Engineering non-haem iron enzymes for enantioselective C(sp3)-F bond formation via radical fluorine transfer

Catalytic Enantioselective Smiles Rearrangement Enabled by the Directed Evolution of P450 Radical Aryl Migratases

Despite its synthetic potential, catalytic enantioselective Smiles rearrangement has remained elusive. Through the directed evolution of P450 radical aryl migratases (P450Smiles's), we describe the first example of catalytic enantioselective Smiles rearrangement. A range of racemic N-arylsulfonyl-α-chloroamides could be transformed by P450Smiles in an enantioconvergent manner, affording acyclic amide products possessing an all-carbon quaternary stereocenter with excellent chemo- and enantioselectivity. Both electron-rich and electron-deficient substituents were compatible with the migrating aryl group, demonstrating this P450-catalyzed Smiles rearrangement is insensitive to the electronic properties of the migrating group. Importantly, our evolved P450 variants were capable of overriding the innate cyclization activity of the N-alkyl amidyl radical intermediate, allowing the chemoselective reductive formation of acyclic products. Classical molecular dynamics (MD) simulations revealed this unusual enzyme-controlled chemoselectivity stems from the restricted conformation of the amidyl radical within the enzyme active site, disfavoring the cyclization pathway. This new-to-nature biocatalytic asymmetric Smiles rearrangement showcases the synthetic potential of enzymatic chemo- and enantioselectivity control over highly reactive radical intermediates eluding small-molecule catalysts.

High-Valent Cobalt-Difluoride in Oxidative Fluorination of Saturated Hydrocarbons

The heme paradigm where Fe=O acts as the C-H oxidant and Fe-OH rebounds with the formed carbon-centered radical guides the design of the prototypical synthetic hydroxylation catalyst. We are exploring methods to evolve beyond the metal-oxo oxidant and hydroxide rebound, to incorporate a wider array of functional group. We have demonstrated the application of CoII(OTf)2 (10 mol% catalyst; OTf=trimfluoromethanesulfonate) in combination with polydentate N-donor ligands (e. g. BPMEN=N,N'-dimethyl-N,N'-bis(pyrid-2-ylmethyl)ethane-1,2-diamine) and Selectfluor in the oxidative fluorination of saturated hydrocarbons in high yields. The addition of CsF to the reaction mixture induced near-quantitative yields of fluorinated saturated hydrocarbons (>90 % yield of fluorinated product). For 1-hydroxy, 1-acetyl, 1-carboxy-, and 1-acetamido-adamantane, we demonstrated selective fluorination at the 3-position. We propose two mechanisms for the CoII-catalyzed reaction: either (i) an N-radical, derived from Selectfluor, acted as the C-H oxidant followed by radical rebound with CoIII-F; or (ii) a CoIV-(F)2 species was the C-H oxidant followed by radical rebound with CoIII-F. Our combined spectroscopic, kinetic, and chemical trapping evidence suggested that an N-radical was not the active oxidant. We concluded that a CoIV-(F)2 species was the likely active oxidant and CoIII-F was the likely F-atom donor to a carbon centered radical producing a C-F bond.

Enantioselective Trifluoromethylazidation of Styrenyl Olefins Catalyzed by an Engineered Nonheme Iron Enzyme

Organofluorines, particularly those containing trifluoromethyl (CF3) groups, play a critical role in medicinal chemistry. While trifluoromethylation of alkenes provides a powerful synthetic route to construct CF3-containing compounds with broad structural and functional diversity, achieving enantioselective control in these reactions remains a formidable challenge. In this study, we engineered a nonheme iron enzyme, quercetin 2,3-dioxygenase from Bacillus subtilis (BsQueD), for the enantioselective trifluoromethylazidation of alkenes. Through directed evolution, the final variant BsQueD-CF3 exhibited excellent enantioselectivity, with an enantiomeric ratio (e.r.) of up to 98 : 2. Preliminary mechanistic studies suggest the involvement of radical intermediates. This work expands biocatalytic organofluorine chemistry by reprogramming metalloenzymes for innovative trifluoromethylation reactions.

Expanding the scope of copper artificial metalloenzymes: A potential fluorinase?

Biocatalysts for fluorination are rare, and thus of great interest for artificial enzyme design. Biohybrid catalysts including Cu-based DNAzymes and dinucleotide catalysts can catalyse enantioselective electrophilic fluorination of β-ketoesters. Here we report the investigation of Cu-based artificial metalloenzymes as catalysts for electrophilic fluorination reactions. A library of artificial copper proteins was prepared by bioconjugation of bidentate and tridentate nitrogen ligands to cysteine variants of the Sterol Carrier Protein 2 L (SCP-2 L) and subsequent addition of Cu(II) salts. The resulting copper proteins were screened for activity for the fluorination of β-ketoesters using Selectfluor. Under aqueous acidic conditions it was observed that the designed catalysts did not outcompete the uncatalysed background reaction. This work highlights that careful consideration of substrate reactivity and background reactions is needed when considering potential reactions for artificial metalloenzyme catalysis.

Copper-dependent halogenase catalyses unactivated C-H bond functionalization

Carbon-hydrogen (C-H) bonds are the foundation of essentially every organic molecule, making them an ideal place to do chemical synthesis. The key challenge is achieving selectivity for one particular C(sp3)-H bond1-3. In recent years, metalloenzymes have been found to perform C(sp3)-H bond functionalization4,5. Despite substantial progresses in the past two decades6,7, enzymatic halogenation and pseudohalogenation of unactivated C(sp3)-H-providing a functional handle for further modification-have been achieved with only non-haem iron/α-ketoglutarate-dependent halogenases, and are therefore limited by the chemistry possible with these enzymes8. Here we report the discovery and characterization of a previously unknown halogenase ApnU, part of a protein family containing domain of unknown function 3328 (DUF3328). ApnU uses copper in its active site to catalyse iterative chlorinations on multiple unactivated C(sp3)-H bonds. By taking advantage of the softer copper centre, we demonstrate that ApnU can catalyse unprecedented enzymatic C(sp3)-H bond functionalization such as iodination and thiocyanation. Using biochemical characterization and proteomics analysis, we identified the functional oligomeric state of ApnU as a covalently linked homodimer, which contains three essential pairs-one interchain and two intrachain-of disulfide bonds. The metal-coordination active site in ApnU consists of binuclear type II copper centres, as revealed by electron paramagnetic resonance spectroscopy. This discovery expands the enzymatic capability of C(sp3)-H halogenases and provides a foundational understanding of this family of binuclear copper-dependent oxidative enzymes.

Ground-state flavin-dependent enzymes catalyzed enantioselective radical trifluoromethylation

The introduction of fluoroalkyl groups into pharmaceutical compounds has the potential to enhance their therapeutic properties. Nevertheless, the synthesis of enantiomerically pure C(sp³)-CF₃ compounds poses a significant challenge. Biocatalysis offers precise stereochemical control, however, the scarcity of fluorine-containing natural products makes it difficult to find enzymes capable of incorporating fluoroalkyl groups. Herein, we develop a ground-state flavin-dependent enzyme-catalyzed strategy for the radical-mediated enantioselective trifluoromethylation. Two engineered flavin-dependent enzymes are successfully developed to catalyze stereoselective hydrotrifluoromethylation and trifluoromethyl-alkyl cross-electrophile coupling reactions using trifluoromethyl thianthrenium triflate as a radical donor. Experimental investigations and computational simulations demonstrate that the reaction is initiated through single-electron transfer from the ground state flavin hydroquinone (FMNhq) and quenched through hydrogen atom transfer by flavin semiquinone (FMNsq). This strategy provides an opportunity to bridge the gap between biocatalysis and organic fluorides but also introduces an alternative approach to address challenging stereoselective fluoroalkylation reactions in organic synthesis.

Nonheme Mononuclear and Dinuclear Iron(II) and Iron(III) Fluoride Complexes and Their Fluorine Radical Transfer Reactivity

The nonheme iron(II) complexes containing a fluoride anion, FeII(BNPAPh2O)(F) (1) and [FeII(BNPAPh2OH)(F)(THF)](BF4) (2), were synthesized and structurally characterized. Addition of dioxygen to either 1 or 2 led to the formation of a fluoride-bridged, dinuclear iron(III) complex [Fe2III(BNPAPh2O)2(F)2(μ-F)]+ (4), which was characterized by single-crystal X-ray diffraction, 1H NMR, and elemental analysis. An iron(II)(iodide) complex, FeII(BNPAPh2O)(I) (3), was prepared and reacted with O2 to give the mononuclear complex cis-FeIII(BNPAPh2O)(OH)(I) (5). Addition of excess fluoride to 5 led to the formation of the oxo-bridged, dinuclear iron(III) complex [Fe2III(BNPAPh2O)2(F)2(μ-O)] (6), while the mononuclear iron(III)(fluoride) complex cis-FeIII(BNPAPh2O)(F)(Cl) (7) was prepared from the addition of excess F- to FeIII(BNPAPh2O)Cl2. The dinuclear complexes 4 and 6 were unreactive to fluorine radical transfer, but mononuclear 7 reacts with the radical substrate (p-MeO-C6H4)3C• to give the fluorine radical transfer products FeII(BNPAPh2O)(Cl) and (p-OMe-C6H4)3CF. These results show that a mononuclear FeIII(F) complex is capable of mediating fluorine radical transfer, even in the presence of second coordination sphere hydrogen bonds to the F- ligand. These findings are placed in context with what is known about the nonheme iron halogenases and related synthetic catalysts regarding their ability, or lack thereof, to mediate fluorine radical transfer reactions.

Biocatalytic Generation of Trifluoromethyl Radicals by Nonheme Iron Enzymes for Enantioselective Alkene Difunctionalization

The trifluoromethyl (-CF3) group represents a highly prevalent functionality in pharmaceuticals. Over the past few decades, significant advances have been made in the development of synthetic methods for trifluoromethylation. In contrast, there are currently no metalloenzymes known to catalyze the formation of C(sp3)-CF3 bonds. In this work, we demonstrate that a nonheme iron enzyme, hydroxymandelate synthase from Amycolatopsis orientalis (AoHMS), is capable of generating CF3 radicals from hypervalent iodine(III) reagents and directing them for enantioselective alkene trifluoromethyl azidation. A high-throughput screening (HTS) platform based on Staudinger ligation was established, enabling the rapid evaluation of AoHMS variants for this abiological transformation. The final optimized variant accepts a range of alkene substrates, producing the trifluoromethyl azidation products in up to 73% yield and 96:4 enantiomeric ratio (e.r.). The biocatalytic platform can be further extended to alkene pentafluoroethyl azidation and diazidation by altering the iodine(III) reagent. In addition, anion competition experiments provide insights into the radical rebound process for this abiological transformation. This study not only expands the catalytic repertoire of metalloenzymes for radical transformations but also creates a new enzymatic space for organofluorine synthesis.

Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction

Non-heme iron (FeII), α-ketoglutarate (α-KG)-dependent oxygenases are a family of enzymes that catalyze an array of transformations that cascade forward after the formation of radical intermediates. Achieving control over the reaction pathway is highly valuable and a necessary step toward broadening the applications of these biocatalysts. Numerous approaches have been used to engineer the reaction pathway of FeII/α-KG-dependent enzymes, including site-directed mutagenesis, DNA shuffling, and site-saturation mutagenesis, among others. Herein, we showcase a novel ancestral sequence reconstruction (ASR)-guided strategy in which evolutionary information is used to pinpoint the residues critical for controlling different reaction pathways. Following this, a combinatorial site-directed mutagenesis approach was used to quickly evaluate the importance of each residue. These results were validated using a DNA shuffling strategy and through quantum mechanical/molecular mechanical (QM/MM) simulations. Using this approach, we identified a set of active site residues together with a key hydrogen bond between the substrate and an active site residue, which are crucial for dictating the dominant reaction pathway. Ultimately, we successfully converted both extant and ancestral enzymes that perform benzylic hydroxylation into variants that can catalyze an oxidative ring-expansion reaction, showcasing the potential of utilizing ASR to accelerate the reaction pathway engineering within enzyme families that share common structural and mechanistic features.

Creating novel metabolic pathways by protein engineering for bioproduction

A diverse array of natural products has been produced by cell biofactories through metabolic engineering, in which enzymes play essential roles in the complex metabolic network. However, the scope of such biotransformation can be limited by the capacities of natural enzymes. To broaden their scope, many natural enzymes have recently been engineered to activate non-native substrates and/or to employ new-to-nature reaction mechanisms, but most of these systems are only demonstrated for in vitro applications. To bridge the gap between in vitro and in vivo biocatalysis, we highlight recent progress in engineering enzymes with non-native substrates or new-to-nature mechanisms that have been successfully applied in living cells to create novel metabolic pathways.

Catalyzing the future: recent advances in chemical synthesis using enzymes

Biocatalysis has the potential to address the need for more sustainable organic synthesis routes. Protein engineering can tune enzymes to perform in cascade reactions and for efficient synthesis of enantiomerically enriched compounds, using both natural and new-to-nature reaction pathways. This review highlights recent achievements in biocatalysis, especially the development of novel enzymatic syntheses to access versatile small molecule intermediates and complex biomolecules. Biocatalytic strategies for the degradation of persistent pollutants and approaches for biomass valorization are also discussed. The transition of chemical synthesis to a greener future will be accelerated by implementing enzymes and engineering them for high performance and new activities.

Recent progress in asymmetric radical reactions enabled by chiral iron catalysts

Transition-metal-catalyzed radical asymmetric reactions offer a versatile and effective platform for accessing chiral organic molecules with high enantiopurity. Given that iron is the most abundant and less toxic transition metalic element available, the application of iron catalysts is considered to be a more sustainable and attractive approach. Over the last decade, several exciting and notable achievements have been witnessed. In this highlight, we aim to provide an overview of the progress in ligand-enabled iron-catalyzed asymmetric radical reactions, with an emphasis on the reaction mechanisms.

Expanding chemistry through in vitro and in vivo biocatalysis

Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.

From Ground-State to Excited-State Activation Modes: Flavin-Dependent "Ene"-Reductases Catalyzed Non-natural Radical Reactions

Enzymes are desired catalysts for chemical synthesis, because they can be engineered to provide unparalleled levels of efficiency and selectivity. Yet, despite the astonishing array of reactions catalyzed by natural enzymes, many reactivity patterns found in small molecule catalysts have no counterpart in the living world. With a detailed understanding of the mechanisms utilized by small molecule catalysts, we can identify existing enzymes with the potential to catalyze reactions that are currently unknown in nature. Over the past eight years, our group has demonstrated that flavin-dependent "ene"-reductases (EREDs) can catalyze various radical-mediated reactions with unparalleled levels of selectivity, solving long-standing challenges in asymmetric synthesis.This Account presents our development of EREDs as general catalysts for asymmetric radical reactions. While we have developed multiple mechanisms for generating radicals within protein active sites, this account will focus on examples where flavin mononucleotide hydroquinone (FMNhq) serves as an electron transfer radical initiator. While our initial mechanistic hypotheses were rooted in electron-transfer-based radical initiation mechanisms commonly used by synthetic organic chemists, we ultimately uncovered emergent mechanisms of radical initiation that are unique to the protein active site. We will begin by covering intramolecular reactions and discussing how the protein activates the substrate for reduction by altering the redox-potential of alkyl halides and templating the charge transfer complex between the substrate and flavin-cofactor. Protein engineering has been used to modify the fundamental photophysics of these reactions, highlighting the opportunity to tune these systems further by using directed evolution. This section highlights the range of coupling partners and radical termination mechanisms available to intramolecular reactions.The next section will focus on intermolecular reactions and the role of enzyme-templated ternary charge transfer complexes among the cofactor, alkyl halide, and coupling partner in gating electron transfer to ensure that it only occurs when both substrates are bound within the protein active site. We will highlight the synthetic applications available to this activation mode, including olefin hydroalkylation, carbohydroxylation, arene functionalization, and nitronate alkylation. This section also discusses how the protein can favor mechanistic steps that are elusive in solution for the asymmetric reductive coupling of alkyl halides and nitroalkanes. We are aware of several recent EREDs-catalyzed photoenzymatic transformations from other groups. We will discuss results from these papers in the context of understanding the nuances of radical initiation with various substrates.These biocatalytic asymmetric radical reactions often complement the state-of-the-art small-molecule-catalyzed reactions, making EREDs a valuable addition to a chemist's synthetic toolbox. Moreover, the underlying principles studied with these systems are potentially operative with other cofactor-dependent proteins, opening the door to different types of enzyme-catalyzed radical reactions. We anticipate that this Account will serve as a guide and inspire broad interest in repurposing existing enzymes to access new transformations.

Radical fluorine transfer catalysed by an engineered nonheme iron enzyme

Nonheme iron enzymes stand out as one of the most versatile biocatalysts for molecular functionalization. They facilitate a wide array of chemical transformations within biological processes, including hydroxylation, chlorination, epimerization, desaturation, cyclization, and more. Beyond their native biological functions, these enzymes possess substantial potential as powerful biocatalytic platforms for achieving abiological metal-catalyzed reactions, owing to their functional and structural diversity and high evolvability. To this end, our group has recently engineered a series of nonheme iron enzymes to employ non-natural radical-relay mechanisms for abiological radical transformations not previously known in biology. Notably, we have demonstrated that a nonheme iron enzyme, (S)-2-hydroxypropylphosphonate epoxidase from Streptomyces viridochromogenes (SvHppE), can be repurposed into an efficient and selective biocatalyst for radical fluorine transfer reactions. This marks the first known instance of a redox enzymatic process for C(sp3)F bond formation. This chapter outlines the detailed experimental protocol for engineering SvHPPE for fluorination reactions. Furthermore, the provided protocol could serve as a general guideline that might facilitate other engineering endeavors targeting nonheme iron enzymes for novel catalytic functions.