a cellular "fingerprint," the glycocalyx is a glycan-enriched cellular coating that plays a crucial role in mediating cell-to-cell interactions. To gain a better understanding of the factors that govern in vivo recognition, artificial glycoproteins were initially created to probe changes made to the accumulation and biodistribution of specific glycan assemblies through biomimicry. As a result, the organ-specific accumulation for a variety of glycoproteins decorated with simple and/or complex glycans was identified. Additionally, binding trends with regard to cancer cell selectivity were also investigated. To exploit the knowledge gained from these studies, numerous groups thus became engaged in developing targeted drug methodologies based on the use of artificial glycoproteins. This has either been done through adopting the glycoprotein scaffold as a drug carrier, or to directly glycosylate therapeutic proteins/enzymes to localize their biological activity. The principle aim of this Review is to present the foundational research that has driven artificial glycoprotein-based targeting and subsequent adaptations with potential therapeutic applications.

Artificial Metalloenzymes: From Selective Chemical Transformations to Biochemical Applications

Artificial metalloenzymes (ArMs) comprise a synthetic metal complex in a protein scaffold. ArMs display performances combining those of both homogeneous catalysts and biocatalysts. Specifically, ArMs selectively catalyze non-natural reactions and reactions inspired by nature in water under mild conditions. In the past few years, the construction of ArMs that possess a genetically incorporated unnatural amino acid and the directed evolution of ArMs have become of great interest in the field. Additionally, biochemical applications of ArMs have steadily increased, owing to the fact that compartmentalization within a protein scaffold allows the synthetic metal complex to remain functional in a sea of inactivating biomolecules. In this review, we present updates on: 1) the newly reported ArMs, according to their type of reaction, and 2) the unique biochemical applications of ArMs, including chemoenzymatic cascades and intracellular/in vivo catalysis. We believe that ArMs have great potential as catalysts for organic synthesis and as chemical biology tools for pharmaceutical applications.

The Quest for Xenobiotic Enzymes: From New Enzymes for Chemistry to a Novel Chemistry of Life

Enzyme engineering has made impressive progress in the past decades, paving the way for the widespread use of enzymes for various purposes. In contrast to "classical" enzyme engineering, which focuses on optimizing specific properties of natural enzymes, a more recent trend towards the creation of artificial enzymes that catalyze fundamentally distinct, new-to-nature reactions is observable. While approaches for creating such enzymes differ significantly, they share the common goal of enabling biocatalytic novelty to broaden the range of applications for enzymes. Although most artificial enzymes reported to date are only moderately active and barely function in vivo, they have the potential to endow cells with capabilities that were previously out of reach and thus herald a new wave of "functional xenobiology". Herein, we highlight recent developments in the field of artificial enzymes with a particular focus on challenges and opportunities for their use in xenobiology.

Molecular Modeling for Artificial Metalloenzyme Design and Optimization

Artificial metalloenzymes (ArMs) are obtained by inserting homogeneous catalysts into biological scaffolds and are among the most promising strategies in the quest for new-to-nature biocatalysts. The quality of their design strongly depends on how three partners interact: the biological host, the "artificial cofactor," and the substrate. However, structural characterization of functional artificial metalloenzymes by X-ray or NMR is often partial, elusive, or absent. How the cofactor binds to the protein, how the receptor reorganizes upon the binding of the cofactor and the substrate, and which are the binding mode(s) of the substrate for the reaction to proceed are key questions that are frequently unresolved yet crucial for ArM design. Such questions may eventually be solved by molecular modeling but require a step change beyond the current state-of-the-art methodologies.Here, we summarize our efforts in the study of ArMs, presenting both the development of computational strategies and their application. We first focus on our integrative computational framework that incorporates a variety of methods such as protein-ligand docking, classical molecular dynamics (MD), and pure quantum mechanical (QM) methods, which, when properly combined, are able to depict questions that range from host-cofactor binding predictions to simulations of entire catalytic mechanisms. We also pay particular attention to the protein-ligand docking strategies that we have developed to accurately predict the binding of transition metal-containing molecules to proteins. While this aspect is fundamental to many bioinorganic fields beyond ArMs, it has been disregarded from the molecular modeling landscape until very recently.Next we describe how to apply this computational framework to particular ArMs including systems previously characterized experimentally as well as others where computation served to guide the design. We start with the prediction of the interactions between homogeneous catalysts and biological hosts. Protein-ligand docking is pivotal at that stage, but it needs to be combined with QM/MM or MD approaches when the binding of the cofactor implies significant conformational changes of the protein or involve changes of the electronic state of the metal.Then, we summarize molecular modeling studies aimed at identifying cofactor-substrate arrangements inside the ArM active pocket that are consistent with its reactivity. These calculations stand on "Theozyme"-like dockings, MD-refined or not, which provide molecular rationale of the catalytic profiles of the artificial systems.In the third section, we present case studies to decode the entire catalytic mechanism of two ArMs: (1) an iridium based asymmetric transfer hydrogenase obtained by insertion of Noyori's catalyst into streptavidin and (2) a metallohydrolase achieved by including a receptor. Transition states, second coordination sphere effects, as well as motions of the cofactors are identified as drivers of the enantiomeric profiles.Finally, we report computer-aided designs of ArMs to guide experiments toward chemical and mutational changes that improve their activity and/or enantioselective profiles and expand toward future directions.

Synthesis and Characterization of a Binuclear Copper(II)-dipyriamethyrin Complex: [Cu2(dipyriamethyrin)(μ2-1,1-acetato)2]

The reaction between dipyriamethyrin and copper(II) acetate [Cu(OAc)₂] afforded what is, to our knowledge, the first transition metal-dipyriamethyrin complex. Molecular and electronic characterization of this binuclear Cu(II) complex via EPR, UV-vis, and single crystal X-ray diffraction analysis revealed marked differences between the present constructs and previously reported binuclear copper(II) hexaphyrin species. UV-vis titration analyses provided evidence for a homotropic positive allosteric effect, wherein the binuclear species is formed without significant intermediacy of a monomeric complex.

The various levels of integration of chemo- and bio-catalysis towards hybrid catalysis

Hybrid catalysis is an emerging concept that combines chemo- and biocatalysts in a wide variety of approaches. Combining the specifications and advantages of multiple disciplines, it is a very promising way to diversify tomorrow's catalysis.

Unlocking the therapeutic potential of artificial metalloenzymes

In order to harness the functionality of metals, nature has evolved over billions of years to utilize metalloproteins as key components in numerous cellular processes. Despite this, transition metals such as ruthenium, palladium, iridium, and gold are largely absent from naturally occurring metalloproteins, likely due to their scarcity as precious metals. To mimic the evolutionary process of nature, the field of artificial metalloenzymes (ArMs) was born as a way to benefit from the unique chemoselectivity and orthogonality of transition metals in a biological setting. In its current state, numerous examples have successfully incorporated transition metals into a variety of protein scaffolds. Using these ArMs, many examples of new-to-nature reactions have been carried out, some of which have shown substantial biocompatibility. Given the rapid rate at which this field is growing, this review aims to highlight some important studies that have begun to take the next step within this field; namely the development of ArM-centered drug therapies or biotechnological tools.

Semiholoenzyme optimizes activity and stability of a hyperthermostable iron-superoxide dismutase

Metal ion coordination is an essential step for the maturation of metalloenzymes. Generally, the metal coordination sites are thought to be fully occupied to achieve the maximum activity and stability. In this research, we compared the structural features, activity and stability of the apo-, semiholo- and holo-forms of a hyperthermostable tetrameric Fe-superoxide dismutase (SOD). Strikingly, the three forms of enzymes had similar compact tetrameric structures. Removal of iron ions destabilized subunit-subunit interactions during guanidine hydrochloride-induced unfolding. The partially metalized semiholoenzyme possessed most of the activity and identical hyperthermostability of the holoenzyme, but weaker propensity to aggregate. Furthermore, both of the iron content and activity of the semiholoenzyme were unaffected by a 200-fold excess iron ions in solutions, suggesting that conformation of the apo-subunits were forced to the close state by the iron-containing subunits. These observations suggest that fully metalized enzyme is probably nonessential for multimeric metalloenzymes and the semiholoenzyme may be a better choice. The unique properties of semiholoenzyme also provide the organisms a compromised solution to survival under metal deficiency conditions.

Harnessing biocompatible chemistry for developing improved and novel microbial cell factories

White biotechnology relies on the sophisticated chemical machinery inside living cells for producing a broad range of useful compounds in a sustainable and environmentally friendly way. However, despite the impressive repertoire of compounds that can be generated using white biotechnology, this approach cannot currently fully replace traditional chemical production, often relying on petroleum as a raw material. One challenge is the limited number of chemical transformations taking place in living organisms. Biocompatible chemistry, that is non‐enzymatic chemical reactions taking place under mild conditions compatible with living organisms, could provide a solution. Biocompatible chemistry is not a novel invention, and has since long been used by living organisms. Examples include Fenton chemistry, used by microorganisms for degrading plant materials, and manganese or ketoacids dependent chemistry used for detoxifying reactive oxygen species. However, harnessing biocompatible chemistry for expanding the chemical repertoire of living cells is a relatively novel approach within white biotechnology, and it could potentially be used for producing valuable compounds which living organisms otherwise are not able to generate. In this mini review, we discuss such applications of biocompatible chemistry, and clarify the potential that lies in using biocompatible chemistry in conjunction with metabolically engineered cell factories for cheap substrate utilization, improved cell physiology, efficient pathway construction and novel chemicals production.

Vancomycin-Iridium (III) Interaction: An Unexplored Route for Enantioselective Imine Reduction

The chiral structure of antibiotic vancomycin (Van) was exploited as an innovative coordination sphere for the preparation of an IrCp* based hybrid catalysts. We found that Van is able to coordinate iridium (Ir(III)) and the complexation was demonstrated by several analytical techniques such as MALDI-TOF, UV, Circular dichroism (CD), Raman IR, and NMR. The hybrid system so obtained was employed in the Asymmetric Transfer Hydrogenation (ATH) of cyclic imines allowing to obtain a valuable 61% e.e. (R) in the asymmetric reduction of quinaldine 2. The catalytic system exhibited a saturation kinetics with a calculated efficiency of K_cat/K_M = 0.688 h⁻¹mM⁻¹.

Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis

This Review is aimed at synthetic organic chemists who may be familiar with organometallic catalysis but have no experience with biocatalysis, and seeks to provide an answer to the perennial question: if it is so attractive, why wasn't it extensively used in the past? The development of biocatalysis in industrial organic synthesis is traced from the middle of the last century. Advances in molecular biology in the last two decades, in particular genome sequencing, gene synthesis and directed evolution of proteins, have enabled remarkable improvements in scope and substantially reduced biocatalyst development times and cost contributions. Additionally, improvements in biocatalyst recovery and reuse have been facilitated by developments in enzyme immobilization technologies. Biocatalysis has become eminently competitive with chemocatalysis and the biocatalytic production of important pharmaceutical intermediates, such as enantiopure alcohols and amines, has become mainstream organic synthesis. The synthetic space of biocatalysis has significantly expanded and is currently being extended even further to include new-to-nature biocatalytic reactions.