Natural and engineered biosynthesis of fluorinated natural products

Chemoenzymatic Synthesis of Fluorinated Mycocyclosin Enabled by the Engineered Cytochrome P450-Catalyzed Biaryl Coupling Reaction

Installing fluorine atoms onto natural products holds great promise for the generation of fluorinated molecules with improved or novel pharmacological properties. The enzymatic oxidative carbon-carbon coupling reaction represents a straightforward strategy for synthesizing biaryl architectures, but the exploration of this method for producing fluorine-substituted derivatives of natural products remains elusive. Here, in this study, we report the protein engineering of cytochrome P450 from Mycobacterium tuberculosis (MtCYP121) for the construction of a series of new-to-nature fluorine-substituted Mycocyclosin derivatives. This protocol takes advantage of a "hybrid" chemoenzymatic procedure consisting of tyrosine phenol lyase-catalyzed fluorotyrosine preparation from commercially available fluorophenols, intermolecular chemical condensation to give cyclodityrosines, and an engineered MtCYP121-catalyzed intramolecular biphenol coupling reaction to complete the strained macrocyclic structure. Computational mechanistic studies reveal that MtCYP121 employs Cpd I to abstract a hydrogen atom from the proximal phenolic hydroxyl group of the substrate to trigger the reaction. Then, conformational change makes the two phenolic hydroxyl groups close enough to undergo intramolecular hydrogen atom transfer with the assistance of a pocket water molecule. The final diradical coupling process completes the intramolecular C-C bond formation. The efficiency of the biaryl coupling reaction was found to be influenced by various fluorine substitutions, primarily due to the presence of distinct binding conformations.

Construction of a high-efficiency GjCCD4a mutant and its application for de novo biosynthesis of five crocins in Escherichia coli

Crocins are bioactive natural products that rarely exist in plants. High costs and resource shortage severely limit its development and application. Synthetic biology studies on crocins are of considerable global interest. However, the lack of high-efficiency genetic tools and complex cascade biocatalytic systems have substantially hindered progress in crocin biosynthesis-related research. Based on mutagenesis, a high-efficiency GjCCD4a mutant (N212m) was constructed with a catalytic efficiency that was 25.08-fold higher than that of the wild-type. Solubilized GjCCD4a was expressed via fusion with an MBP tag. Moreover, N212m and ten other genes were introduced into Escherichia coli for the de novo biosynthesis of five crocins. The engineered E57 strain produced crocins III and V with a total yield of 11.50 mg/L, and the E579 strain produced crocins I-V with a total output of 8.43 mg/L at shake-flask level. This study identified a marvelous genetic element (N212m) for crocin biosynthesis and achieved its de novo biosynthesis in E. coli using glucose. This study provides a reference for the large-scale production of five crocins using E. coli cell factories.

Reasons why life on Earth rarely makes fluorine-containing compounds and their implications for the search for life beyond Earth

Life on Earth is known to rarely make fluorinated carbon compounds, as compared to other halocarbons. We quantify this rarity, based on our exhaustive natural products database curated from available literature. We build on explanations for the scarcity of fluorine chemistry in life on Earth, namely that the exclusion of the C-F bond stems from the unique physico-chemical properties of fluorine, predominantly its extreme electronegativity and strong hydration shell. We further show that the C-F bond is very hard to synthesize and when it is made by life its potential biological functions can be readily provided by alternative functional groups that are much less costly to incorporate into existing biochemistry. As a result, the overall evolutionary cost-to-benefit balance of incorporation of the C-F bond into the chemical repertoire of life is not favorable. We argue that the limitations of organofluorine chemistry are likely universal in that they do not exclusively apply to specifics of Earth's biochemistry. C-F bonds, therefore, will be rare in life beyond Earth no matter its chemical makeup.

Defluorination of monofluorinated alkane by Rhodococcus sp. NJF-7 isolated from soil

Microbial degradation of fluorinated compounds raised significant attention because of their widespread distribution and potential environmental impacts. Here, we report a bacterial isolate, Rhodococcus sp. NJF-7 capable of defluorinating monofluorinated medium-chain length alkanes. This isolate consumed 2.29 ± 0.13 mmol L- 1 of 1-fluorodecane (FD) during a 52 h incubation period, resulting in a significant release of inorganic fluoride amounting to 2.16 ± 0.03 mmol L- 1. The defluorination process was strongly affected by the initial FD concentration and pH conditions, with lower pH increasing fluoride toxicity to bacterial cells and inhibiting enzymatic defluorination activity. Stoichiometric conversion of FD to fluoride was observed at neutral pH with resting cells, while defluorination was significantly lower at reduced pH (6.5). The discovery of the metabolites decanoic acid and methyl decanoate suggests that the initial attack by monooxygenases may be responsible for the biological defluorination of FD. The findings here provide new insights into microbial defluorination processes, specifically aiding in understanding the environmental fate of organic semi-fluorinated alkane chemicals.

The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis

Fluorinated organic chemicals, such as per- and polyfluorinated alkyl substances (PFAS) and fluorinated pesticides, are both broadly useful and unusually long-lived. To combat problems related to the accumulation of these compounds, microbial PFAS and organofluorine degradation and biosynthesis of less-fluorinated replacement chemicals are under intense study. Both efforts are undermined by the substantial toxicity of fluoride, an anion that powerfully inhibits metabolism. Microorganisms have contended with environmental mineral fluoride over evolutionary time, evolving a suite of detoxification mechanisms. In this perspective, we synthesize emerging ideas on microbial defluorination/fluorination and fluoride resistance mechanisms and identify best approaches for bioengineering new approaches for degrading and making organofluorine compounds.

A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules

Halogen-containing molecules are ubiquitous in modern society and present unique chemical possibilities. As a whole, de novo fermentation and synthetic pathway construction for these molecules remain relatively underexplored and could unlock molecules with exciting new applications in industries ranging from textiles to agrochemicals to pharmaceuticals. Here, we report a mix-and-match co-culture platform to de novo generate a large array of halogenated tryptophan derivatives in Escherichia coli from glucose. First, we engineer E. coli to produce between 300 and 700 mg/L of six different halogenated tryptophan precursors. Second, we harness the native promiscuity of multiple downstream enzymes to access unexplored regions of metabolism. Finally, through modular co-culture fermentations, we demonstrate a plug-and-play bioproduction platform, culminating in the generation of 26 distinct halogenated molecules produced de novo including precursors to prodrugs 4-chloro- and 4-bromo-kynurenine and new-to-nature halogenated beta carbolines.

Synthesis of fluorinated amino acids by low-specificity, promiscuous aldolases coupled to in situ fluorodonor generation

Fluorine (F) is an important element in the synthesis of molecules broadly used in medicine, agriculture, and materials. F addition to organic structures represents a unique strategy for tuning molecular properties, yet this atom is rarely found in Nature and approaches to produce fluorometabolites (such as fluorinated amino acids, key building blocks for synthesis) are relatively scarce. This chapter discusses the use of L-threonine aldolase enzymes (LTAs), a class of enzymes that catalyze reversible aldol addition to the α-carbon of glycine. The C-C bond formation ability of LTAs, together with their known substrate promiscuity, make them ideal for in vitro F biocatalysis. Here, we describe protocols to harness the activity of the low-specificity LTAs isolated from Escherichia coli and Pseudomonas putida on 2-fluoroacetaldehyde to efficiently synthesize 4-fluoro-L-threonine in vitro. This chapter also provides a comprehensive account of experimental protocols to implement these activities in vivo. These methods are illustrative and can be adapted to produce other fluorometabolites of interest.

Recombinant Pseudomonas growing on non-natural fluorinated substrates shows stress but overall tolerance to cytoplasmically released fluoride anion

IMPORTANCE

Society uses thousands of organofluorine compounds, sometimes denoted per- and polyfluoroalkyl substances (PFAS), in hundreds of products, but recent studies have shown some to manifest human and environmental health effects. As a class, they are recalcitrant to biodegradation, partly due to the paucity of fluorinated natural products to which microbes have been exposed. Another limit to PFAS biodegradation is the intracellular toxicity of fluoride anion generated from C-F bond cleavage. The present study identified a broader substrate specificity in an enzyme originally studied for its activity on the natural product fluoroacetate. A recombinant Pseudomonas expressing this enzyme was used here as a model system to better understand the limits and effects of a high level of intracellular fluoride generation. A fluoride stress response has evolved in bacteria and has been described in Pseudomonas spp. The present study is highly relevant to organofluorine compound degradation or engineered biosynthesis in which fluoride anion is a substrate.

Microwell fluoride assay screening for enzymatic defluorination

There is intense interest in removing fluorinated compounds from the environment, environments are most efficiently remediated by microbial enzymes, and defluorinating enzymes are readily monitored by fluoride determination. Fluorine is the most electronegative element. Consequently, all mechanisms of enzymatic C-F bond cleavage produce fluoride anion, F-. Therefore, methods for the determination of fluoride are critical for C-F enzymology and apply to any fluorinated organic compounds, including PFAS, or per- and polyfluorinated alkyl substances. The biodegradation of most PFAS chemicals is rare or unknown. Accordingly, identifying new enzymes, or re-engineering the known defluorinases, will require rapid and sensitive methods for measuring fluoride in aqueous media. Most studies currently use ion chromatography or fluoride specific electrodes which are relatively sensitive but low throughput. The methods here describe refashioning a drinking water test to efficiently determine fluoride in enzyme and cell culture reaction mixtures. The method is based on lanthanum alizarin complexone binding of fluoride. Reworking the method to a microtiter well plate format allows detection of as little as 4 nmol of fluoride in 200 μL of assay buffer. The method is amenable to color imaging, spectrophotometric plate reading and automated liquid handling to expedite assays with thousands of enzymes and/or substrates for discovering and improving enzymatic defluorination.

Approaches Towards Better Immunosuppressive Agents

Several classes of compounds are applied in clinics due to their immunosuppressive properties in transplantology and the treatment of autoimmune diseases. Derivatives of mycophenolic acid, corticosteroids and chemotherapeutics bearing heterocyclic moieties like methotrexate, azathioprine, mizoribine, and ruxolitinib are active substances with investigated mechanisms of action. However, improved synthetic approaches of known drugs and novel derivatives are still being reported to attempt better accessibility and therapeutic properties. In this review article, we present the synthesis of the designed chemical structures based on recent literature reports concerning novel compounds as promising immunosuppressive drugs. Moreover, some of the discussed derivers revealed also other types of activities with prospective medicinal potential.

Taming of Furfurylidenes by Chiral Bismuth-Rhodium Paddlewheel Catalysts. Preparation and Functionalization of Optically Active 1,1-Disubstituted (Trifluoromethyl)cyclopropanes

Although 2-furyl-carbenes (furfurylidenes) are prone to instantaneous electrocyclic ring opening, chiral [BiRh]-paddlewheel complexes empowered by London dispersion allow (trifluoromethyl)furfurylidene metal complexes to be generated from a bench-stable triftosylhydrazone precursor. These reactive intermediates engage in asymmetric [2+1] cycloadditions and hence open entry into valuable trifluoromethylated cyclopropane or -cyclopropene derivatives in optically active form, which are important building blocks for medicinal chemistry but difficult to make otherwise.

Photolysis Products of Fluorinated Pharmaceuticals: A Combined Fluorine Nuclear Magnetic Resonance Spectroscopy and Mass Spectrometry Approach

The aqueous photolysis of four pharmaceuticals with varying fluorinated functional groups was assessed under neutral, alkaline, advanced oxidation, and advanced reduction conditions with varying light sources. Solar simulator quantum yields were 2.21 × 10-1  mol Ei-1 for enrofloxacin, 9.36 × 10-3  mol Ei-1 for voriconazole, and 1.49 × 10-2  mol Ei-1 for flecainide. Florfenicol direct photolysis was slow, taking 150 h for three degradation half-lives. Bimolecular rate constants between pharmaceuticals and hydroxyl radicals were 109 to 1010  M-1  s-1 . Using a combined quantitative fluorine nuclear magnetic resonance spectroscopy (19 F-NMR) and mass spectrometry approach, fluorine mass balances and photolysis product structures were elucidated. Enrofloxacin formed a variety of short-lived fluorinated intermediates that retained the aryl F motif. Extended photolysis time led to complete aryl F mineralization to fluoride. The aliphatic F moiety on florfenicol was also mineralized to fluoride, but the resulting product was a known antibiotic (thiamphenicol). For voriconazole, the two aryl Fs contributed more to fluoride production compared with the heteroaromatic F, indicating higher stability of the heteroaromatic F motif. The two aliphatic CF3 moieties in the flecainide structure remained intact under all conditions, further supporting the stability of these moieties found in per- and polyfluoroalkyl substances under a variety of conditions. The advanced treatment conditions generating hydroxyl radicals or hydrated electrons accelerated the degradation, but not the defluorination, of flecainide. The combination of 19 F-NMR and mass spectrometry proved powerful in allowing identification of fluorinated products and verifying the functional groups present in the intermediates and products. The results found in the present study will aid in the understanding of which fluorinated functional groups should be incorporated into pharmaceuticals to ensure organofluorine byproducts are not formed in the environment and help determine the water-treatment processes that effectively remove specific pharmaceuticals and more generally fluorinated motifs. Environ Toxicol Chem 2023;00:1-12. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Biosynthetic incorporation of fluorinated amino acids into the nonribosomal peptide gramicidin S

Fluorine is a key element in medicinal chemistry, as it can significantly enhance the pharmacological properties of drugs. In this study, we aimed to biosynthetically produce fluorinated analogues of the antimicrobial cyclic decapeptide gramicidin S (GS). However, our results show that the A-domain of the NRPS module GrsA rejects 4-fluorinated analogues of its native substrate Phe due to an interrupted T-shaped aromatic interaction in the binding pocket. We demonstrate that GrsA mutant W239S improves the incorporation of 4-fluorinated Phe into GS both in vitro and in vivo. Our findings provide new insights into the behavior of NRPSs towards fluorinated amino acids and strategies for the engineered biosynthesis of fluorinated peptides.

Regioselective C-F Bond Transformations of Silyl Difluoroenolates

Herein, we report the development of a nickel-catalyzed cross-coupling reaction of silyl difluoroenolates with aryl zinc reagents via C-F bond cleavage. Treatment of a stoichiometric amount of Ni(0)/N-heterocyclic carbene (NHC) with silyl difluoroenolates in the presence of a lithium salt resulted in C-F bond cleavage to selectively afford the corresponding (Z)-alkenyl Ni complexes. On the basis of the observations, we developed a catalytic cross-coupling reaction that selectively delivers a single geometric isomer of a fluoroenolate.

Enzymatic Fluoromethylation Enabled by the S-Adenosylmethionine Analog Te-Adenosyl-L-(fluoromethyl)homotellurocysteine

Fluoromethyl, difluoromethyl, and trifluoromethyl groups are present in numerous pharmaceuticals and agrochemicals, where they play critical roles in the efficacy and metabolic stability of these molecules. Strategies for late-stage incorporation of fluorine-containing atoms in molecules have become an important area of organic and medicinal chemistry as well as synthetic biology. Herein, we describe the synthesis and use of Te-adenosyl-L-(fluoromethyl)homotellurocysteine (FMeTeSAM), a novel and biologically relevant fluoromethylating agent. FMeTeSAM is structurally and chemically related to the universal cellular methyl donor S-adenosyl-L-methionine (SAM) and supports the robust transfer of fluoromethyl groups to oxygen, nitrogen, sulfur, and some carbon nucleophiles. FMeTeSAM is also used to fluoromethylate precursors to oxaline and daunorubicin, two complex natural products that exhibit antitumor properties.

Strategies for Nucleophilic C(sp3)-(Radio)Fluorination

This Perspective surveys the progress and current limitations of nucleophilic fluorination methodologies. Despite the long and rich history of C(sp³)-F bond construction in chemical research, the inherent challenges associated with this transformation have largely constrained nucleophilic fluorination to a privileged reaction platform. In recent years, the Doyle group─along with many others─has pursued the study and development of this transformation with the intent of generating deeper mechanistic understanding, developing user-friendly fluorination reagents, and contributing to the invention of synthetic methods capable of enabling radiofluorination. Studies from our laboratory are discussed along with recent developments from others in this field. Fluoride reagent development and the mechanistic implications of reagent identity are highlighted. We also outline the chemical space inaccessible by current synthetic technologies and a series of future directions in the field that can potentially fill the existing dark spaces.

Naturally Occurring Organohalogen Compounds-A Comprehensive Review

The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.

Strategies for the Biodegradation of Polyfluorinated Compounds

Many cite the strength of C–F bonds for the poor microbial biodegradability of polyfluorinated organic compounds (PFCs). However, commercial PFCs almost invariably contain more functionality than fluorine. The additional functionality provides a weak entry point for reactions that activate C–F bonds and lead to their eventual cleavage. This metabolic activation strategy is common in microbial biodegradation pathways and is observed with aromatic hydrocarbons, chlorinated compounds, phosphonates and many other compounds. Initial metabolic activation precedes critical bond breakage and assimilation of nutrients. A similar strategy with commercial PFCs proceeds via initial attack at the non-fluorinated functionalities: sulfonates, carboxylates, chlorines, phenyl rings, or phosphonates. Metabolic transformation of these non-fluorinated groups can activate the C–F bonds, allowing more facile cleavage than a direct attack on the C–F bonds. Given that virtually all compounds denoted as “PFAS” are not perfluorinated and are not alkanes, it is posited here that considering their individual chemical classes is more useful for both chemical and microbiological considerations of their fate.

Identification of Two Novel Fluorinases From Amycolatopsis sp. CA-128772 and Methanosaeta sp. PtaU1.Bin055 and a Mutant With Improved Catalytic Efficiency With Native Substrate

Fluoride plays an important role in the fields of materials and medicine. Compared with chemical synthesis, fluorinases are natural catalysts with more application potential, which provide a green and effective way to obtain organofluorine. However, the application of fluorinases is limited by certain factors, such as the limited number of enzymes and their low activity. In this work, two new fluorinases from Amycolatopsis sp. CA-128772 and Methanosaeta sp. PtaU1.Bin055 were identified by gene mining and named Fam and Fme, respectively. The activities of these two enzymes were reported for the first time, and Fme showed good thermal stability, which was different from the reported fluorinases. In addition, the activity toward natural substrate of Fam was improved by site-directed mutagenesis, the catalytic efficiency (k_cat/K_m) of the best mutant containing two amino acid substitutions (T72A and S164G) toward the substrate S-adenosyl-L-methionine was improved by 2.2-fold compared to the wild-type. Structural modeling analysis revealed that the main reason for the increased enzyme activity might be the formation of a new substrate channel. Experimental evidence suggests that the substrate channel may indeed play a key role in regulating the function of the fluorinases.

Catalytic Stereoconvergent Synthesis of Homochiral β-CF3, β-SCF3, and β-OCF3 Benzylic Alcohols

We describe an efficient catalytic strategy for enantio- and diastereoselective synthesis of homochiral β-CF₃, β-SCF₃, and β-OCF₃ benzylic alcohols. The approach is based on dynamic kinetic resolution (DKR) with Noyori–Ikariya asymmetric transfer hydrogenation leading to simultaneous construction of two contiguous stereogenic centers with up to 99.9% ee, up to 99.9:0.1 dr, and up to 99% isolated yield. The origin of the stereoselectivity and racemization mechanism of DKR is rationalized by density functional theory calculations. Applicability of the previously inaccessible chiral fluorinated alcohols obtained by this method in two directions is further demonstrated: As building blocks for pharmaceuticals, illustrated by the synthesis of heat shock protein 90 inhibitor with in vitro anticancer activity, and in particular, needle-shaped crystals of representative stereopure products that exhibit either elastic or plastic flexibility, which opens the door to functional materials based on mechanically responsive chiral molecular crystals.

A Nonconventional Archaeal Fluorinase Identified by In Silico Mining for Enhanced Fluorine Biocatalysis

Fluorinases, the only enzymes known to catalyze the transfer of fluorine to an organic molecule, are essential catalysts for the biological synthesis of valuable organofluorines. However, the few fluorinases identified so far have low turnover rates that hamper biotechnological applications. Here, we isolated and characterized putative fluorinases retrieved from systematic in silico mining and identified a nonconventional archaeal enzyme from Methanosaeta sp. that mediates the fastest S_N2 fluorination rate reported to date. Furthermore, we demonstrate enhanced production of fluoronucleotides in vivo in a bacterial host engineered with this archaeal fluorinase, paving the way toward synthetic metabolism for efficient biohalogenation.

Recent Advances in Enantioselective Organocatalytic Reactions Enabled by NHCs Containing Triazolium Motifs

N-Heterocyclic carbenes (NHCs) containing triazolium motifs have emerged as a powerful tool in organocatalysis. Recently, various NHC pre-catalyst mediated organic transformations have been developed successfully. This article aims to compile the current state of knowledge on NHC-triazolium catalysed enantioselective name reactions and introduce newly developed catalytic methods. Furthermore, this review article framework provides an excellent opportunity to highlight some of the unique applications of these catalytic procedures in the natural product synthesis of biologically active compounds, notably the wide range of preparation of substituted chiral alcohols, and their derivatives. This article provides an overview of chiral NHC triazolium-catalyst libraries synthesis and their catalytic application in enantioselective reactions.

Microwell Fluoride Screen for Chemical, Enzymatic, and Cellular Reactions Reveals Latent Microbial Defluorination Capacity for -CF3 Groups

The capacity to defluorinate polyfluorinated organic compounds is a rare phenotype in microbes but is increasingly considered important for maintaining the environment. New discoveries will be greatly facilitated by the ability to screen many natural and engineered microbes in a combinatorial manner against large numbers of fluorinated compounds simultaneously. Here, we describe a low-volume, high-throughput screening method to determine defluorination capacity of microbes and their enzymes. The method is based on selective binding of fluoride to a lanthanum chelate complex that gives a purple-colored product. It was miniaturized to determine biodefluorination in 96-well microtiter plates by visual inspection or robotic handling and spectrophotometry. Chemicals commonly used in microbiological studies were examined to define usable buffers and reagents. Base-catalyzed, purified enzyme and whole-cell defluorination reactions were demonstrated with fluoroatrazine and showed correspondence between the microtiter assay and a fluoride electrode. For discovering new defluorination reactions and mechanisms, a chemical library of 63 fluorinated compounds was screened in vivo with Pseudomonas putida F1 in microtiter well plates. These data were also calibrated against a fluoride electrode. Our new method revealed 21 new compounds undergoing defluorination. A compound with four fluorine substituents, 4-fluorobenzotrifluoride, was shown to undergo defluorination to the greatest extent. The mechanism of its defluorination was studied to reveal a latent microbial propensity to defluorinate trifluoromethylphenyl groups, a moiety that is commonly incorporated into numerous pharmaceutical and agricultural chemicals. IMPORTANCE Thousands of organofluorine chemicals are known, and a number are considered to be persistent and toxic environmental pollutants. Environmental bioremediation methods are avidly being sought, but few bacteria biodegrade fluorinated chemicals. To find new organofluoride biodegradation, a rapid screening method was developed. The method is versatile, monitoring chemical, enzymatic, and whole-cell biodegradation. Biodegradation of organofluorine compounds invariably releases fluoride anions, which was sensitively detected. Our method uncovered 21 new microbial defluorination reactions. A general mechanism was delineated for the biodegradation of trifluoromethylphenyl groups that are increasingly being used in drugs and pesticides.

Discovery of Anticancer Agents of Diverse Natural Origin

Research progress from mainly over the last five years is described for a multidisciplinary collaborative program project directed toward the discovery of potential anticancer agents from a broad range of taxonomically defined organisms. Selected lead compounds with potential as new antitumor agents that are representative of considerable structural diversity have continued to be obtained from each of tropical plants, terrestrial and aquatic cyanobacteria, and filamentous fungi. Recently, a new focus has been on the investigation of the constituents of U.S. lichens and their fungal mycobionts. A medicinal chemistry and pharmacokinetics component of the project has optimized structurally selected lead natural products, leading to enhanced cytotoxic potencies against selected cancer cell lines. Biological testing has shown several compounds to have in vivo activity, and relevant preliminary structure-activity relationship and mechanism of action studies have been performed. Several promising lead compounds worthy of further investigation have been identified from the most recent collaborative work performed.

Intramolecular Appel Reaction of Trifluoromethylated β-Keto Diazos Enabling Assembly of Trifluoromethylpyrazoles

A method for the generation of trifluoromethylated β-keto diazos and their applications in intramolecular Appel type reactions are reported. The key success of this reaction is a diazo species as an N-nucleophile in Appel reactions. This reaction is conducted under mild conditions and has a broad substrate scope, affording trifluoromethylpyrazoles in ≤94% yields. This protocol represents a new type of Appel reaction and also a new reaction mode of fluoro diazoalkanes.

Tandem trifluoromethylthiolation and cyclization of N-aryl-3-butenamides with AgSCF3: divergent access to CF3S-substituted 3,4-dihydroquinolin-2-ones and azaspiro[4,5]dienones

A AgSCF3-mediated tandem trifluoromethylthiolaton and cyclization of N-aryl-3-butenamides was developed. It showed divergent reactivities and enabled the selective syntheses of CF3S-substituted 3,4-dihydroquinolin-2-ones and azaspiro[4,5]dienones. The selectivity was achieved through different...

Enantioselective Synthesis of Acyclic Stereotriads Featuring Fluorinated Tetrasubstituted Stereocenters

Elaboration of enantioenriched complex acyclic stereotriads represents a challenge for modern synthesis even more when fluorinated tetrasubstituted stereocenters are targeted. We have been able to develop a simple strategy in a sequence of two unprecedented steps combining a diastereoselective aldol-Tishchenko reaction and an enantioselective organocatalyzed kinetic resolution. The aldol-Tishchenko reaction directly generates a large panel of acyclic 1,3-diols possessing a fluorinated tetrasubstituted stereocenter by condensation of fluorinated ketones with aldehydes under very mild basic conditions. The anti 1,3-diols featuring three contiguous stereogenic centers are generated with excellent diastereocontrol (typically >99 : 1 dr). Depending upon the precursors both diastereomers of stereotriads are accessible through this flexible reaction. Furthermore, from the obtained racemic scaffolds, development of an organocatalyzed kinetic resolution enabled to generate the desired enantioenriched stereotriads with excellent selectivity (typically er >95 : 5).

Why Is the Biodegradation of Polyfluorinated Compounds So Rare?

Thousands of heavily fluorinated chemicals are found in the environment, impact human and ecosystem health, and are relatively resistant to biological and chemical degradation. Their persistence in the environment is due to the inability of most microorganisms to biodegrade them. Only a very few examples of polyfluorinated compound biodegradation are known, and the reported rates are very low. This has been mostly attributed to the low chemical reactivity of the C-F bond. This Perspective goes beyond that explanation to highlight microbiological reasons why polyfluorinated compounds resist metabolism. The evolutionary and physiological impediments must be appreciated to better find, study, and harness microbes that degrade polyfluorinated compounds.

Biomimetic enantioselective synthesis of β,β-difluoro-α-amino acid derivatives

Although utilization of fluorine compounds has a long history, synthesis of chiral fluorinated amino acid derivatives with structural diversity and high stereoselectivity is still very appealing and challenging. Here, we report a biomimetic study of enantioselective [1,3]-proton shift of β,β-difluoro-α-imine amides catalyzed by chiral quinine derivatives. A wide range of corresponding β,β-difluoro-α-amino amides were achieved in good yields with high enantioselectivities. The optically pure β,β-difluoro-α-amino acid derivatives were further obtained, which have high application values in the synthesis of fluoro peptides, fluoro amino alcohols and other valuable fluorine-containing molecules.

Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances

Poly‐ and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today’s society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called ‘forever chemicals’ due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.

Chlorinated metabolites from Streptomyces sp. highlight the role of biosynthetic mosaics and superclusters in the evolution of chemical diversity

LCMS-guided screening of a library of biosynthetically talented bacteria and fungi identified Streptomyces sp. MST- as a prolific producer of chlorinated metabolites. We isolated and characterised six new and nine reported compounds from MST-, belonging to three discrete classes - the depsipeptide svetamycins, the indolocarbazole borregomycins and the aromatic polyketide anthrabenzoxocinones. Following genome sequencing of MST-, we describe, for the first time, the svetamycin biosynthetic gene cluster (sve), its mosaic structure and its relationship to several distantly related gene clusters. Our analysis of the sve cluster suggested that the reported stereostructures of the svetamycins may be incorrect. This was confirmed by single-crystal X-ray diffraction analysis, allowing us to formally revise the absolute configurations of svetamycins A-G. We also show that the borregomycins and anthrabenzoxocinones are encoded by a single supercluster (bab) implicating superclusters as potential nucleation points for the evolution of biosynthetic gene clusters. These clusters highlight how individual enzymes and functional subclusters can be co-opted during the formation of biosynthetic gene clusters, providing a rare insight into the poorly understood mechanisms underpinning the evolution of chemical diversity.

Defluorodearomatization: A Photocatalytic Birch-Like Reduction That Enables C-C Bond Formation and Provides Access to Unnatural Cannabinoids

Within the framework of discovery chemistry, polyfluorination remains a synthetic challenge despite its ability to provide useful characteristics, such as a reduction in the number of hydrogen bond donors and metabolic stability. Coupling a reversal of this methodology with photocatalysis has been demonstrated to allow the rapid synthesis of previously difficult or impossible targets by starting with fluorines everywhere and selectively removing or functionalizing them. Herein, we demonstrate a novel method to synthesize 1,4-cyclohexadienes through a dearomative photocatalytic C-C coupling reaction. This allows for access to materials that are orthogonal to the selectivity of the Birch reaction and are more functional-group-tolerant. The reaction also allows the efficient synthesis of polyfluorinated cannabinoids. While the yields are modest, the access to the new chemical space provided by the reaction is unprecedented by any means. The trifluorinated analog of THC, 1-deoxy-1,2,4-trifluoro-THC, is synthesized, demonstrating the importance of discovery chemistry and the ability to explore otherwise unknown structure-activity relationships.

Diversity-Oriented Synthesis of Aliphatic Fluorides via Reductive C(sp3 )-C(sp3 ) Cross-Coupling Fluoroalkylation

Monofluorinated alkyl compounds are of great importance in pharmaceuticals, agrochemicals and materials. Herein, we describe a direct nickel-catalyzed monofluoromethylation of unactivated alkyl halides using a low-cost industrial raw material, bromofluoromethane, by demonstrating a general and efficient reductive cross-coupling of two alkyl halides. Results with 1-bromo-1-fluoroalkane also demonstrate the viability of monofluoroalkylation, which further established the first example of reductive C(sp³ )-C(sp³ ) cross-coupling fluoroalkylation. These transformations demonstrate high efficiency, mild conditions, and excellent functional-group compatibility, especially for a range of pharmaceuticals and biologically active compounds. Mechanistic studies support a radical pathway. Kinetic studies reveal that the reaction is first-order dependent on catalyst and alkyl bromide whereas the generation of monofluoroalkyl radical is not involved in the rate-determining step. This strategy provides a general and efficient method for the synthesis of aliphatic fluorides.

Low Dose of Fluoride in the Culture Medium of Cordyceps militaris Promotes Its Growth and Enhances Bioactives with Antioxidant and Anticancer Properties

Cordyceps militaris possesses several compounds with medicinal properties, and is commonly used in traditional Chinese functional food and medicine for a variety of health benefits. Because of its rare occurrence in nature, the market demand for artificial C. militaris is on the rise. Furthermore, efforts to increase its bioactive ingredients have also been considered in research. In this study, we aimed to investigate the effect of fluoride on the growth and enrichment of bioactive compounds in C. militaris. A wide range of potassium fluoride concentrations (0, 0.001, 0.01, 0.1, and 1 mM) were added to the culture media as a source of fluoride during the cultivation of C. militaris fruiting bodies. The contents of fluorine and bioactive substances of the fruiting bodies in normal (NM) and fluorine-supplemented (FM) media were measured and compared. C. militaris raised in the growth medium supplemented with 0.01 mM potassium fluoride led to a 44.86% (1.55 ± 0.14 g/bottle) increase in biomass and a 23.43% (3161.38 ± 35.71 µg/g) increase in total carotenoid content in the fruiting bodies. Furthermore, a remarkable increase in superoxide dismutase-like activity (84.75 U/mg) and 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (IC₅₀ = 2.59 mg/mL) was recorded. In human cancer cell-based assays, C. militaris raised in FM caused stronger cytotoxicity, apoptosis, and cell cycle arrest in human osteosarcoma cells. These results demonstrated that a low dose of fluoride could stimulate the growth of C. militaris fruiting bodies and enhance the production of bioactive ingredients that possess useful antioxidant and anticancer activities.

Formal [4 + 1] annulation of fluorinated sulfonium salt with cyclic unsaturated imines to access CF3-substituted pyrroles

Formal [4 + 1] annulation of easily available fluorinated sulfonium salt with cyclic unsaturated imines has been successfully developed. A structurally diverse set of CF₃-substituted dihydropyrroles was efficiently constructed in acceptable to excellent yields with excellent diastereoselectivities. The resulting CF₃-containing dihydropyrroles from this transition metal-free strategy could be easily transformed to pyrroles in good yields under basic conditions.

Catalytic Asymmetric Reduction of α-Trifluoromethylated Imines with Catecholborane by BINOL-Derived Boro-phosphates

A catalytic enantioselective reduction of α-trifluoromethylated imines by a BINOL-derived boro-phosphate employing catecholborane as hydride source has been developed. This method provides an efficient route to prepare synthetically useful chiral α-trifluoromethylated amines in high yields and with excellent enantioselectivities (up to 98% yield and 96% ee) under mild conditions.

The organocatalytic enantiodivergent fluorination of β-ketodiaryl-phosphine oxides for the construction of carbon-fluorine quaternary stereocenters

Commercially available cinchona alkaloids that can catalyze the enantiodivergent fluorination of β-ketodiarylphosphine oxides were developed to construct carbon-fluorine quaternary stereocenters. This protocol features a wide scope of substrates and excellent enantioselectivities, and it is scalable.

The ever-expanding limits of enzyme catalysis and biodegradation: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds

Biodegradation is simply the metabolism of anthropogenic, or otherwise unwanted, chemicals in our environment, typically by microorganisms. The metabolism of compounds commonly found in living things is limited to several thousand metabolites whereas ∼100 million chemical substances have been devised by chemical synthesis, and ∼100 000 are used commercially. Since most of those compounds are not natively found in living things, and some are toxic or carcinogenic, the question arises as to whether there is some organism somewhere with the enzymes that can biodegrade them. Repeatedly, anthropogenic chemicals have been denoted ‘non-biodegradable,’ only to find they are reactive with one or more enzyme(s). Enzyme reactivity has been organized into categories of functional group transformations. The discovery of new functional group transformations has continually expanded our knowledge of enzymes and biodegradation. This expansion of new-chemical biodegradation is driven by the evolution and spread of newly evolved enzymes. This review describes the biodegradation of widespread commercial chemicals with a focus on four classes: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds. Polyaromatic hydrocarbons include some of the most carcinogenic compounds known. Polychlorinated compounds include polychlorinated biphenyls (PCBs) and many pesticides of the twentieth century. Polyfluorinated compounds are a major focus of bioremediation efforts today. Polymers are clogging landfills, killing aquatic species in the oceans and increasingly found in our bodies. All of these classes of compounds, each thought at one time to be non-biodegradable, have been shown to react with natural enzymes. The known limits of enzyme catalysis, and hence biodegradation, are continuing to expand.

Steric-Free Bioorthogonal Labeling of Acetylation Substrates Based on a Fluorine-Thiol Displacement Reaction

We have developed a novel bioorthogonal reaction that can selectively displace fluorine substitutions alpha to amide bonds. This fluorine-thiol displacement reaction (FTDR) allows for fluorinated cofactors or precursors to be utilized as chemical reporters, hijacking acetyltransferase-mediated acetylation both in vitro and in live cells, which cannot be achieved with azide- or alkyne-based chemical reporters. The fluoroacetamide labels can be further converted to biotin or fluorophore tags using FTDR, enabling the general detection and imaging of acetyl substrates. This strategy may lead to a steric-free labeling platform for substrate proteins, expanding our chemical toolbox for functional annotation of post-translational modifications in a systematic manner.

The high persistence of PFAS is sufficient for their management as a chemical class

Per- and polyfluoroalkyl substances (PFAS) are a class of synthetic organic substances with diverse structures, properties, uses, bioaccumulation potentials and toxicities. Despite this high diversity, all PFAS are alike in that they contain perfluoroalkyl moieties that are extremely resistant to environmental and metabolic degradation. The vast majority of PFAS are therefore either non-degradable or transform ultimately into stable terminal transformation products (which are still PFAS). Under the European chemicals regulation this classifies PFAS as very persistent substances (vP). We argue that this high persistence is sufficient concern for their management as a chemical class, and for all "non-essential" uses of PFAS to be phased out. The continual release of highly persistent PFAS will result in increasing concentrations and increasing probabilities of the occurrence of known and unknown effects. Once adverse effects are identified, the exposure and associated effects will not be easily reversible. Reversing PFAS contamination will be technically challenging, energy intensive, and costly for society, as is evident in the efforts to remove PFAS from contaminated land and drinking water sources.

Accessing (Multi)Fluorinated Piperidines Using Heterogeneous Hydrogenation

Fluorinated piperidines are desirable motifs for pharmaceutical and agrochemical research. Nevertheless, general synthetic access remains out of reach. Herein, we describe a simple and robust cis-selective hydrogenation of abundant and cheap fluoropyridines to yield a broad scope of (multi)fluorinated piperidines. This protocol enables the chemoselective reduction of fluoropyridines while tolerating other (hetero)aromatic systems using a commercially available heterogenous catalyst. Fluorinated derivatives of important drug compounds are prepared, and a straightforward strategy for the synthesis of enantioenriched fluorinated piperidines is disclosed.

A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida

Fluorine is a key element in the synthesis of molecules broadly used in medicine, agriculture and materials. Addition of fluorine to organic structures represents a unique strategy for tuning molecular properties, yet this atom is rarely found in Nature and approaches to integrate fluorometabolites into the biochemistry of living cells are scarce. In this work, synthetic gene circuits for organofluorine biosynthesis are implemented in the platform bacterium Pseudomonas putida. By harnessing fluoride-responsive riboswitches and the orthogonal T7 RNA polymerase, biochemical reactions needed for in vivo biofluorination are wired to the presence of fluoride (i.e. circumventing the need of feeding expensive additives). Biosynthesis of fluoronucleotides and fluorosugars in engineered P. putida is demonstrated with mineral fluoride both as only fluorine source (i.e. substrate of the pathway) and as inducer of the synthetic circuit. This approach expands the chemical landscape of cell factories by providing alternative biosynthetic strategies towards fluorinated building-blocks.

Addition of fluorine to organic structures is a unique strategy for tuning molecular properties, but approaches to integrate fluorometabolites into the biochemistry of living cells are scarce. Here, the authors develop a fluoride-responsive genetic circuit to enable in vivo biofluorination in engineered Pseudomonas putida.

Chemoenzymatic Synthesis and Biological Evaluation for Bioactive Molecules Derived from Bacterial Benzoyl Coenzyme A Ligase and Plant Type III Polyketide Synthase

Plant type III polyketide synthases produce diverse bioactive molecules with a great medicinal significance to human diseases. Here, we demonstrated versatility of a stilbene synthase (STS) from Pinus Sylvestris, which can accept various non-physiological substrates to form unnatural polyketide products. Three enzymes (4-coumarate CoA ligase, malonyl-CoA synthetase and engineered benzoate CoA ligase) along with synthetic chemistry was practiced to synthesize starter and extender substrates for STS. Of these, the crystal structures of benzoate CoA ligase (BadA) from Rhodopseudomonas palustris in an apo form or in complex with a 2-chloro-1,3-thiazole-5-carboxyl-AMP or 2-methylthiazole-5-carboxyl-AMP intermediate were determined at resolutions of 1.57 Å, 1.7 Å, and 2.13 Å, respectively, which reinforces its capacity in production of unusual CoA starters. STS exhibits broad substrate promiscuity effectively affording structurally diverse polyketide products. Seven novel products showed desired cytotoxicity against a panel of cancer cell lines (A549, HCT116, Cal27). With the treatment of two selected compounds, the cancer cells underwent cell apoptosis in a dose-dependent manner. The precursor-directed biosynthesis alongside structure-guided enzyme engineering greatly expands the pharmaceutical repertoire of lead compounds with promising/enhanced biological activities.

Fluorine biocatalysis

The introduction of fluorine atoms into organic molecules has received considerable attention as these organofluorines have often found widespread applications in bioorganic chemistry, medicinal chemistry and biomaterial science. Despite innovation of synthetic C-F forming methodologies, selective fluorination is still extremely challenging. Therefore, a biotransformation approach using fluorine biocatalysts is needed to selectively introduce fluorine into structurally diverse molecules. Yet, there are few ways that enable incorporation of fluorine into structurally complex bioactive molecules. One is to extend the substrate scope of the existing enzyme inventory. Another is to expand the biosynthetic pathways to accept fluorinated precursors for producing fluorinated bioactive molecules. Finally, an understanding of the physiological roles of fluorometabolites in the producing microorganisms will advance our ability to engineer a microorganism to produce novel fluorinated commodities. Here, we review the fluorinase biotechnology and fluorine biocatalysts that incorporate fluorine motifs to generate fluorinated molecules, and highlight areas for future developments.