Klein Gebbink, R.J.M.

Artificial Metalloenzymes and MetalloDNAzymes in Catalysis: From Design to Applications 2018, 171-197, 10.1002/9783527804085.ch6

The development of artificial hydrogenases (AHases) and transfer hydrogenases (ATHases) has played a leading and guiding role for the field of artificial metalloenzymes. Starting from the early studies by Whitesides and coworkers, this chapter showcases the conceptual development of AHases and ATHases, highlighting the different conjugation strategies used for their construction and exemplifying the stereoselective control in product formation that can be reached.

DeGrado, W.F.

Nat. Rev. Chem. 2022, 6, 31-50, 10.1038/s41570-021-00339-5

Natural metalloproteins perform many functions — ranging from sensing to electron transfer and catalysis — in which the position and property of each ligand and metal are dictated by protein structure. De novo protein design aims to define an amino acid sequence that encodes a specific structure and function, providing a critical test of the hypothetical inner workings of (metallo)proteins. To date, de novo metalloproteins have used simple, symmetric tertiary structures — uncomplicated by the large size and evolutionary marks of natural proteins — to interrogate structure–function hypotheses. In this Review, we discuss de novo design applications, such as proteins that induce complex, increasingly asymmetric ligand geometries to achieve function, as well as the use of more canonical ligand geometries to achieve stability. De novo design has been used to explore how proteins fine-tune redox potentials and catalyse both oxidative and hydrolytic reactions. With an increased understanding of structure–function relationships, functional proteins including O2-dependent oxidases, fast hydrolases and multi-proton/multielectron reductases have been created. In addition, proteins can now be designed using xenobiological metals or cofactors and principles from inorganic chemistry to derive new-to-nature functions. These results and the advances in computational protein design suggest a bright future for the de novo design of diverse, functional metalloproteins.

Arnold, F.H.

Artificial Metalloenzymes and MetalloDNAzymes in Catalysis: From Design to Applications 2018, 137-170, 10.1002/9783527804085.ch5

Directed evolution is a powerful algorithm for engineering proteins to have novel and useful properties. However, we do not yet fully understand the characteristics of an evolvable system. In this chapter, we present examples where directed evolution has been used to enhance the performance of metalloenzymes, focusing first on “classical” cases such as improving enzyme stability or expanding the scope of natural reactivity. We then discuss how directed evolution has been extended to artificial systems, in which a metalloprotein catalyzes reactions using abiological reagents or in which the protein utilizes a nonnatural cofactor for catalysis. These examples demonstrate that directed evolution can also be applied to artificial systems to improve catalytic properties, such as activity and enantioselectivity, and to favor a different product than that favored by small‐molecule catalysts. Future work will help define the extent to which artificial metalloenzymes can be altered and optimized by directed evolution and the best approaches for doing so.

Roelfes, G.

Artificial Metalloenzymes and MetalloDNAzymes in Catalysis: From Design to Applications 2018, 225-251, 10.1002/9783527804085.ch8

Lewis acid catalysis is undisputedly of great significance for synthetic chemistry. Hence, many hybrid catalysts have been designed that can function as Lewis acid. These hybrid catalysts are based on DNA, protein, or peptide scaffolds. In this chapter an overview of the hybrid catalysts reported for three important classes of Lewis acid‐catalyzed reactions is given: C–C bond‐forming reactions, C–X bond‐forming reactions, and hydrolysis reactions.

Ward, T.R.

Artificial Metalloenzymes and MetalloDNAzymes in Catalysis: From Design to Applications 2018, 253-284, 10.1002/9783527804085.ch9

Herein we summarize the current state of the art in the field of artificial metalloenzymes for enantioselective C–H activation and related X–H insertion as well as cyclopropanation reactions. Three complementary strategies are presented: (i) the creation of artificial metalloenzymes upon incorporation of an organometallic catalyst precursor within a protein scaffold, (ii) metal or cofactor substitution in hemoproteins to access novel reactivities, and (iii) repurposing of hemoproteins. An emphasis is placed on directed evolution strategies to improve the performance of these enantioselective artificial metalloenzymes.

Kamer, P.C.J.

Artificial Metalloenzymes and MetalloDNAzymes in Catalysis: From Design to Applications 2018, 285-319, 10.1002/9783527804085.ch10

In this chapter, applications of hybrid catalysts in some of the most important C–C and C–X bond formation reactions are described. Included are (i) polypeptide and oligonucleotide scaffolds (mostly modified with phosphanes for palladium‐catalyzed allylic substitution), (ii) palladium‐catalyzed cross‐coupling reactions catalyzed by dative, supramolecular, and covalently assembled hybrid catalysts, (iii) rhodium‐modified protein catalysts for hydroformylation reactions, (iv) rhodium hybrid catalysts for phenylacetylene polymerization, and (v) ruthenium‐based hybrid catalysts for the ring‐opening polymerization, cross‐, and ring‐closing metathesis reactions of alkenes. Examples are used to provide insight in the most important aspects for the design of hybrid catalysts for these reactions.

Ménage, S.

Artificial Metalloenzymes and MetalloDNAzymes in Catalysis: From Design to Applications 2018, 199-224, 10.1002/9783527804085.ch7

Artificial metalloenzymes broadens the scope of possibilities for catalysis at the crossroad of biocatalysis and metal‐based catalysis. The content of this chapter illustrates this outline in the field of oxidation, thanks to remarkable achievements for epoxidation and sulfoxidation in particular. Selectivity, especially enantioselectivity, is benchmarked based on six design strategies (ranging from protein engineering to de novo design), revealing that artificial systems may compete natural ones.

Lewis, J.C.

Artificial Metalloenzymes and MetalloDNAzymes in Catalysis: From Design to Applications 2018, 1-40, 10.1002/9783527804085.ch1

Transition metal catalysts and enzymes are ubiquitous tools for chemical synthesis. Potential benefits of combining complementary properties of these catalysts have driven efforts to create artificial metalloenzymes (ArMs), hybrid constructs comprised of synthetic metal centers embedded within protein scaffolds. This unique composition necessitates the use of synthetic chemistry, bioconjugation methodology, and protein engineering for ArM formation. Despite this challenge, a range of approaches for ArM formation has been developed. This chapter provides an overview of these different approaches and discussion of potential advantages and disadvantages of each.

Mayer, C.; Roelfes, G.

Nat. Rev. Chem. 2019, 3, 687-705, 10.1038/s41570-019-0143-x

The ability of one enzyme to catalyse multiple, mechanistically distinct transformations likely played a crucial role in organisms’ abilities to adapt to changing external stimuli in the past and can still be observed in extant enzymes. Given the importance of catalytic promiscuity in nature, enzyme designers have recently begun to create catalytically promiscuous enzymes in order to expand the canon of transformations catalysed by proteins. This article aims to both critically review different strategies for the design of enzymes that display catalytic promiscuity for new-to-nature reactions and highlight the successes of subsequent directed-evolution efforts to fine-tune these novel reactivities. For the former, we put a particular emphasis on the creation, stabilization and repurposing of reaction intermediates, which are key for unlocking new activities in an existing or designed active site. For the directed evolution of the resulting catalysts, we contrast approaches for enzyme design that make use of components found in nature and those that achieve new reactivities by incorporating synthetic components. Following the critical analysis of selected examples that are now available, we close this Review by providing a set of considerations and design principles for enzyme engineers, which will guide the future generation of efficient artificial enzymes for synthetically useful, abiotic transformations.

Happe, T.; Hemschemeier, A.

Nat. Rev. Chem. 2018, 2, 231-243, 10.1038/s41570-018-0029-3

Metal cofactors considerably widen the catalytic space of naturally occurring enzymes whose specific and enantioselective catalytic activity constitutes a blueprint for economically relevant chemical syntheses. To optimize natural enzymes and uncover novel reactivity, we need a detailed understanding of cofactor–protein interactions, which can be challenging to obtain in the case of enzymes with sophisticated cofactors. As a case study, we summarize recent research on the [FeFe]-hydrogenases, which interconvert protons, electrons and dihydrogen at a unique iron-based active site. We can now chemically synthesize the complex cofactor and incorporate it into an apo-protein to afford functional enzymes. By varying both the cofactor and the polypeptide components, we have obtained detailed knowledge on what is required for a metal cluster to process H2. In parallel, the design of artificial proteins and catalytically active nucleic acids are advancing rapidly. In this Perspective, we introduce these fields and outline how chemists and biologists can use this knowledge to develop novel tailored semisynthetic catalysts.