Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis

Catalytic Mechanism of Aromatic Nitration by Cytochrome P450 TxtE: Involvement of a Ferric-Peroxynitrite Intermediate

The cytochromes P450 are heme-dependent enzymes that catalyze many vital reaction processes in the human body related to biodegradation and biosynthesis. They typically act as mono-oxygenases; however, the recently discovered P450 subfamily TxtE utilizes O₂ and NO to nitrate aromatic substrates such as L-tryptophan. A direct and selective aromatic nitration reaction may be useful in biotechnology for the synthesis of drugs or small molecules. Details of the catalytic mechanism are unknown, and it has been suggested that the reaction should proceed through either an iron(III)-superoxo or an iron(II)-nitrosyl intermediate. To resolve this controversy, we used stopped-flow kinetics to provide evidence for a catalytic cycle where dioxygen binds prior to NO to generate an active iron(III)-peroxynitrite species that is able to nitrate l-Trp efficiently. We show that the rate of binding of O₂ is faster than that of NO and also leads to l-Trp nitration, while little evidence of product formation is observed from the iron(II)-nitrosyl complex. To support the experimental studies, we performed density functional theory studies on large active site cluster models. The studies suggest a mechanism involving an iron(III)-peroxynitrite that splits homolytically to form an iron(IV)-oxo heme (Compound II) and a free NO₂ radical via a small free energy of activation. The latter activates the substrate on the aromatic ring, while compound II picks up the ipso-hydrogen to form the product. The calculations give small reaction barriers for most steps in the catalytic cycle and, therefore, predict fast product formation from the iron(III)-peroxynitrite complex. These findings provide the first detailed insight into the mechanism of nitration by a member of the TxtE subfamily and highlight how the enzyme facilitates this novel reaction chemistry.

Single-step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source in Anaerobic Ergothioneine Biosynthesis

Ergothioneine, a natural longevity vitamin and antioxidant, is a thiol-histidine derivative. Recently, two types of biosynthetic pathways were reported. In the aerobic ergothioneine biosynthesis, a non-heme iron enzyme incorporates a sulfoxide to an sp² C-H bond in trimethyl-histidine (hercynine) through oxidation reactions. In contrast, in the anaerobic ergothioneine biosynthetic pathway in a green sulfur bacterium, Chlorobium limicola, a rhodanese domain containing protein (EanB) directly replaces this unreactive hercynine C-H bond with a C-S bond. Herein, we demonstrate that polysulfide (HSS_nSR) is the direct sulfur-source in EanB-catalysis. After identifying EanB's substrates, X-ray crystallography of several intermediate states along with mass spectrometry results provide additional mechanistic details for this reaction. Further, quantum mechanics/molecular mechanics (QM/MM) calculations reveal that protonation of N_π of hercynine by Tyr353 with the assistance of Thr414 is a key activation step for the hercynine sp² C-H bond in this trans-sulfuration reaction.

Electrophilic Chlorine from Chlorosulfonium Salts: A Highly Chemoselective Reduction of Sulfoxides

Herein, we describe a selective late-stage deoxygenation of sulfoxides based on a novel application of chlorosulfonium salts and demonstrate a new process using these species generated in situ from sulfoxides as the source of electrophilic chlorine. The use of highly nucleophilic 1,3,5-trimethoxybenzene (TMB) as the reducing agent is described for the first time and applied in the deoxygenation of simple and functionalized sulfoxides. The method is easy to handle, economic, suitable for gram-scale operations, and readily applied for poly-functionalized molecules, as demonstrated with more than 45 examples, including commercial medicines and analogues. We also report the results of competition experiments that define the more reactive sulfoxide and we present a mechanistic proposal based on substrate and product observations.

The catalytic mechanism of sulfoxide synthases

Sulfoxide synthases are non-heme iron enzymes that catalyze oxidative carbonsulfur bond formation in the biosynthesis of thiohistidines such as ergothioneine and ovothiol. The catalytic mechanism of these enzymes has been studied by protein crystallography, steady-state kinetics, non-natural amino acid incorporation and computational modeling. This review discusses the current status of this research and also highlights similarities between the CS bond forming activity of sulfoxide synthases with that of synthetic coordination compounds.

Introduction to Thiopeptides: Biological Activity, Biosynthesis, and Strategies for Functional Reprogramming

Thiopeptides (also known as thiazolyl peptides) are structurally complex natural products with rich biological activities. Known for over 70 years for potent killing of Gram-positive bacteria, thiopeptides are experiencing a resurgence of interest in the last decade, primarily brought about by the genomic revolution of the 21st century. Every area of thiopeptide research-from elucidating their biological function and biosynthesis to expanding their structural diversity through genome mining-has made great strides in recent years. These advances lay the foundation for and inspire novel strategies for thiopeptide engineering. Accordingly, a number of diverse approaches are being actively pursued in the hope of developing the next generation of natural-product-inspired therapeutics. Here, we review the contemporary understanding of thiopeptide biological activities, biosynthetic pathways, and approaches to structural and functional reprogramming, with a special focus on the latter.

Sulfoxide Reduction/C(sp3)-S Metathesis Cascade in Ionic Liquid

A sulfoxide reduction/C-S bond metathesis cascade between sulfoxides and alkyl bromides has been developed to access high-value sulfides without the use of any catalysts or bases. In this cascade, classical Kornblum oxidation is employed to reduce sulfoxides with alkyl bromides in ionic liquid. This protocol features high functional tolerance, mild conditions, promising scalability, and sustainable solvents.

Convergent Evolution of Fungal Cysteine Dioxygenases

Cupin-type cysteine dioxygenases (CDOs) are non-heme iron enzymes that occur in animals, plants, bacteria and in filamentous fungi. In this report, we show that agaricomycetes contain an entirely unrelated type of CDO that emerged by convergent evolution from enzymes involved in the biosynthesis of ergothioneine. The activity of this CDO type is dependent on the ergothioneine precursor N-α-trimethylhistidine. The metabolic link between ergothioneine production and cysteine oxidation suggests that the two processes might be part of the same chemical response in fungi, for example against oxidative stress.

Sulfonium Acids Loaded onto an Unusual Thiotemplate Assembly Line Construct the Cyclopropanol Warhead of a Burkholderia Virulence Factor

Pathogenic bacteria of the Burkholderia pseudomallei group cause severe infectious diseases such as glanders and melioidosis. Malleicyprols were identified as important bacterial virulence factors, yet the biosynthetic origin of their cyclopropanol warhead has remained enigmatic. By a combination of mutational analysis and metabolomics we found that sulfonium acids, dimethylsulfoniumpropionate (DMSP) and gonyol, known as osmolytes and as crucial components in the global organosulfur cycle, are key intermediates en route to the cyclopropanol unit. Functional genetics and in vitro analyses uncover a specialized pathway to DMSP involving a rare prokaryotic SET‐domain methyltransferase for a cryptic methylation, and show that DMSP is loaded onto the NRPS‐PKS hybrid assembly line by an adenylation domain dedicated to zwitterionic starter units. Then, the megasynthase transforms DMSP into gonyol, as demonstrated by heterologous pathway reconstitution in E. coli.

Highly Efficient Regioselective Decanoylation of Hyperoside Using Nanobiocatalyst of Fe3O4@PDA-Thermomyces lanuginosus Lipase: Insights of Kinetics and Stability Evaluation

The immobilization of Thermomyces lanuginosus lipase on polydopamine-functionalized Fe₃O₄ magnetic nanoparticles (Fe₃O₄@PDA-TLL) as a nanobiocatalyst was successfully performed for the first time, and the Fe₃O₄@PDA-TLL was used for regioselective acylation of natural hyperoside with vinyl decanoate. The effects of several crucial factors, such as the reaction solvent, substrate molar ratio, temperature, and immobilized enzyme dosage, were investigated. Under optimum conditions, the reaction rate, 6″-regioselectivity, and maximum substrate conversion were as high as 12.6 mM/h, 100%, and 100%, respectively. An operational stability study demonstrated that the immobilized enzyme could maintain 90.1% of its initial maximum conversion even after reusing it five times. In addition, further investigations on the kinetic parameters, like V_max, K_m, V_max/K_m, and E_a, also revealed that the biocompatible Fe₃O₄@PDA could act as an alternative carrier for the immobilization of different enzymes.

Recent application of visible-light induced radicals in C-S bond formation

The sulphur centered radicals, produced from various organic compounds, in high efficiency by single-electron-transfer (SET) oxidation. These radicals are highly reactive intermediates having various applications in the construction of organosulphur compounds in the field of synthetic organic chemistry. These S-centred radical-mediated organic transformations have been achieved using photoredox catalysts, including organic dyes and transition metal catalysts, as well as in the absence of any catalyst. Compared with previous methods, photoredox catalysis is inexpensive and features the advantages of being environmentally benign, highly efficient and easy to use. This review focuses on recent developments in the photocatalyzed carbon-sulphur bond formation.

Thiol Activation toward Selective Thiolation of Aromatic C-H Bond

Direct C-S bond coupling is an attractive way to construct aryl sulfur ether, a building block for a variety of biological active molecules. Herein, we disclose an effective model for regioselective thiolation of the aromatic C-H bond by thiol activation instead of arene activation. Strikingly, this method has been applied into anisole derivatives that are not available in the arene activation approach to forge a single thioether isomer with high reactivity.

Disulfide Chromophores Arise from Stereoelectronic Effects

Bonds between sulfur atoms are prevalent in natural products, peptides, and proteins. Disulfide bonds have a distinct chromophore. The wavelength of their maximal absorbance varies widely, from 250 to 500 nm. Here, we demonstrate that this wavelength derives from stereoelectronic effects and is predictable using quantum chemistry. We also provide a sinusoidal equation, analogous to the Karplus equation, that relates the absorbance maximum and the C-S-S-C dihedral angle. These insights provide a facile means to characterize important attributes of disulfide bonds and to design disulfides with specified photophysical properties.

Visible-Light-Induced, Catalyst-Free Radical Cross-Coupling Cyclization of N-Allylbromodifluoroacetamides with Disulfides or Diselenides

A visible-light-induced, catalyst-free radical cross-coupling cyclization of diselenides or disulfides with N-allylbromodifluoroacetamide has been developed. This developed protocol exhibits good functional group tolerance and affords a variety of 4-thio- and 4-seleno-substituted 3,3-difluoro-γ-lactams in moderate to good yields. Based on control experiments, a plausible radical-radical cross-coupling pathway is proposed.

Reconstitution of polythioamide antibiotic backbone formation reveals unusual thiotemplated assembly strategy

Nonribosomal peptides (NRPs) are a vast class of natural products and an important source of therapeutics. Typically, these secondary metabolites are assembled by NRP synthetases (NRPSs) that function on substrates covalently linked to the enzyme by a thioester, in a process known as thiotemplated biosynthesis. Although NRPS-independent assembly pathways are known, all are nonthiotemplated. Here we report an NRPS-independent yet thiotemplated pathway for NRP biosynthesis and demonstrate that members of the ATP-grasp and cysteine protease families form the β-peptide backbone of an antibiotic. Armed with this knowledge, we provide genomic evidence that this noncanonical assembly pathway is widespread in bacteria. Our results will inspire future genome mining efforts for the discovery of potential therapeutics that otherwise would be overlooked.

Closthioamide (CTA) is a rare example of a thioamide-containing nonribosomal peptide and is one of only a handful of secondary metabolites described from obligately anaerobic bacteria. Although the biosynthetic gene cluster responsible for CTA production and the thioamide synthetase that catalyzes sulfur incorporation were recently discovered, the logic for peptide backbone assembly has remained a mystery. Here, through the use of in vitro biochemical assays, we demonstrate that the amide backbone of CTA is assembled in an unusual thiotemplated pathway involving the cooperation of a transacylating member of the papain-like cysteine protease family and an iteratively acting ATP-grasp protein. Using the ATP-grasp protein as a bioinformatic handle, we identified hundreds of such thiotemplated yet nonribosomal peptide synthetase (NRPS)-independent biosynthetic gene clusters across diverse bacterial phyla. The data presented herein not only clarify the pathway for the biosynthesis of CTA, but also provide a foundation for the discovery of additional secondary metabolites produced by noncanonical biosynthetic pathways.

Thioamycolamides A-E, Sulfur-Containing Cycliclipopeptides Produced by the Rare Actinomycete Amycolatopsis sp

A series of novel sulfur-containing cycliclipopeptides named thioamycolamides A-E, with thiazoline, thioether rings, and fatty acid moieties, were identified from the culture broth of the rare actinomycete Amycolatopsis sp. 26-4. The planar structural elucidation was accomplished by HRMS and 1D/2D NMR spectroscopic data analyses. The absolute configurations were unambiguously determined by Marfey's method, CD spectroscopy, and synthesis of partial structures. Moreover, their growth inhibitory activities against human tumor cell lines were investigated.

Cu(I)-Catalyzed Enantioselective Alkynylation of Thiochromones

A highly efficient asymmetric synthesis of chiral thiochromanones is developed via Cu(I)/phosphoramidite catalyzed asymmetric alkynylation of thiochromones under mild reaction conditions. The catalyst system is tolerant of various thiochromone precursors and terminal alkynes. The established asymmetric transformation provides different enatiomeric-enriched thiochromanones with more molecular complexity and enables access to chiral thioflavanones, a subgroup of flavonoid by further functionalization.

Exploiting a C-N Bond Forming Cytochrome P450 Monooxygenase for C-S Bond Formation

C-S bond formation reactions are widely distributed in the biosynthesis of biologically active molecules, and thus have received much attention over the past decades. Herein, we report intramolecular C-S bond formation by a P450 monooxygenase, TleB, which normally catalyzes a C-N bond formation in teleocidin biosynthesis. Based on the proposed reaction mechanism of TleB, a thiol-substituted substrate analogue was synthesized and tested in the enzyme reaction, which afforded the unprecedented sulfur-containing thio-indolactam V, in addition to an unusual indole-fused 6/5/8-tricyclic product whose structure was determined by the crystalline sponge method. Interestingly, conformational analysis revealed that the SOFA conformation is stable in thio-indolactam V, in sharp contrast to the major TWIST form in indolactam V, resulting in differences in their biological activities.

Acid-Controlled Access to β-Sulfenyl Ketones and α,β-Disulfonyl Ketones by Pummerer Reaction of β-Keto Sulfones and Sulfoxides

A convenient acid-mediated reaction of β-keto sulfones with sulfoxides under metal-free conditions has been developed, thereby delivering the acid-controlled synthesis of β-sulfenyl ketones and α,β-disulfonyl ketones in good to excellent yields. The mechanism of the transformations has been studied carefully, which suggested the involvement of a radical process in the formation of α,β-disulfonyl ketones.

Electrochemical Synthesis of β-Ketosulfones from Switchable Starting Materials

A synthesis of β-ketosulfones via sulfination of aryl methyl ketones and aryl acetylenes with sodium sulfinates under mild electrochemical conditions, in moderate to good chemical yields, is described. In particular, an electrochemical sulfination reaction of alkynes with sulfinate salts has never been explored. An environmentally friendly characteristic of this reaction is that it uses electricity as a valuable energy source for electrochemical synthesis of β-ketosulfones. This strategy is more convenient and practical compared to previous approaches.

NIS-promoted intermolecular bis-sulfenylation of allenamides via a two-step radical process: synthesis of 1,3-dithioethers

The first report of NIS-promoted two-step radical addition of thiols to allenamides to provide an efficient route for accessing 1,3-dithioethers.

Cross-linking of aromatic phenolate groups by cytochrome P450 enzymes: a model for the biosynthesis of vancomycin by OxyB

Aromatic cross-linking by cytochrome P450 enzymes was studied computationally. P450 Compound I rapidly abstracts two weak phenolic H-atoms that link up via a rate-determining C–O bond formation.

Room temperature nickel-catalyzed cross-coupling of aryl-boronic acids with thiophenols: synthesis of diarylsulfides

A mild and easy to operate NiCl₂/2,2′-bipyridine-catalyzed cross-coupling of thiophenols with arylboronic acids has been developed for the synthesis of symmetric and unsymmetric diarylsulfides at room temperature and in air.

Construction of sulfur-containing moieties in the total synthesis of natural products

This review surveys the total syntheses of sulfur-containing natural products where sulfur atoms are introduced with different sulfurization agents to construct related sulfur-containing moieties.

Advances in Cu and Ni-catalyzed Chan–Lam-type coupling: synthesis of diarylchalcogenides, Ar2–X (X = S, Se, Te)

Advances in the Cu and Ni-catalyzed Chan–Lam-type coupling of aryl/heteroarylboronic acids with various chalcogen sources for diarylsulfide, diarylselenide and diaryltelluride synthesis are covered in this review.

Nickel-Catalyzed Inter- and Intramolecular Aryl Thioether Metathesis by Reversible Arylation

A nickel‐catalyzed aryl thioether metathesis has been developed to access high‐value thioethers. 1,2‐Bis(dicyclohexylphosphino)ethane (dcype) is essential to promote this highly functional‐group‐tolerant reaction. Furthermore, synthetically challenging macrocycles could be obtained in good yield in an unusual example of ring‐closing metathesis that does not involve alkene bonds. In‐depth organometallic studies support a reversible Ni⁰/Ni^II pathway to product formation. Overall, this work not only provides a more sustainable alternative to previous catalytic systems based on Pd, but also presents new applications and mechanistic information that are highly relevant to the further development and application of unusual single‐bond metathesis reactions.

Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool

The rational discovery of new specialized metabolites by genome mining represents a very promising strategy in the quest for new bioactive molecules. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural product that derive from genetically encoded precursor peptides. However, RiPP gene clusters are particularly refractory to reliable bioinformatic predictions due to the absence of a common biosynthetic feature across all pathways. Here, we describe RiPPER, a new tool for the family-independent identification of RiPP precursor peptides and apply this methodology to search for novel thioamidated RiPPs in Actinobacteria. Until now, thioamidation was believed to be a rare post-translational modification, which is catalyzed by a pair of proteins (YcaO and TfuA) in Archaea. In Actinobacteria, the thioviridamide-like molecules are a family of cytotoxic RiPPs that feature multiple thioamides, which are proposed to be introduced by YcaO-TfuA proteins. Using RiPPER, we show that previously undescribed RiPP gene clusters encoding YcaO and TfuA proteins are widespread in Actinobacteria and encode a highly diverse landscape of precursor peptides that are predicted to make thioamidated RiPPs. To illustrate this strategy, we describe the first rational discovery of a new structural class of thioamidated natural products, the thiovarsolins from Streptomyces varsoviensis.

Carbene-Catalyzed Enantioselective Addition of Thioamides to Bromoenals for Access to Thiazinone Heterocycles

A carbene-catalyzed reaction between α-bromoenals and thioamides was developed. Key steps include enantioselective 1,4-addition of thioamide sulfur atoms to α,β-unsaturated acyl azolium intermediate. Subsequent intramolecular annulation eventually affords thiazinone heterocycles with high optical purities. The introduction of Lewis acid additives such as Cu(OTf)₂ to this NHC catalytic reaction could provide small but consistent improvements to reaction enantioselectivities.