Exploring the Biocatalytic Potential of Fe/α-Ketoglutarate-Dependent Halogenases

Freestanding Fe/α-ketoglutarate-dependent halogenases are oxidoreductases that catalyze the installation of halogen atoms into unactivated sp³-hybridized carbon centers with high stereo- and regioselectivity. Since their discovery in 2014, a small number of indole alkaloid and amino acid halogenases have been identified and characterized. First enzyme engineering examples suggest that the accessible substrate range of these enzymes may be expanded through the use of rational enzyme design and directed evolution. Structural investigations of non-heme iron halogenases acting on freestanding as well as tethered substrates are beginning to inform about the principles of the underlying halogenation mechanism.     

Evolved Aliphatic Halogenases Enable Regiocomplementary C−H Functionalization of a Pharmaceutically Relevant Compound

Non‐heme iron halogenases are synthetically valuable biocatalysts that are capable of halogenating unactivated sp³‐hybridized carbon centers with high stereo‐ and regioselectivity. The reported substrate scope of these enzymes, however, is limited primarily to the natural substrates and their analogues. We engineered the halogenase WelO5* for chlorination of a martinelline‐derived fragment. Using structure‐guided evolution, a halogenase variant with a more than 290‐fold higher total turnover number and a 400‐fold higher apparent k_cat compared to the wildtype enzyme was generated. Moreover, we identified key positions in the active site that allow direction of the halogen to different positions in the target substrate. This is the first example of enzyme engineering to expand the substrate scope of a non‐heme iron halogenase beyond the native indole‐alkaloid‐type substrates. The highly evolvable nature of WelO5* underscores the usefulness of this enzyme family for late‐stage halogenation.     

Enzymatic Halogenation of Tryptophan on a Gram Scale

Halogenated arenes are important building blocks in medicinal and agrochemistry. Chemical electrophilic aromatic halogenation requires molecular halogen, whereas FAD‐dependent halogenases form halogenated arenes with high regioselectivity while only halide salts and O₂ are required. This reaction proceeds at room temperature in aqueous media. However, enzymatic halogenation is considered inefficient, mainly because halogenases are not stable. Thus, the preparative application remained elusive. We were able to show that the long‐term stability and, hence, the preparative efficiency of the tryptophan‐7‐halogenase RebH can be significantly improved by immobilization together with the other enzymes required for cofactor regeneration. We established a facile scalable method suitable for the halogenation of tryptophan and its derivatives on a gram scale using a solid, multifunctional, and recyclable biocatalyst; this immobilization strategy might also be applicable for other FAD‐dependent halogenases.     

卤过氧化物酶在绿色卤化反应中的研究进展

卤化反应是一类极其重要的有机合成反应,在实验室研究和化工生产领域占据重要地位.传统卤化反应因存在使用有毒有害试剂、反应缺乏选择性等问题而亟待改进,生物酶催化策略则为突破上述瓶颈提供了可能.自然界已经进化出多种可对有机物中催化引入卤素的卤化酶.酶催化卤化反应的突出优势在于常温常压下,可使用来源温和的卤素进行高效的催化反应.催化范围包括卤化、羟卤化、卤环合和氧化脱羧等多种具有挑战性的反应.鉴于酶催化卤化反应展示出巨大的潜力,从催化活性、酶稳定性、底物浓度、催化范围等几个方面着重介绍了卤过氧化物酶在绿色卤化反应中的最新研究进展,为进一步开发绿色的卤化酶催化卤化反应提供参考.     

Halogenation of unactivated carbon centers in natural product biosynthesis: trichlorination of leucine during barbamide biosynthesis

The in vitro reconstitution of leucine halogenation during barbamide biosynthesis has been accomplished. It has been demonstrated that the triple chlorination of the unactivated pro-R methyl group of the peptidyl carrier protein-tethered l-Leu substrate is carried out by the tandem action of two nonheme iron(II)-dependent halogenases, BarB1 and BarB2. Investigation of the substrate specificities of each of the halogenating enzymes revealed their complementary roles in the generation of trichloroleucine.     

A Collaborative Journey towards the Late-Stage Functionalization of Added-Value Chemicals Using Engineered Halogenases

In 2017, two companies, Novartis AG and Syngenta AG, joined forces with the group of Prof. Buller, head of the Competence Center for Biocatalysis (CCBIO), to tackle the challenge of enzymatic late-stage halogenation. This biocatalytic method was considered to provide a more sustainable approach to late-stage halogenation of complex molecules than traditional synthetic approaches. Using machine-learning guided protein engineering, α-ketoglutarate dependent halogenases were evolved into versatile catalysts capable of selectively chlorinating inactivated C−H bonds. Structurally diverse molecules, namely an analogue of martinelline as well as two members of the soraphen natural product family, were enzymatically chlorinated at two distinct positions in a regio- and stereoselective manner, thus demonstrating the synthetic usefulness of such a strategy. As part of our three-year collaboration, flavin-dependent halogenases were also studied.     

Specific Enzymatic Halogenation—From the Discovery of Halogenated Enzymes to Their Applications In Vitro and In Vivo

During the last 20 years, focus has shifted from haloperoxidases to flavin‐dependent and non‐heme‐iron halogenases because of their proven involvement in the biosynthesis of halogenated metabolites in different organisms and the regioselectivity of their reactions. During the first 10–12 years, the main research topics were the detection of halogenases as well as the elucidation of three‐dimensional structures and reaction mechanisms. This Review mainly deals with studies on halogenating enzymes published between 2010 and 2015. It focusses on the elucidation of the involvement of halogenating enzymes in halometabolite biosynthesis, application of halogenases in in vivo and in vitro systems, in vivo modification of biosynthetic pathways in bacteria and plants, improvement of enzyme stability, broadening of substrate specificity, and the combination of biocatalysis with chemical synthesis to produce new compounds.     

Repurposing Iron- and 2-Oxoglutarate-Dependent Oxygenases to Catalyze Olefin Hydration

Mononuclear nonheme iron(II) and 2-oxoglutarate (Fe/2OG)-dependent oxygenases and halogenases are known to catalyze a diverse set of oxidative reactions, including hydroxylation, halogenation, epoxidation, and desaturation in primary metabolism and natural product maturation. However, their use in abiotic transformations has mainly been limited to C−H oxidation. Herein, we show that various enzymes of this family, when reconstituted with Fe(II) or Fe(III), can catalyze Mukaiyama hydration—a redox neutral transformation. Distinct from the native reactions of the Fe/2OG enzymes, wherein oxygen atom transfer (OAT) catalyzed by an iron-oxo species is involved, this nonnative transformation proceeds through a hydrogen atom transfer (HAT) pathway in a 2OG-independent manner. Additionally, in contrast to conventional inorganic catalysts, wherein a dinuclear iron species is responsible for HAT, the Fe/2OG enzymes exploit a mononuclear iron center to support this reaction. Collectively, our work demonstrates that Fe/2OG enzymes have utility in catalysis beyond the current scope of catalytic oxidation.     

Fluorogenic Diversification of Unprotected Bromotryptophan by Aqueous Mizoroki–Heck Cross-Coupling

Fluorescent styryl-tryptophans have been synthesized by a Mizoroki–Heck cross-coupling from unprotected bromotryptophan in aqueous medium showing promising spectrophotometric properties for possible application in fluorescence labelling of biomolecules. Moreover, this strategy permits a modular combination of biocatalytic halogenation by using immobilized FAD-dependent tryptophan halogenases and Pd-mediated chemocatalysis in a multistep one-pot process.     

A High‐Throughput Fluorescence Assay to Determine the Activity of Tryptophan Halogenases

Biocatalytic halogenation with tryptophan halogenases is hampered by severe limitations such as low activity and stability. These drawbacks can be overcome by directed evolution, but for screening large mutant libraries, a facile high‐throughput method is required. Therefore, we developed a quantitative halogenase assay based on a Suzuki–Miyaura cross‐coupling towards the formation of a fluorescent aryltryptophan. The technique was optimized for application in crude E. coli lysate without intermediary purification steps, and was used for quantitatively monitoring the formation of halogenated tryptophans with high specificity by facile fluorescence screening in microtiter plates. This novel screening approach was exploited to engineer a thermostable tryptophan 6‐halogenase. Libraries were constructed by error‐prone PCR and selected for improved thermal resistance simply by fluorogenic cross‐coupling. Our method led to an enzyme variant with substantially increased thermal stability and 2.5‐fold improved activity.     

Identification and Spectroscopic Characterization of Nonheme Iron(III) Hypochlorite Intermediates

Fe^III–hypohalite complexes have been implicated in a wide range of important enzyme‐catalyzed halogenation reactions including the biosynthesis of natural products and antibiotics and post‐translational modification of proteins. The absence of spectroscopic data on such species precludes their identification. Herein, we report the generation and spectroscopic characterization of nonheme Fe^III–hypohalite intermediates of possible relevance to iron halogenases. We show that Fe^III‐OCl polypyridylamine complexes can be sufficiently stable at room temperature to be characterized by UV/Vis absorption, resonance Raman and EPR spectroscopies, and cryo‐ESIMS. DFT methods rationalize the pathways to the formation of the Fe^III‐OCl, and ultimately Fe^IV?O, species and provide indirect evidence for a short‐lived Fe^II‐OCl intermediate. The species observed and the pathways involved offer insight into and, importantly, a spectroscopic database for the investigation of iron halogenases.     

Second-Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes

Mononuclear iron-containing enzymes are highly versatile oxidants that often react stereospecifically and/or regioselectively with substrates. Combined experimental and computational studies on heme monooxygenases, nonheme iron dioxygenases and halogenases have revealed the intricate details of the second-coordination sphere, which determine this specificity and selectivity. These second-coordination sphere effects originate from the positioning of the substrate and oxidant, which involve the binding of the co-factors and substrate into the active site of the protein. In addition, some enzymes affect the selectivity and reactivity through charge-stabilization from nearby bound cations/anions, an induced electric field or through the positioning of salt bridges and hydrogen-bonding interactions to first-coordination sphere iron ligands and/or the substrate. Examples of all of these second-coordination sphere effects in iron-containing enzymes and how these influence structure and reactivity are given.     

Selective C−H Halogenation with a Highly Fluorinated Manganese Porphyrin

The selective C?H functionalization of aliphatic molecules remains a challenge in organic synthesis. While radical chain halogenation reactions provide efficient access to many halogenated molecules, the use of typical protocols for the selective halogenation of electron‐deficient and strained aliphatic molecules is rare. Herein, we report selective C?H chlorination and fluorination reactions promoted by an electron‐deficient manganese pentafluorophenyl porphyrin catalyst, Mn(TPFPP)Cl. This catalyst displays superior properties for the aliphatic halogenation of recalcitrant, electron‐deficient, and strained substrates with unique regio‐ and stereoselectivity. UV/Vis analysis during the course of the reaction indicated that an oxo‐Mn^V species is responsible for hydrogen‐atom abstraction. The observed stereoselectivity results from steric interactions between the bulky porphyrin ligand and the intermediate substrate radical in the halogen rebound step.     

Reengineering a tryptophan halogenase to preferentially chlorinate a direct alkaloid precursor

Installing halogens onto natural products can generate compounds with novel or improved properties. Notably, enzymatic halogenation is now possible as a result of the discovery of several classes of halogenases; however, applications are limited because of the narrow substrate specificity of these enzymes. Here we demonstrate that the flavin-dependent halogenase RebH can be engineered to install chlorine preferentially onto tryptamine rather than the native substrate tryptophan. Tryptamine is a direct precursor to many alkaloid natural products, including approximately 3000 monoterpene indole alkaloids. To validate the function of this engineered enzyme in vivo, we transformed the tryptamine-specific RebH mutant (Y455W) into the alkaloid-producing plant Madagascar periwinkle ( Catharanthus roseus ) and observed the de novo production of the halogenated alkaloid 12-chloro-19,20-dihydroakuammicine. While wild-type (WT) RebH has been integrated into periwinkle metabolism previously, the resulting tissue cultures accumulated substantial levels of 7-chlorotryptophan. Tryptophan decarboxylase, the enzyme that converts tryptophan to tryptamine, accepts 7-chlorotryptophan at only 3% of the efficiency of the native substrate tryptophan, thereby creating a bottleneck. The RebH Y455W mutant circumvents this bottleneck by installing chlorine onto tryptamine, a downstream substrate. In comparison with cultures harboring RebH and WT RebF, tissue cultures containing mutant RebH Y455W and RebF also accumulate microgram per gram fresh-weight quantities of 12-chloro-19,20-dihydroakuammicine but, in contrast, do not accumulate 7-chlorotryptophan, demonstrating the selectivity and potential utility of this mutant in metabolic engineering applications.     

Flavin-dependent biocatalysts in synthesis

The diverse chemistry possible with flavin cofactors positions flavin-dependent enzymes as versatile synthetic tools. This focused review highlights applications of flavin-dependent enzymes in organic synthesis. Select examples of monoamine oxidases, ene-reductases, monooxygenases and halogenases in target-oriented synthesis are presented.     

Total synthesis and biochemical characterization of mirror image barnase

In this study we synthesized and characterized mirror image barnase (B. amyloliquefaciens ribonuclease). d-Barnase was identical to l-barnase, when analyzed by liquid chromatography and mass-spectrometry. Proteolysis of the mirror image enzyme revealed that in contrast to its native counterpart, d-barnase was completely stable to digestive proteases. In enzymatic assays, d-barnase had the reciprocal chiral specificity and was fully active towards mirror image substrates. Interestingly, d-barnase also hydrolyzed the substrate of the native chirality, albeit 4000 times less efficiently. This effect was further confirmed by digesting a native 112-mer RNA with the enzyme. Additional studies revealed that barnase accommodates a range of substrates with various chiralities, but the prime requirement for guanosine remains. These studies point toward using mirror image enzymes as modern agents in biotechnology.     

Advances in Iodine(III)‐Mediated Halogenations: A Versatile Tool to Explore New Reactivities and Selectivities

Within the repertoire of organic chemical transformations, the halogenation of substrates is among the most versatile, reliable, and broadly applicable reactions. Although a multitude of different methods are known today, there is still a huge demand for novel and, in particular, catalytic halogenation methods that exhibit new reactivities and selectivities. The class of hypervalent iodanes meets exactly these needs and thus offers a great opportunity to fuel this highly desirable direction within the field of halogenation chemistry. This Concept gives a short overview of recent examples focusing on selective and/or mechanistically unusual halogenations.     

Halogenation in Fungi: What Do We Know and What Remains to Be Discovered?

In nature, living organisms produce a wide variety of specialized metabolites to perform many biological functions. Among these specialized metabolites, some carry halogen atoms on their structure, which can modify their chemical characteristics. Research into this type of molecule has focused on how organisms incorporate these atoms into specialized metabolites. Several families of enzymes have been described gathering metalloenzymes, flavoproteins, or S-adenosyl-L-methionine (SAM) enzymes that can incorporate these atoms into different types of chemical structures. However, even though the first halogenation enzyme was discovered in a fungus, this clade is still lagging behind other clades such as bacteria, where many enzymes have been discovered. This review will therefore focus on all halogenation enzymes that have been described in fungi and their associated metabolites by searching for proteins available in databases, but also by using all the available fungal genomes. In the second part of the review, the chemical diversity of halogenated molecules found in fungi will be discussed. This will allow the highlighting of halogenation mechanisms that are still unknown today, therefore, highlighting potentially new unknown halogenation enzymes.     

RadH: A Versatile Halogenase for Integration into Synthetic Pathways

Flavin‐dependent halogenases are useful enzymes for providing halogenated molecules with improved biological activity, or intermediates for synthetic derivatization. We demonstrate how the fungal halogenase RadH can be used to regioselectively halogenate a range of bioactive aromatic scaffolds. Site‐directed mutagenesis of RadH was used to identify catalytic residues and provide insight into the mechanism of fungal halogenases. A high‐throughput fluorescence screen was also developed, which enabled a RadH mutant to be evolved with improved properties. Finally we demonstrate how biosynthetic genes from fungi, bacteria, and plants can be combined to encode a new pathway to generate a novel chlorinated coumarin “non‐natural” product in E. coli.     

Ion-Pair Version of the Chemo- and Regioselectivity of Halogen Addition to Double Bond

Analysis of the stereoselectivity of halogenation of alkenes shows that the notion of the reaction intermediate as a three-membered halogenium state is contrary to fact. It is assumed that the precursors of the halogenation products are the ion pairs formed by step heterolysis of the C = C bond. This allows a logical connection to be revealed between the electronic properties of substituents in substrates and reagents, on the one hand, and the overall stereoselectivity and direction of halogenation, on the other.