Chloramphenicol biosynthesis: the structure of CmlS, a flavin-dependent halogenase showing a covalent flavin-aspartate bond

Coupling and regulation mechanisms of the flavin-dependent halogenase PyrH observed by infrared difference spectroscopy

Flavin-dependent halogenases are central enzymes in the production of halogenated secondary metabolites in various organisms and they constitute highly promising biocatalysts for regioselective halogenation. The mechanism of these monooxygenases includes formation of hypohalous acid from a reaction of fully reduced flavin with oxygen and halide. The hypohalous acid then diffuses via a tunnel to the substrate-binding site for halogenation of tryptophan and other substrates. Oxidized flavin needs to be reduced for regeneration of the enzyme, which can be performed in vitro by a photoreduction with blue light. Here, we employed this photoreduction to study characteristic structural changes associated with the transition from oxidized to fully reduced flavin in PyrH from Streptomyces rugosporus as a model for tryptophan-5-halogenases. The effect of the presence of bromide and chloride or the absence of any halides on the UV-vis spectrum of the enzyme demonstrated a halide-dependent structure of the flavin-binding pocket. Light-induced FTIR difference spectroscopy was applied and the signals assigned by selective isotope labeling of the protein moiety. The identified structural changes in α-helix and β-sheet elements were strongly dependent on the presence of bromide, chloride, the substrate tryptophan, and the product 5-chloro-tryptophan, respectively. We identified a clear allosteric coupling in solution at ambient conditions between cofactor-binding site and substrate-binding site that is active in both directions, despite their separation by a tunnel. We suggest that this coupling constitutes a fine-tuned mechanism for the promotion of the enzymatic reaction of flavin-dependent halogenases in dependence of halide and substrate availability.

Selective C-H Halogenation of Alkenes and Alkynes Using Flavin-Dependent Halogenases

Single component flavin-dependent halogenases (FDHs) possess both flavin reductase and FDH activity in a single enzyme. We recently reported that the single component FDH AetF catalyzes site-selective bromination and iodination of a variety of aromatic substrates and enantioselective bromolactonization and iodoetherification of styrenes bearing pendant carboxylic acid or alcohol substituents. Given this inherent reactivity and selectivity, we explored the utility of AetF as catalyst for alkene and alkyne C-H halogenation. We find that AetF catalyzes halogenation of a range of 1,1-disubstituted styrenes, often with high stereoselectivity. Despite the utility of haloalkenes for cross-coupling and other applications, accessing these compounds in a stereoselective manner typically requires functional group interconversion processes, and selective halogenation of 1,1'-disubstituted olefins remains rare. We also establish that AetF and homologues of this enzyme can halogenate terminal alkynes. Mutagenesis studies and deuterium kinetic isotope effects are used to support a mechanistic proposal involving covalent catalysis for halogenation of unactivated alkynes by AetF homologues. These findings expand the scope of FDH catalysis and continue to show the unique utility of single component FDHs for biocatalysis.

The Lichen Flavin-Dependent Halogenase, DnHal: Identification, Heterologous Expression and Functional Characterization

Enzymatic halogenation captures scientific interest considering its feasibility in modifying compounds for chemical diversity. Currently, majority of flavin-dependent halogenases (F-Hals) were reported from bacterial origin, and as far as we know, none from lichenized fungi. Fungi are well-known producers of halogenated compounds, so using available transcriptomic dataset of Dirinaria sp., we mined for putative gene encoding for F-Hal. Phylogenetic-based classification of the F-Hal family suggested a non-tryptophan F-Hals, similar to other fungal F-Hals, which mainly act on aromatic compounds. However, after the putative halogenase gene from Dirinaria sp., dnhal was codon-optimized, cloned, and expressed in Pichia pastoris, the ~63 kDa purified enzyme showed biocatalytic activity towards tryptophan and an aromatic compound methyl haematommate, which gave the tell-tale isotopic pattern of a chlorinated product at m/z 239.0565 and 241.0552; and m/z 243.0074 and 245.0025, respectively. This study is the start of understanding the complexities of lichenized fungal F-hals and its ability to halogenate tryptophan and other aromatic. compounds which can be used as green alternatives for biocatalysis of halogenated compounds.

Non-Native Site-Selective Enzyme Catalysis

The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.

Genome- and metabolome-guided discovery of marine BamA inhibitors revealed a dedicated darobactin halogenase

Darobactins represent a class of ribosomally synthesized and post-translationally modified peptide (RiPP) antibiotics featuring a rare bicyclic structure. They target the Bam-complex of Gram-negative bacteria and exhibit in vivo activity against drug-resistant pathogens. First isolated from Photorhabdus species, the corresponding biosynthetic gene clusters (BGCs) are widespread among γ-proteobacteria, including the genera Vibrio, Yersinia, and Pseudoalteromonas (P.). While the organization of the BGC core is highly conserved, a small subset of Pseudoalteromonas carries an extended BGC with additional genes. Here, we report the identification of brominated and dehydrated darobactin derivatives from P. luteoviolacea strains. The marine derivatives are active against multidrug-resistant (MDR) Gram-negative bacteria and showed solubility and plasma protein binding ability different from darobactin A, rendering it more active than darobactin A. The halogenation reaction is catalyzed by DarH, a new class of flavin-dependent halogenases with a novel fold.

Simultaneous removal of norfloxacin and chloramphenicol using cold atmospheric plasma jet (CAPJ): Enhanced performance, synergistic effect, plasma-activated water (PAW) contribution, mechanism and toxicity evaluation

The extensive abuse and inadvertent discharge of various antibiotics into the environment has become a serious problem for posing a big threat to human health. In order to deal with this problem, we utilized cold atmospheric plasma jet (CAPJ) to treat two different antibiotics, namely, norfloxacin and chloramphenicol, and investigated the efficiencies and corresponding mechanisms for removing the mixed antibiotics. In the application of the CAPJ technique, we made use of not only the direct plasma processing, but also the indirect plasma-activated water (PAW) treatment. The efficiency for mixed antibiotics treatment was considerably enhanced as compared to the efficiency for treatment of single antibiotics. The contributions from the CAPJ-induced reactive oxygen/nitrogen species (RONS) were examined, showing that ·OH and ¹O₂ played a major role in the degradation of norfloxacin and chloramphenicol in the direct plasma treatment, while ¹O₂ played a major role in the PAW treatment. The bio-toxicity evaluation was also provided to verify the ecological safety of the CAPJ treatment. As such, this work has not only showed the effectiveness of CAPJ treatment of mixed antibiotics, but also elucidated the mechanisms for the enhanced treatment efficiency, which may provide a new solution for treatment of antibiotics in the environment.

Efficient Electrochemical Oxidation of Chloramphenicol by Novel Reduced TiO2 Nanotube Array Anodes: Kinetics, Reaction Parameters, Degradation Pathway and Biotoxicity Forecast

The key component of electrochemical advanced oxidation technology are high-efficiency anodes, and highly efficient and simple-to-prepare materials have generated a lot of interest. In this study, novel self-supported Ti³⁺-doped titanium dioxide nanotube arrays (R-TNTs) anodes were successfully prepared by a two-step anodic oxidation and straightforward electrochemical reduction technique. The electrochemical reduction self-doping treatment produced more Ti³⁺ sites with stronger absorption in the UV-vis region, a band gap reduction from 2.86 to 2.48 ev, and a significant increase in electron transport rate. The electrochemical degradation effect of R-TNTs electrode on chloramphenicol (CAP) simulated wastewater was investigated. At pH = 5, current density of 8 mA cm^-2, electrolyte concentration of 0.1 M sodium sulfate (Na₂SO₄), initial CAP concentration of 10 mg L^-1, CAP degradation efficiency exceeded 95% after 40 min. In addition, molecular probe experiments and electron paramagnetic resonance (EPR) tests revealed that the active species were mainly •OH and SO₄^-, among which •OH played a major role. The CAP degradation intermediates were discovered using high-performance liquid chromatography-mass spectrometry (HPLC-MS), and three possible degradation mechanisms were postulated. In cycling experiments, the R-TNTs anode demonstrated good stability. The R-TNTs prepared in this paper were an anode electrocatalytic material with high catalytic activity and stability, which could provide a new approach for the preparation of electrochemical anode materials for difficult-to-degrade organic compounds.

Synergy between Genome Mining, Metabolomics, and Bioinformatics Uncovers Antibacterial Chlorinated Carbazole Alkaloids and Their Biosynthetic Gene Cluster from Streptomyces tubbatahanensis sp. nov., a Novel Actinomycete Isolated from Sulu Sea, Philippines

In this study, a novel actinomycete strain, DSD3025T, isolated from the underexplored marine sediments in Tubbataha Reefs Natural Park, Sulu Sea, Philippines, with the proposed name Streptomyces tubbatahanensis sp. nov., was described using polyphasic approaches and characterized using whole-genome sequencing. Its specialized metabolites were profiled using mass spectrometry and nuclear magnetic resonance analyses, followed by antibacterial, anticancer, and toxicity screening. The S. tubbatahanensis DSD3025T genome was comprised of 7.76 Mbp with a 72.3% G+C content. The average nucleotide identity and digital DNA-DNA hybridization values were 96.5% and 64.1%, respectively, compared with its closest related species, thus delineating the novelty of Streptomyces species. The genome encoded 29 putative biosynthetic gene clusters (BGCs), including a BGC region containing tryptophan halogenase and its associated flavin reductase, which were not found in its close Streptomyces relatives. The metabolite profiling unfolded six rare halogenated carbazole alkaloids, with chlocarbazomycin A as the major compound. A biosynthetic pathway for chlocarbazomycin A was proposed using genome mining, metabolomics, and bioinformatics platforms. Chlocarbazomycin A produced by S. tubbatahanensis DSD3025T has antibacterial activities against Staphylococcus aureus ATCC BAA-44 and Streptococcus pyogenes and showed antiproliferative activity against colon (HCT-116) and ovarian (A2780) human cancer cell lines. Chlocarbazomycin A exhibited no toxicity to liver cells but moderate and high toxicity to kidney and cardiac cell lines, respectively. IMPORTANCE Streptomyces tubbatahanensis DSD3025T is a novel actinomycete with antibiotic and anticancer activities from Tubbataha Reefs Natural Park, a United Nations Educational, Scientific and Cultural Organization World Heritage Site in Sulu Sea and considered one of the Philippines' oldest and most-well-protected marine ecosystems. In silico genome mining tools were used to identify putative BGCs that led to the discovery of genes involved in the production of halogenated carbazole alkaloids and new natural products. By integrating bioinformatics-driven genome mining and metabolomics, we unearthed the hidden biosynthetic richness and mined the associated chemical entities from the novel Streptomyces species. The bioprospecting of novel Streptomyces species from marine sediments of underexplored ecological niches serves as an important source of antibiotic and anticancer drug leads with unique chemical scaffolds.

Enhanced adsorptional-photocatalytic degradation of chloramphenicol by reduced graphene oxide-zinc oxide nanocomposite

Improper discharge of waste dry cell batteries and untreated antibiotics laden effluents to the environment pose serious threat to the sustenance of the ecosystem. In this study, synthesis of reduced graphene oxide-ZnO (rGO-ZnO) nanocomposite was achieved via a bioreduction process using waste dry cell battery rod as graphene oxide (GO) precursor. The nanocomposite was applied in the ultraviolet photocatalytic degradation of chloramphenicol (CAP) at 290 nm in the presence of hydrogen peroxide. RGO-ZnO nanocomposite was characterized by SEM, TEM, XRD, BET and FTIR. TEM image of the nanocomposite revealed a polydispersed, quasi-spherical zinc oxide on a coarse reduced graphene oxide surface. XRD patterns showed sharp, prominent crystalline wurtzite hexagonal phases of ZnO and rGO. BET surface area of the nanocomposite was 722 m²/g with pore size of 2 nm and pore volume of 0.4 cc/g. % photo-removal efficiency increased with increasing irradiation time but diminished at higher pH, temperature and CAP concentration. Photocatalytic adsorption process fitted more accurately into the Freundlich model (R² = 0.99) indicating a multilayer adsorption mechanism. 92.74% reduction in chemical oxygen demand (COD) level of veterinary effluent was obtained after treatment with the nanocomposite thus affirming its effectiveness in real waste water samples.

Synergic degradation Chloramphenicol in photo-electrocatalytic microbial fuel cell over Ni/MXene photocathode

The abuse of Chloramphenicol (CAP) has become the increasingly serious environmental problem for its harmfulness and toxicity. A novel strategy was achieved by photocatalysis coupled with microbial fuel cell (Photo-MFC) over Ni/MXene photocathode for enhancing the degradation efficiency of (CAP). It was demonstrated that the best degradation efficiency of CAP can reach 82.62% (original concentration of 30 mg/L) after 36 h under the optimal conditions (pH = 2). Based on density functional theory (DFT) calculations and high-performance liquid chromatography-mass (HPLC-MS) spectrometry, it was speculated that the degradation mechanism of CAP in Photo-MFC over Ni/MXene photoelectrode was achieved by destroying the two asymmetric centers and nitro, including the hydrodechlorination, nitro reduction reaction, hydroxylation reaction, cleavage of CN bond and ring-opening reaction of benzene ring. Finally, the ecotoxicity evaluation of the degradation products showed that the CAP degradation in the Ni/MXene modified photo-MFC system showed a remarkable tendency to the low-toxicity level.

Engineered RebH Halogenase Variants Demonstrating a Specificity Switch from Tryptophan towards Novel Indole Compounds

Activating industrially important aromatic hydrocarbons by installing halogen atoms is extremely important in organic synthesis and often improves the pharmacological properties of drug molecules. To this end, tryptophan halogenase enzymes are potentially valuable tools for regioselective halogenation of arenes, including various industrially important indole derivatives and similar scaffolds. Although endogenous enzymes show reasonable substrate scope towards indole compounds, their efficacy can often be improved by engineering. Using a structure-guided semi-rational mutagenesis approach, we have developed two RebH variants with expanded biocatalytic repertoires that can efficiently halogenate several novel indole substrates and produce important pharmaceutical intermediates. Interestingly, the engineered enzymes are completely inactive towards their natural substrate tryptophan in spite of their high tolerance to various functional groups in the indole ring. Computational modelling and molecular dynamics simulations provide mechanistic insights into the role of gatekeeper residues in the substrate binding site and the dramatic switch in substrate specificity when these are mutated.

Halogenases: a palette of emerging opportunities for synthetic biology-synthetic chemistry and C-H functionalisation

The enzymatic generation of carbon-halogen bonds is a powerful strategy used by both nature and synthetic chemists to tune the bioactivity, bioavailability and reactivity of compounds, opening up the opportunity for selective C-H functionalisation. Genes encoding halogenase enzymes have recently been shown to transcend all kingdoms of life. These enzymes install halogen atoms into aromatic and less activated aliphatic substrates, achieving selectivities that are often challenging to accomplish using synthetic methodologies. Significant advances in both halogenase discovery and engineering have provided a toolbox of enzymes, enabling the ready use of these catalysts in biotransformations, synthetic biology, and in combination with chemical catalysis to enable late stage C-H functionalisation. With a focus on substrate scope, this review outlines the mechanisms employed by the major classes of halogenases, while in parallel, it highlights key advances in the utilisation of the combination of enzymatic halogenation and chemical catalysis for C-H activation and diversification.

Flavin-dependent halogenases catalyze enantioselective olefin halocyclization

Halocyclization of alkenes is a powerful bond-forming tool in synthetic organic chemistry and a key step in natural product biosynthesis, but catalyzing halocyclization with high enantioselectivity remains a challenging task. Identifying suitable enzymes that catalyze enantioselective halocyclization of simple olefins would therefore have significant synthetic value. Flavin-dependent halogenases (FDHs) catalyze halogenation of arene and enol(ate) substrates. Herein, we reveal that FDHs engineered to catalyze site-selective aromatic halogenation also catalyze non-native bromolactonization of olefins with high enantioselectivity and near-native catalytic proficiency. Highly selective halocyclization is achieved by characterizing and mitigating the release of HOBr from the FDH active site using a combination of reaction optimization and protein engineering. The structural origins of improvements imparted by mutations responsible for the emergence of halocyclase activity are discussed. This expansion of FDH catalytic activity presages the development of a wide range of biocatalytic halogenation reactions.

Catalytic enantioselective halocyclization of alkenes is an important bond forming tool and a key step in natural product biosynthesis, but so far no examples of the enzymatic counterpart of this reaction on simple achiral olefins have been reported. Here, the authors describe examples of engineered flavin-dependent halogenases that catalyze halolactonization of olefins with high enantioselectivity and near-native catalytic activity.

Genomic Determinants Encode the Reactivity and Regioselectivity of Flavin-Dependent Halogenases in Bacterial Genomes and Metagenomes

Halogenases create diverse natural products by utilizing halide ions and are of great interest in the synthesis of potential pharmaceuticals and agrochemicals. An increasing number of halogenases discovered in microorganisms are annotated as flavin-dependent halogenases (FDHs), but their chemical reactivities are markedly different and the genomic contents associated with such functional distinction have not been revealed yet. Even though the reactivity and regioselectivity of FDHs are essential in the halogenation activity, these FDHs are annotated inaccurately in the protein sequence repositories without characterizing their functional activities. We carried out a comprehensive sequence analysis and biochemical characterization of FDHs. Using a probabilistic model that we built in this study, FDHs were discovered from 2,787 bacterial genomes and 17 sediment metagenomes. We analyzed the essential genomic determinants that are responsible for substrate binding and subsequent reactions: four flavin adenine dinucleotide-binding, one halide-binding, and four tryptophan-binding sites. Compared with previous studies, our study utilizes large-scale genomic information to propose a comprehensive set of sequence motifs that are related to the active sites and regioselectivity. We reveal that the genomic patterns and phylogenetic locations of the FDHs determine the enzymatic reactivities, which was experimentally validated in terms of the substrate scope and regioselectivity. A large portion of publicly available FDHs needs to be reevaluated to designate their correct functions. Our genomic models establish comprehensive links among genotypic information, reactivity, and regioselectivity of FDHs, thereby laying an important foundation for future discovery and classification of novel FDHs.

IMPORTANCE Halogenases are playing an important role as tailoring enzymes in biosynthetic pathways. Flavin-dependent tryptophan halogenases (Trp-FDHs) are among the enzymes that have broad substrate scope and high selectivity. From bacterial genomes and metagenomes, we found highly diverse halogenase sequences by using a well-trained profile hidden Markov model built from the experimentally validated halogenases. The characterization of genotype, steady-state activity, substrate scope, and regioselectivity has established comprehensive links between the information encoded in the genomic sequence and reactivity of FDHs reported here. By constructing models for accurate and detailed sequence markers, our work should guide future discovery and classification of novel FDHs.

AoiQ Catalyzes Geminal Dichlorination of 1,3-Diketone Natural Products

Enzymes that can perform halogenation of aliphatic carbons are of significant interest to the synthetic and biocatalysis communities. Here we describe the characterization of AoiQ, a single-component flavin-dependent halogenase (FDH) that catalyzes gem-dichlorination of 1,3-diketone substrates in the biosynthesis of dichlorodiaporthin. AoiQ represents the first biochemically reconstituted FDH that can halogenate an enolizable sp3-hybridized carbon atom.

Two Novel, Flavin-Dependent Halogenases from the Bacterial Consortia of Botryococcus braunii Catalyze Mono- and Dibromination

Halogen substituents often lead to a profound effect on the biological activity of organic compounds. Flavin-dependent halogenases offer the possibility of regioselective halogenation at non-activated carbon atoms, while employing only halide salts and molecular oxygen. However, low enzyme activity, instability, and narrow substrate scope compromise the use of enzymatic halogenation as an economical and environmentally friendly process. To overcome these drawbacks, it is of tremendous interest to identify novel halogenases with high enzymatic activity and novel substrate scopes. Previously, Neubauer et al. developed a new hidden Markov model (pHMM) based on the PFAM tryptophan halogenase model, and identified 254 complete and partial putative flavin-dependent halogenase genes in eleven metagenomic data sets. In the present study, the pHMM was used to screen the bacterial associates of the Botryococcus braunii consortia (PRJEB21978), leading to the identification of several putative, flavin-dependent halogenase genes. Two of these new halogenase genes were found in one gene cluster of the Botryococcus braunii symbiont Sphingomonas sp. In vitro activity tests revealed that both heterologously expressed enzymes are active flavin-dependent halogenases able to halogenate indole and indole derivatives, as well as phenol derivatives, while preferring bromination over chlorination. Interestingly, SpH1 catalyses only monohalogenation, while SpH2 can catalyse both mono- and dihalogenation for some substrates.

Flavoprotein monooxygenases: Versatile biocatalysts

Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.

Functional and structural characterization of a flavoprotein monooxygenase essential for biogenesis of tryptophylquinone cofactor

Bioconversion of peptidyl amino acids into enzyme cofactors is an important post-translational modification. Here, we report a flavoprotein, essential for biosynthesis of a protein-derived quinone cofactor, cysteine tryptophylquinone, contained in a widely distributed bacterial enzyme, quinohemoprotein amine dehydrogenase. The purified flavoprotein catalyzes the single-turnover dihydroxylation of the tryptophylquinone-precursor, tryptophan, in the protein substrate containing triple intra-peptidyl crosslinks that are pre-formed by a radical S-adenosylmethionine enzyme within the ternary complex of these proteins. Crystal structure of the peptidyl tryptophan dihydroxylase reveals a large pocket that may dock the protein substrate with the bound flavin adenine dinucleotide situated close to the precursor tryptophan. Based on the enzyme-protein substrate docking model, we propose a chemical reaction mechanism of peptidyl tryptophan dihydroxylation catalyzed by the flavoprotein monooxygenase. The diversity of the tryptophylquinone-generating systems suggests convergent evolution of the peptidyl tryptophan-derived cofactors in different proteins.

Flavin Adenine Dinucleotide-Dependent Halogenase XanH and Engineering of Multifunctional Fusion Halogenases

Xantholipin (compound 1), a polycyclic xanthone antibiotic, exhibited strong antibacterial activities and showed potent cytotoxicity. The biosynthetic gene cluster of compound 1 has been identified in our previous work, and the construction of xanthone nucleus has been well demonstrated. However, limited information of the halogenation involved in compound 1 biosynthesis is available. In this study, based on the genetic manipulation and biochemical assay, we characterized XanH as an indispensable flavin adenine dinucleotide (FAD)-dependent halogenase (FDH) for the biosynthesis of compound 1. XanH was found to be a bifunctional protein capable of flavin reduction and chlorination and exclusively used the NADH. However, the reduced flavin could not be fully and effectively utilized, and the presence of an extra flavin reductase (FDR) and chemical-reducing agent could promote the halogenation. XanH accepted its natural free-standing substrate with angular fused polycyclic aromatic systems. Meanwhile, it exhibited moderate halogenation activity and possessed high substrate specificity. The requirement of extra FDR for higher halogenation activity is tedious for future engineering. To facilitate efforts in engineering XanH derivative proteins, we constructed the self-sufficient FDR-XanH fusion proteins. The fusion protein E1 with comparable activities to that of XanH could be used as a good alternative for future protein engineering. Taken together, these findings reported here not only improve the understanding of polycyclic xanthones biosynthesis but also expand the substrate scope of FDH and pave the way for future engineering of biocatalysts for new active substance synthesis.IMPORTANCE Halogenation is important in medicinal chemistry and plays an essential role in the biosynthesis of active secondary metabolites. Halogenases have evolved to catalyze reactions with high efficiency and selectivity, and engineering efforts have been made to engage the selective reactivity in natural product biosynthesis. The enzymatic halogenations are an environmentally friendly approach with high regio- and stereoselectivity, which make it a potential complement to organic synthesis. FDHs constitute one of the most extensively elucidated class of halogenases; however, the inventory awaits to be expanded for biotechnology applications and for the generation of halogenated natural product analogues. In this study, XanH was found to reduce flavin and halogenated the freely diffusing natural substrate with an angular fused hexacyclic scaffold, findings which were different from those for the exclusively studied FDHs. Moreover, the FDR-XanH fusion protein E1 with comparable reactivity to that of XanH serves as a successful example of genetic fusions and sets an important stage for future protein engineering.

Structures, mechanisms and applications of flavin-dependent halogenases

Overall, this review highlights the structures, mechanisms and applications of flavin-dependent halogenases (FDHs) for future development of FDHs as potential biocatalysts. FDHs catalyze incorporation of halogen atoms into a broad range of substrates. The reactions involved in the production of various halogenated natural products which are important drugs. Typical substrates for FDHs include indole, pyrrole, phenolic and aliphatic compounds. In addition to organic substrates, all FDHs utilize reduced FAD (FADH^-), oxygen and halides as co-substrates. Structural studies reveal that FDHs all have similar FAD binding sites. However, FDHs have variations between the different isotypes including different recognition residues for substrate binding and some unique loop structures and conformations. These different structural differences suggest that variations in reaction catalysis exist. However, limited knowledge of the reaction mechanisms of FDHs is currently available. Various biocatalytic applications of FDHs have been explored. Further investigation of the catalytic reactions of FDHs is essential for improving enzyme engineering work to enable FDHs catalysis of challenging reactions.

Photoinduced monooxygenation involving NAD(P)H-FAD sequential single-electron transfer

Light-dependent or light-stimulated catalysis provides a multitude of perspectives for implementation in technological or biomedical applications. Despite substantial progress made in the field of photobiocatalysis, the number of usable light-responsive enzymes is still very limited. Flavoproteins have exceptional potential for photocatalytic applications because the name-giving cofactor intrinsically features light-dependent reactivity, undergoing photoreduction with a variety of organic electron donors. However, in the vast majority of these enzymes, photoreactivity of the enzyme-bound flavin is limited or even suppressed. Here, we present a flavoprotein monooxygenase in which catalytic activity is controllable by blue light illumination. The reaction depends on the presence of nicotinamide nucleotide-type electron donors, which do not support the reaction in the absence of light. Employing various experimental approaches, we demonstrate that catalysis depends on a protein-mediated photoreduction of the flavin cofactor, which proceeds via a radical mechanism and a transient semiquinone intermediate.

Hydrothermal Enhanced Nanoscale Zero-Valent Iron Activated Peroxydisulfate Oxidation of Chloramphenicol in Aqueous Solutions: Fe-Speciation Analysis and Modeling Optimization

The efficiencies of the nanoscale zero-valent iron (nZVI) and hydrothermal and nZVI-heat activation of peroxydisulfate (PS) were studied for the decomposition of chloramphenicol (CAP) in aqueous solutions. The nZVI heat combined with activation of PS provided a significant synergistic effect. A central composite design (CCD) with response surface methodology (RSM) was employed to explore the influences of single parameter and interactions of selected variables (initial pH, PS concentration, nZVI and temperature) on degradation rates with the purpose of condition optimization. A quadratic model was established based on the experimental results with excellent correlation coefficients of 0.9908 and 0.9823 for R2 and R2adj. The optimized experimental condition for 97.12% CAP removal was predicted with the quadratic model as 15 mg/L, 0.5 mmol/L, 7.08 and 70 °C for nZVI dosage, PS, initial pH, and temperature, respectively. This study demonstrated the effectiveness of RSM for the modeling and prediction of CAP removal processes. In the optimal condition, Fe2O3 and Fe3O4 were the predominant solid products after reactions based on X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) analysis, which could also act as the activators along with the reaction. Overall, it could be concluded that hydrothermal enhanced nZVI activation of PS was a promising and efficient choice for CAP degradation.

Site-Selective C-H Halogenation Using Flavin-Dependent Halogenases Identified via Family-Wide Activity Profiling

Enzymes are powerful catalysts for site-selective C-H bond functionalization. Identifying suitable enzymes for this task and for biocatalysis in general remains challenging, however, due to the fundamental difficulty of predicting catalytic activity from sequence information. In this study, family-wide activity profiling was used to obtain sequence-function information on flavin-dependent halogenases (FDHs). This broad survey provided a number of insights into FDH activity, including halide specificity and substrate preference, that were not apparent from the more focused studies reported to date. Regions of FDH sequence space that are most likely to contain enzymes suitable for halogenating small-molecule substrates were also identified. FDHs with novel substrate scope and complementary regioselectivity on large, three-dimensionally complex compounds were characterized and used for preparative-scale late-stage C-H functionalization. In many cases, these enzymes provide activities that required several rounds of directed evolution to accomplish in previous efforts, highlighting that this approach can achieve significant time savings for biocatalyst identification and provide advanced starting points for further evolution.

Halogenating Enzymes for Active Agent Synthesis: First Steps Are Done and Many Have to Follow

Halogens can be very important for active agents as vital parts of their binding mode, on the one hand, but are on the other hand instrumental in the synthesis of most active agents. However, the primary halogenating compound is molecular chlorine which has two major drawbacks, high energy consumption and hazardous handling. Nature bypassed molecular halogens and evolved at least six halogenating enzymes: Three kind of haloperoxidases, flavin-dependent halogenases as well as α-ketoglutarate and S-adenosylmethionine (SAM)-dependent halogenases. This review shows what is known today on these enzymes in terms of biocatalytic usage. The reader may understand this review as a plea for the usage of halogenating enzymes for fine chemical syntheses, but there are many steps to take until halogenating enzymes are reliable, flexible, and sustainable catalysts for halogenation.

XszenFHal, a novel tryptophan 5-halogenase from Xenorhabdus szentirmaii

Flavin-dependent halogenases (FHals) catalyse the halogenation of electron-rich substrates, mainly aromatics. Halogenated compounds have many applications, as pharmaceutical, agrochemicals or as starting materials for the synthesis of complex molecules. By exploring the sequenced bacterial diversity, we discovered and characterized XszenFHal, a novel FHal from Xenorhabdus szentirmaii, a symbiotic bacterium of entomopathogenic nematode. The substrate scope of XszenFHal was examined and revealed activities towards tryptophan, indole and indole derivatives, leading to the formation of the corresponding 5-chloro products. XszenFHal makes a valuable addition to the panel of flavin-dependent halogenases already discovered and enriches the potential for biotechnology applications by allowing access to 5-halogenated indole derivatives.

The photocatalytic degradation of chloramphenicol with electrospun Bi2O2CO3-poly(ethylene oxide) nanofibers: the synthesis of crosslinked polymer, degradation kinetics, mechanism and cytotoxicity

Insoluble poly(ethylene oxide) (PEO) nanofibers were synthesized by adding pentaerythrotol triacrylate (PETA) into precursor solutions prior to electrospinning, and then the obtained fibers were exposed to an electron beam (EB) irradiation. Bi2O2CO3 was incorporated into these fibers to extend their photocatalytic properties. Studies confirmed that EB irradiation induced characteristic changes in PEO and led to the formation of a crosslinked structure, from which we optimized the irradiation dose of fibers as 210 kGy. The optimum PEO/Bi2O2CO3 membranes achieved 99.5% CPL degradation within 60 min, and we also proposed the possible degradation pathways of CPL in this study. Besides, all the water samples and extracts of nanomaterials showed no cytotoxicity on L-929 cells. The subtle variations in the cell viability of treated and untreated water samples could be due to the toxic intermediates arising from the photocatalytic process. Therefore, this photocatalyst-polymer membrane can be considered as a biocompatible composite system that can change the solubility of a polymer and also act as a highly efficient photocatalyst for organic wastewater treatments.

Characterization of PlGoxB, a flavoprotein required for cysteine tryptophylquinone biosynthesis in glycine oxidase from Pseudoalteromonas luteoviolacea

LodA-like proteins are oxidases with a protein-derived cysteine tryptophylquinone (CTQ) prosthetic group. In Pseudoalteromonas luteoviolacea glycine oxidase (PlGoxA), CTQ biosynthesis requires post-translational modifications catalyzed by a modifying enzyme encoded by PlgoxB. The PlGoxB protein was expressed and shown to possess a flavin cofactor. PlGoxB was unstable in solution as it readily lost the flavin and precipitated. PlGoxB precipitation was significantly reduced by incubation with either excess FAD or an equal concentration of prePlGoxA, the precursor protein that is its substrate. In contrast, the mature CTQ-bearing PlGoxA had no stabilizing effect. A homology model of PlGoxB was generated using the structure of Alkylhalidase CmIS. The FAD-binding site of PlGoxB in the model was nearly identical to that of the template structure. The bound FAD in PlGoxB had significant solvent exposure, consistent with the observed tendency to lose FAD. This also suggested that interaction of prePlGoxA with PlGoxB at the exposed FAD-binding site could prevent the observed loss of FAD and subsequent precipitation of PlGoxB. A docking model of the putative PlGoxB-prePlGoxA complex was consistent with these hypotheses. The experimental results and computational analysis implicate structural features of PlGoxB that contribute to its stability and function.

Degradation of chloramphenicol using Ti-Sb/attapulgite ceramsite particle electrodes

Ti-Sb/attapulgite ceramsite particle electrodes were prepared for the efficient degradation of chloramphenicol (CAP) in wastewater. To observe the surface morphology and structural characteristics of the Ti-Sb/attapulgite ceramsite particle electrodes, Fourier transform infrared spectroscopy, X-ray fluorescence, scanning electron microscopy, and X-ray diffraction were used for characterization. Parameters affecting the degradation efficiency and the energy consumption of the Ti-Sb/attapulgite ceramsite particle electrodes, such as current density, electrode distance, initial pH, conductivity, air flow, and packing ratio, were examined. Results showed that the optimal conditions were 20 mA/cm² current intensity, 3 cm electrode distance, 5,000 μS/cm conductivity, 2.0 L/min air flow, 50.0% packing ratio, and initial pH 1. The removal efficiency of chloramphenicol was 73.7% under the optimal conditions, and the energy consumption was 191.3 (kW h)/kg CAP. PRACTITIONER POINTS: Attapulgite ceramsite with good physical performance was prepared. The removal efficiencies for CAP in water by Ti-Sb/attapulgite ceramsite particle electrodes were studied. CAP was effectively removed by 3-D electrode system. CAP removal was significantly influenced by operational parameters. Three-dimensional electrode system shows good degradation ability.

Degradation of antibiotic chloramphenicol in water by pulsed discharge plasma combined with TiO2/WO3 composites: mechanism and degradation pathway

Pulsed discharge plasma (PDP) combined with TiO₂/WO₃ composites for chloramphenicol (CAP) degradation was investigated. The prepared TiO₂/WO₃ composites were characterized by scanning electron microscope, transmission electron microscope, nitrogen adsorption apparatus, zeta sizer, X-ray diffraction, Raman spectra, UV-Vis absorption spectroscopy, X-ray photoelectron spectroscopy, photocurrent and electrochemical impedance spectroscopy. The degradation performance showed that the addition of TiO₂/WO₃ composites significantly enhanced the removal efficiency of CAP in PDP system. At a peak voltage of 18 kV, the highest removal efficiency of CAP could reach 88.1% in PDP system with 4 wt% TiO₂/WO₃, which was 36.8% and 26.0% higher than that in sole PDP system and PDP/TiO₂ system, respectively. The TiO₂/WO₃ composites significantly accelerated interfacial charge transfer process compared to the pure TiO₂. Besides, the effect of catalyst dosage and peak voltage on CAP removal was evaluated. OH, O₃O₂^-, h⁺ and high-energy electrons contributed to CAP degradation in PDP-TiO₂/WO₃ system. Addition of TiO₂/WO₃ composites can decompose O₃ and produce more OH and H₂O₂. The degradation intermediates were measured by liquid chromatography-mass spectrometry (LC-MS) and ion chromatography (IC). The cycling degradation experiment showed that the TiO₂/WO₃ composites have good reusability as well as stability.

Unusual substrate and halide versatility of phenolic halogenase PltM

Controlled halogenation of chemically versatile substrates is difficult to achieve. Here we describe a unique flavin-dependent halogenase, PltM, which is capable of utilizing a wide range of halides for installation on a diverse array of phenolic compounds, including FDA-approved drugs and natural products, such as terbutaline, fenoterol, resveratrol, and catechin. Crystal structures of PltM in complex with phloroglucinol and FAD in different states yield insight into substrate recognition and the FAD recycling mechanism of this halogenase.

Halogenase enzymes are of interest as halogenating tools for organic synthesis. Here the authors show that the bacterial FAD-dependent phenolic halogenase PltM chlorinates, brominates and iodinates a variety of substrates and reveal the structural basis for its substrate versatility and provide insights into the FAD recycling mechanism of PltM.

Two-Component FAD-Dependent Monooxygenases: Current Knowledge and Biotechnological Opportunities

Flavoprotein monooxygenases create valuable compounds that are of high interest for the chemical, pharmaceutical, and agrochemical industries, among others. Monooxygenases that use flavin as cofactor are either single- or two-component systems. Here we summarize the current knowledge about two-component flavin adenine dinucleotide (FAD)-dependent monooxygenases and describe their biotechnological relevance. Two-component FAD-dependent monooxygenases catalyze hydroxylation, epoxidation, and halogenation reactions and are physiologically involved in amino acid metabolism, mineralization of aromatic compounds, and biosynthesis of secondary metabolites. The monooxygenase component of these enzymes is strictly dependent on reduced FAD, which is supplied by the reductase component. More and more representatives of two-component FAD-dependent monooxygenases have been discovered and characterized in recent years, which has resulted in the identification of novel physiological roles, functional properties, and a variety of biocatalytic opportunities.

Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris

Flavin-dependent halogenases can be used as biocatalysts because they regioselectively halogenate their substrates under mild reaction conditions. New halogenases with novel substrate specificities will add to the toolbox of enzymes available to organic chemists. HalX, the product of the xcc-b100_4193 gene, is a putative flavin-dependent halogenase from Xanthomonas campestris. The enzyme was recombinantly expressed and crystallized in order to aid in identifying its hitherto unknown substrate. Native data collected to a resolution of 2.5 Å showed indications of merohedral twinning in a hexagonal lattice. Attempts to solve the phase problem by molecular replacement failed. Here, a detailed analysis of the suspected twinning is presented. It is most likely that the crystals are trigonal (point group 3) and exhibit perfect hemihedral twinning so that they appear to be hexagonal (point group 6). As there are several molecules in the asymmetric unit, noncrystallographic symmetry may complicate twinning analysis and structure determination.

A flavin-dependent halogenase from metagenomic analysis prefers bromination over chlorination

Flavin-dependent halogenases catalyse halogenation of aromatic compounds. In most cases, this reaction proceeds with high regioselectivity and requires only the presence of FADH2, oxygen, and halide salts. Since marine habitats contain high concentrations of halides, organisms populating the oceans might be valuable sources of yet undiscovered halogenases. A new Hidden-Markov-Model (HMM) based on the PFAM tryptophan halogenase model was used for the analysis of marine metagenomes. Eleven metagenomes were screened leading to the identification of 254 complete or partial putative flavin-dependent halogenase genes. One predicted halogenase gene (brvH) was selected, codon optimised for E. coli, and overexpressed. Substrate screening revealed that this enzyme represents an active flavin-dependent halogenase able to convert indole to 3-bromoindole. Remarkably, bromination prevails also in a large excess of chloride. The BrvH crystal structure is very similar to that of tryptophan halogenases but reveals a substrate binding site that is open to the solvent instead of being covered by a loop.

Halogenase engineering and its utility in medicinal chemistry

Halogenation is commonly used in medicinal chemistry to improve the potency of pharmaceutical leads. While synthetic methods for halogenation present selectivity and reactivity challenges, halogenases have evolved over time to perform selective reactions under benign conditions. The optimization of halogenation biocatalysts has utilized enzyme evolution and structure-based engineering alongside biotransformation in a variety of systems to generate stable site-selective variants. The recent improvements in halogenase-catalyzed reactions has demonstrated the utility of these biocatalysts for industrial purposes, and their ability to achieve a broad substrate scope implies a synthetic tractability with increasing relevance in medicinal chemistry.

In Vitro Analysis of Cyanobacterial Nonheme Iron-Dependent Aliphatic Halogenases WelO5 and AmbO5

Aliphatic carbon-halogen (C-X) bonds are prevalent in modern pharmaceuticals and bioactive natural products. Three distinct chemical strategies are known in Nature to generate these structural motifs. The first is via the nucleophilic substitution at a prefunctionalized electrophilic carbon center with a halide anion (X^-), known for the S-adenosyl-l-methionine-dependent halogenases. The second is via the electrophilic activation of an alkene or its equivalent by a halenium ion (X⁺) donor, known for the haloperoxidases and flavin-dependent halogenases. The third is via the direct functionalization of an unactivated aliphatic C-H bond with a halogen radical (X) equivalent, known for the 2-oxo-glutarate and nonheme iron-dependent halogenases. Due to the ubiquitous nature of aliphatic C-H groups in organic molecules, transformations that permit chemo-, regio-, and stereo-selective modification(s) at an unactivated sp³-carbon center have been a long sought-after goal in chemical science. Two nonheme iron-dependent halogenases, WelO5 and AmbO5 involved in the biogenesis of cyanobacterial hapalindole-type alkaloids, have been recently shown able to perform this type of challenging transformation. In this chapter, experimental details for the in vitro reconstitution of WelO5 and AmbO5 enzymatic activities are presented.

Understanding and Improving the Activity of Flavin-Dependent Halogenases via Random and Targeted Mutagenesis

Flavin-dependent halogenases (FDHs) catalyze the halogenation of organic substrates by coordinating reactions of reduced flavin, molecular oxygen, and chloride. Targeted and random mutagenesis of these enzymes have been used to both understand and alter their reactivity. These studies have led to insights into residues essential for catalysis and FDH variants with improved stability, expanded substrate scope, and altered site selectivity. Mutations throughout FDH structures have contributed to all of these advances. More recent studies have sought to rationalize the impact of these mutations on FDH function and to identify new FDHs to deepen our understanding of this enzyme class and to expand their utility for biocatalytic applications.

Chemoenzymatic Synthesis of Starting Materials and Characterization of Halogenases Requiring Acyl Carrier Protein-Tethered Substrates

Flavin-adenine dinucleotide (FAD)-dependent halogenases are widespread in natural product biosynthetic gene clusters and have been demonstrated to employ small organic molecules as substrates for halogenation, as well as substrates that are tethered to carrier proteins (CPs). Despite numerous reports of FAD-dependent halogenases utilizing CP-tethered substrates, only a few have been biochemically characterized due to limited accessibility to the physiological substrates. Here, we describe a method for the preparation of acyl-S-CP substrates and their use in biochemical assays to query the activity of FAD-dependent halogenases. Furthermore, we describe a mass spectrometry-based method for the characterization of acyl-S-CP substrates and the corresponding halogenated products generated by the halogenases. Finally, we test the substrate specificity of a physiological chlorinase and a physiological brominase from marine bacteria, and, for the first time, demonstrate the distinct halide specificity of halogenases. The methodology described here will enable characterization of new halogenases employing CP-tethered substrates.

Electrolytic and electro-irradiated technologies for the removal of chloramphenicol in synthetic urine with diamond anodes

Hospital effluents are a major source for the occurrence of pharmaceuticals in the environment. In this work, the treatment of synthetic urine polluted with chloramphenicol is studied by using three different conductive-diamond electrochemical oxidation technologies: electrolysis (single electrolysis), photoelectrolysis and high-frequency ultrasound sonoelectrolysis. These technologies were evaluated at 10 and 100 mA cm^-2. Results shows that not only chloramphenicol but also other organics contained in urine are completely mineralized by electrolysis. Ammonium is the main inorganic nitrogen species formed and it can react with the electrogenerated hypochlorite, favouring the formation of chloramines. These species prevent the potential formation of perchlorate from chlorides contained in urine at low current densities (10 mA cm^-2) and delay its occurrence at high current densities (100 mA cm^-2). On the other hand, irradiation of ultraviolet (UV) light or high-frequency ultrasound (US) produce changes in the performance of the electrolytic treatment, but these changes are not as important as in other cases of study shown in the literature. Nonetheless, the effect of electroirradiated technologies seems to be higher and depends on the type of pollutant when working at low current densities (10 mA cm^-2). It is positive in the case of the degradation of the antibiotic and the uric acid and negative in the case of urea where there is a clear antagonistic effect. Production of oxidants increases with the current density although in lower ratio than expected. These results are of great importance because clearly point out that electrolytic technologies can be applied to minimize the diffuse pollution associated to pharmaceuticals before discharge into municipal sewers.

Function and Structure of MalA/MalA', Iterative Halogenases for Late-Stage C-H Functionalization of Indole Alkaloids

Malbrancheamide is a dichlorinated fungal indole alkaloid isolated from both Malbranchea aurantiaca and Malbranchea graminicola that belongs to a family of natural products containing a characteristic bicyclo[2.2.2]diazaoctane core. The introduction of chlorine atoms on the indole ring of malbrancheamide differentiates it from other members of this family and contributes significantly to its biological activity. In this study, we characterized the two flavin-dependent halogenases involved in the late-stage halogenation of malbrancheamide in two different fungal strains. MalA and MalA' catalyze the iterative dichlorination and monobromination of the free substrate premalbrancheamide as the final steps in the malbrancheamide biosynthetic pathway. Two unnatural bromo-chloro-malbrancheamide analogues were generated through MalA-mediated chemoenzymatic synthesis. Structural analysis and computational studies of MalA' in complex with three substrates revealed that the enzyme represents a new class of zinc-binding flavin-dependent halogenases and provides new insights into a potentially unique reaction mechanism.

Development of Halogenase Enzymes for Use in Synthesis

Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo. Consequently, a high proportion of pharmaceuticals and agrochemicals on the market today possess halogens. Halogenated organic compounds are also common intermediates in synthesis and are particularly valuable in metal-catalyzed cross-coupling reactions. Despite the potential utility of organohalogens, traditional nonenzymatic halogenation chemistry utilizes deleterious reagents and often lacks regiocontrol. Reliable, facile, and cleaner methods for the regioselective halogenation of organic compounds are therefore essential in the development of economical and environmentally friendly industrial processes. A potential avenue toward such methods is the use of halogenase enzymes, responsible for the biosynthesis of halogenated natural products, as biocatalysts. This Review will discuss advances in developing halogenases for biocatalysis, potential untapped sources of such biocatalysts and how further optimization of these enzymes is required to achieve the goal of industrial scale biohalogenation.

Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse

Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.