Design of Artificial Enzymes: Insights into Protein Scaffolds

The design of artificial enzymes has emerged as a promising tool for the generation of potent biocatalysts able to promote new-to-nature reactions with improved catalytic performances, providing a powerful platform for wide-ranging applications and a better understanding of protein functions and structures. The selection of an appropriate protein scaffold plays a key role in the design process. This review aims to give a general overview of the most common protein scaffolds that can be exploited for the generation of artificial enzymes. Several examples are discussed and categorized according to the strategy used for the design of the artificial biocatalyst, namely the functionalization of natural enzymes, the creation of a new catalytic site in a protein scaffold bearing a wide hydrophobic pocket and de novo protein design. The review is concluded by a comparison of these different methods and by our perspective on the topic.

Synthesis of Tetrapeptides Containing Dehydroalanine, Dehydrophenylalanine and Oxazole as Building Blocks for Construction of Foldamers and Bioinspired Catalysts

The incorporation of dehydroamino acid or fragments of oxazole into peptide chain is accompanied by a distorted three-dimensional structure and additionally enables the introduction of non-typical side-chain substituents. Thus, such compounds could be building blocks for obtaining novel foldamers and/or artificial enzymes (artzymes). In this paper, effective synthetic procedures leading to such building blocks-tetrapeptides containing glycyldehydroalanine, glycyldehydrophenylalanine, and glycyloxazole subunits-are described. Peptides containing serine were used as substrates for their conversion into peptides containing dehydroalanine and aminomethyloxazole-4-carboxylic acid while considering possible requirements for the introduction of these fragments into long-chain peptides at the last steps of synthesis.

Artificial Enzymes for Diels-Alder Reactions

The Diels-Alder (DA) reaction is a cycloaddition of a conjugated diene and an alkene (dienophile) leading to the formation of a cyclohexene derivative through a concerted mechanism. As DA reactions generally proceed with a high degree of regio- and stereoselectivity, they are widely used in synthetic organic chemistry. Considering eco-conscious public and governmental movements, efforts are now directed towards the development of synthetic processes that meet environmental concerns. Artificial enzymes, which can be developed to catalyze abiotic reactions, appear to be important synthetic tools in the synthetic biology field. This review describes the different strategies used to develop protein-based artificial enzymes for DA reactions, including for in cellulo approaches.

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 Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase

Acireductone dioxygenase (ARD) from the methionine salvage pathway (MSP) is a unique enzyme that exhibits dual chemistry determined solely by the identity of the divalent transition-metal ion (Fe²⁺ or Ni²⁺) in the active site. The Fe²⁺-containing isozyme catalyzes the on-pathway reaction using substrates 1,2-dihydroxy-3-keto-5-methylthiopent-1-ene (acireductone) and dioxygen to generate formate and the ketoacid precursor of methionine, 2-keto-4-methylthiobutyrate, whereas the Ni²⁺-containing isozyme catalyzes an off-pathway shunt with the same substrates, generating methylthiopropionate, carbon monoxide, and formate. The dual chemistry of ARD was originally discovered in the bacterium Klebsiella oxytoca, but it has recently been shown that mammalian ARD enzymes (mouse and human) are also capable of catalyzing metal-dependent dual chemistry in vitro. This is particularly interesting, since carbon monoxide, one of the products of off-pathway reaction, has been identified as an antiapoptotic molecule in mammals. In addition, several biochemical and genetic studies have indicated an inhibitory role of human ARD in cancer. This comprehensive review describes the biochemical and structural characterization of the ARD family, the proposed experimental and theoretical approaches to establishing mechanisms for the dual chemistry, insights into the mechanism based on comparison with structurally and functionally similar enzymes, and the applications of this research to the field of artificial metalloenzymes and synthetic biology.

Artificial Metalloenzymes: Reaction Scope and Optimization Strategies

The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.

Adsorption of Papain on solid substrates of different hydrophobicity

Adsorption properties of protein Papain at the solid|liquid (0.1 M KCl) interfaces of different hydrophobicity [highly oriented pyrolytic graphite (HOPG), bare gold, CH3, OH, and COOH-terminated self-assembled monolayers on gold] were studied by a combined quartz crystal microbalance and atomic force microscopy techniques. It was found that Papain forms an incomplete monolayer at hydrophobic interfaces (HOPG and CH3-terminated substrate), whereas on more hydrophilic ones, a complete monolayer formation was always observed with either the onset of the formation of a second layer (bare gold substrate) or adsorption in a multilayer fashion, possibly a bilayer formation (OH-terminated substrate). The surface concentration and compact monolayer film thickness was much lower on the COOH-terminated substrate compared to other surfaces studied. This result was explained by partial dissociation of the interfacial COOH groups leading to additional electrostatic interactions between the positively charged protein domains and negatively charged carboxylate anions, as well as to local pH changes promoting protein denaturation.

Neocarzinostatin-based hybrid biocatalysts for oxidation reactions

An anionic iron(III)-porphyrin-testosterone conjugate 1-Fe has been synthesized and fully characterized. It has been further associated with a neocarzinostatin variant, NCS-3.24, to generate a new artificial metalloenzyme following the so-called 'Trojan Horse' strategy. This new 1-Fe-NCS-3.24 biocatalyst showed an interesting catalytic activity as it was found able to catalyze the chemoselective and slightly enantioselective (ee = 13%) sulfoxidation of thioanisole by H2O2. Molecular modelling studies show that a synergy between the binding of the steroid moiety and that of the porphyrin macrocycle into the protein binding site can explain the experimental results, indicating a better affinity of 1-Fe for the NCS-3.24 variant than testosterone and testosterone-hemisuccinate themselves. They also show that the Fe-porphyrin complex is sandwiched between the two subdomains of the protein providing with good complementarities. However, the artificial cofactor entirely fills the cavity and its metal ion remains widely exposed to the solvent which explains the moderate enantioselectivity observed. Some possible improvements in the "Trojan Horse" strategy for obtaining better catalysts of selective oxidations are presented.

Various strategies for obtaining oxidative artificial hemoproteins with a catalytic oxidative activity: from "Hemoabzymes" to "Hemozymes"?

The design of artificial hemoproteins that could lead to new biocatalysts for selective oxidation reactions using clean oxidants such as O 2 or H 2 O 2 under ecocompatible conditions constitutes a really promising challenge for a wide range of industrial applications. In vivo, such reactions are performed by heme-thiolate proteins, cytochromes P450, that catalyze the oxidation of drugs by dioxygen in the presence of electrons delivered from NADPH by cytochrome P450 reductase. Several strategies were used to design new artificial hemoproteins to mimic these enzymes, that associate synthetic metalloporphyrin derivatives to a protein that is supposed to induce a selectivity in the catalyzed reaction. A first generation of artificial hemoproteins or "hemoabzymes" was obtained by the non-covalent association of synthetic hemes such as N-methyl-mesoporphyrin IX, Fe(III) -α3β-tetra-o-carboxyphenylporphyrin or microperoxidase 8 with monoclonal antibodies raised against these cofactors. The obtained antibody-metalloporphyrin complexes displayed a peroxidase activity and some of them catalyzed the regio-selective nitration of phenols by H 2 O 2/ NO 2 and the stereo-selective oxidation of sulphides by H 2 O 2. A second generation of artificial hemoproteins or "hemozymes", was obtained by the non-covalent association of non-relevant proteins with metalloporphyrin derivatives. Several strategies were used, the most successful of which, named "host-guest" strategy involved the non-covalent incorporation of metalloporphyrin derivatives into easily affordable proteins. The artificial hemoproteins obtained were found to be able to perform efficiently the stereoselective oxidation of organic compounds such as sulphides and alkenes by H 2 O 2 and KHSO 5.

From “hemoabzymes” to “hemozymes”: towards new biocatalysts for selective oxidations

Two generations of artificial hemoproteins have been obtained: “hemoabzymes”, by non-covalent association of synthetic hemes with monoclonal antibodies raised against these cofactors and “hemozymes”, by non-covalent association of non-relevant proteins with metalloporphyrin derivatives. A review of the different strategies employed as well as their structural and catalytic properties is presented here.

Unravelling novel synergies between organometallic and biological partners: a quantum mechanics/molecular mechanics study of an artificial metalloenzyme

In recent years, the design of artificial metalloenzymes obtained by the insertion of homogeneous catalysts into biological macromolecules has become a major field of research. These hybrids, and the corresponding X-ray structures of several of them, are offering opportunities to better understand the synergy between organometallic and biological subsystems. In this work, we investigate the resting state and activation process of a hybrid inspired by an oxidative haemoenzyme but presenting an unexpected reactivity and structural features. An extensive series of quantum mechanics/molecular mechanics calculations show that the resting state and the activation processes of the novel enzyme differ from naturally occurring haemoenzymes in terms of the electronic state of the metal, participation of the first coordination sphere of the metal and the dynamic process. This study presents novel insights into the sensitivity of the association between organometallic and biological partners and illustrates the molecular challenge that represents the design of efficient enzymes based on this strategy.

Neocarzinostatin-based hybrid biocatalysts with a RNase like activity

A new zinc(II)-cofactor coupled to a testosterone anchor, zinc(II)-N,N-bis(2-pyridylmethyl)-1,3-diamino-propa-2-ol-N'(17'-succinimidyltestosterone) (Zn-Testo-BisPyPol) 1-Zn has been synthesized and fully characterized. It has been further associated with a neocarzinostatin variant, NCS-3.24, to generate a new artificial metalloenzyme following the so-called 'Trojan horse' strategy. This new 1-Zn-NCS-3.24 biocatalyst showed an interesting catalytic activity as it was found able to catalyze the hydrolysis of the RNA model HPNP with a good catalytic efficiency (kcat/KM=13.6M(-1)s(-1) at pH 7) that places it among the best artificial catalysts for this reaction. Molecular modeling studies showed that a synergy between the binding of the steroid moiety and that of the BisPyPol into the protein binding site can explain the experimental results, indicating a better affinity of 1-Zn for the NCS-3.24 variant than testosterone and testosterone-hemisuccinate themselves. They also show that the artificial cofactor entirely fills the cavity, the testosterone part of 1-Zn being bound to one the two subdomains of the protein providing with good complementarities whereas its metal ion remains widely exposed to the solvent which made it a valuable tool for the catalysis of hydrolysis reactions, such as that of HPNP. Some possible improvements in the 'Trojan horse' strategy for obtaining better catalysts of selective reactions will be further studied.

Artificial metalloenzymes derived from bovine β-lactoglobulin for the asymmetric transfer hydrogenation of an aryl ketone – synthesis, characterization and catalytic activity

Protein hybrids resulting from the supramolecular anchoring to bovine β-lactoglobulin of fatty acid-derived Rh(iii) diimine complexes catalysed the asymmetric transfer hydrogenation of trifluoroacetophenone with up to 32% ee.

Chemically engineered papain as artificial formate dehydrogenase for NAD(P)H regeneration

Organometallic complexes of the general formula [(η(6)-arene)Ru(N⁁N)Cl](+) and [(η(5)-Cp*)Rh(N⁁N)Cl](+) where N⁁N is a 2,2'-dipyridylamine (DPA) derivative carrying a thiol-targeted maleimide group, 2,2'-bispyridyl (bpy), 1,10-phenanthroline (phen) or ethylenediamine (en) and arene is benzene, 2-chloro-N-[2-(phenyl)ethyl]acetamide or p-cymene were identified as catalysts for the stereoselective reduction of the enzyme cofactors NAD(P)(+) into NAD(P)H with formate as a hydride donor. A thorough comparison of their effectiveness towards NAD(+) (expressed as TOF) revealed that the Rh(III) complexes were much more potent catalysts than the Ru(II) complexes. Within the Ru(II) complex series, both the N⁁N and arene ligands forming the coordination sphere had a noticeable influence on the activity of the complexes. Covalent anchoring of the maleimide-functionalized Ru(II) and Rh(III) complexes to the cysteine endoproteinase papain yielded hybrid metalloproteins, some of them displaying formate dehydrogenase activity with potentially interesting kinetic parameters.